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Sample records for direct mri mapping

  1. Intraoperative MRI and functional mapping.

    PubMed

    Gasser, Thomas; Szelenyi, Andrea; Senft, Christian; Muragaki, Yoshihiro; Sandalcioglu, I Erol; Sure, Ulrich; Nimsky, Christopher; Seifert, Volker

    2011-01-01

    The integration of functional and anatomical data into neuronavigation is an established standard of care in many neurosurgical departments. Yet, this method has limitations as in most cases the data are acquired prior to surgery. Due to brain-shift the accurate presentation of functional as well as anatomical structures declines in the course of surgery. In consequence, the acquisition of information during surgery about the brain's current functional state is of specific interest. The advancement of imaging technologies (e.g. fMRI, MEG, Intraoperative Optical Intrinsic Signal Imaging--IOIS) and neurophysiological techniques and the advent of intraoperative MRI all had a major impact on neurosurgery. The combination of modalities such as neurophysiology and intraoperative MRI (ioMRI), as well as the acquisition of functional MRI during surgery (ifMRI) are in the focus of this work. Especially the technical aspects and safety issues are elucidated.

  2. Neuroethics and fMRI: mapping a fledgling relationship.

    PubMed

    Garnett, Alex; Whiteley, Louise; Piwowar, Heather; Rasmussen, Edie; Illes, Judy

    2011-01-01

    Human functional magnetic resonance imaging (fMRI) informs the understanding of the neural basis of mental function and is a key domain of ethical enquiry. It raises questions about the practice and implications of research, and reflexively informs ethics through the empirical investigation of moral judgments. It is at the centre of debate surrounding the importance of neuroscience findings for concepts such as personhood and free will, and the extent of their practical consequences. Here, we map the landscape of fMRI and neuroethics, using citation analysis to uncover salient topics. We find that this landscape is sparsely populated: despite previous calls for debate, there are few articles that discuss both fMRI and ethical, legal, or social implications (ELSI), and even fewer direct citations between the two literatures. Recognizing that practical barriers exist to integrating ELSI discussion into the research literature, we argue nonetheless that the ethical challenges of fMRI, and controversy over its conceptual and practical implications, make this essential. PMID:21526115

  3. Large-Scale, High-Resolution Neurophysiological Maps Underlying fMRI of Macaque Temporal Lobe

    PubMed Central

    Papanastassiou, Alex M.; DiCarlo, James J.

    2013-01-01

    Maps obtained by functional magnetic resonance imaging (fMRI) are thought to reflect the underlying spatial layout of neural activity. However, previous studies have not been able to directly compare fMRI maps to high-resolution neurophysiological maps, particularly in higher level visual areas. Here, we used a novel stereo microfocal x-ray system to localize thousands of neural recordings across monkey inferior temporal cortex (IT), construct large-scale maps of neuronal object selectivity at subvoxel resolution, and compare those neurophysiology maps with fMRI maps from the same subjects. While neurophysiology maps contained reliable structure at the sub-millimeter scale, fMRI maps of object selectivity contained information at larger scales (>2.5 mm) and were only partly correlated with raw neurophysiology maps collected in the same subjects. However, spatial smoothing of neurophysiology maps more than doubled that correlation, while a variety of alternative transforms led to no significant improvement. Furthermore, raw spiking signals, once spatially smoothed, were as predictive of fMRI maps as local field potential signals. Thus, fMRI of the inferior temporal lobe reflects a spatially low-passed version of neurophysiology signals. These findings strongly validate the widespread use of fMRI for detecting large (>2.5 mm) neuronal domains of object selectivity but show that a complete understanding of even the most pure domains (e.g., faces vs nonface objects) requires investigation at fine scales that can currently only be obtained with invasive neurophysiological methods. PMID:24048850

  4. Complete fourier direct magnetic resonance imaging (CFD-MRI) for diffusion MRI

    PubMed Central

    Özcan, Alpay

    2013-01-01

    The foundation for an accurate and unifying Fourier-based theory of diffusion weighted magnetic resonance imaging (DW–MRI) is constructed by carefully re-examining the first principles of DW–MRI signal formation and deriving its mathematical model from scratch. The derivations are specifically obtained for DW–MRI signal by including all of its elements (e.g., imaging gradients) using complex values. Particle methods are utilized in contrast to conventional partial differential equations approach. The signal is shown to be the Fourier transform of the joint distribution of number of the magnetic moments (at a given location at the initial time) and magnetic moment displacement integrals. In effect, the k-space is augmented by three more dimensions, corresponding to the frequency variables dual to displacement integral vectors. The joint distribution function is recovered by applying the Fourier transform to the complete high-dimensional data set. In the process, to obtain a physically meaningful real valued distribution function, phase corrections are applied for the re-establishment of Hermitian symmetry in the signal. Consequently, the method is fully unconstrained and directly presents the distribution of displacement integrals without any assumptions such as symmetry or Markovian property. The joint distribution function is visualized with isosurfaces, which describe the displacement integrals, overlaid on the distribution map of the number of magnetic moments with low mobility. The model provides an accurate description of the molecular motion measurements via DW–MRI. The improvement of the characterization of tissue microstructure leads to a better localization, detection and assessment of biological properties such as white matter integrity. The results are demonstrated on the experimental data obtained from an ex vivo baboon brain. PMID:23596401

  5. Sources of Variation Influencing Concordance between Functional MRI and Direct Cortical Stimulation in Brain Tumor Surgery

    PubMed Central

    Morrison, Melanie A.; Tam, Fred; Garavaglia, Marco M.; Hare, Gregory M. T.; Cusimano, Michael D.; Schweizer, Tom A.; Das, Sunit; Graham, Simon J.

    2016-01-01

    Object: Preoperative functional magnetic resonance imaging (fMRI) remains a promising method to aid in the surgical management of patients diagnosed with brain tumors. For patients that are candidates for awake craniotomies, surgical decisions can potentially be improved by fMRI but this depends on the level of concordance between preoperative brain maps and the maps provided by the gold standard intraoperative method, direct cortical stimulation (DCS). There have been numerous studies of the concordance between fMRI and DCS using sensitivity and specificity measures, however the results are variable across studies and the key factors influencing variability are not well understood. Thus, the present work addresses the influence of technical factors on fMRI and DCS concordance. Methods: Motor and language mapping data were collected for a group of glioma patients (n = 14) who underwent both preoperative fMRI and intraoperative DCS in an awake craniotomy procedure for tumor removal. Normative fMRI data were also acquired in a healthy control group (n = 12). The fMRI and DCS mapping data were co-registered; true positive (TP), true negative (TN), false positive (FP), and false negative (FN) occurrences were tabulated over the exposed brain surface. Sensitivity and specificity were measured for the total group, and for the motor and language sub-groups. The influence of grid placement, fMRI statistical thresholding, and task standardization were assessed. Correlations between proportions of agreement and error were also carefully scrutinized to evaluate concordance in more detail. Results: Concordance was significantly better for motor vs. language mapping. There was an inverse relationship between TP and TN with increasing statistical threshold, and FP dominated the total error. Sensitivity and specificity were reduced when tasks were not standardized across fMRI and DCS. Conclusions: Although the agreement between fMRI and DCS is good, variability is introduced by

  6. NOTE: MRI temperature mapping during thermal balloon angioplasty

    NASA Astrophysics Data System (ADS)

    Shmatukha, Andriy V.; Bakker, Chris J. G.

    2006-04-01

    Knowledge on the thermal dose delivered during thermal balloon angioplasty (TBA) is desirable to understand why TBA's outcome varies widely among patients and why it is subject to high restenosis rates. In its conventional implementation, TBA involves injection of a heated medium into a balloon positioned within a stenotic blood vessel. The medium injection causes flow, motion and susceptibility-redistribution artefacts that are devastating to the proton resonance frequency shift (PRFS) technique of MRI temperature mapping. Here, we propose to separate in time medium injection and heating by first inflating a balloon with a medium at an initial temperature, and then by heating the medium up using laser light. The separation is shown to eliminate all the mentioned artefacts and to enable real-time MRI temperature mapping using the PRFS technique. Accurate and reliable temperature maps were acquired in a TBA balloon itself and in the surrounding phantom tissue during heat application.

  7. Direct MRI detection of the neuronal magnetic field: the effect of the dendrite branch.

    PubMed

    Huang, Ying-Ling; Xiong, Hong-Chuan; Yao, De-Zhong

    2010-09-21

    In recent years, neuronal current MRI (nc-MRI) was proposed as a new imaging method to directly map the magnetic field change caused by neuronal activity. Nc-MRI could offer improved spatial and temporal resolution compared to blood hemodynamics-based functional magnetic resonance imaging (fMRI). In this paper, with a finite current dipole as the model of dendrite or dendrite branch, we investigated the spatial distribution of the magnetic field generated by synchronously activated neurons to evaluate the possibility of nc-MRI. Our simulations imply that the existence of a dendrite branch may not only increase the strength of the neuronal magnetic field (NMF), but also raise the non-uniform and unsymmetry of the NMF; therefore, it can enhance the detectability of the neuronal current magnetic field by MRI directly. The results show that the signal phase shift is enlarged, but it is unstable and is still very small, <1 radian, while the magnitude signal may be strong enough for a typical MRI voxel to be detected. We suggest making further efforts to measure the magnitude signal which may induce a large effect in an nc-MRI experiment.

  8. Contour tracking and probabilistic segmentation of tissue phase mapping MRI

    NASA Astrophysics Data System (ADS)

    Chitiboi, Teodora; Hennemuth, Anja; Schnell, Susanne; Chowdhary, Varun; Honarmand, Amir; Markl, Michael; Linsen, Lars; Hahn, Horst

    2016-03-01

    Many cardiovascular diseases manifest as an abnormal motion pattern of the heart muscle (myocardium). Local cardiac motion can be non-invasively quantified with magnetic resonance imaging (MRI), using methods such as tissue phase mapping (TPM), which directly measures the local myocardial velocities over time with high temporal and spatial resolution. The challenges for routine clinical use of TPM for the diagnosis and monitoring of cardiac function lie in providing a fast and accurate myocardium segmentation and a robust quantitative analysis of the velocity field. Both of these tasks are difficult to automate on routine clinical data because of the reduced contrast in the presence of noise. In this work, we propose to address these challenges with a segmentation approach that combines smooth, iterative contour displacement and probabilistic segmentation using particle tracing, based on the underlying velocity field. The proposed solution enabled the efficient and reproducible segmentation of TPM datasets from 27 patients and 14 volunteers, showing good potential for routine use in clinical studies. Our method allows for a more reliable quantitative analysis of local myocardial velocities, by giving a higher weight to velocity vectors corresponding to pixels more likely to belong to the myocardium. The accuracy of the contour propagation was evaluated on nine subjects, showing an average error smaller than the spatial resolution of the image data. Statistical analysis concluded that the difference between the segmented contours and the ground truths was not significantly higher than the variability between the manual ground truth segmentations.

  9. Mapping of electrical muscle stimulation using MRI

    NASA Technical Reports Server (NTRS)

    Adams, Gregory R.; Harris, Robert T.; Woodard, Daniel; Dudley, Gary A.

    1993-01-01

    The pattern of muscle contractile activity elicited by electromyostimulation (EMS) was mapped and compared to the contractile-activity pattern produced by voluntary effort. This was done by examining the patterns and the extent of contrast shift, as indicated by T2 values, im magnetic resonance (MR) images after isometric activity of the left m. quadriceps of human subjects was elicited by EMS (1-sec train of 500-microsec sine wave pulses at 50 Hz) or voluntary effort. The results suggest that, whereas EMS stimulates the same fibers repeatedly, thereby increasing the metabolic demand and T2 values, the voluntary efforts are performed by more diffuse asynchronous activation of skeletal muscle even at forces up to 75 percent of maximal to maintain performance.

  10. COMPARISON OF THE COMPLETE FOURIER DIRECT MRI WITH EXISTING DIFFUSION WEIGHTED MRI METHODS

    PubMed Central

    Özcan, Alpay

    2011-01-01

    The Complete Fourier Direct (CFD) MRI method introduced in earlier work for modeling the diffusion weighted MRI signal is compared with the existing methods. The preservation of Hermitian symmetry in the diffusion weighted MRI signal without affecting its energy is the key point that differentiates CFD–MRI from the existing methods. By keeping the correct Fourier relationship intact, the joint distribution function is represented ‘as it is’, without any constraints, e.g. being symmetric. The necessity to model or assume models for spin motion and try to fit the model to the samples of the Fourier transform as in case of model matching methods is not required because the Discrete Fourier Transform applied to correctly processed signal in CFD–MRI gives more accurate results. PMID:21918715

  11. Quantitative β mapping for calibrated fMRI.

    PubMed

    Shu, Christina Y; Sanganahalli, Basavaraju G; Coman, Daniel; Herman, Peter; Rothman, Douglas L; Hyder, Fahmeed

    2016-02-01

    The metabolic and hemodynamic dependencies of the blood oxygenation level-dependent (BOLD) signal form the basis for calibrated fMRI, where the focus is on oxidative energy demanded by neural activity. An important part of calibrated fMRI is the power-law relationship between the BOLD signal and the deoxyhemoglobin concentration, which in turn is related to the ratio between oxidative demand (CMRO2) and blood flow (CBF). The power-law dependence between BOLD signal and deoxyhemoglobin concentration is signified by a scaling exponent β. Until recently most studies assumed a β value of 1.5, which is based on numerical simulations of the extravascular BOLD component. Since the basal value of CMRO2 and CBF can vary from subject-to-subject and/or region-to-region, a method to independently measure β in vivo should improve the accuracy of calibrated fMRI results. We describe a new method for β mapping through characterizing R2' - the most sensitive relaxation component of BOLD signal (i.e., the reversible magnetic susceptibility component that is predominantly of extravascular origin at high magnetic field) - as a function of intravascular magnetic susceptibility induced by an FDA-approved superparamagnetic contrast agent. In α-chloralose anesthetized rat brain, at 9.4 T, we measured β values of ~0.8 uniformly across large neocortical swathes, with lower magnitude and more heterogeneity in subcortical areas. Comparison of β maps in rats anesthetized with medetomidine and α-chloralose revealed that β is independent of neural activity levels at these resting states. We anticipate that this method for β mapping can help facilitate calibrated fMRI for clinical studies. PMID:26619788

  12. Directly detected 55Mn MRI: Application to phantoms for human hyperpolarized 13C MRI development

    PubMed Central

    von Morze, Cornelius; Carvajal, Lucas; Reed, Galen D.; Swisher, Christine Leon; Tropp, James; Vigneron, Daniel B.

    2014-01-01

    In this work we demonstrate for the first time directly detected manganese-55 (55Mn) MRI using a clinical 3T MRI scanner designed for human hyperpolarized 13C clinical studies with no additional hardware modifications. Due to the similar frequency of the 55Mn and 13C resonances, the use of aqueous permanganate for large, signal-dense, and cost-effective “13C” MRI phantoms was investigated, addressing the clear need for new phantoms for these studies. Due to 100% natural abundance, higher intrinsic sensitivity, and favorable relaxation properties, 55Mn MRI of aqueous permanganate demonstrates dramatically increased sensitivity over typical 13C phantom MRI, at greatly reduced cost as compared with large 13C-enriched phantoms. A large sensitivity advantage (22-fold) was demonstrated. A cylindrical phantom (d= 8 cm) containing concentrated aqueous sodium permanganate (2.7M) was scanned rapidly by 55Mn MRI in a human head coil tuned for 13C, using a balanced SSFP acquisition. The requisite penetration of RF magnetic fields into concentrated permanganate was investigated by experiments and high frequency electromagnetic simulations, and found to be sufficient for 55Mn MRI with reasonably sized phantoms. A sub-second slice-selective acquisition yielded mean image SNR of ~60 at 0.5cm3 spatial resolution, distributed with minimum central signal ~40% of the maximum edge signal. We anticipate that permanganate phantoms will be very useful for testing HP 13C coils and methods designed for human studies. PMID:25179135

  13. MAPPING DIRECTLY IMAGED GIANT EXOPLANETS

    SciTech Connect

    Kostov, Veselin; Apai, Daniel

    2013-01-01

    With the increasing number of directly imaged giant exoplanets, the current atmosphere models are often not capable of fully explaining the spectra and luminosity of the sources. A particularly challenging component of the atmosphere models is the formation and properties of condensate cloud layers, which fundamentally impact the energetics, opacity, and evolution of the planets. Here we present a suite of techniques that can be used to estimate the level of rotational modulations these planets may show. We propose that the time-resolved observations of such periodic photometric and spectroscopic variations of extrasolar planets due to their rotation can be used as a powerful tool to probe the heterogeneity of their optical surfaces. In this paper, we develop simulations to explore the capabilities of current and next-generation ground- and space-based instruments for this technique. We address and discuss the following questions: (1) what planet properties can be deduced from the light curve and/or spectra, and in particular can we determine rotation periods, spot coverage, spot colors, and spot spectra?; (2) what is the optimal configuration of instrument/wavelength/temporal sampling required for these measurements?; and (3) can principal component analysis be used to invert the light curve and deduce the surface map of the planet? Our simulations describe the expected spectral differences between homogeneous (clear or cloudy) and patchy atmospheres, outline the significance of the dominant absorption features of H{sub 2}O, CH{sub 4}, and CO, and provide a method to distinguish these two types of atmospheres. Assuming surfaces with and without clouds for most currently imaged planets the current models predict the largest variations in the J band. Simulated photometry from current and future instruments is used to estimate the level of detectable photometric variations. We conclude that future instruments will be able to recover not only the rotation periods

  14. Passive fMRI mapping of language function for pediatric epilepsy surgical planning: validation using Wada, ECS, and FMAER

    PubMed Central

    Suarez, Ralph O.; Taimouri, Vahid; Boyer, Katrina; Vega, Clemente; Rotenberg, Alexander; Madsen, Joseph R.; Loddenkemper, Tobias; Duffy, Frank; Prabhu, Sanjay; Warfield, Simon K.

    2014-01-01

    In this study we validate passive language fMRI protocols designed for clinical application in pediatric epilepsy surgical planning as they do not require overt participation from patients. We introduced a set of quality checks that assess reliability of noninvasive fMRI mappings utilized for clinical purposes. We initially compared two fMRI language mapping paradigms, one active in nature (requiring participation from the patient) and the other passive in nature (requiring no participation from the patient). Group-level analysis in a healthy control cohort demonstrated similar activation of the putative language centers of the brain in the inferior frontal (IFG) and temporoparietal (TPG) regions. Additionally, we showed that passive language fMRI produced more left-lateralized activation in TPG (LI = +0.45) compared to the active task; with similarly robust left-lateralized IFG (LI = +0.24) activations using the passive task. We validated our recommended fMRI mapping protocols in a cohort of 15 pediatric epilepsy patients by direct comparison against the invasive clinical gold-standards. We found that language-specific TPG activation by fMRI agreed to within 9.2 mm to subdural localizations by invasive functional mapping in the same patients, and language dominance by fMRI agreed with Wada test results at 80% congruency in TPG and 73% congruency in IFG. Lastly, we tested the recommended passive language fMRI protocols in a cohort of very young patients and confirmed reliable language-specific activation patterns in that challenging cohort. We concluded that language activation maps can be reliably achieved using the passive language fMRI protocols we proposed even in very young (average 7.5 years old) or sedated pediatric epilepsy patients. PMID:25445239

  15. [Study on cine view of relative enhancement ratio map in O2-enhanced MRI].

    PubMed

    Fujii, Keita; Watanabe, Yasushi; Hanaoka, Shouhei; Motoyoshi, Kouichi; Goto, Masami; Amemiya, Shiori; Ino, Kenji; Akahane, Masaaki; Yano, Keiichi; Ohtomo, Kuni

    2014-11-01

    Magnetic resonance imaging (MRI) enables the evaluation of organ structure and function. Oxygen-enhanced MRI (O2-enhanced MRI) is a method for evaluating the pulmonary ventilation function using oxygen as a contrast agent. We created the Cine View of Relative Enhancement Ratio Map (Cine RER map) in O2-enhanced MRI to easily observe the contrast effect for clinical use. Relative enhancement ratio (RER) was determined as the pixel values of the Cine RER map. Moreover, six healthy volunteers underwent O2-enhanced MRI to determine the appropriate scale width of the Cine RER map. We calculated each RER and set 0 to 1.27 as the scale width of the Cine RER map based on the results. The Cine RER map made it possible to observe the contrast effect over time and thus is a convenient tool for evaluating the pulmonary ventilation function in O2-enhanced MRI.

  16. Mean Apparent Propagator (MAP) MRI: a novel diffusion imaging method for mapping tissue microstructure

    PubMed Central

    Özarslan, Evren; Koay, Cheng Guan; Shepherd, Timothy M.; Komlosh, Michal E.; İrfanoğlu, M. Okan; Pierpaoli, Carlo; Basser, Peter J.

    2014-01-01

    Diffusion-weighted magnetic resonance (MR) signals reflect information about underlying tissue microstructure and cytoarchitecture. We propose a quantitative, efficient, and robust mathematical and physical framework for representing diffusion-weighted MR imaging (MRI) data obtained in “q-space,” and the corresponding “mean apparent propagator (MAP)” describing molecular displacements in “r-space.” We also define and map novel quantitative descriptors of diffusion that can be computed robustly using this MAP-MRI framework. We describe efficient analytical representation of the three-dimensional q-space MR signal in a series expansion of basis functions that accurately describes diffusion in many complex geometries. The lowest order term in this expansion contains a diffusion tensor that characterizes the Gaussian displacement distribution, equivalent to diffusion tensor MRI (DTI). Inclusion of higher order terms enables the reconstruction of the true average propagator whose projection onto the unit “displacement” sphere provides an orientational distribution function (ODF) that contains only the orientational dependence of the diffusion process. The representation characterizes novel features of diffusion anisotropy and the non-Gaussian character of the three-dimensional diffusion process. Other important measures this representation provides include the return-to-the-origin probability (RTOP), and its variants for diffusion in one- and two-dimensions—the return-to-the-plane probability (RTPP), and the return-to-the-axis probability (RTAP), respectively. These zero net displacement probabilities measure the mean compartment (pore) volume and cross-sectional area in distributions of isolated pores irrespective of the pore shape. MAP-MRI represents a new comprehensive framework to model the three-dimensional q-space signal and transform it into diffusion propagators. Experiments on an excised marmoset brain specimen demonstrate that MAP-MRI

  17. An Atlas-Based Electron Density Mapping Method for Magnetic Resonance Imaging (MRI)-Alone Treatment Planning and Adaptive MRI-Based Prostate Radiation Therapy

    SciTech Connect

    Dowling, Jason A.; Lambert, Jonathan; Parker, Joel; Salvado, Olivier; Fripp, Jurgen; Capp, Anne; Wratten, Chris; Denham, James W.; Greer, Peter B.

    2012-05-01

    Purpose: Prostate radiation therapy dose planning directly on magnetic resonance imaging (MRI) scans would reduce costs and uncertainties due to multimodality image registration. Adaptive planning using a combined MRI-linear accelerator approach will also require dose calculations to be performed using MRI data. The aim of this work was to develop an atlas-based method to map realistic electron densities to MRI scans for dose calculations and digitally reconstructed radiograph (DRR) generation. Methods and Materials: Whole-pelvis MRI and CT scan data were collected from 39 prostate patients. Scans from 2 patients showed significantly different anatomy from that of the remaining patient population, and these patients were excluded. A whole-pelvis MRI atlas was generated based on the manually delineated MRI scans. In addition, a conjugate electron-density atlas was generated from the coregistered computed tomography (CT)-MRI scans. Pseudo-CT scans for each patient were automatically generated by global and nonrigid registration of the MRI atlas to the patient MRI scan, followed by application of the same transformations to the electron-density atlas. Comparisons were made between organ segmentations by using the Dice similarity coefficient (DSC) and point dose calculations for 26 patients on planning CT and pseudo-CT scans. Results: The agreement between pseudo-CT and planning CT was quantified by differences in the point dose at isocenter and distance to agreement in corresponding voxels. Dose differences were found to be less than 2%. Chi-squared values indicated that the planning CT and pseudo-CT dose distributions were equivalent. No significant differences (p > 0.9) were found between CT and pseudo-CT Hounsfield units for organs of interest. Mean {+-} standard deviation DSC scores for the atlas-based segmentation of the pelvic bones were 0.79 {+-} 0.12, 0.70 {+-} 0.14 for the prostate, 0.64 {+-} 0.16 for the bladder, and 0.63 {+-} 0.16 for the rectum

  18. Rapid MRI method for mapping the longitudinal relaxation time

    NASA Astrophysics Data System (ADS)

    Hsu, Jung-Jiin; Glover, Gary H.

    2006-07-01

    A novel method for mapping the longitudinal relaxation time in a clinically acceptable time is developed based on a recent proposal [J.-J. Hsu, I.J. Lowe, Spin-lattice relaxation and a fast T1-map acquisition method in MRI with transient-state magnetization, J. Magn. Reson. 169 (2004) 270-278] and the speed of the spiral pulse sequence. The method acquires multiple curve-fitting samples with one RF pulse train. It does not require RF pulses of specific flip angles (e.g., 90° or 180°), nor are the long recovery waiting time and the measurement of the magnetization at thermal equilibrium needed. Given the value of the flip angle, the curve fitting is semi-logarithmic and not computationally intensive. On a heterogeneous phantom, the average percentage difference between measurements of the present method and those of an inversion-recovery method is below 2.7%. In mapping the human brain, the present method, for example, can obtain four curve-fitting samples for five 128 × 128 slices in less than 3.2 s and the results are in agreement with other studies in the literature.

  19. Using qualitative maps to direct reactive robots

    NASA Technical Reports Server (NTRS)

    Bertin, Randolph; Pendleton, Tom

    1992-01-01

    The principal advantage of mobile robots is that they are able to go to specific locations to perform useful tasks rather than have the tasks brought to them. It is important therefore that the robot be used to reach desired locations efficiently and reliably. A mobile robot whose environment extends significantly beyond its sensory horizon must maintain a representation of the environment, a map, in order to attain these efficiency and reliability requirements. We believe that qualitative mapping methods provide useful and robust representation schemes and that such maps may be used to direct the actions of a reactively controlled robot. In this paper we describe our experience in employing qualitative maps to direct, through the selection of desired control strategies, a reactive-behavior based robot. This mapping capability represents the development of one aspect of a successful deliberative/reactive hybrid control architecture.

  20. Characterizing fiber directional uncertainty in diffusion tensor MRI.

    PubMed

    Jeong, Ha-Kyu; Anderson, Adam W

    2008-12-01

    Image noise in diffusion tensor MRI (DT-MRI) causes errors in the measured tensor and hence variance in the estimated fiber orientation. Uncertainty in fiber orientation has been described using a circular "cone of uncertainty" (CU) around the principal eigenvector of the DT. The CU has proved to be a useful construct for quantifying and visualizing the variability of DT-MRI parameters and fiber tractography. The assumption of circularity of the CU has not been tested directly, however. In this work, bootstrap analysis and simple theoretical arguments were used to show that the CU is elliptical and multivariate normal in the vast majority of white matter (WM) voxels for typical measurement conditions. The dependence of the cone angle on the signal-to-noise ratio (SNR) and eigenvalue contrast was established. The major and minor cone axes are shown to be coincident with the second and third eigenvectors of the tensor, respectively, in the limit of many uniformly spaced diffusion-encoding directions. The deviation between the major cone axis and the second eigenvector was quantified for typical sets of diffusion-weighting (DW) directions. The elliptical CU provides more realistic error information for fiber-tracking algorithms and a quantitative basis for selecting DT imaging acquisition protocols.

  1. Mapping Fetal Brain Development in utero Using MRI: The Big Bang of Brain Mapping

    PubMed Central

    Studholme, Colin

    2012-01-01

    The development of tools to construct and investigate probabilistic maps of the adult human brain from MRI have led to advances in both basic neuroscience and clinical diagnosis. These tools are increasingly being applied to brain development in adolescence, childhood and even neonatal and premature neonatal imaging. Looking even earlier in development, parallel developments in clinical fetal Magnetic Resonance Imaging (MRI) have led to its growing use as a tool in challenging medical conditions. This has motivated new engineering developments that combine optimal fast MRI scans with techniques derived from computer vision that allow full 3D imaging of the moving fetal brain in utero without sedation. These promise to provide a new and unprecedented window into early human brain growth. This article will review the developments that have led us to this point, and examine the current state of the art in the fields of fast fetal imaging, motion correction and the tools to analyze dynamically changing fetal brain structure. New methods to deal with developmental tissue segmentation and the construction of spatio-temporal atlases will be examined, together with techniques to map fetal brain growth patterns. PMID:21568716

  2. Reading sequence-directed computational nucleosome maps.

    PubMed

    Nibhani, Reshma; Trifonov, Edward N

    2015-01-01

    Recently developed latest version of the sequence-directed single-base resolution nucleosome mapping reveals existence of strong nucleosomes and chromatin columnar structures (columns). Broad application of this simple technique for further studies of chromatin and chromosome structure requires some basic understanding as to how it works and what information it affords. The paper provides such an introduction to the method. The oscillating maps of singular nucleosomes, of short and long oligonucleosome columns, are explained, as well as maps of chromatin on satellite DNA and occurrences of counter-phase (antiparallel) nucleosome neighbors.

  3. Current and New Directions in MRI in Multiple Sclerosis

    PubMed Central

    Klawiter, Eric C.

    2013-01-01

    Purpose of Review This article summarizes the use of MRI in the diagnosis and treatment of multiple sclerosis (MS). Current and emerging imaging techniques are reviewed pertaining to their utility in MS. Recent Findings Conventional T1-weighted and T2-weighted sequences are used to identify and characterize disease pathology in MS. T2 lesion burden, postcontrast enhancement, T1 hypointensities, and regional and global atrophy are all informative and correlate to clinical measures, such as disease disability, to a variable extent. Newer techniques such as diffusion tensor imaging, magnetization transfer imaging, and MR spectroscopy are increasingly being incorporated into clinical trials and may provide improved specificity to the underlying pathology. Double inversion recovery and ultrahigh-field-strength MRI have direct application in MS for evaluating cortical pathology. Newer functional MRI techniques such as resting-state functional connectivity are increasingly being applied in MS. Summary Conventional and emerging imaging techniques greatly inform our understanding of MS. These techniques are integral in diagnosis, in evaluating new treatments for MS, and for following patients in the clinical setting. PMID:23917101

  4. MRI thermometry: Fast mapping of RF-induced heating along conductive wires.

    PubMed

    Ehses, Philipp; Fidler, Florian; Nordbeck, Peter; Pracht, Eberhard D; Warmuth, Marcus; Jakob, Peter M; Bauer, Wolfgang R

    2008-08-01

    Conductive implants are in most cases a strict contraindication for MRI examinations, as RF pulses applied during the MRI measurement can lead to severe heating of the surrounding tissue. Understanding and mapping of these heating effects is therefore crucial for determining the circumstances under which patient examinations are safe. The use of fluoroptic probes is the standard procedure for monitoring these heating effects. However, the observed temperature increase is highly dependent on the positioning of such a probe, as it can only determine the temperature locally. Temperature mapping with MRI after RF heating can be used, but cooling effects during imaging lead to a significant underestimation of the heating effect. In this work, an MRI thermometry method was combined with an MRI heating sequence, allowing for temperature mapping during RF heating. This technique may provide new opportunities for implant safety investigations.

  5. Asymmetric Weighting to Optimize Regional Sensitivity in Combined fMRI-MEG Maps.

    PubMed

    McWhinney, Sean R; Bardouille, Timothy; D'Arcy, Ryan C N; Newman, Aaron J

    2016-01-01

    Functional magnetic resonance imaging (fMRI) and magnetoencephalography (MEG) are neuroimaging techniques that measure inherently different physiological processes, resulting in complementary estimates of brain activity in different regions. Combining the maps generated by each technique could thus provide a richer understanding of brain activation. However, present approaches to integration rely on a priori assumptions, such as expected patterns of brain activation in a task, or use fMRI to bias localization of MEG sources, diminishing fMRI-invisible sources. We aimed to optimize sensitivity to neural activity by developing a novel method of integrating data from the two imaging techniques. We present a data-driven method of integration that weights fMRI and MEG imaging data by estimates of data quality for each technique and region. This method was applied to a verbal object recognition task. As predicted, the two imaging techniques demonstrated sensitivity to activation in different regions. Activity was seen using fMRI, but not MEG, throughout the medial temporal lobes. Conversely, activation was seen using MEG, but not fMRI, in more lateral and anterior temporal lobe regions. Both imaging techniques were sensitive to activation in the inferior frontal gyrus. Importantly, integration maps retained activation from individual activation maps, and showed an increase in the extent of activation, owing to greater sensitivity of the integration map than either fMRI or MEG alone.

  6. A new paradigm for individual subject language mapping: Movie-watching fMRI

    PubMed Central

    Tie, Yanmei; Rigolo, Laura; Ovalioglu, Aysegul Ozdemir; Olubiyi, Olutayo; Doolin, Kelly L.; Mukundan, Srinivasan; Golby, Alexandra J.

    2015-01-01

    Background Functional MRI (fMRI) based on language tasks has been used in pre-surgical language mapping in patients with lesions in or near putative language areas. However, if the patients have difficulty performing the tasks due to neurological deficits, it leads to unreliable or non-interpretable results. In this study, we investigate the feasibility of using a movie-watching fMRI for language mapping. Methods A 7-min movie clip with contrasting speech and non-speech segments was shown to 22 right-handed healthy subjects. Based on all subjects' language functional regions-of-interest, six language response areas were defined, within which a language response model (LRM) was derived by extracting the main temporal activation profile. Using a leave-one-out procedure, individuals' language areas were identified as the areas that expressed highly correlated temporal responses with the LRM derived from an independent group of subjects. Results Compared with an antonym generation task-based fMRI, the movie-watching fMRI generated language maps with more localized activations in the left frontal language area, larger activations in the left temporoparietal language area, and significant activations in their right-hemisphere homologues. Results of two brain tumor patients' movie-watching fMRI using the LRM derived from the healthy subjects indicated its ability to map putative language areas; while their task-based fMRI maps were less robust and noisier. Conclusions These results suggest that it is feasible to use this novel “task-free” paradigm as a complementary tool for fMRI language mapping when patients cannot perform the tasks. Its deployment in more neurosurgical patients and validation against gold-standard techniques need further investigation. PMID:25962953

  7. Interpreting fMRI data: maps, modules and dimensions

    PubMed Central

    Op de Beeck, Hans P.; Haushofer, Johannes; Kanwisher, Nancy G.

    2009-01-01

    Neuroimaging research over the past decade has revealed a detailed picture of the functional organization of the human brain. Here we focus on two fundamental questions that are raised by the detailed mapping of sensory and cognitive functions and illustrate these questions with findings from the object-vision pathway. First, are functionally specific regions that are located close together best understood as distinct cortical modules or as parts of a larger-scale cortical map? Second, what functional properties define each cortical map or module? We propose a model in which overlapping continuous maps of simple features give rise to discrete modules that are selective for complex stimuli. PMID:18200027

  8. fMRI activation maps based on the NN-ARx model.

    PubMed

    Riera, J; Bosch, J; Yamashita, O; Kawashima, R; Sadato, N; Okada, T; Ozaki, T

    2004-10-01

    The most significant progresses in the understanding of human brain functions have been possible due to the use of functional magnetic resonance imaging (fMRI), which when used in combination with other standard neuroimaging techniques (i.e., EEG) provides researchers with a potential tool to elucidate many biophysical principles, established previously by animal comparative studies. However, to date, most of the methods proposed in the literature seeking fMRI signs have been limited to the use of a top-down data analysis approach, thus ignoring a pool of physiological facts. In spite of the important contributions achieved by applying these methods to actual data, there is a disproportionate gap between theoretical models and data-analysis strategies while trying to focus on several new prospects, like for example fMRI/EEG data fusion, causality/connectivity patterns, and nonlinear BOLD signal dynamics. In this paper, we propose a new approach which will allow many of the abovementioned hot topics to be addressed in the near future with an underlying interpretability based on bottom-up modeling. In particular, the theta-MAP presented in the paper to test brain activation corresponds very well with the standardized t test of the SPM99 toolbox. Additionally, a new Impulse Response Function (IRF) has been formulated, directly related to the well-established concept of the hemodynamics response function (HRF). The model uses not only the information contained in the signal but also that in the structure of the background noise to simultaneously estimate the IRF and the autocorrelation function (ACF) by using an autoregressive (AR) model with a filtered Poisson process driving the dynamics. The short-range contributions of voxels within the near-neighborhood are also included, and the potential drift was characterized by a polynomial series. Since our model originated from an immediate extension of the hemodynamics approach [Friston, K.J., Mechelli, A., Turner, R

  9. Shape based MRI prostate image segmentation using local information driven directional distance Bayesian method

    NASA Astrophysics Data System (ADS)

    Gao, Yi; Tannenbaum, Allen

    2010-03-01

    In this paper, we present a shape based segmentation methodology for magnetic resonance prostate images. We first propose a new way to represent shapes via the hyperbolic tangent of the signed distance function. This effectively corrects the drawbacks of the signed distance function and yields very reasonable results for the shape registration and learning. Secondly, under a Bayesian statistical framework, instead of computing the posterior using a uniform prior, a directional distance map is introduced in order to incorporate a priori knowledge of image content as well as the estimated center of target object. Essentially, the image is modeled as a Finsler manifold and the metric is computed out of the directional derivative of the image. Then the directional distance map is computed to suppress the posterior remote from the object center. Thirdly, in the posterior image, a localized region based cost functional is designed to drive the shape based segmentation. Such cost functional utilizes the local regional information and is robust to both image noise and remote/irrelevant disturbances. With these three major components, the entire shape based segmentation procedure is provided as a complete open source pipeline and is applied to magnetic resonance image (MRI) prostate data.

  10. Integrated Analysis of EEG and fMRI Using Sparsity of Spatial Maps.

    PubMed

    Samadi, S; Soltanian-Zadeh, H; Jutten, C

    2016-09-01

    Integration of electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) is an open problem, which has motivated many researches. The most important challenge in EEG-fMRI integration is the unknown relationship between these two modalities. In this paper, we extract the same features (spatial map of neural activity) from both modality. Therefore, the proposed integration method does not need any assumption about the relationship of EEG and fMRI. We present a source localization method from scalp EEG signal using jointly fMRI analysis results as prior spatial information and source separation for providing temporal courses of sources of interest. The performance of the proposed method is evaluated quantitatively along with multiple sparse priors method and sparse Bayesian learning with the fMRI results as prior information. Localization bias and source distribution index are used to measure the performance of different localization approaches with or without a variety of fMRI-EEG mismatches on simulated realistic data. The method is also applied to experimental data of face perception of 16 subjects. Simulation results show that the proposed method is significantly stable against the noise with low localization bias. Although the existence of an extra region in the fMRI data enlarges localization bias, the proposed method outperforms the other methods. Conversely, a missed region in the fMRI data does not affect the localization bias of the common sources in the EEG-fMRI data. Results on experimental data are congruent with previous studies and produce clusters in the fusiform and occipital face areas (FFA and OFA, respectively). Moreover, it shows high stability in source localization against variations in different subjects. PMID:27460558

  11. Decision forests for learning prostate cancer probability maps from multiparametric MRI

    NASA Astrophysics Data System (ADS)

    Ehrenberg, Henry R.; Cornfeld, Daniel; Nawaf, Cayce B.; Sprenkle, Preston C.; Duncan, James S.

    2016-03-01

    Objectives: Advances in multiparametric magnetic resonance imaging (mpMRI) and ultrasound/MRI fusion imaging offer a powerful alternative to the typical undirected approach to diagnosing prostate cancer. However, these methods require the time and expertise needed to interpret mpMRI image scenes. In this paper, a machine learning framework for automatically detecting and localizing cancerous lesions within the prostate is developed and evaluated. Methods: Two studies were performed to gather MRI and pathology data. The 12 patients in the first study underwent an MRI session to obtain structural, diffusion-weighted, and dynamic contrast enhanced image vol- umes of the prostate, and regions suspected of being cancerous from the MRI data were manually contoured by radiologists. Whole-mount slices of the prostate were obtained for the patients in the second study, in addition to structural and diffusion-weighted MRI data, for pathology verification. A 3-D feature set for voxel-wise appear- ance description combining intensity data, textural operators, and zonal approximations was generated. Voxels in a test set were classified as normal or cancer using a decision forest-based model initialized using Gaussian discriminant analysis. A leave-one-patient-out cross-validation scheme was used to assess the predictions against the expert manual segmentations confirmed as cancer by biopsy. Results: We achieved an area under the average receiver-operator characteristic curve of 0.923 for the first study, and visual assessment of the probability maps showed 21 out of 22 tumors were identified while a high level of specificity was maintained. In addition to evaluating the model against related approaches, the effects of the individual MRI parameter types were explored, and pathological verification using whole-mount slices from the second study was performed. Conclusions: The results of this paper show that the

  12. Imaging whole-brain cytoarchitecture of mouse with MRI-based quantitative susceptibility mapping.

    PubMed

    Wei, Hongjiang; Xie, Luke; Dibb, Russell; Li, Wei; Decker, Kyle; Zhang, Yuyao; Johnson, G Allan; Liu, Chunlei

    2016-08-15

    The proper microstructural arrangement of complex neural structures is essential for establishing the functional circuitry of the brain. We present an MRI method to resolve tissue microstructure and infer brain cytoarchitecture by mapping the magnetic susceptibility in the brain at high resolution. This is possible because of the heterogeneous magnetic susceptibility created by varying concentrations of lipids, proteins and irons from the cell membrane to cytoplasm. We demonstrate magnetic susceptibility maps at a nominal resolution of 10-μm isotropic, approaching the average cell size of a mouse brain. The maps reveal many detailed structures including the retina cell layers, olfactory sensory neurons, barrel cortex, cortical layers, axonal fibers in white and gray matter. Olfactory glomerulus density is calculated and structural connectivity is traced in the optic nerve, striatal neurons, and brainstem nerves. The method is robust and can be readily applied on MRI scanners at or above 7T. PMID:27181764

  13. T₂ distribution mapping profiles with phase-encode MRI.

    PubMed

    Petrov, Oleg V; Ersland, Geir; Balcom, Bruce J

    2011-03-01

    Two 1-D phase-encode sequences for T₂ mapping, namely CPMG-prepared SPRITE and spin-echo SPI, are presented and compared in terms of image quality, accuracy of T₂ measurements and the measurement time. The sequences implement two different approaches to acquiring T₂-weighted images: in the CPMG-prepared SPRITE, the T₂-weighting of magnetization precedes the spatial encoding, while in the spin-echo SPI, the T₂-weighting follows the spatial encoding. The sequences are intended primarily for T₂ mapping of fluids in porous solids, where using frequency encode techniques may be problematic either due to local gradient distortions or too short T₂. Their possible applications include monitoring fluid-flow processes in rocks, cement paste hydration, curing of rubber, filtering paramagnetic impurities and other processes accomplished by changing site-specific T₂. PMID:21239194

  14. Transspinal direct current stimulation immediately modifies motor cortex sensorimotor maps

    PubMed Central

    Song, Weiguo; Truong, Dennis Q.; Bikson, Marom

    2015-01-01

    Motor cortex (MCX) motor representation reorganization occurs after injury, learning, and different long-term stimulation paradigms. The neuromodulatory approach of transspinal direct current stimulation (tsDCS) has been used to promote evoked cortical motor responses. In the present study, we used cathodal tsDCS (c-tsDCS) of the rat cervical cord to determine if spinal cord activation can modify the MCX forelimb motor map. We used a finite-element method model based on coregistered high-resolution rat MRI and microcomputed tomography imaging data to predict spinal current density to target stimulation to the caudal cervical enlargement. We examined the effects of cathodal and anodal tsDCS on the H-reflex and c-tsDCS on responses evoked by intracortical microstimulation (ICMS). To determine if cervical c-tsDCS also modified MCX somatic sensory processing, we examined sensory evoked potentials (SEPs) produced by wrist electrical stimulation and induced changes in ongoing activity. Cervical c-tsDCS enhanced the H-reflex, and anodal depressed the H-reflex. Using cathodal stimulation to examine cortical effects, we found that cervical c-tsDCS immediately modified the forelimb MCX motor map, with decreased thresholds and an expanded area. c-tsDCS also increased SEP amplitude in the MCX. The magnitude of changes produced by c-tsDCS were greater on the motor than sensory response. Cervical c-tsDCS more strongly enhanced forelimb than hindlimb motor representation and had no effect on vibrissal representation. The finite-element model indicated current density localized to caudal cervical segments, informing forelimb motor selectivity. Our results suggest that c-tsDCS augments spinal excitability in a spatially selective manner and may improve voluntary motor function through MCX representational plasticity. PMID:25673738

  15. Probabilistic atlas-based segmentation of combined T1-weighted and DUTE MRI for calculation of head attenuation maps in integrated PET/MRI scanners

    PubMed Central

    Poynton, Clare B; Chen, Kevin T; Chonde, Daniel B; Izquierdo-Garcia, David; Gollub, Randy L; Gerstner, Elizabeth R; Batchelor, Tracy T; Catana, Ciprian

    2014-01-01

    We present a new MRI-based attenuation correction (AC) approach for integrated PET/MRI systems that combines both segmentation- and atlas-based methods by incorporating dual-echo ultra-short echo-time (DUTE) and T1-weighted (T1w) MRI data and a probabilistic atlas. Segmented atlases were constructed from CT training data using a leave-one-out framework and combined with T1w, DUTE, and CT data to train a classifier that computes the probability of air/soft tissue/bone at each voxel. This classifier was applied to segment the MRI of the subject of interest and attenuation maps (μ-maps) were generated by assigning specific linear attenuation coefficients (LACs) to each tissue class. The μ-maps generated with this “Atlas-T1w-DUTE” approach were compared to those obtained from DUTE data using a previously proposed method. For validation of the segmentation results, segmented CT μ-maps were considered to the “silver standard”; the segmentation accuracy was assessed qualitatively and quantitatively through calculation of the Dice similarity coefficient (DSC). Relative change (RC) maps between the CT and MRI-based attenuation corrected PET volumes were also calculated for a global voxel-wise assessment of the reconstruction results. The μ-maps obtained using the Atlas-T1w-DUTE classifier agreed well with those derived from CT; the mean DSCs for the Atlas-T1w-DUTE-based μ-maps across all subjects were higher than those for DUTE-based μ-maps; the atlas-based μ-maps also showed a lower percentage of misclassified voxels across all subjects. RC maps from the atlas-based technique also demonstrated improvement in the PET data compared to the DUTE method, both globally as well as regionally. PMID:24753982

  16. Functional Topography of Human Corpus Callosum: An fMRI Mapping Study

    PubMed Central

    Fabri, Mara; Polonara, Gabriele

    2013-01-01

    The concept of a topographical map of the corpus callosum (CC) has emerged from human lesion studies and from electrophysiological and anatomical tracing investigations in other mammals. Over the last few years a rising number of researchers have been reporting functional magnetic resonance imaging (fMRI) activation in white matter, particularly the CC. In this study the scope for describing CC topography with fMRI was explored by evoking activation through simple sensory stimulation and motor tasks. We reviewed our published and unpublished fMRI and diffusion tensor imaging data on the cortical representation of tactile, gustatory, auditory, and visual sensitivity and of motor activation, obtained in 36 normal volunteers and in 6 patients with partial callosotomy. Activation foci were consistently detected in discrete CC regions: anterior (taste stimuli), central (motor tasks), central and posterior (tactile stimuli), and splenium (auditory and visual stimuli). Reconstruction of callosal fibers connecting activated primary gustatory, motor, somatosensory, auditory, and visual cortices by diffusion tensor tracking showed bundles crossing, respectively, through the genu, anterior and posterior body, and splenium, at sites harboring fMRI foci. These data confirm that the CC commissure has a topographical organization and demonstrate that its functional topography can be explored with fMRI. PMID:23476810

  17. Mapping the mouse brain with rs-fMRI: An optimized pipeline for functional network identification.

    PubMed

    Zerbi, Valerio; Grandjean, Joanes; Rudin, Markus; Wenderoth, Nicole

    2015-12-01

    The use of resting state fMRI (rs-fMRI) in translational research is a powerful tool to assess brain connectivity and investigate neuropathology in mouse models. However, despite encouraging initial results, the characterization of consistent and robust resting state networks in mice remains a methodological challenge. One key reason is that the quality of the measured MR signal is degraded by the presence of structural noise from non-neural sources. Notably, in the current pipeline of the Human Connectome Project, a novel approach has been introduced to clean rs-fMRI data, which involves automatic artifact component classification and data cleaning (FIX). FIX does not require any external recordings of physiology or the segmentation of CSF and white matter. In this study, we evaluated the performance of FIX for analyzing mouse rs-fMRI data. Our results showed that FIX can be easily applied to mouse datasets and detects true signals with 100% accuracy and true noise components with very high accuracy (>98%), thus reducing both within- and between-subject variability of rs-fMRI connectivity measurements. Using this improved pre-processing pipeline, maps of 23 resting state circuits in mice were identified including two networks that displayed default mode network-like topography. Hierarchical clustering grouped these neural networks into meaningful larger functional circuits. These mouse resting state networks, which are publicly available, might serve as a reference for future work using mouse models of neurological disorders.

  18. MRI

    MedlinePlus

    MRI does not use ionizing radiation. No side effects from the magnetic fields and radio waves have been reported. The most common type of contrast (dye) used is gadolinium. It is very safe. Allergic reactions rarely ...

  19. Accelerating patch-based directional wavelets with multicore parallel computing in compressed sensing MRI.

    PubMed

    Li, Qiyue; Qu, Xiaobo; Liu, Yunsong; Guo, Di; Lai, Zongying; Ye, Jing; Chen, Zhong

    2015-06-01

    Compressed sensing MRI (CS-MRI) is a promising technology to accelerate magnetic resonance imaging. Both improving the image quality and reducing the computation time are important for this technology. Recently, a patch-based directional wavelet (PBDW) has been applied in CS-MRI to improve edge reconstruction. However, this method is time consuming since it involves extensive computations, including geometric direction estimation and numerous iterations of wavelet transform. To accelerate computations of PBDW, we propose a general parallelization of patch-based processing by taking the advantage of multicore processors. Additionally, two pertinent optimizations, excluding smooth patches and pre-arranged insertion sort, that make use of sparsity in MR images are also proposed. Simulation results demonstrate that the acceleration factor with the parallel architecture of PBDW approaches the number of central processing unit cores, and that pertinent optimizations are also effective to make further accelerations. The proposed approaches allow compressed sensing MRI reconstruction to be accomplished within several seconds.

  20. Quantitative NumART2* mapping in functional MRI studies at 1.5 T.

    PubMed

    Hagberg, Gisela E; Bianciardi, Marta; Patria, Fabiana; Indovina, Iole

    2003-12-01

    Quantitative mapping of the effective transverse relaxation time, T2* and proton density was performed in a motor activation functional MRI (fMRI) study using multi-echo, echo planar imaging (EPI) and NumART2* (Numerical Algorithm for Real time T2*). Comparisons between NumART2* and conventional single echo EPI with an echo time of 64 ms were performed for five healthy participants examined twice. Simulations were also performed to address specific issues associated with the two techniques, such as echo time-dependent signal variation. While the single echo contrast varied with the baseline T2* value, relative changes in T2* remained unaffected. Statistical analysis of the T2* maps yielded fMRI activation patterns with an improved statistical detection relative to conventional EPI but with less activated voxels, suggesting that NumART2* has superior spatial specificity. Two effects, inflow and dephasing, that may explain this finding were investigated. Particularly, a statistically significant increase in proton density was found in a brain area that was detected as activated by conventional EPI but not by NumART2* while no such changes were observed in brain areas that showed stimulus correlated signal changes on T2* maps.

  1. Head direction maps remain stable despite grid map fragmentation

    PubMed Central

    Whitlock, Jonathan R.; Derdikman, Dori

    2012-01-01

    Areas encoding space in the brain contain both representations of position (place cells and grid cells) and representations of azimuth (head direction cells). Previous studies have already suggested that although grid cells and head direction cells reside in the same brain areas, the calculation of head direction is not dependent on the calculation of position. Here we demonstrate that realignment of grid cells does not affect head direction tuning. We analyzed head direction cell data collected while rats performed a foraging task in a multi-compartment environment (the hairpin maze) vs. an open-field environment, demonstrating that the tuning of head direction cells did not change when the environment was divided into multiple sub-compartments, in the hairpin maze. On the other hand, as we have shown previously (Derdikman et al., 2009), the hexagonal firing pattern expressed by grid cells in the open-field broke down into repeating patterns in similar alleys when rats traversed the multi-compartment hairpin maze. The grid-like firing of conjunctive cells, which express both grid properties and head direction properties in the open-field, showed a selective fragmentation of grid-like firing properties in the hairpin maze, while the head directionality property of the same cells remained unaltered. These findings demonstrate that head direction is not affected during the restructuring of grid cell firing fields as a rat actively moves between compartments, thus strengthening the claim that the head direction system is upstream from or parallel to the grid-place system. PMID:22479237

  2. Recovery of directed intracortical connectivity from fMRI data

    NASA Astrophysics Data System (ADS)

    Gilson, Matthieu; Ritter, Petra; Deco, Gustavo

    2016-06-01

    The brain exhibits complex spatio-temporal patterns of activity. In particular, its baseline activity at rest has a specific structure: imaging techniques (e.g., fMRI, EEG and MEG) show that cortical areas experience correlated fluctuations, which is referred to as functional connectivity (FC). The present study relies on our recently developed model in which intracortical white-matter connections shape noise-driven fluctuations to reproduce FC observed in experimental data (here fMRI BOLD signal). Here noise has a functional role and represents the variability of neural activity. The model also incorporates anatomical information obtained using diffusion tensor imaging (DTI), which estimates the density of white-matter fibers (structural connectivity, SC). After optimization to match empirical FC, the model provides an estimation of the efficacies of these fibers, which we call effective connectivity (EC). EC differs from SC, as EC not only accounts for the density of neural fibers, but also the concentration of synapses formed at their end, the type of neurotransmitters associated and the excitability of target neural populations. In summary, the model combines anatomical SC and activity FC to evaluate what drives the neural dynamics, embodied in EC. EC can then be analyzed using graph theory to understand how it generates FC and to seek for functional communities among cortical areas (parcellation of 68 areas). We find that intracortical connections are not symmetric, which affects the dynamic range of cortical activity (i.e., variety of states it can exhibit).

  3. Assessing the sensitivity of diffusion MRI to detect neuronal activity directly.

    PubMed

    Bai, Ruiliang; Stewart, Craig V; Plenz, Dietmar; Basser, Peter J

    2016-03-22

    Functional MRI (fMRI) is widely used to study brain function in the neurosciences. Unfortunately, conventional fMRI only indirectly assesses neuronal activity via hemodynamic coupling. Diffusion fMRI was proposed as a more direct and accurate fMRI method to detect neuronal activity, yet confirmative findings have proven difficult to obtain. Given that the underlying relation between tissue water diffusion changes and neuronal activity remains unclear, the rationale for using diffusion MRI to monitor neuronal activity has yet to be clearly established. Here, we studied the correlation between water diffusion and neuronal activity in vitro by simultaneous calcium fluorescence imaging and diffusion MR acquisition. We used organotypic cortical cultures from rat brains as a biological model system, in which spontaneous neuronal activity robustly emerges free of hemodynamic and other artifacts. Simultaneous fluorescent calcium images of neuronal activity are then directly correlated with diffusion MR signals now free of confounds typically encountered in vivo. Although a simultaneous increase of diffusion-weighted MR signals was observed together with the prolonged depolarization of neurons induced by pharmacological manipulations (in which cell swelling was demonstrated to play an important role), no evidence was found that diffusion MR signals directly correlate with normal spontaneous neuronal activity. These results suggest that, whereas current diffusion MR methods could monitor pathological conditions such as hyperexcitability, e.g., those seen in epilepsy, they do not appear to be sensitive or specific enough to detect or follow normal neuronal activity.

  4. Assessing the sensitivity of diffusion MRI to detect neuronal activity directly

    PubMed Central

    Bai, Ruiliang; Stewart, Craig V.; Plenz, Dietmar; Basser, Peter J.

    2016-01-01

    Functional MRI (fMRI) is widely used to study brain function in the neurosciences. Unfortunately, conventional fMRI only indirectly assesses neuronal activity via hemodynamic coupling. Diffusion fMRI was proposed as a more direct and accurate fMRI method to detect neuronal activity, yet confirmative findings have proven difficult to obtain. Given that the underlying relation between tissue water diffusion changes and neuronal activity remains unclear, the rationale for using diffusion MRI to monitor neuronal activity has yet to be clearly established. Here, we studied the correlation between water diffusion and neuronal activity in vitro by simultaneous calcium fluorescence imaging and diffusion MR acquisition. We used organotypic cortical cultures from rat brains as a biological model system, in which spontaneous neuronal activity robustly emerges free of hemodynamic and other artifacts. Simultaneous fluorescent calcium images of neuronal activity are then directly correlated with diffusion MR signals now free of confounds typically encountered in vivo. Although a simultaneous increase of diffusion-weighted MR signals was observed together with the prolonged depolarization of neurons induced by pharmacological manipulations (in which cell swelling was demonstrated to play an important role), no evidence was found that diffusion MR signals directly correlate with normal spontaneous neuronal activity. These results suggest that, whereas current diffusion MR methods could monitor pathological conditions such as hyperexcitability, e.g., those seen in epilepsy, they do not appear to be sensitive or specific enough to detect or follow normal neuronal activity. PMID:26941239

  5. Direction Estimation Using Square Lattice and Cadastral Map Assembling

    NASA Astrophysics Data System (ADS)

    Takahashi, Yusuke; Fei, Liu; Ohyama, Wataru; Wakabayashi, Tetsushi; Kimura, Fumitaka

    This paper proposes a technique for direction estimation by means of square grid points in order to improve the performance of cadastral map assembling technique based on Merlin-Farber (MF) algorithm. The MF algorithm requires direction normalization of the segments (of cadastral map) preceding the assembling. Proposed direction estimation technique is based on the spatial frequency analysis of autocorrelation by MF algorithm for the square grid points regularly drawn with constant intervals on the segments. Since many square grid points are drawn over entire area of the segments the direction can be estimated more accurately with those points when compared the direction is estimated with single north arrow. To assemble two adjacent segments the longest common boundary is detected by MF algorithm. Evaluation experiments are performed to compare the accuracy and the success rate of map assembling when the direction is estimated and normalized based on the square grid points and when estimated and normalized based on the north arrow. Total of 324 map segments of 47 district provided by Institut Geographique National France are used in the experiments. While the map assembling based on the north arrow tends to form inaccurate cadastral maps the proposed technique assembles the map more accurately. The results of experiments shows that the proposed technique achieves sufficient success rate and accuracy so that it effectively reduces the labor cost and time of the cadastral map assembling.

  6. Univalent harmonic mappings convex in one direction

    NASA Astrophysics Data System (ADS)

    Ponnusamy, S.; Kaliraj, A. Sairam

    2014-09-01

    In this paper, we present a criterion for a harmonic function to be convex in one direction. Also, we discuss the class of harmonic functions starlike in one direction in the unit disk and obtain a method to construct univalent harmonic functions convex in one direction. Although the converse of classical Alexander's theorem for harmonic functions was proved to be false, we obtain a version of converse of it under a suitable additional condition.

  7. Response Properties of Human Amygdala Subregions: Evidence Based on Functional MRI Combined with Probabilistic Anatomical Maps

    PubMed Central

    Rahm, Benjamin; Eickhoff, Simon B.; Schulze-Bonhage, Andreas; Speck, Oliver

    2007-01-01

    The human amygdala is thought to play a pivotal role in the processing of emotionally significant sensory information. The major subdivisions of the human amygdala—the laterobasal group (LB), the superficial group (SF), and the centromedial group (CM)—have been anatomically delineated, but the functional response properties of these amygdala subregions in humans are still unclear. We combined functional MRI with cyto-architectonically defined probabilistic maps to analyze the response characteristics of amygdala subregions in subjects presented with auditory stimuli. We found positive auditory stimulation-related signal changes predominantly in probabilistically defined LB, and negative responses predominantly in SF and CM. In the left amygdala, mean response magnitude in the core area of LB with 90–100% assignment probability was significantly larger than in the core areas of SF and CM. These differences were observed for pleasant and unpleasant stimuli. Our findings reveal that the probabilistically defined anatomical subregions of the human amygdala show distinctive fMRI response patterns. The stronger auditory responses in LB as compared with SF and CM may reflect a predominance of auditory inputs to human LB, similar to many animal species in which the majority of sensory, including auditory, afferents project to this subdivision of the amygdala. Our study indicates that the intrinsic functional differentiation of the human amygdala may be probed using fMRI combined with probabilistic anatomical maps. PMID:17375193

  8. Anatomically-adapted graph wavelets for improved group-level fMRI activation mapping.

    PubMed

    Behjat, Hamid; Leonardi, Nora; Sörnmo, Leif; Van De Ville, Dimitri

    2015-12-01

    A graph based framework for fMRI brain activation mapping is presented. The approach exploits the spectral graph wavelet transform (SGWT) for the purpose of defining an advanced multi-resolutional spatial transformation for fMRI data. The framework extends wavelet based SPM (WSPM), which is an alternative to the conventional approach of statistical parametric mapping (SPM), and is developed specifically for group-level analysis. We present a novel procedure for constructing brain graphs, with subgraphs that separately encode the structural connectivity of the cerebral and cerebellar gray matter (GM), and address the inter-subject GM variability by the use of template GM representations. Graph wavelets tailored to the convoluted boundaries of GM are then constructed as a means to implement a GM-based spatial transformation on fMRI data. The proposed approach is evaluated using real as well as semi-synthetic multi-subject data. Compared to SPM and WSPM using classical wavelets, the proposed approach shows superior type-I error control. The results on real data suggest a higher detection sensitivity as well as the capability to capture subtle, connected patterns of brain activity.

  9. Extensive Cochleotopic Mapping of Human Auditory Cortical Fields Obtained with Phase-Encoding fMRI

    PubMed Central

    Amedi, Amir

    2011-01-01

    The primary sensory cortices are characterized by a topographical mapping of basic sensory features which is considered to deteriorate in higher-order areas in favor of complex sensory features. Recently, however, retinotopic maps were also discovered in the higher-order visual, parietal and prefrontal cortices. The discovery of these maps enabled the distinction between visual regions, clarified their function and hierarchical processing. Could such extension of topographical mapping to high-order processing regions apply to the auditory modality as well? This question has been studied previously in animal models but only sporadically in humans, whose anatomical and functional organization may differ from that of animals (e.g. unique verbal functions and Heschl's gyrus curvature). Here we applied fMRI spectral analysis to investigate the cochleotopic organization of the human cerebral cortex. We found multiple mirror-symmetric novel cochleotopic maps covering most of the core and high-order human auditory cortex, including regions considered non-cochleotopic, stretching all the way to the superior temporal sulcus. These maps suggest that topographical mapping persists well beyond the auditory core and belt, and that the mirror-symmetry of topographical preferences may be a fundamental principle across sensory modalities. PMID:21448274

  10. Mapping mean axon diameter and axonal volume fraction by MRI using temporal diffusion spectroscopy

    PubMed Central

    Xu, Junzhong; Li, Hua; Harkins, Kevin D.; Jiang, Xiaoyu; Xie, Jingping; Kang, Hakmook; Does, Mark D.; Gore, John C.

    2014-01-01

    Mapping mean axon diameter and intra-axonal volume fraction may have significant clinical potential because nerve conduction velocity is directly dependent on axon diameter, and several neurodegenerative diseases affect axons of specific sizes and alter axon counts. Diffusion-weighted MRI methods based on the pulsed gradient spin echo (PGSE) sequence have been reported to be able to assess axon diameter and volume fraction non-invasively. However, due to the relatively long diffusion times used, e.g. > 20 ms, the sensitivity to small axons (diameter < 2 µm) is low, and the derived mean axon diameter has been reported to be overestimated. In the current study, oscillating gradient spin echo (OGSE) diffusion sequences with variable frequency gradients were used to assess rat spinal white matter tracts with relatively short effective diffusion times (1 – 5 ms). In contrast to previous PGSE-based methods, the extra-axonal diffusion cannot be modeled as hindered (Gaussian) diffusion when short diffusion times are used. Appropriate frequency-dependent rates are therefore incorporated into our analysis and validated by histology-based computer simulation of water diffusion. OGSE data were analyzed to derive mean axon diameters and intra-axonal volume fractions of rat spinal white matter tracts (mean axon diameter ~ 1.27 – 5.54 µm). The estimated values were in good agreement with histology, including the small axon diameters (< 2.5 µm). This study establishes a framework for quantification of nerve morphology using the OGSE method with high sensitivity to small axons. PMID:25225002

  11. Quantitative susceptibility mapping (QSM): Decoding MRI data for a tissue magnetic biomarker

    PubMed Central

    Wang, Yi; Liu, Tian

    2015-01-01

    In MRI, the main magnetic field polarizes the electron cloud of a molecule, generating a chemical shift for observer protons within the molecule and a magnetic susceptibility inhomogeneity field for observer protons outside the molecule. The number of water protons surrounding a molecule for detecting its magnetic susceptibility is vastly greater than the number of protons within the molecule for detecting its chemical shift. However, the study of tissue magnetic susceptibility has been hindered by poor molecular specificities of hitherto used methods based on MRI signal phase and T2* contrast, which depend convolutedly on surrounding susceptibility sources. Deconvolution of the MRI signal phase can determine tissue susceptibility but is challenged by the lack of MRI signal in the background and by the zeroes in the dipole kernel. Recently, physically meaningful regularizations, including the Bayesian approach, have been developed to enable accurate quantitative susceptibility mapping (QSM) for studying iron distribution, metabolic oxygen consumption, blood degradation, calcification, demyelination, and other pathophysiological susceptibility changes, as well as contrast agent biodistribution in MRI. This paper attempts to summarize the basic physical concepts and essential algorithmic steps in QSM, to describe clinical and technical issues under active development, and to provide references, codes, and testing data for readers interested in QSM. Magn Reson Med 73:82–101, 2015. © 2014 The Authors. Magnetic Resonance in Medicine Published by Wiley Periodicals, Inc. on behalf of International Society of Medicine in Resonance. This is an open access article under the terms of the Creative commons Attribution License, which permits use, distribution, and reproduction in any medium, provided the original work is properly cited. PMID:25044035

  12. Mapping human preictal and ictal haemodynamic networks using simultaneous intracranial EEG-fMRI.

    PubMed

    Chaudhary, Umair J; Centeno, Maria; Thornton, Rachel C; Rodionov, Roman; Vulliemoz, Serge; McEvoy, Andrew W; Diehl, Beate; Walker, Matthew C; Duncan, John S; Carmichael, David W; Lemieux, Louis

    2016-01-01

    Accurately characterising the brain networks involved in seizure activity may have important implications for our understanding of epilepsy. Intracranial EEG-fMRI can be used to capture focal epileptic events in humans with exquisite electrophysiological sensitivity and allows for identification of brain structures involved in this phenomenon over the entire brain. We investigated ictal BOLD networks using the simultaneous intracranial EEG-fMRI (icEEG-fMRI) in a 30 year-old male undergoing invasive presurgical evaluation with bilateral depth electrode implantations in amygdalae and hippocampi for refractory temporal lobe epilepsy. One spontaneous focal electrographic seizure was recorded. The aims of the data analysis were firstly to map BOLD changes related to the ictal activity identified on icEEG and secondly to compare different fMRI modelling approaches. Visual inspection of the icEEG showed an onset dominated by beta activity involving the right amygdala and hippocampus lasting 6.4 s (ictal onset phase), followed by gamma activity bilaterally lasting 14.8 s (late ictal phase). The fMRI data was analysed using SPM8 using two modelling approaches: firstly, purely based on the visually identified phases of the seizure and secondly, based on EEG spectral dynamics quantification. For the visual approach the two ictal phases were modelled as 'ON' blocks convolved with the haemodynamic response function; in addition the BOLD changes during the 30 s preceding the onset were modelled using a flexible basis set. For the quantitative fMRI modelling approach two models were evaluated: one consisting of the variations in beta and gamma bands power, thereby adding a quantitative element to the visually-derived models, and another based on principal components analysis of the entire spectrogram in attempt to reduce the bias associated with the visual appreciation of the icEEG. BOLD changes related to the visually defined ictal onset phase were revealed in the medial and

  13. Decoding the subjective rotation direction of the spinning dancer from fMRI data

    NASA Astrophysics Data System (ADS)

    Song, SuTao; Liu, Yang; Zhang, JiaCai

    2015-03-01

    A challenging goal in neuroscience is to decode the mental states from brain activity. Recently, researchers have successfully deciphered the objective and static visual stimuli (such as orientation of stripes and category of objects) from brain activity recorded by functional magnetic resonance imaging (fMRI) technology. However, few studies focused on the decoding of the rotation direction perception of the actual three-dimensional world with two-dimensional representations. In this study, the brain activities when subjects viewed the animation of the spinning dancer in the front were recorded using fMRI, and subjects reported the viewing-from-bottom motion direction (clockwise or counterclockwise) by press different buttons. One multivariate pattern analysis method, support vector machine was trained to predict the rotation direction. The 5-fold cross-validation result showed that the subjective rotation direction reported by the subjects can be predicted from fMRI with a possibility above the chance level, which imply that fMRI activity of the brain contains detailed rotation direction information that can reliably predict the subjective perception.

  14. Direct Mapping of Hippocampal Surfaces with Intrinsic Shape Context

    PubMed Central

    Shi, Yonggang; Thompson, Paul M.; de Zubicaray, Greig I.; Rose, Stephen E.; Tu, Zhuowen; Dinov, Ivo; Toga, Arthur W.

    2007-01-01

    We propose in this paper a new method for the mapping of hippocampal (HC) surfaces to establish correspondences between points on HC surfaces and enable localized HC shape analysis. A novel geometric feature, the intrinsic shape context, is defined to capture the global characteristics of the HC shapes. Based on this intrinsic feature, an automatic algorithm is developed to detect a set of landmark curves that are stable across population. The direct map between a source and target HC surface is then solved as the minimizer of a harmonic energy function defined on the source surface with landmark constraints. For numerical solutions, we compute the map with the approach of solving partial differential equations on implicit surfaces. The direct mapping method has the following properties: 1) it has the advantage of being automatic; 2) it is invariant to the pose of HC shapes. In our experiments, we apply the direct mapping method to study temporal changes of HC asymmetry in Alzheimer disease (AD) using HC surfaces from 12 AD patients and 14 normal controls. Our results show that the AD group has a different trend in temporal changes of HC asymmetry than the group of normal controls. We also demonstrate the flexibility of the direct mapping method by applying it to construct spherical maps of HC surfaces. Spherical harmonics (SPHARM) analysis is then applied and it confirms our results about temporal changes of HC asymmetry in AD. PMID:17625918

  15. Resting-state fMRI can reliably map neural networks in children.

    PubMed

    Thomason, Moriah E; Dennis, Emily L; Joshi, Anand A; Joshi, Shantanu H; Dinov, Ivo D; Chang, Catie; Henry, Melissa L; Johnson, Rebecca F; Thompson, Paul M; Toga, Arthur W; Glover, Gary H; Van Horn, John D; Gotlib, Ian H

    2011-03-01

    Resting-state MRI (rs-fMRI) is a powerful procedure for studying whole-brain neural connectivity. In this study we provide the first empirical evidence of the longitudinal reliability of rs-fMRI in children. We compared rest-retest measurements across spatial, temporal and frequency domains for each of six cognitive and sensorimotor intrinsic connectivity networks (ICNs) both within and between scan sessions. Using Kendall'sW, concordance of spatial maps ranged from .60 to .86 across networks, for various derived measures. The Pearson correlation coefficient for temporal coherence between networks across all Time 1-Time 2 (T1/T2) z-converted measures was .66 (p<.001). There were no differences between T1/T2 measurements in low-frequency power of the ICNs. For the visual network, within-session T1 correlated with the T2 low-frequency power, across participants. These measures from resting-state data in children were consistent across multiple domains (spatial, temporal, and frequency). Resting-state connectivity is therefore a reliable method for assessing large-scale brain networks in children. PMID:21134471

  16. MRI-based elastic-mapping method for inter-subject comparison of brain FDG-PET images

    SciTech Connect

    Yang, J.; Huang, S.C.; Lin, K.P.; Small, G.; Phelps, M.E.

    1996-12-31

    Inter-subject anatomic differences prohibits direct image-wise statistical evaluation of brain FDG-PET images of Alzheimer`s disease (AD) patients. In this study, we propose a MRI-based elastic-mapping method which enables image-wise evaluation. The method involves intra-subject MR-PET registration, 3-D elastic mapping of two set of MR images, and elastically transforming the co-registered PET images. The MR-PET registration used simulated PET images, which were based on segmentation of MR images. In the 3-D elastic mapping stage, first a global linear scaling was applied to compensate for brain size difference, then a deformation field was obtained by minimizing the regional sum of squared difference between the two sets of MR images. Two groups (AD patient and normal control), each with three subjects, were included in the current study. After processing, images from all subjects have similar shapes. Averaging the images across all subjects (either within the individual group or for both groups) give images indistinguishable from original single subject FDG images (i.e. without much spatial resolution loss), except with lower image noise level. The method is expected to allow statistical image-wise analysis to be performed across different subjects.

  17. Fine-grained mapping of mouse brain functional connectivity with resting-state fMRI.

    PubMed

    Mechling, Anna E; Hübner, Neele S; Lee, Hsu-Lei; Hennig, Jürgen; von Elverfeldt, Dominik; Harsan, Laura-Adela

    2014-08-01

    Understanding the intrinsic circuit-level functional organization of the brain has benefited tremendously from the advent of resting-state fMRI (rsfMRI). In humans, resting-state functional network has been consistently mapped and its alterations have been shown to correlate with symptomatology of various neurological or psychiatric disorders. To date, deciphering the mouse brain functional connectivity (MBFC) with rsfMRI remains a largely underexplored research area, despite the plethora of human brain disorders that can be modeled in this specie. To pave the way from pre-clinical to clinical investigations we characterized here the intrinsic architecture of mouse brain functional circuitry, based on rsfMRI data acquired at 7T using the Cryoprobe technology. High-dimensional spatial group independent component analysis demonstrated fine-grained segregation of cortical and subcortical networks into functional clusters, overlapping with high specificity onto anatomical structures, down to single gray matter nuclei. These clusters, showing a high level of stability and reliability in their patterning, formed the input elements for computing the MBFC network using partial correlation and graph theory. Its topological architecture conserved the fundamental characteristics described for the human and rat brain, such as small-worldness and partitioning into functional modules. Our results additionally showed inter-modular interactions via "network hubs". Each major functional system (motor, somatosensory, limbic, visual, autonomic) was found to have representative hubs that might play an important input/output role and form a functional core for information integration. Moreover, the rostro-dorsal hippocampus formed the highest number of relevant connections with other brain areas, highlighting its importance as core structure for MBFC.

  18. Two-dimensional T2 distribution mapping in porous solids with phase encode MRI.

    PubMed

    Petrov, Oleg V; Balcom, Bruce J

    2011-09-01

    Two pure phase encode MRI sequences, CPMG-prepared SPRITE and spin-echo SPI with compressed sensing, for two-dimensional (2-D) T2 distribution mapping have been presented. The sequences are 2-D extensions of their 1-D predecessors previously described and are intended for studying processes in porous solids and other samples with short relaxation times whenever 2-D T2 maps are preferable to simple 1-D profiling. The sequences were tested on model samples and natural water-saturated rocks, in a low field MRI instrument. 2-D spin-echo SPI and CPMG-SPRITE demonstrate a similar performance, enabling measurement of T2 down to 1-2 ms. Both experiments are time consuming (up to 2-2.5 h sample dependent). As such, they can be recommended mostly for measurement during steady state conditions or when studying relatively slow dynamic processes (e.g. enhanced oil recovery, cement paste hydration, curing rubber, infiltration of paramagnetic ions). PMID:21757381

  19. The brain mapping on reinforcement acupuncture stimulation at ST36 (zusanli) evidenced by fMRI.

    PubMed

    Xiao, Y Y; Chen, X K; Du, L; Pei, R Q; Chen, F Y; Liu, G R; Wu, R H

    2006-01-01

    To characterize the brain mapping on reinforcement acupuncture stimulation at ST36 (zusanli), and to discuss the mechanisms of acupuncture to treat diseases. fMRI was performed on 26 healthy Chinese student volunteers. Sixteen subjects were acupunctured at the acupoint ST36, while 10 others at sham-acupoint (lateral from ST36 about 3 cm). The fMRI studies were performed using a gradient echo-EPI sequence. Brain mapping were generated using GE Functool program. Cerebral blood flow and correlation coefficient (CC) of ROl were analyzed. Stimulation at the right ST36 elicited 13 brain functional areas, and 10 of these areas were the same with the sham-acupoint group. However, only the temporal gyrus was specificity while by using reinforcement manual acupuncture (MA) at ST36 (Fisher's Exact test, P=0.022), and the contralateral hemisphere activation was prominent (McNemer test, P=0.020). Our results support the theory of acupuncture about meridian distribution overlapping on the whole body. The special transmission channel of meridian may exists, and it may be consist of spinal nerve and autonomic nerve. However, our results may oppose the theory concerning on stomach meridian walking lateral.

  20. Functional MRI mapping of dynamic visual features during natural viewing in the macaque

    PubMed Central

    Russ, Brian E.; Leopold, David A.

    2015-01-01

    The ventral visual pathway of the primate brain is specialized to respond to stimuli in certain categories, such as the well-studied face selective patches in the macaque inferotemporal cortex. To what extent does response selectivity determined using brief presentations of isolated stimuli predict activity during the free viewing of a natural, dynamic scene, where features are superimposed in space and time? To approach this question, we obtained fMRI activity from the brains of three macaques viewing extended video clips containing a range of social and nonsocial content and compared the fMRI time courses to a family of feature models derived from the movie content. Starting with more than two dozen feature models extracted from each movie, we created functional maps based on features whose time courses were nearly orthogonal, focusing primarily on faces, motion content, and contrast level. Activity mapping using the face feature model readily yielded functional regions closely resembling face patches obtained using a block design in the same animals. Overall, the motion feature model dominated responses in nearly all visually driven areas, including the face patches as well as ventral visual areas V4, TEO, and TE. Control experiments presenting dynamic movies, whose content was free of animals, demonstrated that biological movement critically contributed to the predominance of motion in fMRI responses. These results highlight the value of natural viewing paradigms for studying the brain’s functional organization and also underscore the paramount contribution of magnocellular input to the ventral visual pathway during natural vision. PMID:25579448

  1. Functional MRI mapping of dynamic visual features during natural viewing in the macaque.

    PubMed

    Russ, Brian E; Leopold, David A

    2015-04-01

    The ventral visual pathway of the primate brain is specialized to respond to stimuli in certain categories, such as the well-studied face selective patches in the macaque inferotemporal cortex. To what extent does response selectivity determined using brief presentations of isolated stimuli predict activity during the free viewing of a natural, dynamic scene, where features are superimposed in space and time? To approach this question, we obtained fMRI activity from the brains of three macaques viewing extended video clips containing a range of social and nonsocial content and compared the fMRI time courses to a family of feature models derived from the movie content. Starting with more than two dozen feature models extracted from each movie, we created functional maps based on features whose time courses were nearly orthogonal, focusing primarily on faces, motion content, and contrast level. Activity mapping using the face feature model readily yielded functional regions closely resembling face patches obtained using a block design in the same animals. Overall, the motion feature model dominated responses in nearly all visually driven areas, including the face patches as well as ventral visual areas V4, TEO, and TE. Control experiments presenting dynamic movies, whose content was free of animals, demonstrated that biological movement critically contributed to the predominance of motion in fMRI responses. These results highlight the value of natural viewing paradigms for studying the brain's functional organization and also underscore the paramount contribution of magnocellular input to the ventral visual pathway during natural vision. PMID:25579448

  2. Accelerating patch-based directional wavelets with multicore parallel computing in compressed sensing MRI.

    PubMed

    Li, Qiyue; Qu, Xiaobo; Liu, Yunsong; Guo, Di; Lai, Zongying; Ye, Jing; Chen, Zhong

    2015-06-01

    Compressed sensing MRI (CS-MRI) is a promising technology to accelerate magnetic resonance imaging. Both improving the image quality and reducing the computation time are important for this technology. Recently, a patch-based directional wavelet (PBDW) has been applied in CS-MRI to improve edge reconstruction. However, this method is time consuming since it involves extensive computations, including geometric direction estimation and numerous iterations of wavelet transform. To accelerate computations of PBDW, we propose a general parallelization of patch-based processing by taking the advantage of multicore processors. Additionally, two pertinent optimizations, excluding smooth patches and pre-arranged insertion sort, that make use of sparsity in MR images are also proposed. Simulation results demonstrate that the acceleration factor with the parallel architecture of PBDW approaches the number of central processing unit cores, and that pertinent optimizations are also effective to make further accelerations. The proposed approaches allow compressed sensing MRI reconstruction to be accomplished within several seconds. PMID:25620521

  3. Sodium 3D COncentration MApping (COMA 3D) using 23Na and proton MRI

    NASA Astrophysics Data System (ADS)

    Truong, Milton L.; Harrington, Michael G.; Schepkin, Victor D.; Chekmenev, Eduard Y.

    2014-10-01

    Functional changes of sodium 3D MRI signals were converted into millimolar concentration changes using an open-source fully automated MATLAB toolbox. These concentration changes are visualized via 3D sodium concentration maps, and they are overlaid over conventional 3D proton images to provide high-resolution co-registration for easy correlation of functional changes to anatomical regions. Nearly 5000/h concentration maps were generated on a personal computer (ca. 2012) using 21.1 T 3D sodium MRI brain images of live rats with spatial resolution of 0.8 × 0.8 × 0.8 mm3 and imaging matrices of 60 × 60 × 60. The produced concentration maps allowed for non-invasive quantitative measurement of in vivo sodium concentration in the normal rat brain as a functional response to migraine-like conditions. The presented work can also be applied to sodium-associated changes in migraine, cancer, and other metabolic abnormalities that can be sensed by molecular imaging. The MATLAB toolbox allows for automated image analysis of the 3D images acquired on the Bruker platform and can be extended to other imaging platforms. The resulting images are presented in a form of series of 2D slices in all three dimensions in native MATLAB and PDF formats. The following is provided: (a) MATLAB source code for image processing, (b) the detailed processing procedures, (c) description of the code and all sub-routines, (d) example data sets of initial and processed data. The toolbox can be downloaded at: http://www.vuiis.vanderbilt.edu/~truongm/COMA3D/.

  4. Sodium 3D COncentration MApping (COMA 3D) using (23)Na and proton MRI.

    PubMed

    Truong, Milton L; Harrington, Michael G; Schepkin, Victor D; Chekmenev, Eduard Y

    2014-10-01

    Functional changes of sodium 3D MRI signals were converted into millimolar concentration changes using an open-source fully automated MATLAB toolbox. These concentration changes are visualized via 3D sodium concentration maps, and they are overlaid over conventional 3D proton images to provide high-resolution co-registration for easy correlation of functional changes to anatomical regions. Nearly 5000/h concentration maps were generated on a personal computer (ca. 2012) using 21.1T 3D sodium MRI brain images of live rats with spatial resolution of 0.8×0.8×0.8 mm(3) and imaging matrices of 60×60×60. The produced concentration maps allowed for non-invasive quantitative measurement of in vivo sodium concentration in the normal rat brain as a functional response to migraine-like conditions. The presented work can also be applied to sodium-associated changes in migraine, cancer, and other metabolic abnormalities that can be sensed by molecular imaging. The MATLAB toolbox allows for automated image analysis of the 3D images acquired on the Bruker platform and can be extended to other imaging platforms. The resulting images are presented in a form of series of 2D slices in all three dimensions in native MATLAB and PDF formats. The following is provided: (a) MATLAB source code for image processing, (b) the detailed processing procedures, (c) description of the code and all sub-routines, (d) example data sets of initial and processed data. The toolbox can be downloaded at: http://www.vuiis.vanderbilt.edu/~truongm/COMA3D/.

  5. Sodium 3D COncentration MApping (COMA 3D) using (23)Na and proton MRI.

    PubMed

    Truong, Milton L; Harrington, Michael G; Schepkin, Victor D; Chekmenev, Eduard Y

    2014-10-01

    Functional changes of sodium 3D MRI signals were converted into millimolar concentration changes using an open-source fully automated MATLAB toolbox. These concentration changes are visualized via 3D sodium concentration maps, and they are overlaid over conventional 3D proton images to provide high-resolution co-registration for easy correlation of functional changes to anatomical regions. Nearly 5000/h concentration maps were generated on a personal computer (ca. 2012) using 21.1T 3D sodium MRI brain images of live rats with spatial resolution of 0.8×0.8×0.8 mm(3) and imaging matrices of 60×60×60. The produced concentration maps allowed for non-invasive quantitative measurement of in vivo sodium concentration in the normal rat brain as a functional response to migraine-like conditions. The presented work can also be applied to sodium-associated changes in migraine, cancer, and other metabolic abnormalities that can be sensed by molecular imaging. The MATLAB toolbox allows for automated image analysis of the 3D images acquired on the Bruker platform and can be extended to other imaging platforms. The resulting images are presented in a form of series of 2D slices in all three dimensions in native MATLAB and PDF formats. The following is provided: (a) MATLAB source code for image processing, (b) the detailed processing procedures, (c) description of the code and all sub-routines, (d) example data sets of initial and processed data. The toolbox can be downloaded at: http://www.vuiis.vanderbilt.edu/~truongm/COMA3D/. PMID:25261742

  6. Probing neuronal activation by functional quantitative susceptibility mapping under a visual paradigm: A group level comparison with BOLD fMRI and PET.

    PubMed

    Özbay, Pinar Senay; Warnock, Geoffrey; Rossi, Cristina; Kuhn, Felix; Akin, Burak; Pruessmann, Klaas Paul; Nanz, Daniel

    2016-08-15

    Dynamic changes of brain-tissue magnetic susceptibility provide the basis for functional MR imaging (fMRI) via T2*-weighted signal-intensity modulations. Promising initial work on a detection of neuronal activity via quantitative susceptibility mapping (fQSM) has been published but consistently reported on ill-understood positive and negative activation patterns (Balla et al., 2014; Chen and Calhoun, 2015a). We set out to (i) demonstrate that fQSM can exploit established fMRI data acquisition and processing methods and to (ii) better describe aspects of the apparent activation patterns using fMRI and PET as standards of reference. Under a standardized visual-stimulation paradigm PET and 3-T gradient-echo EPI-based fQSM, fMRI data from 9 healthy volunteers were acquired and analyzed by means of Independent Component Analysis (ICA) at subject level and, for the first time, at group level. Numbers of activated (z-score>2.0) voxels were counted and their mean z-scores calculated in volumes of interest (occipital lobe (Nocc_lobe), segmented occipital gray-matter (NGM_occ_lobe), large veins (Nveins)), and in occipital-lobe voxels commonly activated in fQSM and fMRI component maps. Common but not entirely congruent regions of apparent activation were found in the occipital lobe in z-score maps from all modalities, fQSM, fMRI and PET, with distinct BOLD-negatively correlated regions in fQSM data. At subject-level, Nocc_lobe, NGM_occ_lobe and their mean z-scores were significantly smaller in fQSM than in fMRI, but their ratio, NGM_occ_lobe/Nocc_lobe, was comparable. Nveins did not statistically differ and the ratio Nveins/NGM_occ_lobe as well as the mean z-scores were higher for fQSM than for fMRI. In veins and immediate vicinity, z-score maps derived from both phase and fQSM-data showed positive and negative lobes resembling dipole shapes in simulated field and phase maps with no correlate in fMRI or PET data. Our results show that standard fMRI tools can directly be used

  7. Dynamic contrast-enhanced quantitative susceptibility mapping with ultrashort echo time MRI for evaluating renal function.

    PubMed

    Xie, Luke; Layton, Anita T; Wang, Nian; Larson, Peder E Z; Zhang, Jeff L; Lee, Vivian S; Liu, Chunlei; Johnson, G Allan

    2016-01-15

    Dynamic contrast-enhanced (DCE) MRI can provide key insight into renal function. DCE MRI is typically achieved through an injection of a gadolinium (Gd)-based contrast agent, which has desirable T1 quenching and tracer kinetics. However, significant T2* blooming effects and signal voids can arise when Gd becomes very concentrated, especially in the renal medulla and pelvis. One MRI sequence designed to alleviate T2* effects is the ultrashort echo time (UTE) sequence. In the present study, we observed T2* blooming in the inner medulla of the mouse kidney, despite using UTE at an echo time of 20 microseconds and a low dose of 0.03 mmol/kg Gd. We applied quantitative susceptibility mapping (QSM) and resolved the signal void into a positive susceptibility signal. The susceptibility values [in parts per million (ppm)] were converted into molar concentrations of Gd using a calibration curve. We determined the concentrating mechanism (referred to as the concentrating index) as a ratio of maximum Gd concentration in the inner medulla to the renal artery. The concentrating index was assessed longitudinally over a 17-wk course (3, 5, 7, 9, 13, 17 wk of age). We conclude that the UTE-based DCE method is limited in resolving extreme T2* content caused by the kidney's strong concentrating mechanism. QSM was able to resolve and confirm the source of the blooming effect to be the large positive susceptibility of concentrated Gd. UTE with QSM can complement traditional magnitude UTE and offer a powerful tool to study renal pathophysiology. PMID:26447222

  8. Radiomic Texture Analysis Mapping Predicts Areas of True Functional MRI Activity.

    PubMed

    Hassan, Islam; Kotrotsou, Aikaterini; Bakhtiari, Ali Shojaee; Thomas, Ginu A; Weinberg, Jeffrey S; Kumar, Ashok J; Sawaya, Raymond; Luedi, Markus M; Zinn, Pascal O; Colen, Rivka R

    2016-01-01

    Individual analysis of functional Magnetic Resonance Imaging (fMRI) scans requires user-adjustment of the statistical threshold in order to maximize true functional activity and eliminate false positives. In this study, we propose a novel technique that uses radiomic texture analysis (TA) features associated with heterogeneity to predict areas of true functional activity. Scans of 15 right-handed healthy volunteers were analyzed using SPM8. The resulting functional maps were thresholded to optimize visualization of language areas, resulting in 116 regions of interests (ROIs). A board-certified neuroradiologist classified different ROIs into Expected (E) and Non-Expected (NE) based on their anatomical locations. TA was performed using the mean Echo-Planner Imaging (EPI) volume, and 20 rotation-invariant texture features were obtained for each ROI. Using forward stepwise logistic regression, we built a predictive model that discriminated between E and NE areas of functional activity, with a cross-validation AUC and success rate of 79.84% and 80.19% respectively (specificity/sensitivity of 78.34%/82.61%). This study found that radiomic TA of fMRI scans may allow for determination of areas of true functional activity, and thus eliminate clinician bias. PMID:27151623

  9. Functional diffusion map: a noninvasive MRI biomarker for early stratification of clinical brain tumor response.

    PubMed

    Moffat, Bradford A; Chenevert, Thomas L; Lawrence, Theodore S; Meyer, Charles R; Johnson, Timothy D; Dong, Qian; Tsien, Christina; Mukherji, Suresh; Quint, Douglas J; Gebarski, Stephen S; Robertson, Patricia L; Junck, Larry R; Rehemtulla, Alnawaz; Ross, Brian D

    2005-04-12

    Assessment of radiation and chemotherapy efficacy for brain cancer patients is traditionally accomplished by measuring changes in tumor size several months after therapy has been administered. The ability to use noninvasive imaging during the early stages of fractionated therapy to determine whether a particular treatment will be effective would provide an opportunity to optimize individual patient management and avoid unnecessary systemic toxicity, expense, and treatment delays. We investigated whether changes in the Brownian motion of water within tumor tissue as quantified by using diffusion MRI could be used as a biomarker for early prediction of treatment response in brain cancer patients. Twenty brain tumor patients were examined by standard and diffusion MRI before initiation of treatment. Additional images were acquired 3 weeks after initiation of chemo- and/or radiotherapy. Images were coregistered to pretreatment scans, and changes in tumor water diffusion values were calculated and displayed as a functional diffusion map (fDM) for correlation with clinical response. Of the 20 patients imaged during the course of therapy, 6 were classified as having a partial response, 6 as stable disease, and 8 as progressive disease. The fDMs were found to predict patient response at 3 weeks from the start of treatment, revealing that early changes in tumor diffusion values could be used as a prognostic indicator of subsequent volumetric tumor response. Overall, fDM analysis provided an early biomarker for predicting treatment response in brain tumor patients. PMID:15805192

  10. Radiomic Texture Analysis Mapping Predicts Areas of True Functional MRI Activity

    PubMed Central

    Hassan, Islam; Kotrotsou, Aikaterini; Bakhtiari, Ali Shojaee; Thomas, Ginu A.; Weinberg, Jeffrey S.; Kumar, Ashok J.; Sawaya, Raymond; Luedi, Markus M.; Zinn, Pascal O.; Colen, Rivka R.

    2016-01-01

    Individual analysis of functional Magnetic Resonance Imaging (fMRI) scans requires user-adjustment of the statistical threshold in order to maximize true functional activity and eliminate false positives. In this study, we propose a novel technique that uses radiomic texture analysis (TA) features associated with heterogeneity to predict areas of true functional activity. Scans of 15 right-handed healthy volunteers were analyzed using SPM8. The resulting functional maps were thresholded to optimize visualization of language areas, resulting in 116 regions of interests (ROIs). A board-certified neuroradiologist classified different ROIs into Expected (E) and Non-Expected (NE) based on their anatomical locations. TA was performed using the mean Echo-Planner Imaging (EPI) volume, and 20 rotation-invariant texture features were obtained for each ROI. Using forward stepwise logistic regression, we built a predictive model that discriminated between E and NE areas of functional activity, with a cross-validation AUC and success rate of 79.84% and 80.19% respectively (specificity/sensitivity of 78.34%/82.61%). This study found that radiomic TA of fMRI scans may allow for determination of areas of true functional activity, and thus eliminate clinician bias. PMID:27151623

  11. Quantitative MRI Evaluation of Articular Cartilage Using T2 Mapping Following Hip Arthroscopy for Femoroacetabular Impingement

    PubMed Central

    Mayer, Stephanie W.; Wagner, Naomi; Fields, Kara G.; Wentzel, Catherine; Burge, Alissa; Potter, Hollis G.; Lyman, Stephen; Kelly, Bryan T.

    2016-01-01

    Objectives: Cam-type femoroacetabular impingement (FAI) causes a shearing and delamination injury to the acetabular articular cartilage due to a mismatch between the size of the femoral head and the acetabulum. This mechanism is thought to lead to early osteoarthritis in this population. Cam decompression has been advocated to eliminate impingement, with the ultimate goal of halting the progression of articular cartilage delamination. Although outcomes following this procedure in the young adult population have been favorable at short and medium term follow up, it is not known whether the articular cartilage itself is protected from further injury by changing the biomechanics of the joint with decompression of the cam morphology. The purpose of this study is to compare the pre- and post-operative integrity of the acetabular articular cartilage using T2 mapping to determine if hip arthroscopy is protective of the articular cartilage at short- to medium term follow up. Methods: Males between 18 and 35 years of age who had pre-operative T2 mapping MRIs, underwent hip arthroscopy for cam or mixed-type FAI with an alpha angle greater than 50°, and had at least 2 year follow-up were identified. Post-operative MRIs were performed and T2 relaxation times in the transition zone and weight bearing articular cartilage in the anterosuperior acetabulum at deep and superficial chondral layers were recorded at nine points on three sagittal sequences on pre and post-operative MRIs. A paired t-test was used to compare T2 relaxation values between pre-operative and post-operative scans. Results: Eleven hips were evaluated. Mean age was 26.3 years (range 21 - 35). Mean follow up time to post-operative T2 mapping MRI was 2.6 years (range 2.4 - 2.7). The change in T2 relaxation time was not significantly different between pre- and post-operative MRI scans for any of the nine regions in the deep zone of the acetabular cartilage (p=0.065 - 0.969) or the superficial zone of the

  12. Correlation of Scar in Cardiac MRI and High‐Resolution Contact Mapping of Left Ventricle in a Chronic Infarct Model

    PubMed Central

    THAJUDEEN, ANEES; STEWART, BRIAN; COKIC, IVAN; NAKAGAWA, HIROSHI; SHEHATA, MICHAEL; AMORN, ALLEN M.; KALI, AVINASH; LIU, EZH; HARLEV, DORON; BENNETT, NATHAN; DHARMAKUMAR, ROHAN; CHUGH, SUMEET S.; WANG, XUNZHANG

    2015-01-01

    Background Endocardial mapping for scars and abnormal electrograms forms the most essential component of ventricular tachycardia ablation. The utility of ultra‐high resolution mapping of ventricular scar was assessed using a multielectrode contact mapping system in a chronic canine infarct model. Methods Chronic infarcts were created in five anesthetized dogs by ligating the left anterior descending coronary artery. Late gadolinium‐enhanced magnetic resonance imaging (LGE MRI) was obtained 4.9 ± 0.9 months after infarction, with three‐dimensional (3D) gadolinium enhancement signal intensity maps at 1‐mm and 5‐mm depths from the endocardium. Ultra‐high resolution electroanatomical maps were created using a novel mapping system (Rhythmia Mapping System, Rhythmia Medical/Boston Scientific, Marlborough, MA, USA) Rhythmia Medical, Boston Scientific, Marlborough, MA, USA with an 8.5F catheter with mini‐basket electrode array (64 tiny electrodes, 2.5‐mm spacing, center‐to‐center). Results The maps contained 7,754 ± 1,960 electrograms per animal with a mean resolution of 2.8 ± 0.6 mm. Low bipolar voltage (<2 mV) correlated closely with scar on the LGE MRI and the 3D signal intensity map (1‐mm depth). The scar areas between the MRI signal intensity map and electroanatomic map matched at 87.7% of sites. Bipolar and unipolar voltages, compared in 592 electrograms from four MRI‐defined scar types (endocardial scar, epicardial scar, mottled transmural scar, and dense transmural scar) as well as normal tissue, were significantly different. A unipolar voltage of <13 mV correlated with transmural extension of scar in MRI. Electrograms exhibiting isolated late potentials (ILPs) were manually annotated and ILP maps were created showing ILP location and timing. ILPs were identified in 203 ± 159 electrograms per dog (within low‐voltage areas) and ILP maps showed gradation in timing of ILPs at different locations in the scar. Conclusions Ultra

  13. Mapping the Voxel-Wise Effective Connectome in Resting State fMRI

    PubMed Central

    Wu, Guo-Rong; Stramaglia, Sebastiano; Chen, Huafu; Liao, Wei; Marinazzo, Daniele

    2013-01-01

    A network approach to brain and dynamics opens new perspectives towards understanding of its function. The functional connectivity from functional MRI recordings in humans is widely explored at large scale, and recently also at the voxel level. The networks of dynamical directed connections are far less investigated, in particular at the voxel level. To reconstruct full brain effective connectivity network and study its topological organization, we present a novel approach to multivariate Granger causality which integrates information theory and the architecture of the dynamical network to efficiently select a limited number of variables. The proposed method aggregates conditional information sets according to community organization, allowing to perform Granger causality analysis avoiding redundancy and overfitting even for high-dimensional and short datasets, such as time series from individual voxels in fMRI. We for the first time depicted the voxel-wise hubs of incoming and outgoing information, called Granger causality density (GCD), as a complement to previous repertoire of functional and anatomical connectomes. Analogies with these networks have been presented in most part of default mode network; while differences suggested differences in the specific measure of centrality. Our findings could open the way to a new description of global organization and information influence of brain function. With this approach is thus feasible to study the architecture of directed networks at the voxel level and individuating hubs by investigation of degree, betweenness and clustering coefficient. PMID:24069220

  14. Mapping individual cosmid DNAs by direct AFM imaging.

    PubMed

    Allison, D P; Kerper, P S; Doktycz, M J; Thundat, T; Modrich, P; Larimer, F W; Johnson, D K; Hoyt, P R; Mucenski, M L; Warmack, R J

    1997-05-01

    Individual cosmid clones have been restriction mapped by directly imaging, with the atomic force microscope (AFM), a mutant EcoRI endonuclease site-specifically bound to DNA. Images and data are presented that locate six restriction sites, predicted from gel electrophoresis, on a 35-kb cosmid isolated from mouse chromosome 7. Measured distances between endonuclease molecules bound to lambda DNA, when compared to known values, demonstrate the accuracy of AFM mapping to better than 1%. These results may be extended to identify other important site-specific protein-DNA interactions, such as transcription factor and mismatch repair enzyme binding, difficult to resolve by current techniques.

  15. Bloch simulations towards direct detection of oscillating magnetic fields using MRI with spin-lock sequence.

    PubMed

    Nagahara, Shizue; Kobayashi, Tetsuo

    2013-01-01

    A new MRI method using the spin-lock sequence has attracted wide attention because of its potential for detecting small oscillating magnetic fields. However, as the mechanism involved is complicated, we visualized the magnetization performance during the spin-lock sequence in order to better understand interaction of the spin-lock pulse and the externally applied oscillating magnetic fields by means of a fast-and-simple method using matrix operations to solve a time-dependent Bloch equation. To improve spin-lock imaging in the detection of small magnetic fields (in an fMRI experiment that modeled neural magnetic fields), we observed that the phenomenon decreases MR signals, which led us to investigate how spin-lock parameters cause the MR signal to decrease; based on this, we determined that MR signals decrease in oscillating magnetic fields that are resonant with the spin-lock pulse. We also determined that MR signals decrease is directly proportional to spin-lock duration. Our results suggest that MRI can feasibly detect oscillating magnetic fields directly by using of the spin-lock sequence.

  16. Detecting directional influence in fMRI connectivity analysis using PCA based Granger causality

    PubMed Central

    Zhou, Zhenyu; Ding, Mingzhou; Chen, Yonghong; Wright, Paul; Lu, Zuhong; Liu, Yijun

    2009-01-01

    A fMRI connectivity analysis approach combining both principal component analysis (PCA) and Granger causality method (GCM) is proposed to study directional influence between functional brain regions. Both simulated data and human fMRI data obtained during behavioral tasks were used to validate this method. If PCA is first used to reduce number of fMRI time series, then more energy and information features in the signal can be preserved than using averaged values from brain regions of interest. Subsequently, GCM can be applied to principal components extracted in order to further investigate effective connectivity. The simulation demonstrated that by using GCM with PCA, between-region causalities were better represented than using GCM with average values. Furthermore, after localizing an emotion task-induced activation in the anterior cingulate cortex, inferior frontal sulcus and amygdala, the directional influences among these brain regions were resolved using our new approach. These results indicate that using PCA may improve upon application of existing GCMs in study of human brain effective connectivity. PMID:19595679

  17. Differentiation of motor cortical representation of hand muscles by navigated mapping of optimal TMS current directions in healthy subjects

    PubMed Central

    Bashir, Shahid; Perez, Jennifer; Horvath, Jared Cooney; Pascual-Leone, Alvaro

    2013-01-01

    The precision of navigated transcranial magnetic stimulation (TMS) to map the human primary motor cortex may be effected the direction of TMS-induced current in the brain as determined by the orientation of the stimulation coil. In this study, we investigated the effect of current directionality on motor output mapping using navigated brain stimulation (NBS). Our goal was to determine the optimal coil orientation (and, thus, induced brain current) to activate hand musculature representations relative to each subject’s unique neuroanatomical landmarks. We studied motor output maps for the first dorsal interosseous (FDI), abductor pollicis brevis (APB), and abductor digiti minimi (ADM) muscles in 10 normal volunteers. Monopolar current pulses were delivered through a figure-of-eight shaped TMS coil and motor evoked potentials (MEPs) were recorded using electromyography (EMG). At each targeted brain region, we systematically rotated the TMS coil to determine the direction of induced current in the brain for induction of the largest MEPs. These optimal current directions were expressed as an angle relative to each subject’s central sulcus. Consistency of the optimal current direction was assessed by repeating the entire mapping procedure on two different occasions across subjects. We demonstrate that systematic optimization of current direction as guided by MRI based neuronavigation improves the resolution of cortical output motor mapping with TMS. PMID:23912579

  18. Isotropic diffusion weighting for measurement of a high-resolution apparent diffusion coefficient map using a single radial scan in MRI

    NASA Astrophysics Data System (ADS)

    Seo, Hyunseok; Choi, Joonsung; Oh, Changheun; Han, Yeji; Park, HyunWook

    2014-10-01

    This work proposes an isotropic diffusion weighting method for a high-resolution diffusion-weighted image and for a high-resolution apparent diffusion coefficient (ADC) map using a single radial scan in MRI. By using a conventional radial imaging technique, a high-resolution diffusion-weighted (DW) image can be obtained at the cost of a long imaging time. To reduce the imaging time, the proposed method acquires a DW image by altering the diffusion gradient directions for each radial spoke. The acquisition order and directions of the diffusion gradients for an accurate DW image and an ADC map are also proposed by modifying the golden angle ratio in 3D space. In addition, an individual-direction diffusion-weighted (id-DW) image can also be obtained by a diffusion gradient direction, which is one of the multiple directions used in isotropic diffusion weighting. Computer simulations and experiment results show that the proposed method is more accurate and faster than the conventional radial diffusion-weighted imaging. This study suggests that the proposed isotropic diffusion-weighted imaging can be used to obtain a DW image and a high-resolution ADC map accurately in a single radial scan, while reducing the artifacts caused by the diffusion anisotropy, compared to the diffusion-weighted echo-planar-imaging.

  19. Superparamagnetic iron oxide nanoparticles for direct labeling of stem cells and in vivo MRI tracking.

    PubMed

    Kim, Saejeong J; Lewis, Bobbi; Steiner, Mark-Steven; Bissa, Ursula V; Dose, Christian; Frank, Joseph A

    2016-01-01

    To develop effective stem cell therapies, it is important to track therapeutic cells non-invasively and monitor homing to areas of pathology. The purpose of this study was to design and evaluate the labeling efficiency of commercially available dextran-coated superparamagnetic iron oxide nanoparticles, FeraTrack Direct (FTD), in various stem and immune cells; assess the cytotoxicity and tolerability of the FTD in stem cells; and monitor stem cell homing using FTD-labeled bone-marrow-derived mesenchymal stromal cells (BMSCs) and neural stem cells (NSCs) in a tumor model by in vivo MRI. BMSCs, NSCs, hematopoietic stem cells (HSCs), T-lymphocytes, and monocytes were labeled effectively with FTD without the need for transfection agents, and Prussian blue (PB) staining and transmission electron microscopy (TEM) confirmed intracellular uptake of the agent. The viability, proliferation, and functionality of the labeled cells were minimally or not affected after labeling. When 10(6) FTD-labeled BMSCs or NSCs were injected into C6 glioma bearing nude mice, the cells homing to the tumors were detected as hypointense regions within the tumor using 3 T clinical MRI up to 10 days post injection. Histological analysis confirmed the homing of injected cells to the tumor by the presence of PB positive cells that are not macrophages. Labeling of stem cells or immune cells with FTD was non-toxic, and should facilitate the translation of this agent to clinical trials for evaluation of trafficking of cells by MRI.

  20. Directional patterns of cross frequency phase and amplitude coupling within the resting state mimic patterns of fMRI functional connectivity.

    PubMed

    Weaver, Kurt E; Wander, Jeremiah D; Ko, Andrew L; Casimo, Kaitlyn; Grabowski, Thomas J; Ojemann, Jeffrey G; Darvas, Felix

    2016-03-01

    Functional imaging investigations into the brain's resting state interactions have yielded a wealth of insight into the intrinsic and dynamic neural architecture supporting cognition and behavior. Electrophysiological studies however have highlighted the fact that synchrony across large-scale cortical systems is composed of spontaneous interactions occurring at timescales beyond the traditional resolution of fMRI, a feature that limits the capacity of fMRI to draw inference on the true directional relationship between network nodes. To approach the question of directionality in resting state signals, we recorded resting state functional MRI (rsfMRI) and electrocorticography (ECoG) from four human subjects undergoing invasive epilepsy monitoring. Using a seed-point based approach, we employed phase-amplitude coupling (PAC) and biPhase Locking Values (bPLV), two measures of cross-frequency coupling (CFC) to explore both outgoing and incoming connections between the seed and all non-seed, site electrodes. We observed robust PAC between a wide range of low-frequency phase and high frequency amplitude estimates. However, significant bPLV, a CFC measure of phase-phase synchrony, was only observed at specific narrow low and high frequency bandwidths. Furthermore, the spatial patterns of outgoing PAC connectivity were most closely associated with the rsfMRI connectivity maps. Our results support the hypothesis that PAC is relatively ubiquitous phenomenon serving as a mechanism for coordinating high-frequency amplitudes across distant neuronal assemblies even in absence of overt task structure. Additionally, we demonstrate that the spatial distribution of a seed-point rsfMRI sensorimotor network is strikingly similar to specific patterns of directional PAC. Specifically, the high frequency activities of distal patches of cortex owning membership in a rsfMRI sensorimotor network were most likely to be entrained to the phase of a low frequency rhythm engendered from the

  1. Mapping epitopes and antigenicity by site-directed masking

    NASA Astrophysics Data System (ADS)

    Paus, Didrik; Winter, Greg

    2006-06-01

    Here we describe a method for mapping the binding of antibodies to the surface of a folded antigen. We first created a panel of mutant antigens (-lactamase) in which single surface-exposed residues were mutated to cysteine. We then chemically tethered the cysteine residues to a solid phase, thereby masking a surface patch centered on each cysteine residue and blocking the binding of antibodies to this region of the surface. By these means we mapped the epitopes of several mAbs directed to -lactamase. Furthermore, by depleting samples of polyclonal antisera to the masked antigens and measuring the binding of each depleted sample of antisera to unmasked antigen, we mapped the antigenicity of 23 different epitopes. After immunization of mice and rabbits with -lactamase in Freund's adjuvant, we found that the antisera reacted with both native and denatured antigen and that the antibody response was mainly directed to an exposed and flexible loop region of the native antigen. By contrast, after immunization in PBS, we found that the antisera reacted only weakly with denatured antigen and that the antibody response was more evenly distributed over the antigenic surface. We suggest that denatured antigen (created during emulsification in Freund's adjuvant) elicits antibodies that bind mainly to the flexible regions of the native protein and that this explains the correlation between antigenicity and backbone flexibility. Denaturation of antigen during vaccination or natural infections would therefore be expected to focus the antibody response to the flexible loops. backbone flexibility | Freund's adjuvant | conformational epitope | antisera

  2. Statistical modeling and MAP estimation for body fat quantification with MRI ratio imaging

    NASA Astrophysics Data System (ADS)

    Wong, Wilbur C. K.; Johnson, David H.; Wilson, David L.

    2008-03-01

    We are developing small animal imaging techniques to characterize the kinetics of lipid accumulation/reduction of fat depots in response to genetic/dietary factors associated with obesity and metabolic syndromes. Recently, we developed an MR ratio imaging technique that approximately yields lipid/{lipid + water}. In this work, we develop a statistical model for the ratio distribution that explicitly includes a partial volume (PV) fraction of fat and a mixture of a Rician and multiple Gaussians. Monte Carlo hypothesis testing showed that our model was valid over a wide range of coefficient of variation of the denominator distribution (c.v.: 0-0:20) and correlation coefficient among the numerator and denominator (ρ 0-0.95), which cover the typical values that we found in MRI data sets (c.v.: 0:027-0:063, ρ: 0:50-0:75). Then a maximum a posteriori (MAP) estimate for the fat percentage per voxel is proposed. Using a digital phantom with many PV voxels, we found that ratio values were not linearly related to PV fat content and that our method accurately described the histogram. In addition, the new method estimated the ground truth within +1.6% vs. +43% for an approach using an uncorrected ratio image, when we simply threshold the ratio image. On the six genetically obese rat data sets, the MAP estimate gave total fat volumes of 279 +/- 45mL, values 21% smaller than those from the uncorrected ratio images, principally due to the non-linear PV effect. We conclude that our algorithm can increase the accuracy of fat volume quantification even in regions having many PV voxels, e.g. ectopic fat depots.

  3. Mapping MRI/MRS Parameters with Genetic Over-expression Profiles In Human Prostate Cancer: Demonstrating the Potential

    PubMed Central

    Lenkinski, Robert E.; Bloch, B. Nicholas; Liu, Fangbing; Frangioni, John V.; Perner, Sven; Rubin, Mark A.; Genega, Elizabeth; Rofsky, Neil M.; Gaston, Sandra M.

    2009-01-01

    Magnetic resonance imaging (MRI) and MR spectroscopy can probe a variety of physiological (e.g. blood vessel permeability) and metabolic characteristics of prostate cancer. However, little is known about the changes in gene expression that underlie the spectral and imaging features observed in prostate cancer. Tumor induced changes in vascular permeability and angiogenesis are thought to contribute to patterns of dynamic contrast enhanced (DCE) MRI images of prostate cancer even though the genetic basis of tumor vasculogenesis is complex and the specific mechanisms underlying these DCEMRI features have not yet been determined. In order to identify the changes in gene expression that correspond to MRS and DCEMRI patterns in human prostate cancers, we have utilized tissue print micropeel techniques to generate “whole mount” molecular maps of radical prostatectomy specimens that correspond to pre-surgical MRI/MRS studies. These molecular maps include RNA expression profiles from both Affymetrix GeneChip microarrays and quantitative reverse transcriptase PCR (qrt-PCR) analysis, as well as immunohistochemical studies. Using these methods on patients with prostate cancer, we found robust over-expression of choline kinase a in the majority of primary tumors. We also observed overexpression of neuropeptide Y (NPY), a newly identified angiogenic factor, in a subset of DCEMRI positive prostate cancers. These studies set the stage for establishing MRI/MRS parameters as validated biomarkers for human prostate cancer. PMID:18752015

  4. Regional fractional ventilation mapping in spontaneously breathing mice using hyperpolarized ¹²⁹Xe MRI.

    PubMed

    Imai, Hirohiko; Matsumoto, Hironobu; Miyakoshi, Erika; Okumura, Shintaro; Fujiwara, Hideaki; Kimura, Atsuomi

    2015-01-01

    The feasibility of ventilation imaging with hyperpolarized (HP) (129) Xe MRI has been investigated for quantitative and regional assessment of ventilation in spontaneously breathing mice. The multiple breath ventilation imaging technique was modified to the protocol of spontaneous inhalation of HP (129) Xe delivered continuously from a (129) Xe polarizer. A series of (129) Xe ventilation images was obtained by varying the number of breaths before the (129) Xe lung imaging. The fractional ventilation, r, was successfully evaluated for spontaneously breathing mice. An attempt was made to detect ventilation dysfunction in the emphysematous mouse lung induced by intratracheal administration of porcine pancreatic elastase (PPE). As a result, the distribution of fractional ventilation could be visualized by the r map. Significant dysfunction of ventilation was quantitatively identified in the PPE-treated group. The whole-lung r value of 0.34 ± 0.01 for control mice (N = 4) was significantly reduced, to 0.25 ± 0.07, in PPE-treated mice (N = 4) (p = 0.038). This study is the first application of multiple breath ventilation imaging to spontaneously breathing mice, and shows that this methodology is sensitive to differences in the pulmonary ventilation. This methodology is expected to improve simplicity as well as noninvasiveness when assessing regional ventilation in small rodents.

  5. Quantitative evaluation of fMRI retinotopic maps, from V1 to V4, for cognitive experiments

    PubMed Central

    Bordier, Cécile; Hupé, Jean-Michel; Dojat, Michel

    2015-01-01

    FMRI retinotopic mapping is a non-invasive technique for the delineation of low-level visual areas in individual subjects. It generally relies upon the analysis of functional responses to periodic visual stimuli that encode eccentricity or polar angle in the visual field. This technique is used in vision research when the precise assignation of brain activation to retinotopic areas is an issue. It involves processing steps computed with different algorithms and embedded in various software suites. Manual intervention may be needed for some steps. Although the diversity of the available processing suites and manual interventions may potentially introduce some differences in the final delineation of visual areas, no documented comparison between maps obtained with different procedures has been reported in the literature. To explore the effect of the processing steps on the quality of the maps obtained, we used two tools, BALC, which relies on a fully automated procedure, and BrainVoyager, where areas are delineated “by hand” on the brain surface. To focus on the mapping procedures specifically, we used the same SPM pipeline for pretreatment and the same tissue segmentation tool. We document the consistency and differences of the fMRI retinotopic maps obtained from “routine retinotopy” experiments on 10 subjects. The maps obtained by skilled users are never fully identical. However, the agreement between the maps, around 80% for low-level areas, is probably sufficient for most applications. Our results also indicate that assigning cognitive activations, following a specific experiment (here, color perception), to individual retinotopic maps is not free of errors. We provide measurements of this error, that may help for the cautious interpretation of cognitive activation projection onto fMRI retinotopic maps. On average, the magnitude of the error is about 20%, with much larger differences in a few subjects. More variability may even be expected with less

  6. In Vivo MRI Mapping of Brain Iron Deposition across the Adult Lifespan

    PubMed Central

    Betts, Matthew J.; Cardenas-Blanco, Arturo; Yang, Shan; Nestor, Peter J.

    2016-01-01

    Disruption of iron homeostasis as a consequence of aging is thought to cause iron levels to increase, potentially promoting oxidative cellular damage. Therefore, understanding how this process evolves through the lifespan could offer insights into both the aging process and the development of aging-related neurodegenerative brain diseases. This work aimed to map, in vivo for the first time with an unbiased whole-brain approach, age-related iron changes using quantitative susceptibility mapping (QSM)—a new postprocessed MRI contrast mechanism. To this end, a full QSM standardization routine was devised and a cohort of N = 116 healthy adults (20–79 years of age) was studied. The whole-brain and ROI analyses confirmed that the propensity of brain cells to accumulate excessive iron as a function of aging largely depends on their exact anatomical location. Whereas only patchy signs of iron scavenging were observed in white matter, strong, bilateral, and confluent QSM–age associations were identified in several deep-brain nuclei—chiefly the striatum and midbrain—and across motor, premotor, posterior insular, superior prefrontal, and cerebellar cortices. The validity of QSM as a suitable in vivo imaging technique with which to monitor iron dysregulation in the human brain was demonstrated by confirming age-related increases in several subcortical nuclei that are known to accumulate iron with age. The study indicated that, in addition to these structures, there is a predilection for iron accumulation in the frontal lobes, which when combined with the subcortical findings, suggests that iron accumulation with age predominantly affects brain regions concerned with motor/output functions. SIGNIFICANCE STATEMENT This study used a whole-brain imaging approach known as quantitative susceptibility mapping (QSM) to provide a novel insight into iron accumulation in the brain across the adult lifespan. Validity of the method was demonstrated by showing concordance with ROI

  7. Fast T2 Mapping With Improved Accuracy Using Undersampled Spin-Echo MRI and Model-Based Reconstructions With a Generating Function

    PubMed Central

    Petrovic, Andreas; Uecker, Martin; Knoll, Florian; Frahm, Jens

    2015-01-01

    A model-based reconstruction technique for accelerated T2 mapping with improved accuracy is proposed using under-sampled Cartesian spin-echo magnetic resonance imaging (MRI) data. The technique employs an advanced signal model for T2 relaxation that accounts for contributions from indirect echoes in a train of multiple spin echoes. An iterative solution of the nonlinear inverse reconstruction problem directly estimates spin-density and T2 maps from undersampled raw data. The algorithm is validated for simulated data as well as phantom and human brain MRI at 3T. The performance of the advanced model is compared to conventional pixel-based fitting of echo-time images from fully sampled data. The proposed method yields more accurate T2 values than the mono-exponential model and allows for retrospective under-sampling factors of at least 6. Although limitations are observed for very long T2 relaxation times, respective reconstruction problems may be overcome by a gradient dampening approach. The analytical gradient of the utilized cost function is included as Appendix. The source code is made available to the community. PMID:24988592

  8. Non-invasive pulmonary blood flow analysis and blood pressure mapping derived from 4D flow MRI

    NASA Astrophysics Data System (ADS)

    Delles, Michael; Rengier, Fabian; Azad, Yoo-Jin; Bodenstedt, Sebastian; von Tengg-Kobligk, Hendrik; Ley, Sebastian; Unterhinninghofen, Roland; Kauczor, Hans-Ulrich; Dillmann, Rüdiger

    2015-03-01

    In diagnostics and therapy control of cardiovascular diseases, detailed knowledge about the patient-specific behavior of blood flow and pressure can be essential. The only method capable of measuring complete time-resolved three-dimensional vector fields of the blood flow velocities is velocity-encoded magnetic resonance imaging (MRI), often denoted as 4D flow MRI. Furthermore, relative pressure maps can be computed from this data source, as presented by different groups in recent years. Hence, analysis of blood flow and pressure using 4D flow MRI can be a valuable technique in management of cardiovascular diseases. In order to perform these tasks, all necessary steps in the corresponding process chain can be carried out in our in-house developed software framework MEDIFRAME. In this article, we apply MEDIFRAME for a study of hemodynamics in the pulmonary arteries of five healthy volunteers. The study included measuring vector fields of blood flow velocities by phase-contrast MRI and subsequently computing relative blood pressure maps. We visualized blood flow by streamline depictions and computed characteristic values for the left and the right pulmonary artery (LPA and RPA). In all volunteers, we observed a lower amount of blood flow in the LPA compared to the RPA. Furthermore, we visualized blood pressure maps using volume rendering and generated graphs of pressure differences between the LPA, the RPA and the main pulmonary artery. In most volunteers, blood pressure was increased near to the bifurcation and in the proximal LPA, leading to higher average pressure values in the LPA compared to the RPA.

  9. MRI technique for the snapshot imaging of quantitative velocity maps using RARE.

    PubMed

    Shiko, G; Sederman, A J; Gladden, L F

    2012-03-01

    A quantitative PGSE-RARE pulse sequence was developed and successfully applied to the in situ dissolution of two pharmaceutical formulations dissolving over a range of timescales. The new technique was chosen over other existing fast velocity imaging techniques because it is T(2) weighted, not T(2)(∗) weighted, and is, therefore, robust for imaging time-varying interfaces and flow in magnetically heterogeneous systems. The complex signal was preserved intact by separating odd and even echoes to obtain two phase maps which are then averaged in post-processing. Initially, the validity of the technique was shown when imaging laminar flow in a pipe. Subsequently, the dissolution of two drugs was followed in situ, where the technique enables the imaging and quantification of changes in the form of the tablet and the flow field surrounding it at high spatial and temporal resolution. First, the complete 3D velocity field around an eroding salicylic acid tablet was acquired at a resolution of 98×49 μm(2), within 20 min, and monitored over ∼13 h. The tablet was observed to experience a heterogeneous flow field and, hence a heterogeneous shear field, which resulted in the non-symmetric erosion of the tablet. Second, the dissolution of a fast dissolving immediate release tablet was followed using one-shot 2D velocity images acquired every 5.2 s at a resolution of 390×390 μm(2). The quantitative nature of the technique and fast acquisition times provided invaluable information on the dissolution behaviour of this tablet, which had not been attainable previously with conventional quantitative MRI techniques.

  10. MRI technique for the snapshot imaging of quantitative velocity maps using RARE

    NASA Astrophysics Data System (ADS)

    Shiko, G.; Sederman, A. J.; Gladden, L. F.

    2012-03-01

    A quantitative PGSE-RARE pulse sequence was developed and successfully applied to the in situ dissolution of two pharmaceutical formulations dissolving over a range of timescales. The new technique was chosen over other existing fast velocity imaging techniques because it is T2 weighted, not T2∗ weighted, and is, therefore, robust for imaging time-varying interfaces and flow in magnetically heterogeneous systems. The complex signal was preserved intact by separating odd and even echoes to obtain two phase maps which are then averaged in post-processing. Initially, the validity of the technique was shown when imaging laminar flow in a pipe. Subsequently, the dissolution of two drugs was followed in situ, where the technique enables the imaging and quantification of changes in the form of the tablet and the flow field surrounding it at high spatial and temporal resolution. First, the complete 3D velocity field around an eroding salicylic acid tablet was acquired at a resolution of 98 × 49 μm2, within 20 min, and monitored over ˜13 h. The tablet was observed to experience a heterogeneous flow field and, hence a heterogeneous shear field, which resulted in the non-symmetric erosion of the tablet. Second, the dissolution of a fast dissolving immediate release tablet was followed using one-shot 2D velocity images acquired every 5.2 s at a resolution of 390 × 390 μm2. The quantitative nature of the technique and fast acquisition times provided invaluable information on the dissolution behaviour of this tablet, which had not been attainable previously with conventional quantitative MRI techniques.

  11. Intraoperative, real-time, functional MRI.

    PubMed

    Gering, D T; Weber, D M

    1998-01-01

    Functional MRI (fMRI) methods have been demonstrated to noninvasively identify motor-sensory, visual, and other areas of eloquent cortex for guiding surgical intervention. Typically, fMRI data are acquired preoperatively during a conventional surgical planning MRI examination. Unlike direct cortical stimulation at the time of surgery, however, preoperative fMRI methods do not account for the potential movement of tissues (relative to the time of functional imaging) that may occur in the surgical suite as a direct result of the intervention. Recently, an MRI device has been demonstrated for use in the surgical suite that has the potential to reduce the extent of cortical exposure required for the intervention. However, the invasive requirements of cortical mapping may supersede the invasive requirements of the surgical intervention itself. Consequently, we demonstrate here a modification to the intraoperative MRI device that facilitates a noninvasive, real-time, functional MR examination in the surgical suite.

  12. Simultaneous measures of kinematics and fMRI: relation between movement parameters and activation maps in healthy subjects

    NASA Astrophysics Data System (ADS)

    Gandolla, M.; Casellato, C.; Ferrante, S.; Ferrigno, G.; Baselli, G.; Molteni, F.; Martegani, A.; Frattini, T.; Pedrocchi, A.

    2010-03-01

    The objective of this study was to identify on healthy subjects the correlation between motor performances and brain activation maps, by the simultaneous use of functional magnetic resonance imaging (fMRI) and optoelectronic motion analysis system. The specific goal was to individuate how amplitude affects the related cerebral flow maps in active, passive and electrical stimulated (FES) movements. Ankle DorsiFlexion (ADF) was chosen as analyzed task because of its importance in the gait cycle. Firstly FES compatibility with fMRI images acquisition was assessed, both for the safety of the subject and of the device, and for mutual disturbances evaluation. We identified the experimental protocol so as to optimize the measured cerebral maps and the repeatability of the results. Intra-subject analysis of movement parameters along with brain activation mapping was performed. First level analysis to compare different execution modalities have been studied and preliminary qualitative results are reported. The long term application is the exploitation of the combined system in the evaluation of neurological patients where the definition of the motor tasks could be only partially accomplished depending on the patient residual functionality.

  13. Improved Quantification and Mapping of Anomalous Pulmonary Venous Flow With Four-Dimensional Phase-Contrast MRI and Interactive Streamline Rendering

    PubMed Central

    Hsiao, Albert; Yousaf, Ufra; Alley, Marcus T.; Lustig, Michael; Chan, Frandics Pak; Newman, Beverley; Vasanawala, Shreyas S.

    2016-01-01

    Background Cardiac MRI is routinely performed for quantification of shunt flow in patients with anomalous pulmonary veins, but can be technically-challenging to perform. Four-dimensional phase-contrast (4D-PC) MRI has potential to simplify this exam. We sought to determine whether 4D-PC may be a viable clinical alternative to conventional 2D phase-contrast MR imaging. Methods With institutional review board approval and HIPAA-compliance, we retrospectively identified all patients with anomalous pulmonary veins who underwent cardiac MRI at either 1.5 Tesla (T) or 3T with parallel-imaging compressed-sensing (PI-CS) 4D-PC between April, 2011 and October, 2013. A total of 15 exams were included (10 male, 5 female). Algorithms for interactive streamline visualization were developed and integrated into in-house software. Blood flow was measured at the valves, pulmonary arteries and veins, cavae, and any associated shunts. Pulmonary veins were mapped to their receiving atrial chamber with streamlines. The intraobserver, interobserver, internal consistency of flow measurements, and consistency with conventional MRI were then evaluated with Pearson correlation and Bland-Altman analysis. Results Triplicate measurements of blood flow from 4D-PC were highly consistent, particularly at the aortic and pulmonary valves (cv 2–3%). Flow measurements were reproducible by a second observer (ρ = 0.986–0.999). Direct measurements of shunt volume from anomalous veins and intracardiac shunts matched indirect estimates from the outflow valves (ρ = 0.966). Measurements of shunt fraction using 4D-PC using any approach were more consistent with ventricular volumetric displacements than conventional 2D-PC (ρ = 0.972–0.991 versus 0.929). Conclusion Shunt flow may be reliably quantified with 4D-PC MRI, either indirectly or with detailed delineation of flow from multiple shunts. The 4D-PC may be a more accurate alternative to conventional MRI. PMID:25914149

  14. Highly directional transurethral ultrasound applicators with rotational control for MRI-guided prostatic thermal therapy

    NASA Astrophysics Data System (ADS)

    Ross, Anthony B.; Diederich, Chris J.; Nau, William H.; Gill, Harcharan; Bouley, Donna M.; Daniel, Bruce; Rieke, Viola; Butts, R. Kim; Sommer, Graham

    2004-01-01

    Transurethral ultrasound applicators with highly directional energy deposition and rotational control were investigated for precise treatment of benign prostatic hyperplasia (BPH) and adenocarcinoma of the prostate (CaP). Two types of catheter-based applicators were fabricated, using either 90° sectored tubular (3.5 mm OD × 10 mm) or planar transducers (3.5 mm × 10 mm). They were constructed to be MRI compatible, minimally invasive and allow for manual rotation of the transducer array within a 10 mm cooling balloon. In vivo evaluations of the applicators were performed in canine prostates (n = 3) using MRI guidance (0.5 T interventional magnet). MR temperature imaging (MRTI) utilizing the proton resonance frequency shift method was used to acquire multiple-slice temperature overlays in real time for monitoring and guiding the thermal treatments. Post-treatment T1-weighted contrast-enhanced imaging and triphenyl tetrazolium chloride stained tissue sections were used to define regions of tissue coagulation. Single sonications with the 90° tubular applicator (9-15 W, 12 min, 8 MHz) produced coagulated zones covering an 80° wedge of the prostate extending from 1-2 mm outside the urethra to the outer boundary of the gland (16 mm radial coagulation). Single sonications with the planar applicator (15-20 W, 10 min, ~8 MHz) generated thermal lesions of ~30° extending to the prostate boundary. Multiple sequential sonications (sweeping) of a planar applicator (12 W with eight rotations of 30° each) demonstrated controllable coagulation of a 270° contiguous section of the prostate extending to the capsule boundary. The feasibility of using highly directional transurethral ultrasound applicators with rotational capabilities to selectively coagulate regions of the prostate while monitoring and controlling the treatments with MRTI was demonstrated in this study.

  15. Anatomo-clinical overlapping maps (AnaCOM): a new method to create anatomo-functional maps from neuropsychological tests and structural MRI scan of subjects with brain lesions

    NASA Astrophysics Data System (ADS)

    Kinkingnehun, Serge R. J.; du Boisgueheneuc, Foucaud; Golmard, Jean-Louis; Zhang, Sandy X.; Levy, Richard; Dubois, Bruno

    2004-04-01

    We have developed a new technique to analyze correlations between brain anatomy and its neurological functions. The technique is based on the anatomic MRI of patients with brain lesions who are administered neuropsychological tests. Brain lesions of the MRI scans are first manually segmented. The MRI volumes are then normalized to a reference map, using the segmented area as a mask. After normalization, the brain lesions of the MRI are segmented again in order to redefine the border of the lesions in the context of the normalized brain. Once the MRI is segmented, the patient's score on the neuropsychological test is assigned to each voxel in the lesioned area, while the rest of the voxels of the image are set to 0. Subsequently, the individual patient's MRI images are superimposed, and each voxel is reassigned the average score of the patients who have a lesion at that voxel. A threshold is applied to remove regions having less than three overlaps. This process leads to an anatomo-functional map that links brain areas to functional loss. Other maps can be created to aid in analyzing the functional maps, such as one that indicates the 95% confidence interval of the averaged scores for each area. This anatomo-clinical overlapping map (AnaCOM) method was used to obtain functional maps from patients with lesions in the superior frontal gyrus. By finding particular subregions more responsible for a particular deficit, this method can generate new hypotheses to be tested by conventional group methods.

  16. MAPL: Tissue microstructure estimation using Laplacian-regularized MAP-MRI and its application to HCP data.

    PubMed

    Fick, Rutger H J; Wassermann, Demian; Caruyer, Emmanuel; Deriche, Rachid

    2016-07-01

    The recovery of microstructure-related features of the brain's white matter is a current challenge in diffusion MRI. To robustly estimate these important features from multi-shell diffusion MRI data, we propose to analytically regularize the coefficient estimation of the Mean Apparent Propagator (MAP)-MRI method using the norm of the Laplacian of the reconstructed signal. We first compare our approach, which we call MAPL, with competing, state-of-the-art functional basis approaches. We show that it outperforms the original MAP-MRI implementation and the recently proposed modified Spherical Polar Fourier (mSPF) basis with respect to signal fitting and reconstruction of the Ensemble Average Propagator (EAP) and Orientation Distribution Function (ODF) in noisy, sparsely sampled data of a physical phantom with reference gold standard data. Then, to reduce the variance of parameter estimation using multi-compartment tissue models, we propose to use MAPL's signal fitting and extrapolation as a preprocessing step. We study the effect of MAPL on the estimation of axon diameter using a simplified Axcaliber model and axonal dispersion using the Neurite Orientation Dispersion and Density Imaging (NODDI) model. We show the positive effect of using it as a preprocessing step in estimating and reducing the variances of these parameters in the Corpus Callosum of six different subjects of the MGH Human Connectome Project. Finally, we correlate the estimated axon diameter, dispersion and restricted volume fractions with Fractional Anisotropy (FA) and clearly show that changes in FA significantly correlate with changes in all estimated parameters. Overall, we illustrate the potential of using a well-regularized functional basis together with multi-compartment approaches to recover important microstructure tissue parameters with much less variability, thus contributing to the challenge of better understanding microstructure-related features of the brain's white matter.

  17. Oxygen-Enhanced MRI Accurately Identifies, Quantifies, and Maps Tumor Hypoxia in Preclinical Cancer Models.

    PubMed

    O'Connor, James P B; Boult, Jessica K R; Jamin, Yann; Babur, Muhammad; Finegan, Katherine G; Williams, Kaye J; Little, Ross A; Jackson, Alan; Parker, Geoff J M; Reynolds, Andrew R; Waterton, John C; Robinson, Simon P

    2016-02-15

    There is a clinical need for noninvasive biomarkers of tumor hypoxia for prognostic and predictive studies, radiotherapy planning, and therapy monitoring. Oxygen-enhanced MRI (OE-MRI) is an emerging imaging technique for quantifying the spatial distribution and extent of tumor oxygen delivery in vivo. In OE-MRI, the longitudinal relaxation rate of protons (ΔR1) changes in proportion to the concentration of molecular oxygen dissolved in plasma or interstitial tissue fluid. Therefore, well-oxygenated tissues show positive ΔR1. We hypothesized that the fraction of tumor tissue refractory to oxygen challenge (lack of positive ΔR1, termed "Oxy-R fraction") would be a robust biomarker of hypoxia in models with varying vascular and hypoxic features. Here, we demonstrate that OE-MRI signals are accurate, precise, and sensitive to changes in tumor pO2 in highly vascular 786-0 renal cancer xenografts. Furthermore, we show that Oxy-R fraction can quantify the hypoxic fraction in multiple models with differing hypoxic and vascular phenotypes, when used in combination with measurements of tumor perfusion. Finally, Oxy-R fraction can detect dynamic changes in hypoxia induced by the vasomodulator agent hydralazine. In contrast, more conventional biomarkers of hypoxia (derived from blood oxygenation-level dependent MRI and dynamic contrast-enhanced MRI) did not relate to tumor hypoxia consistently. Our results show that the Oxy-R fraction accurately quantifies tumor hypoxia noninvasively and is immediately translatable to the clinic.

  18. Goal-Directed Modulation of Neural Memory Patterns: Implications for fMRI-Based Memory Detection.

    PubMed

    Uncapher, Melina R; Boyd-Meredith, J Tyler; Chow, Tiffany E; Rissman, Jesse; Wagner, Anthony D

    2015-06-01

    Remembering a past event elicits distributed neural patterns that can be distinguished from patterns elicited when encountering novel information. These differing patterns can be decoded with relatively high diagnostic accuracy for individual memories using multivoxel pattern analysis (MVPA) of fMRI data. Brain-based memory detection--if valid and reliable--would have clear utility beyond the domain of cognitive neuroscience, in the realm of law, marketing, and beyond. However, a significant boundary condition on memory decoding validity may be the deployment of "countermeasures": strategies used to mask memory signals. Here we tested the vulnerability of fMRI-based memory detection to countermeasures, using a paradigm that bears resemblance to eyewitness identification. Participants were scanned while performing two tasks on previously studied and novel faces: (1) a standard recognition memory task; and (2) a task wherein they attempted to conceal their true memory state. Univariate analyses revealed that participants were able to strategically modulate neural responses, averaged across trials, in regions implicated in memory retrieval, including the hippocampus and angular gyrus. Moreover, regions associated with goal-directed shifts of attention and thought substitution supported memory concealment, and those associated with memory generation supported novelty concealment. Critically, whereas MVPA enabled reliable classification of memory states when participants reported memory truthfully, the ability to decode memory on individual trials was compromised, even reversing, during attempts to conceal memory. Together, these findings demonstrate that strategic goal states can be deployed to mask memory-related neural patterns and foil memory decoding technology, placing a significant boundary condition on their real-world utility. PMID:26041920

  19. Infant-directed prosody helps infants map sounds to meanings

    PubMed Central

    Estes, Katharine Graf; Hurley, Karinna

    2012-01-01

    Adults typically use an exaggerated, distinctive speaking style when addressing infants. However, the effects of infant-directed (ID) speech on infants’ learning is not yet well understood. This research investigates how ID speech affects how infants perform a key function in language acquisition, associating the sounds of words with their meanings. Seventeen-month-old infants were presented with two label-object pairs in a habituation-based word learning task. In Experiment 1, the labels were produced in adult-directed (AD) speech. In Experiment 2, the labels were produced in ID prosody; they had higher pitch, greater pitch variation, and longer durations than the AD labels. We found that infants failed to learn the labels in AD speech, but succeeded in learning the same labels when they were produced in ID speech. Experiment 3 investigated the role of variability in learning from ID speech. When the labels were presented in ID prosody with no variation across tokens, infants failed to learn them. Our findings indicate that ID prosody can affect how readily infants map sounds to meanings and that the variability in prosody that is characteristic of ID speech may play a key role in its effect on learning new words. PMID:24244106

  20. The use of error-category mapping in pharmacokinetic model analysis of dynamic contrast-enhanced MRI data

    PubMed Central

    Gill, Andrew B.; Anandappa, Gayathri; Patterson, Andrew J.; Priest, Andrew N.; Graves, Martin J.; Janowitz, Tobias; Jodrell, Duncan I.; Eisen, Tim; Lomas, David J.

    2015-01-01

    This study introduces the use of ‘error-category mapping’ in the interpretation of pharmacokinetic (PK) model parameter results derived from dynamic contrast-enhanced (DCE-) MRI data. Eleven patients with metastatic renal cell carcinoma were enrolled in a multiparametric study of the treatment effects of bevacizumab. For the purposes of the present analysis, DCE-MRI data from two identical pre-treatment examinations were analysed by application of the extended Tofts model (eTM), using in turn a model arterial input function (AIF), an individually-measured AIF and a sample-average AIF. PK model parameter maps were calculated. Errors in the signal-to-gadolinium concentration ([Gd]) conversion process and the model-fitting process itself were assigned to category codes on a voxel-by-voxel basis, thereby forming a colour-coded ‘error-category map’ for each imaged slice. These maps were found to be repeatable between patient visits and showed that the eTM converged adequately in the majority of voxels in all the tumours studied. However, the maps also clearly indicated sub-regions of low Gd uptake and of non-convergence of the model in nearly all tumours. The non-physical condition ve ≥ 1 was the most frequently indicated error category and appeared sensitive to the form of AIF used. This simple method for visualisation of errors in DCE-MRI could be used as a routine quality-control technique and also has the potential to reveal otherwise hidden patterns of failure in PK model applications. PMID:25460333

  1. Direct Cortical Mapping via Solving Partial Differential Equations on Implicit Surfaces

    PubMed Central

    Shi, Yonggang; Thompson, Paul M.; Dinov, Ivo; Osher, Stanley; Toga, Arthur W.

    2007-01-01

    In this paper, we propose a novel approach for cortical mapping that computes a direct map between two cortical surfaces while satisfying constraints on sulcal landmark curves. By computing the map directly, we can avoid conventional intermediate parameterizations and help simplify the cortical mapping process. The direct map in our method is formulated as the minimizer of a flexible variational energy under landmark constraints. The energy can include both a harmonic term to ensure smoothness of the map and general data terms for the matching of geometric features. Starting from a properly designed initial map, we compute the map iteratively by solving a partial differential equation (PDE) defined on the source cortical surface. For numerical implementation, a set of adaptive numerical schemes are developed to extend the technique of solving PDEs on implicit surfaces such that landmark constraints are enforced. In our experiments, we show the flexibility of the direct mapping approach by computing smooth maps following landmark constraints from two different energies. We also quantitatively compare the metric preserving property of the direct mapping method with a parametric mapping method on a group of 30 subjects. Finally, we demonstrate the direct mapping method in the brain mapping applications of atlas construction and variability analysis. PMID:17379568

  2. High-Resolution fMRI Maps of Cortical Activation in Nonhuman Primates: Correlation with Intrinsic Signal Optical Images

    PubMed Central

    Roe, Anna W.; Chen, Li Min

    2009-01-01

    One of the most widely used functional brain mapping tools is blood oxygen level–dependent (BOLD) functional magnetic resonance imaging (fMRI). This method has contributed to new understandings of the functional roles of different areas in the human brain. However, its ability to map cerebral cortex at high spatial (submillimeter) resolution is still unknown. Other methods such as single- and multiunit electrophysiology and intrinsic signal optical imaging have revealed submillimeter resolution of sensory topography and cortical columnar activations. However, they are limited either by spatial scale (electrophysiology characterizes only local groups of neurons) or by the inability to monitor deep structures in the brain (i.e., cortical regions buried in sulci or subcortical structures). A method that could monitor all regions of the brain at high spatial resolution would be ideal. This capacity would open the doors to investigating, for example, how networks of cerebral cortical columns relate to or produce behavior. In this article we demonstrate that, without benefit of contrast agents, at a magnetic field strength of 9.4 tesla, BOLD fMRI can reveal millimeter-sized topographic maps of digit representation in the somatosensory cortex of the anesthetized squirrel monkey. Furthermore, by mapping the “funneling illusion,” it is possible to detect even submillimeter shifts in activation in the cortex. Our data suggest that at high magnetic field strength, the positive BOLD signal can be used to reveal high spatial resolution maps of brain activity, a finding that weakens previous notions about the ultimate spatial specificity of the positive BOLD signal. PMID:18172338

  3. On-the-Fly Mapping for Calibrating Directional Antennas

    NASA Technical Reports Server (NTRS)

    Rochblatt, David; Richter, Paul; Withington, Philip

    2004-01-01

    An improved method of calibrating a large directional radio antenna of the type used in deep-space communication and radio astronomy has been developed. This method involves a raster-scanning-and-measurement technique denoted on-the-fly (OTF) mapping, applied in consideration of the results of a systematic analysis of the entire measurement procedure. Phenomena to which particular attention was paid in the analysis include (1) the noise characteristics of a total-power radiometer (TPR) that is used in the measurements and (2) tropospherically induced radiometer fluctuations. The method also involves the use of recently developed techniques for acquisition and reduction of data. In comparison with prior methods used to calibrate such antennas, this method yields an order-of-magnitude improvement in the precision of determinations of antenna aperture efficiency, and improvement by a factor of five or more in the precision of determination of pointing error and beam width. Prerequisite to a meaningful description of the present method is some background information concerning three aspects of the problem of calibrating an antenna of the type in question: In OTF mapping measurements in which a TPR is used, the desired data are the peak temperature corresponding to a radio source, the pointing offset when the antenna is commanded to point toward the source, and the shape of the main lobe of the antenna beam, all as functions of the antenna beam elevation and azimuth angles. These data enable one to calculate the (1) antenna aperture efficiency by comparing the measured peak temperature with that expected for a 100-percent-efficient antenna, (2) the mechanical pointing error resulting from small misalignments of various parts of the antenna structure, and (3) misalignments of the antenna subreflector and other mirrors. For practical reasons having to do with obtaining adequate angular resolution and all-sky coverage, it is necessary to perform azimuth and elevation scans

  4. Compensation for z-directional non-uniformity of a monopole antenna at 7T MRI

    NASA Astrophysics Data System (ADS)

    Kim, Nambeom; Woo, Myung-Kyun; Kang, Chang-Ki

    2016-06-01

    The research was conducted to find ways to compensate for z-directional non-uniformity at a monopole antenna array (MA) coil by using a tilted optimized non-saturating excitation (TONE) pulse and to evaluate the feasibility of using the MA coil with the TONE pulse for anatomical and angiographic imaging. The sensitivity of a MA coil along the z-direction was measured by using an actual flip angle imaging pulse sequence with an oil phantom to evaluate the flip angle distributions of the MA coil for 7T magnetic resonance imaging (MRI). The effects on the z-directional uniformity were examined by using slow and fast TONE pulses, i.e., TONE SLOW and TONE FAST. T1- and T2* -weighted images of the human brain were also examined. The z-directional profiles of the TONE pulses were analyzed by using the average signal intensity throughout the brain. The effect of the TONE pulses on cerebral vessels was further examined by analyzing maximal intensity projections of T1-weighted images. With increasing the applied flip angles, the sensitivity slope slightly increased (0.044 per degree). For the MA coil, the TONE SLOWpulse yielded a compensated profile along the z-direction while the TONE HIGH pulse, which has a flat excitation profile along the z-direction, exhibited a tilted signal intensity toward the coil end, clearly indicating an intrinsic property of the MA coil. Similar to the phantom study, human brain images revealed z-directional symmetry around the peak value for the averaged signal intensity of the TONE SLOW pulse while the TONE HIGH pulse exhibited a tilted signal intensity toward the coil end. In vascular system imaging, the MA coil also clearly demonstrated a beneficial effect on the cerebral vessels, either with or without the TONE pulses. This study demonstrates that TONE pulses could compensate for the intrinsic z-directional non-uniformity of MA coils that exhibit strong uniformity in the x-y plane. Furthermore, tilted pulses, such as TONE pulses, were

  5. MRI-based anatomical model of the human head for specific absorption rate mapping

    PubMed Central

    Makris, Nikos; Angelone, Leonardo; Tulloch, Seann; Sorg, Scott; Kaiser, Jonathan; Kennedy, David

    2009-01-01

    In this study, we present a magnetic resonance imaging (MRI)-based, high-resolution, numerical model of the head of a healthy human subject. In order to formulate the model, we performed quantitative volumetric segmentation on the human head, using T1-weighted MRI. The high spatial resolution used (1 × 1 × 1 mm3), allowed for the precise computation and visualization of a higher number of anatomical structures than provided by previous models. Furthermore, the high spatial resolution allowed us to study individual thin anatomical structures of clinical relevance not visible by the standard model currently adopted in computational bioelectromagnetics. When we computed the electromagnetic field and specific absorption rate (SAR) at 7 Tesla MRI using this high-resolution model, we were able to obtain a detailed visualization of such fine anatomical structures as the epidermis/dermis, bone structures, bone-marrow, white matter and nasal and eye structures. PMID:18985401

  6. Mapping of motor and sensory activity in the human spinal cord with functional magnetic resonance imaging (fMRI)

    NASA Astrophysics Data System (ADS)

    Morales, Dinorah; Rojas, Rafael; Barrios, Fernando A.

    2001-10-01

    Spinal cord fMRI images in control human volunteers were obtained at 1.5 T. Using a T2* weighted EPI-BOLD GE pulse sequence during a motor task activation scheme. The images were centered at C7 with five axial slices, 8 mm thick with zero separation. All the images were analyzed off-line with GE's Functool software to construct a functional map. This study was compared with a previous one at 1.5 T using FLASH sequences. After a small group of volunteers we can conclude that the EPI sequences are highly sensitive to flow effects in the CSF and may not have the functional resolution to use them in functional mapping in the human spine at 1.5 T.

  7. Direct MRI-guided biopsy of the prostate: use of post-biopsy needle track imaging to confirm targeting

    PubMed Central

    Nicholson, Alexander J.; Pettersson, David R.; Korngold, Elena K.; Foster, Bryan R.; Hung, Arthur Y.; Amling, Christopher L.; Coakley, Fergus V.

    2015-01-01

    Purpose To report the observation that in-plane post-biopsy T2-weighted MRI often demonstrates the needle track as a transient visible linear tissue distortion during direct MRI-guided biopsy. Materials and methods We retrospectively identified 11 prostatic lesions in 9 men that underwent direct MRI-guided biopsy and in which post-biopsy images were obtained in the plane of the biopsy needle. Results In 9 of 11 targets, a post-biopsy needle track was visible as a linear tissue distortion on in-plane T2-weighted images obtained at a mean interval of 6 min (range 3–15). In these nine cases, the needle track traversed the intended target, and the biopsy was positive for malignancy in six. Biopsy was positive in one of two cases where the needle track was not visible. In five targets, one or more delayed series were obtained after a mean interval of 21 min (range 8–33), showing the track was no longer visible (n = 3) or was of progressively decreased conspicuity (n = 2). Conclusion Accurate targeting during direct MRI-guided biopsy of the prostate can be confirmed by obtaining post-biopsy in-plane images, since the needle track is usually visible as a transient linear tissue distortion. PMID:25687631

  8. Sentence translation in proficient bilinguals: a direct electrostimulation brain mapping.

    PubMed

    Borius, Pierre-Yves; Giussani, Carlo; Draper, Louisa; Roux, Franck-Emmanuel

    2012-05-01

    Direct cortical electrostimulation was used to study cortical areas hypothetically involved in translation in bilinguals during brain tumour resections, with a view to sparing these functional areas. A series of seven proficient bilingual patients was studied: two left-handed and five right-handed individuals with no pre-existing language deficit. Hemispheric cortex (on the side contralateral to the patient's hand-dominance) was directly stimulated whilst the patient performed naming and reading tasks in both languages and a translation task (of a written text from their second 'learned' language to their first or 'native' language). Of the 147 different cortical sites studied, 26 'language functional sites' were detected, where electrostimulation affected reading and/or naming in the patient's native and/or second learned language. Of these, 8 sites (in 4 patients) were "task-specific" and "language-specific" i.e., affecting only naming or reading in only one of the patient's languages. Of the 26 "language sites", only 3 produced any interferences in translation. All of these were located in frontal regions. Electrostimulation at these sites caused the patient to stop translating abruptly, but no language switching or other translation-related phenomenon was observed. No site was found that was involved only in translation and not other language tasks. Overall, in contrast to other language tasks, cortical structures of the convexity were rarely involved in translation. We suggest that translation interference could be more readily detected by subcortical stimulations. This spatial dissociation within the brain of translation function versus other language functions could explain the cases of dissociated language impairments observed in some bilingual patients with brain lesions. On a practical level, because the cortical sites found by translation tasks are few and related with other cortical language sites, we think that translation tasks provide little

  9. DT-MRI measurement of myolaminar structure: accuracy and sensitivity to time post-fixation, b-value and number of directions.

    PubMed

    Gilbert, Stephen H; Smaill, Bruce H; Walton, Richard D; Trew, Mark L; Bernus, Olivier

    2013-01-01

    DT-MRI has been widely used to quantify myocardial fiber and laminar orientations. These structural orientations influence both the spread of excitation and the reorganization of the myocardium during contraction and are altered in disease states. Studies have sought to validate DT-MRI but questions remain about the accuracy of the method and its sensitivity to the time post-fixation and imaging parameters, including b-value, number of diffusion directions and image voxel size. The advent of high-spatial resolution ex vivo MRI and structure tensor (ST) analysis provides a means of direct validation of DT-MRI and assessment of sensitivity to the b-value, the number of diffusion directions and the image voxel size. We find that, with the fixation method we used, structure does not change with time (up to 72 hours). We show that DT-MRI and ST/HR-MRI are markedly similar measures of fiber orientation but DT-MRI and ST are much less similar measures of laminar orientation. DT-MRI performance is not sensitive to the number of directions, with similar structural orientations measured with 6 or 12 directions. Likewise, DT-MRI performance is generally insensitive to b-value, but laminar measurement is moderately more accurate at b = 500 than for higher b-values.

  10. Temperature mapping in bread dough using SE and GE two-point MRI methods: experimental and theoretical estimation of uncertainty.

    PubMed

    Lucas, Tiphaine; Musse, Maja; Bornert, Mélanie; Davenel, Armel; Quellec, Stéphane

    2012-04-01

    Two-dimensional (2D)-SE, 2D-GE and tri-dimensional (3D)-GE two-point T(1)-weighted MRI methods were evaluated in this study in order to maximize the accuracy of temperature mapping of bread dough during thermal processing. Uncertainties were propagated throughout each protocol of measurement, and comparisons demonstrated that all the methods with comparable acquisition times minimized the temperature uncertainty to similar extent. The experimental uncertainties obtained with low-field MRI were also compared to the theoretical estimations. Some discrepancies were reported between experimental and theoretical values of uncertainties of temperature; however, experimental and theoretical trends with varying parameters agreed to a large extent for both SE and GE methods. The 2D-SE method was chosen for further applications on prefermented dough because of its lower sensitivity to susceptibility differences in porous media. It was applied for temperature mapping in prefermented dough during chilling prior to freezing and compared locally to optical fiber measurements.

  11. Temperature mapping in bread dough using SE and GE two-point MRI methods: experimental and theoretical estimation of uncertainty.

    PubMed

    Lucas, Tiphaine; Musse, Maja; Bornert, Mélanie; Davenel, Armel; Quellec, Stéphane

    2012-04-01

    Two-dimensional (2D)-SE, 2D-GE and tri-dimensional (3D)-GE two-point T(1)-weighted MRI methods were evaluated in this study in order to maximize the accuracy of temperature mapping of bread dough during thermal processing. Uncertainties were propagated throughout each protocol of measurement, and comparisons demonstrated that all the methods with comparable acquisition times minimized the temperature uncertainty to similar extent. The experimental uncertainties obtained with low-field MRI were also compared to the theoretical estimations. Some discrepancies were reported between experimental and theoretical values of uncertainties of temperature; however, experimental and theoretical trends with varying parameters agreed to a large extent for both SE and GE methods. The 2D-SE method was chosen for further applications on prefermented dough because of its lower sensitivity to susceptibility differences in porous media. It was applied for temperature mapping in prefermented dough during chilling prior to freezing and compared locally to optical fiber measurements. PMID:22227351

  12. The Effects of Reciprocal Teaching and Direct Instruction Approaches on Knowledge Map (K-Map) Generation Skill

    ERIC Educational Resources Information Center

    Görgen, Izzet

    2014-01-01

    The primary purpose of the present study is to investigate whether reciprocal teaching approach or direct instruction approach is more effective in the teaching of k-map generation skill. Secondary purpose of the study is to determine which of the k-map generation principles are more challenging for students to apply. The results of the study…

  13. The Effects of Reciprocal Teaching and Direct Instruction Approaches on Knowledge Map (k-map) Generation Skill

    ERIC Educational Resources Information Center

    Gorgen, Izzet

    2014-01-01

    The primary purpose of the present study is to investigate whether reciprocal teaching approach or direct instruction approach is more effective in the teaching of k-map generation skill. Secondary purpose of the study is to determine which of the k-map generation principles are more challenging for students to apply. The results of the study…

  14. FUNCTIONAL BRAIN MAPPING AT 9.4T USING A NEW MRI COMPATIBLE ELECTRODE CHRONICALLY IMPLANTED IN RATS

    PubMed Central

    Dunn, Jeff F.; Tuor, Ursula I.; Kmech, Jonn; Young, Nicole A.; Henderson, Amy K.; Jackson, Jesse C.; Valentine, Pamela A.; Teskey, G. Campbell

    2009-01-01

    There is a need for acute and chronic stimulation of the brain within the MRI for studies of epilepsy, as well as of deep brain stimulation for movement and behavioral disorders. This paper describes the production and characteristics of carbon fiber based electrodes for acute and chronic stimulation in the brain. Increasing MRI field strengths are making it increasingly difficult to introduce foreign objects without a susceptibility artifact. This paper describes the production of, and the characteristics of carbon fiber based electrodes. These are biocompatible and can be implanted for chronic studies. We show the use of these electrodes at 9.4T for studying functional activation. Data are presented showing regional connectivity. Activation not only occurs near the electrode, but at sites distant and often contralateral to the electrode. In addition, there were sites showing strong negative activation to stimulation both with direct stimulation and during a kindling associated seizure. PMID:19097225

  15. Characterizing Information Flux Within the Distributed Pediatric Expressive Language Network: A Core Region Mapped Through fMRI-Constrained MEG Effective Connectivity Analyses

    PubMed Central

    Dimitrijevic, Andrew; Toro-Serey, Claudio A.; Smith, Mary Lou; Holland, Scott K.

    2016-01-01

    Abstract Using noninvasive neuroimaging, researchers have shown that young children have bilateral and diffuse language networks, which become increasingly left lateralized and focal with development. Connectivity within the distributed pediatric language network has been minimally studied, and conventional neuroimaging approaches do not distinguish task-related signal changes from those that are task essential. In this study, we propose a novel multimodal method to map core language sites from patterns of information flux. We retrospectively analyze neuroimaging data collected in two groups of children, ages 5–18 years, performing verb generation in functional magnetic resonance imaging (fMRI) (n = 343) and magnetoencephalography (MEG) (n = 21). The fMRI data were conventionally analyzed and the group activation map parcellated to define node locations. Neuronal activity at each node was estimated from MEG data using a linearly constrained minimum variance beamformer, and effective connectivity within canonical frequency bands was computed using the phase slope index metric. We observed significant (p ≤ 0.05) effective connections in all subjects. The number of suprathreshold connections was significantly and linearly correlated with participant's age (r = 0.50, n = 21, p ≤ 0.05), suggesting that core language sites emerge as part of the normal developmental trajectory. Across frequencies, we observed significant effective connectivity among proximal left frontal nodes. Within the low frequency bands, information flux was rostrally directed within a focal, left frontal region, approximating Broca's area. At higher frequencies, we observed increased connectivity involving bilateral perisylvian nodes. Frequency-specific differences in patterns of information flux were resolved through fast (i.e., MEG) neuroimaging. PMID:26456242

  16. Characterizing Information Flux Within the Distributed Pediatric Expressive Language Network: A Core Region Mapped Through fMRI-Constrained MEG Effective Connectivity Analyses.

    PubMed

    Kadis, Darren S; Dimitrijevic, Andrew; Toro-Serey, Claudio A; Smith, Mary Lou; Holland, Scott K

    2016-02-01

    Using noninvasive neuroimaging, researchers have shown that young children have bilateral and diffuse language networks, which become increasingly left lateralized and focal with development. Connectivity within the distributed pediatric language network has been minimally studied, and conventional neuroimaging approaches do not distinguish task-related signal changes from those that are task essential. In this study, we propose a novel multimodal method to map core language sites from patterns of information flux. We retrospectively analyze neuroimaging data collected in two groups of children, ages 5-18 years, performing verb generation in functional magnetic resonance imaging (fMRI) (n = 343) and magnetoencephalography (MEG) (n = 21). The fMRI data were conventionally analyzed and the group activation map parcellated to define node locations. Neuronal activity at each node was estimated from MEG data using a linearly constrained minimum variance beamformer, and effective connectivity within canonical frequency bands was computed using the phase slope index metric. We observed significant (p ≤ 0.05) effective connections in all subjects. The number of suprathreshold connections was significantly and linearly correlated with participant's age (r = 0.50, n = 21, p ≤ 0.05), suggesting that core language sites emerge as part of the normal developmental trajectory. Across frequencies, we observed significant effective connectivity among proximal left frontal nodes. Within the low frequency bands, information flux was rostrally directed within a focal, left frontal region, approximating Broca's area. At higher frequencies, we observed increased connectivity involving bilateral perisylvian nodes. Frequency-specific differences in patterns of information flux were resolved through fast (i.e., MEG) neuroimaging. PMID:26456242

  17. CRISPR-directed mitotic recombination enables genetic mapping without crosses.

    PubMed

    Sadhu, Meru J; Bloom, Joshua S; Day, Laura; Kruglyak, Leonid

    2016-05-27

    Linkage and association studies have mapped thousands of genomic regions that contribute to phenotypic variation, but narrowing these regions to the underlying causal genes and variants has proven much more challenging. Resolution of genetic mapping is limited by the recombination rate. We developed a method that uses CRISPR (clustered, regularly interspaced, short palindromic repeats) to build mapping panels with targeted recombination events. We tested the method by generating a panel with recombination events spaced along a yeast chromosome arm, mapping trait variation, and then targeting a high density of recombination events to the region of interest. Using this approach, we fine-mapped manganese sensitivity to a single polymorphism in the transporter Pmr1. Targeting recombination events to regions of interest allows us to rapidly and systematically identify causal variants underlying trait differences.

  18. The connectome mapper: an open-source processing pipeline to map connectomes with MRI.

    PubMed

    Daducci, Alessandro; Gerhard, Stephan; Griffa, Alessandra; Lemkaddem, Alia; Cammoun, Leila; Gigandet, Xavier; Meuli, Reto; Hagmann, Patric; Thiran, Jean-Philippe

    2012-01-01

    Researchers working in the field of global connectivity analysis using diffusion magnetic resonance imaging (MRI) can count on a wide selection of software packages for processing their data, with methods ranging from the reconstruction of the local intra-voxel axonal structure to the estimation of the trajectories of the underlying fibre tracts. However, each package is generally task-specific and uses its own conventions and file formats. In this article we present the Connectome Mapper, a software pipeline aimed at helping researchers through the tedious process of organising, processing and analysing diffusion MRI data to perform global brain connectivity analyses. Our pipeline is written in Python and is freely available as open-source at www.cmtk.org.

  19. Mapping three-dimensional oil distribution with π-EPI MRI measurements at low magnetic field.

    PubMed

    Li, Ming; Xiao, Dan; Romero-Zerón, Laura; Marica, Florea; MacMillan, Bryce; Balcom, Bruce J

    2016-08-01

    Magnetic resonance imaging (MRI) is a robust tool to image oil saturation distribution in rock cores during oil displacement processes. However, a lengthy measurement time for 3D measurements at low magnetic field can hinder monitoring the displacement. 1D and 2D MRI measurements are instead often undertaken to monitor the oil displacement since they are faster. However, 1D and 2D images may not completely reflect the oil distribution in heterogeneous rock cores. In this work, a high-speed 3D MRI technique, π Echo Planar Imaging (π-EPI), was employed at 0.2T to monitor oil displacement. Centric scan interleaved sampling with view sharing in k-t space was employed to improve the temporal resolution of the π-EPI measurements. A D2O brine was employed to distinguish the hydrocarbon and water phases. A relatively homogenous glass bead pack and a heterogeneous Spynie core plug were employed to show different oil displacement behaviors. High quality 3D images were acquired with π-EPI MRI measurements. Fluid quantification with π-EPI compared favorably with FID, CPMG, 1D-DHK-SPRITE, 3D Fast Spin Echo (FSE) and 3D Conical SPRITE measurements. π-EPI greatly reduced the gradient duty cycle and improved sensitivity, compared to FSE and Conical SPRITE measurements, enabling dynamic monitoring of oil displacement processes. For core plug samples with sufficiently long lived T2, T2(∗), π-EPI is an ideal method for rapid 3D saturation imaging. PMID:27208417

  20. Mapping three-dimensional oil distribution with π-EPI MRI measurements at low magnetic field.

    PubMed

    Li, Ming; Xiao, Dan; Romero-Zerón, Laura; Marica, Florea; MacMillan, Bryce; Balcom, Bruce J

    2016-08-01

    Magnetic resonance imaging (MRI) is a robust tool to image oil saturation distribution in rock cores during oil displacement processes. However, a lengthy measurement time for 3D measurements at low magnetic field can hinder monitoring the displacement. 1D and 2D MRI measurements are instead often undertaken to monitor the oil displacement since they are faster. However, 1D and 2D images may not completely reflect the oil distribution in heterogeneous rock cores. In this work, a high-speed 3D MRI technique, π Echo Planar Imaging (π-EPI), was employed at 0.2T to monitor oil displacement. Centric scan interleaved sampling with view sharing in k-t space was employed to improve the temporal resolution of the π-EPI measurements. A D2O brine was employed to distinguish the hydrocarbon and water phases. A relatively homogenous glass bead pack and a heterogeneous Spynie core plug were employed to show different oil displacement behaviors. High quality 3D images were acquired with π-EPI MRI measurements. Fluid quantification with π-EPI compared favorably with FID, CPMG, 1D-DHK-SPRITE, 3D Fast Spin Echo (FSE) and 3D Conical SPRITE measurements. π-EPI greatly reduced the gradient duty cycle and improved sensitivity, compared to FSE and Conical SPRITE measurements, enabling dynamic monitoring of oil displacement processes. For core plug samples with sufficiently long lived T2, T2(∗), π-EPI is an ideal method for rapid 3D saturation imaging.

  1. Mapping three-dimensional oil distribution with π-EPI MRI measurements at low magnetic field

    NASA Astrophysics Data System (ADS)

    Li, Ming; Xiao, Dan; Romero-Zerón, Laura; Marica, Florea; MacMillan, Bryce; Balcom, Bruce J.

    2016-08-01

    Magnetic resonance imaging (MRI) is a robust tool to image oil saturation distribution in rock cores during oil displacement processes. However, a lengthy measurement time for 3D measurements at low magnetic field can hinder monitoring the displacement. 1D and 2D MRI measurements are instead often undertaken to monitor the oil displacement since they are faster. However, 1D and 2D images may not completely reflect the oil distribution in heterogeneous rock cores. In this work, a high-speed 3D MRI technique, π Echo Planar Imaging (π-EPI), was employed at 0.2 T to monitor oil displacement. Centric scan interleaved sampling with view sharing in k-t space was employed to improve the temporal resolution of the π-EPI measurements. A D2O brine was employed to distinguish the hydrocarbon and water phases. A relatively homogenous glass bead pack and a heterogeneous Spynie core plug were employed to show different oil displacement behaviors. High quality 3D images were acquired with π-EPI MRI measurements. Fluid quantification with π-EPI compared favorably with FID, CPMG, 1D-DHK-SPRITE, 3D Fast Spin Echo (FSE) and 3D Conical SPRITE measurements. π-EPI greatly reduced the gradient duty cycle and improved sensitivity, compared to FSE and Conical SPRITE measurements, enabling dynamic monitoring of oil displacement processes. For core plug samples with sufficiently long lived T2, T2∗, π-EPI is an ideal method for rapid 3D saturation imaging.

  2. Quantitative susceptibility mapping: current status and future directions.

    PubMed

    Haacke, E Mark; Liu, Saifeng; Buch, Sagar; Zheng, Weili; Wu, Dongmei; Ye, Yongquan

    2015-01-01

    Quantitative susceptibility mapping (QSM) is a new technique for quantifying magnetic susceptibility. It has already found various applications in quantifying in vivo iron content, calcifications and changes in venous oxygen saturation. The accuracy of susceptibility mapping is dependent on several factors. In this review, we evaluate the entire process of QSM from data acquisition to individual data processing steps. We also show preliminary results of several new concepts introduced in this review in an attempt to improve the quality and accuracy for certain steps. The uncertainties in estimating susceptibility differences using susceptibility maps, phase images, and T2* maps are analyzed and compared. Finally, example clinical applications are presented. We conclude that QSM holds great promise in quantifying iron and becoming a standard clinical tool. PMID:25267705

  3. Connectivity of the Primate Superior Colliculus Mapped by Concurrent Microstimulation and Event-Related fMRI

    PubMed Central

    Field, Courtney B.; Johnston, Kevin; Gati, Joseph S.; Menon, Ravi S.; Everling, Stefan

    2008-01-01

    Background Neuroanatomical studies investigating the connectivity of brain areas have heretofore employed procedures in which chemical or viral tracers are injected into an area of interest, and connected areas are subsequently identified using histological techniques. Such experiments require the sacrifice of the animals and do not allow for subsequent electrophysiological studies in the same subjects, rendering a direct investigation of the functional properties of anatomically identified areas impossible. Methodology/Principal Findings Here, we used a combination of microstimulation and fMRI in an anesthetized monkey preparation to study the connectivity of the superior colliculus (SC). Microstimulation of the SC resulted in changes in the blood oxygenation level-dependent (BOLD) signals in the SC and in several cortical and subcortical areas consistent with the known connectivity of the SC in primates. Conclusions/Significance These findings demonstrates that the concurrent use of microstimulation and fMRI can be used to identify brain networks for further electrophysiological or fMRI investigation. PMID:19079541

  4. Bi-Directional Tuning of Amygdala Sensitivity in Combat Veterans Investigated with fMRI

    PubMed Central

    Brashers-Krug, Tom; Jorge, Ricardo

    2015-01-01

    Objectives Combat stress can be followed by persistent emotional consequences. It is thought that these emotional consequences are caused in part by increased amygdala reactivity. It is also thought that amygdala hyper-reactivity results from decreased inhibition from portions of the anterior cingulate cortex (ACC) in which activity is negatively correlated with activity in the amygdala. However, experimental support for these proposals has been inconsistent. Methods We showed movies of combat and civilian scenes during a functional magnetic resonance imaging (fMRI) session to 50 veterans of recent combat. We collected skin conductance responses (SCRs) as measures of emotional arousal. We examined the relation of blood oxygenation-level dependent (BOLD) signal in the amygdala and ACC to symptom measures and to SCRs. Results Emotional arousal, as measured with SCR, was greater during the combat movie than during the civilian movie and did not depend on symptom severity. As expected, amygdala signal during the less-arousing movie increased with increasing symptom severity. Surprisingly, during the more-arousing movie amygdala signal decreased with increasing symptom severity. These differences led to the unexpected result that amygdala signal in highly symptomatic subjects was lower during the more-arousing movie than during the less-arousing movie. Also unexpectedly, we found no significant inverse correlation between any portions of the amygdala and ACC. Rather, signal throughout more than 80% of the ACC showed a strong positive correlation with signal throughout more than 90% of the amygdala. Conclusions Amygdala reactivity can be tuned bi-directionally, either up or down, in the same person depending on the stimulus and the degree of post-traumatic symptoms. The exclusively positive correlations in BOLD activity between the amygdala and ACC contrast with findings that have been cited as evidence for inhibitory control of the amygdala by the ACC. The

  5. Noninvasive quantitative mapping of conductivity and dielectric distributions using RF wave propagation effects in high-field MRI

    NASA Astrophysics Data System (ADS)

    Wen, Han

    2003-06-01

    In this paper I show with phantom and animal experiments a non-invasive and quantitative method for measuring the conductivity and dielectric distributions based on high field magnetic resonance imaging. High field MRI is accompanied by significant RF wave propagation effects. They are observed as phase and magnitude variations of the image that cannot be removed by optimizing the static field homogeneity, or by improving the RF coils. These variations reflect the RF field distribution in the sample, and in fact obey a modified Helmholtz equation. By mapping both the phase and magnitude of the field with MRI techniques, both the conductivity and the dielectric constant are determined non-invasively. In phantom experiments at 1.5 tesla, conductivity values were measured at 4 mm resolution to 0.5 S/m accuracy. At 4.7 tesla, the accuracy was improved to 0.2 S/m, and the dielectric constant was measured to an accuracy of 5 (relative to vacuum) for 2cm regions.

  6. Radiogenomic Mapping of Edema/Cellular Invasion MRI-Phenotypes in Glioblastoma Multiforme

    PubMed Central

    Zinn, Pascal O.; Majadan, Bhanu; Sathyan, Pratheesh; Singh, Sanjay K.; Majumder, Sadhan; Jolesz, Ferenc A.; Colen, Rivka R.

    2011-01-01

    Background Despite recent discoveries of new molecular targets and pathways, the search for an effective therapy for Glioblastoma Multiforme (GBM) continues. A newly emerged field, radiogenomics, links gene expression profiles with MRI phenotypes. MRI-FLAIR is a noninvasive diagnostic modality and was previously found to correlate with cellular invasion in GBM. Thus, our radiogenomic screen has the potential to reveal novel molecular determinants of invasion. Here, we present the first comprehensive radiogenomic analysis using quantitative MRI volumetrics and large-scale gene- and microRNA expression profiling in GBM. Methods Based on The Cancer Genome Atlas (TCGA), discovery and validation sets with gene, microRNA, and quantitative MR-imaging data were created. Top concordant genes and microRNAs correlated with high FLAIR volumes from both sets were further characterized by Kaplan Meier survival statistics, microRNA-gene correlation analyses, and GBM molecular subtype-specific distribution. Results The top upregulated gene in both the discovery (4 fold) and validation (11 fold) sets was PERIOSTIN (POSTN). The top downregulated microRNA in both sets was miR-219, which is predicted to bind to POSTN. Kaplan Meier analysis demonstrated that above median expression of POSTN resulted in significantly decreased survival and shorter time to disease progression (P<0.001). High POSTN and low miR-219 expression were significantly associated with the mesenchymal GBM subtype (P<0.0001). Conclusion Here, we propose a novel diagnostic method to screen for molecular cancer subtypes and genomic correlates of cellular invasion. Our findings also have potential therapeutic significance since successful molecular inhibition of invasion will improve therapy and patient survival in GBM. PMID:21998659

  7. Director orientations in lyotropic liquid crystals: diffusion MRI mapping of the Saupe order tensor.

    PubMed

    Topgaard, Daniel

    2016-03-28

    The macroscopic physical properties of a liquid crystalline material depend on both the properties of the individual crystallites and the details of their spatial arrangement. We propose a diffusion MRI method to estimate the director orientations of a lyotropic liquid crystal as a spatially resolved field of Saupe order tensors. The method relies on varying the shape of the diffusion-encoding tensor to disentangle the effects of voxel-scale director orientational order and the local diffusion anisotropy of the solvent. Proof-of-concept experiments are performed on water in lamellar and reverse hexagonal liquid crystalline systems with intricate patterns of director orientations.

  8. Dynamic in vivo mapping of model moisturiser ingress into human skin by GARfield MRI.

    PubMed

    Ciampi, Elisabetta; van Ginkel, Michael; McDonald, Peter J; Pitts, Simon; Bonnist, Eleanor Y M; Singleton, Scott; Williamson, Ann-Marie

    2011-02-01

    We describe the development of in vivo one-dimensional MRI (profiling) using a GARField (Gradient At Right angles to Field) magnet for the characterisation of side-of-hand human skin. For the first time and in vivo, we report measurements of the NMR longitudinal and transverse relaxation parameters and self-diffusivity of the upper layers of human skin with a nominal spatial resolution better than 10 µm. The results are correlated with in vivo confocal Raman spectroscopy measurements of water concentration and natural moisturiser factors, and discussed in terms of known skin biology and microstructure of the stratum corneum and viable epidermis. The application of model moisturiser solutions to the skin is followed and their dynamics of ingress are characterised using the MRI methodology developed. Selected hydrophilic and lipophilic formulations are studied. The results are corroborated by standard in vivo measurements of transepidermal water loss and hydration status. A further insight into moisturisation mechanisms is gained. The effect of two different penetration enhancers on a commonly used skin care oil is also discussed, and different timescales of oil penetration into the skin are reported depending on the type of enhancer. PMID:20842757

  9. Dynamic in vivo mapping of model moisturiser ingress into human skin by GARfield MRI.

    PubMed

    Ciampi, Elisabetta; van Ginkel, Michael; McDonald, Peter J; Pitts, Simon; Bonnist, Eleanor Y M; Singleton, Scott; Williamson, Ann-Marie

    2011-02-01

    We describe the development of in vivo one-dimensional MRI (profiling) using a GARField (Gradient At Right angles to Field) magnet for the characterisation of side-of-hand human skin. For the first time and in vivo, we report measurements of the NMR longitudinal and transverse relaxation parameters and self-diffusivity of the upper layers of human skin with a nominal spatial resolution better than 10 µm. The results are correlated with in vivo confocal Raman spectroscopy measurements of water concentration and natural moisturiser factors, and discussed in terms of known skin biology and microstructure of the stratum corneum and viable epidermis. The application of model moisturiser solutions to the skin is followed and their dynamics of ingress are characterised using the MRI methodology developed. Selected hydrophilic and lipophilic formulations are studied. The results are corroborated by standard in vivo measurements of transepidermal water loss and hydration status. A further insight into moisturisation mechanisms is gained. The effect of two different penetration enhancers on a commonly used skin care oil is also discussed, and different timescales of oil penetration into the skin are reported depending on the type of enhancer.

  10. Choosing the polarity of the phase-encoding direction in diffusion MRI: Does it matter for group analysis?

    PubMed

    Kennis, M; van Rooij, S J H; Kahn, R S; Geuze, E; Leemans, A

    2016-01-01

    Notorious for degrading diffusion MRI data quality are so-called susceptibility-induced off-resonance fields, which cause non-linear geometric image deformations. While acquiring additional data to correct for these distortions alleviates the adverse effects of this artifact drastically - e.g., by reversing the polarity of the phase-encoding (PE) direction - this strategy is often not an option due to scan time constraints. Especially in a clinical context, where patient comfort and safety are of paramount importance, acquisition specifications are preferred that minimize scan time, typically resulting in data obtained with only one PE direction. In this work, we investigated whether choosing a different polarity of the PE direction would affect the outcome of a specific clinical research study. To address this methodological question, fractional anisotropy (FA) estimates of FreeSurfer brain regions were obtained in civilian and combat controls, remitted posttraumatic stress disorder (PTSD) patients, and persistent PTSD patients before and after trauma-focused therapy and were compared between diffusion MRI data sets acquired with different polarities of the PE direction (posterior-to-anterior, PA and anterior-to-posterior, AP). Our results demonstrate that regional FA estimates differ on average in the order of 5% between AP and PA PE data. In addition, when comparing FA estimates between different subject groups for specific cingulum subdivisions, the conclusions for AP and PA PE data were not in agreement. These findings increase our understanding of how one of the most pronounced data artifacts in diffusion MRI can impact group analyses and should encourage users to be more cautious when interpreting and reporting study outcomes derived from data acquired along a single PE direction. PMID:27158586

  11. Choosing the polarity of the phase-encoding direction in diffusion MRI: Does it matter for group analysis?

    PubMed Central

    Kennis, M.; van Rooij, S.J.H.; Kahn, R.S.; Geuze, E.; Leemans, A.

    2016-01-01

    Notorious for degrading diffusion MRI data quality are so-called susceptibility-induced off-resonance fields, which cause non-linear geometric image deformations. While acquiring additional data to correct for these distortions alleviates the adverse effects of this artifact drastically – e.g., by reversing the polarity of the phase-encoding (PE) direction – this strategy is often not an option due to scan time constraints. Especially in a clinical context, where patient comfort and safety are of paramount importance, acquisition specifications are preferred that minimize scan time, typically resulting in data obtained with only one PE direction. In this work, we investigated whether choosing a different polarity of the PE direction would affect the outcome of a specific clinical research study. To address this methodological question, fractional anisotropy (FA) estimates of FreeSurfer brain regions were obtained in civilian and combat controls, remitted posttraumatic stress disorder (PTSD) patients, and persistent PTSD patients before and after trauma-focused therapy and were compared between diffusion MRI data sets acquired with different polarities of the PE direction (posterior-to-anterior, PA and anterior-to-posterior, AP). Our results demonstrate that regional FA estimates differ on average in the order of 5% between AP and PA PE data. In addition, when comparing FA estimates between different subject groups for specific cingulum subdivisions, the conclusions for AP and PA PE data were not in agreement. These findings increase our understanding of how one of the most pronounced data artifacts in diffusion MRI can impact group analyses and should encourage users to be more cautious when interpreting and reporting study outcomes derived from data acquired along a single PE direction. PMID:27158586

  12. In vivo isotropic 3D diffusion tensor mapping of the rat brain using diffusion-weighted 3D MP-RAGE MRI.

    PubMed

    Numano, Tomokazu; Homma, Kazuhiro; Iwasaki, Nobuaki; Hyodo, Koji; Nitta, Naotaka; Hirose, Takeshi

    2006-04-01

    The purpose of this study was to examine the potential of diffusion-weighted (DW) three-dimensional (3D) MP-RAGE MRI for diffusion-tensor mapping of the rat brain in vivo. A DW-3D-MP-RAGE (3D-DWI) sequence was implemented at 2.0 T using six gradient orientations and a b value of 1000 s/mm2. In this sequence, the preparation sequence with a "90 degrees RF-motion proving gradient (MPG): MPG-180 degrees RF-MPG-90 degrees RF" pulse train (DW driven equilibrium Fourier transform) was used to sensitize the magnetization to diffusion. A centric k-space acquisition order was necessary to minimize saturation effects (T1 contamination) from tissues with short relaxation time. The image matrix was 128x128x128 (interpolated from 64x64x64 acquisitions), which resulted in small isotropic DW image data (voxel size: 0.273x0.273x0.273 mm3). Moreover, 3D-DWI-derived maps of the fractional anisotropy (FA), relative anisotropy (RA) and main-diffusion direction were completely free of susceptibility-induced signal losses and geometric distortions. Two well-known commissural fibers, the corpus callosum and anterior commissure, were indicated and shown to be in agreement with the locations of these known stereotaxic atlases. The experiment took 45 min, and shorter times should be possible in clinical application. The 3D-DWI sequence allows for in vivo 3D diffusion-tensor mapping of the rat brain without motion artifacts and susceptibility to distortion. PMID:16563958

  13. Asymmetric control mechanisms of bimanual coordination: an application of directed connectivity analysis to kinematic and functional MRI data.

    PubMed

    Maki, Yohko; Wong, Kin Foon Kevin; Sugiura, Motoaki; Ozaki, Tohru; Sadato, Norihiro

    2008-10-01

    Mirror-symmetrical bimanual movement is more stable than parallel bimanual movement. This is well established at the kinematic level. We used functional MRI (fMRI) to evaluate the neural substrates of the stability of mirror-symmetrical bimanual movement. Right-handed participants (n=17) rotated disks with their index fingers bimanually, both in mirror-symmetrical and asymmetrical parallel modes. We applied the Akaike causality model to both kinematic and fMRI time-series data. We hypothesized that kinematic stability is represented by the extent of neural "cross-talk": as the fraction of signals that are common to controlling both hands increases, the stability also increases. The standard deviation of the phase difference for the mirror mode was significantly smaller than that for the parallel mode, confirming that the former was more stable. We used the noise-contribution ratio (NCR), which was computed using a multivariate autoregressive model with latent variables, as a direct measure of the cross-talk between both the two hands and the bilateral primary motor cortices (M1s). The mode-by-direction interaction of the NCR was significant in both the kinematic and fMRI data. Furthermore, in both sets of data, the NCR from the right hand (left M1) to the left (right M1) was more prominent than vice versa during the mirror-symmetrical mode, whereas no difference was observed during parallel movement or rest. The asymmetric interhemispheric interaction from the left M1 to the right M1 during symmetric bimanual movement might represent cortical-level cross-talk, which contributes to the stability of symmetric bimanual movements.

  14. Connectivity Concordance Mapping: A New Tool for Model-Free Analysis of fMRI Data of the Human Brain

    PubMed Central

    Lohmann, Gabriele; Ovadia-Caro, Smadar; Jungehülsing, Gerhard Jan; Margulies, Daniel S.; Villringer, Arno; Turner, Robert

    2011-01-01

    Functional magnetic resonance data acquired in a task-absent condition (“resting state”) require new data analysis techniques that do not depend on an activation model. Here, we propose a new analysis method called Connectivity Concordance Mapping (CCM). The main idea is to assign a label to each voxel based on the reproducibility of its whole-brain pattern of connectivity. Specifically, we compute the correlations of time courses of each voxel with every other voxel for each measurement. Voxels whose correlation pattern is consistent across measurements receive high values. The result of a CCM analysis is thus a voxel-wise map of concordance values. Regions of high inter-subject concordance can be assumed to be functionally consistent, and may thus be of specific interest for further analysis. Here we present two fMRI studies to demonstrate the possible applications of the algorithm. The first is a eyes-open/eyes-closed paradigm designed to highlight the potential of the method in a relatively simple domain. The second study is a longitudinal repeated measurement of a patient following stroke. Longitudinal clinical studies such as this may represent the most interesting domain of applications for this algorithm. PMID:22470320

  15. Visualising inter-subject variability in fMRI using threshold-weighted overlap maps.

    PubMed

    Seghier, Mohamed L; Price, Cathy J

    2016-01-01

    Functional neuroimaging studies are revealing the neural systems sustaining many sensory, motor and cognitive abilities. A proper understanding of these systems requires an appreciation of the degree to which they vary across subjects. Some sources of inter-subject variability might be easy to measure (demographics, behavioural scores, or experimental factors), while others are more difficult (cognitive strategies, learning effects, and other hidden sources). Here, we introduce a simple way of visualising whole-brain consistency and variability in brain responses across subjects using threshold-weighted voxel-based overlap maps. The output quantifies the proportion of subjects activating a particular voxel or region over a wide range of statistical thresholds. The sensitivity of our approach was assessed in 30 healthy adults performing a matching task with their dominant hand. We show how overlap maps revealed many effects that were only present in a subsample of our group; we discuss how overlap maps can provide information that may be missed or misrepresented by standard group analysis, and how this information can help users to understand their data. In particular, we emphasize that functional overlap maps can be particularly useful when it comes to explaining typical (or atypical) compensatory mechanisms used by patients following brain damage. PMID:26846561

  16. New perspectives in EEG/MEG brain mapping and PET/fMRI neuroimaging of human pain.

    PubMed

    Chen, A C

    2001-10-01

    With the maturation of EEG/MEG brain mapping and PET/fMRI neuroimaging in the 1990s, greater understanding of pain processing in the brain now elucidates and may even challenge the classical theory of pain mechanisms. This review scans across the cultural diversity of pain expression and modulation in man. It outlines the difficulties in defining and studying human pain. It then focuses on methods of studying the brain in experimental and clinical pain, the cohesive results of brain mapping and neuroimaging of noxious perception, the implication of pain research in understanding human consciousness and the relevance to clinical care as well as to the basic science of human psychophysiology. Non-invasive brain studies in man start to unveil the age-old puzzles of pain-illusion, hypnosis and placebo in pain modulation. The neurophysiological and neurohemodynamic brain measures of experimental pain can now largely satisfy the psychophysiologist's dream, unimaginable only a few years ago, of modelling the body-brain, brain-mind, mind-matter duality in an inter-linking 3-P triad: physics (stimulus energy); physiology (brain activities); and psyche (perception). For neuropsychophysiology greater challenges lie ahead: (a) how to integrate a cohesive theory of human pain in the brain; (b) what levels of analyses are necessary and sufficient; (c) what constitutes the structural organisation of the pain matrix; (d) what are the modes of processing among and across the sites of these structures; and (e) how can neural computation of these processes in the brain be carried out? We may envision that modular identification and delineation of the arousal-attention, emotion-motivation and perception-cognition neural networks of pain processing in the brain will also lead to deeper understanding of the human mind. Two foreseeable impacts on clinical sciences and basic theories from brain mapping/neuroimaging are the plausible central origin in persistent pain and integration of

  17. Refining the Sensory and Motor Ratunculus of the Rat Upper Extremity Using fMRI and Direct Nerve Stimulation

    PubMed Central

    Cho, Younghoon R.; Pawela, Christopher P.; Li, Rupeng; Kao, Dennis; Schulte, Marie L.; Runquist, Matthew L.; Yan, Ji-Geng; Matloub, Hani S.; Jaradeh, Safwan S.; Hudetz, Anthony G.; Hyde, James S.

    2008-01-01

    It is well understood that the different regions of the body have cortical representations in proportion to the degree of innervation. Our current understanding of the rat upper extremity has been enhanced using functional MRI (fMRI), but these studies are often limited to the rat forepaw. The purpose of this study is to describe a new technique that allows us to refine the sensory and motor representations in the cerebral cortex by surgically implanting electrodes on the major nerves of the rat upper extremity and providing direct electrical nerve stimulation while acquiring fMRI images. This technique was used to stimulate the ulnar, median, radial, and musculocutaneous nerves in the rat upper extremity using four different stimulation sequences that varied in frequency (5 Hz vs. 10 Hz) and current (0.5 mA vs. 1.0 mA). A distinct pattern of cortical activation was found for each nerve. The higher stimulation current resulted in a dramatic increase in the level of cortical activation. The higher stimulation frequency resulted in both increases and attenuation of cortical activation in different regions of the brain, depending on which nerve was stimulated. PMID:17969116

  18. MRI in Chronic Aortic Dissection: A Systematic Review and Future Directions

    PubMed Central

    Sherrah, Andrew G.; Grieve, Stuart M.; Jeremy, Richmond W.; Bannon, Paul G.; Vallely, Michael P.; Puranik, Rajesh

    2015-01-01

    The acute event of thoracic aortic dissection carries with it high mortality and morbidity. Despite optimal initial surgical or medical management strategies, the risk of further complications in the long-term, including aneurysmal dilatation and false lumen (FL) expansion, are not insignificant. Adequate follow-up of such conditions requires dedicated imaging where relevant prognostic indicators are accurately assessed. We perform a systematic review of the literature and report the current evidence for the use of magnetic resonance imaging (MRI) in assessment of chronic aortic dissection. We then make a comparison with traditional imaging modalities including computed tomography and echocardiography. We discuss new ways in which MRI may extend existing aortic assessment, including identification of blood-flow dynamics within the TL and FL using phase-contrast imaging. PMID:26664877

  19. Diagnostic Performance of Dual-Energy CT Stress Myocardial Perfusion Imaging: Direct Comparison With Cardiovascular MRI

    PubMed Central

    Ko, Sung Min; Song, Meong Gun; Chee, Hyun Kun; Hwang, Hweung Kon; Feuchtner, Gudrun Maria; Min, James K.

    2014-01-01

    OBJECTIVE The purpose of this study was to assess the diagnostic performance of stress perfusion dual-energy CT (DECT) and its incremental value when used with coronary CT angiography (CTA) for identifying hemodynamically significant coronary artery disease. SUBJECTS AND METHODS One hundred patients with suspected or known coronary artery disease without chronic myocardial infarction detected with coronary CTA underwent stress perfusion DECT, stress cardiovascular perfusion MRI, and invasive coronary angiography (ICA). Stress perfusion DECT and cardiovascular stress perfusion MR images were used for detecting perfusion defects. Coronary CTA and ICA were evaluated in the detection of ≥ 50% coronary stenosis. The diagnostic performance of coronary CTA for detecting hemodynamically significant stenosis was assessed before and after stress perfusion DECT on a pervessel basis with ICA and cardiovascular stress perfusion MRI as the reference standard. RESULTS The performance of stress perfusion DECT compared with cardiovascular stress perfusion MRI on a per-vessel basis in the detection of perfusion defects was sensitivity, 89%; specificity, 74%; positive predictive value, 73%; negative predictive value, 90%. Per segment, these values were sensitivity, 76%; specificity, 80%; positive predictive value, 63%; and negative predictive value, 88%. Compared with ICA and cardiovascular stress perfusion MRI per vessel territory the sensitivity, specificity, positive predictive value, and negative predictive value of coronary CTA were 95%, 61%, 61%, and 95%. The values for stress perfusion DECT were 92%, 72%, 68%, and 94%. The values for coronary CTA and stress perfusion DECT were 88%, 79%, 73%, and 91%. The ROC AUC increased from 0.78 to 0.84 (p = 0.02) with the use of coronary CTA and stress perfusion DECT compared with coronary CTA alone. CONCLUSION Stress perfusion DECT plays a complementary role in enhancing the accuracy of coronary CTA for identifying hemodynamically

  20. The average baboon brain: MRI templates and tissue probability maps from 89 individuals.

    PubMed

    Love, Scott A; Marie, Damien; Roth, Muriel; Lacoste, Romain; Nazarian, Bruno; Bertello, Alice; Coulon, Olivier; Anton, Jean-Luc; Meguerditchian, Adrien

    2016-05-15

    The baboon (Papio) brain is a remarkable model for investigating the brain. The current work aimed at creating a population-average baboon (Papio anubis) brain template and its left/right hemisphere symmetric version from a large sample of T1-weighted magnetic resonance images collected from 89 individuals. Averaging the prior probability maps output during the segmentation of each individual also produced the first baboon brain tissue probability maps for gray matter, white matter and cerebrospinal fluid. The templates and the tissue probability maps were created using state-of-the-art, freely available software tools and are being made freely and publicly available: http://www.nitrc.org/projects/haiko89/ or http://lpc.univ-amu.fr/spip.php?article589. It is hoped that these images will aid neuroimaging research of the baboon by, for example, providing a modern, high quality normalization target and accompanying standardized coordinate system as well as probabilistic priors that can be used during tissue segmentation. PMID:26975558

  1. Feasibility of similarity coefficient map for improving morphological evaluation of T2* weighted MRI for renal cancer

    NASA Astrophysics Data System (ADS)

    Wang, Hao-Yu; Hu, Jiani; Xie, Yao-Qin; Chen, Jie; Yu, Amy; Wei, Xin-Hua; Dai, Yong-Ming; Li, Meng; Bao, Shang-Lian; M. Haacke, E.

    2013-03-01

    The purpose of this paper is to investigate the feasibility of using a similarity coefficient map (SCM) in improving the morphological evaluation of T2* weighted (T2*W) magnatic resonance imaging (MRI) for renal cancer. Simulation studies and in vivo 12-echo T2*W experiments for renal cancers were performed for this purpose. The results of the first simulation study suggest that an SCM can reveal small structures which are hard to distinguish from the background tissue in T2*W images and the corresponding T2* map. The capability of improving the morphological evaluation is likely due to the improvement in the signal-to-noise ratio (SNR) and the carrier-to-noise ratio (CNR) by using the SCM technique. Compared with T2*W images, an SCM can improve the SNR by a factor ranging from 1.87 to 2.47. Compared with T2* maps, an SCM can improve the SNR by a factor ranging from 3.85 to 33.31. Compared with T2*W images, an SCM can improve the CNR by a factor ranging from 2.09 to 2.43. Compared with T2* maps, an SCM can improve the CNR by a factor ranging from 1.94 to 8.14. For a given noise level, the improvements of the SNR and the CNR depend mainly on the original SNRs and CNRs in T2*W images, respectively. In vivo experiments confirmed the results of the first simulation study. The results of the second simulation study suggest that more echoes are used to generate the SCM, and higher SNRs and CNRs can be achieved in SCMs. In conclusion, an SCM can provide improved morphological evaluation of T2*W MR images for renal cancer by unveiling fine structures which are ambiguous or invisible in the corresponding T2*W MR images and T2* maps. Furthermore, in practical applications, for a fixed total sampling time, one should increase the number of echoes as much as possible to achieve SCMs with better SNRs and CNRs.

  2. Mapping the distribution of malaria: current approaches and future directions

    USGS Publications Warehouse

    Johnson, Leah R.; Lafferty, Kevin D.; McNally, Amy; Mordecai, Erin A.; Paaijmans, Krijn P.; Pawar, Samraat; Ryan, Sadie J.; Chen, Dongmei; Moulin, Bernard; Wu, Jianhong

    2015-01-01

    Mapping the distribution of malaria has received substantial attention because the disease is a major source of illness and mortality in humans, especially in developing countries. It also has a defined temporal and spatial distribution. The distribution of malaria is most influenced by its mosquito vector, which is sensitive to extrinsic environmental factors such as rainfall and temperature. Temperature also affects the development rate of the malaria parasite in the mosquito. Here, we review the range of approaches used to model the distribution of malaria, from spatially explicit to implicit, mechanistic to correlative. Although current methods have significantly improved our understanding of the factors influencing malaria transmission, significant gaps remain, particularly in incorporating nonlinear responses to temperature and temperature variability. We highlight new methods to tackle these gaps and to integrate new data with models.

  3. The Role of Gaze Direction and Mutual Exclusivity in Guiding 24-Month-Olds' Word Mappings

    ERIC Educational Resources Information Center

    Graham, Susan A.; Nilsen, Elizabeth S.; Collins, Sarah; Olineck, Kara

    2010-01-01

    In these studies, we examined how a default assumption about word meaning, the mutual exclusivity assumption and an intentional cue, gaze direction, interacted to guide 24-month-olds' object-word mappings. In Expt 1, when the experimenter's gaze was consistent with the mutual exclusivity assumption, novel word mappings were facilitated. When the…

  4. Directly labeled fluorescent DNA probes for chromosome mapping

    SciTech Connect

    Marrone, B.L.; Deaven, L.L.; Chen, D.J.; Park, Min S.; MacInnes, M.A.; Salzman, G.C.; Yoshida, T.M.

    1995-12-31

    A new strategy is briefly described for employing nucleic acid probes that are directly labeled with fluorochromes in fluorescence in situ hybridization techniques. These probes will permit the detection, quantitation, and high-precision spatial analysis of multiple DNA sequences along a single chromosome using video-enhanced fluorescence microscopy and digital image processing and analysis. Potential advantages of direct labeled DNA probes for fluorescence in situ hybridization far surpass currently available, indirect DNA probe labeling techniques in ease of use, versatility, and increased signal- to-noise ratio.

  5. Late emergence of the vibrissa direction selectivity map in the rat barrel cortex.

    PubMed

    Kremer, Yves; Léger, Jean-François; Goodman, Dan; Brette, Romain; Bourdieu, Laurent

    2011-07-20

    In the neocortex, neuronal selectivities for multiple sensorimotor modalities are often distributed in topographical maps thought to emerge during a restricted period in early postnatal development. Rodent barrel cortex contains a somatotopic map for vibrissa identity, but the existence of maps representing other tactile features has not been clearly demonstrated. We addressed the issue of the existence in the rat cortex of an intrabarrel map for vibrissa movement direction using in vivo two-photon imaging. We discovered that the emergence of a direction map in rat barrel cortex occurs long after all known critical periods in the somatosensory system. This map is remarkably specific, taking a pinwheel-like form centered near the barrel center and aligned to the barrel cortex somatotopy. We suggest that this map may arise from intracortical mechanisms and demonstrate by simulation that the combination of spike-timing-dependent plasticity at synapses between layer 4 and layer 2/3 and realistic pad stimulation is sufficient to produce such a map. Its late emergence long after other classical maps suggests that experience-dependent map formation and refinement continue throughout adult life.

  6. Writing Direction Affects How People Map Space Onto Time

    PubMed Central

    Bergen, Benjamin K.; Chan Lau, Ting Ting

    2012-01-01

    What determines which spatial axis people use to represent time? We investigate effects of writing direction. English, like Mandarin Chinese in mainland China, is written left to right and then top to bottom. But in Taiwan, characters are written predominantly top to bottom and then right to left. Because being a fluent reader–writer entails thousands of hours of experience with eye and hand movement in the direction dictated by one’s writing system, it could be that writing system direction affects the axis used to represent time in terms of space. In a behavioral experiment, we had native speakers of English, Mandarin Chinese from mainland China, and Mandarin Chinese from Taiwan place sets of cards in temporal order. These cards depicted stages of development of plants and animals, for instance: tadpole, froglet, frog. Results showed that English speakers always represented time as moving from left to right (LR). Mainland Chinese participants trended in the same direction, but a small portion laid the cards out from top to bottom. Taiwanese participants were just as likely to depict time as moving from LR as from top to bottom, with a large minority depicting it as moving from right to left. Native writing system affects how people represent time spatially. PMID:22514546

  7. Noninvasive functional cardiac electrical source imaging: combining MRI and ECG mapping for imaging electrical function

    NASA Astrophysics Data System (ADS)

    Tilg, Bernhard; Modre, Robert; Fischer, Gerald; Hanser, Friedrich; Messnarz, Bernd; Schocke, Michael F. H.; Kremser, Christian; Roithinger, Franz

    2002-04-01

    Inverse electrocardiography has been developing for several years. By coupling electrocardiographic mapping and 3D+time anatomical data, the electrical excitation sequence can be imaged completely noninvasively in the human heart. In this study, a bidomain theory based surface heart model activation time imaging approach was applied to single beat data of atrial and ventricular depolarization. For sinus and paced rhythms, the sites of early activation and the areas with late activation were estimated with sufficient accuracy. In particular for focal arrhythmias, this model-based imaging approach might allow the guidance and evaluation of antiarrhythmic interventions, for instance, in case of catheter ablation or drug therapy.

  8. Analysis of 2D Phase Contrast MRI in Renal Arteries by Self Organizing Maps

    NASA Astrophysics Data System (ADS)

    Zöllner, Frank G.; Schad, Lothar R.

    We present an approach based on self organizing maps to segment renal arteries from 2D PC Cine MR, images to measure blood velocity and flow. Such information are important in grading renal artery stenosis and support the decision on surgical interventions like percu-tan transluminal angioplasty. Results show that the renal arteries could be extracted automatically. The corresponding velocity profiles show high correlation (r=0.99) compared those from manual delineated vessels. Furthermore, the method could detect possible blood flow patterns within the vessel.

  9. A Method for Automated Classification of Parkinson's Disease Diagnosis Using an Ensemble Average Propagator Template Brain Map Estimated from Diffusion MRI.

    PubMed

    Banerjee, Monami; Okun, Michael S; Vaillancourt, David E; Vemuri, Baba C

    2016-01-01

    Parkinson's disease (PD) is a common and debilitating neurodegenerative disorder that affects patients in all countries and of all nationalities. Magnetic resonance imaging (MRI) is currently one of the most widely used diagnostic imaging techniques utilized for detection of neurologic diseases. Changes in structural biomarkers will likely play an important future role in assessing progression of many neurological diseases inclusive of PD. In this paper, we derived structural biomarkers from diffusion MRI (dMRI), a structural modality that allows for non-invasive inference of neuronal fiber connectivity patterns. The structural biomarker we use is the ensemble average propagator (EAP), a probability density function fully characterizing the diffusion locally at a voxel level. To assess changes with respect to a normal anatomy, we construct an unbiased template brain map from the EAP fields of a control population. Use of an EAP captures both orientation and shape information of the diffusion process at each voxel in the dMRI data, and this feature can be a powerful representation to achieve enhanced PD brain mapping. This template brain map construction method is applicable to small animal models as well as to human brains. The differences between the control template brain map and novel patient data can then be assessed via a nonrigid warping algorithm that transforms the novel data into correspondence with the template brain map, thereby capturing the amount of elastic deformation needed to achieve this correspondence. We present the use of a manifold-valued feature called the Cauchy deformation tensor (CDT), which facilitates morphometric analysis and automated classification of a PD versus a control population. Finally, we present preliminary results of automated discrimination between a group of 22 controls and 46 PD patients using CDT. This method may be possibly applied to larger population sizes and other parkinsonian syndromes in the near future.

  10. A Method for Automated Classification of Parkinson’s Disease Diagnosis Using an Ensemble Average Propagator Template Brain Map Estimated from Diffusion MRI

    PubMed Central

    Banerjee, Monami; Okun, Michael S.; Vaillancourt, David E.; Vemuri, Baba C.

    2016-01-01

    Parkinson’s disease (PD) is a common and debilitating neurodegenerative disorder that affects patients in all countries and of all nationalities. Magnetic resonance imaging (MRI) is currently one of the most widely used diagnostic imaging techniques utilized for detection of neurologic diseases. Changes in structural biomarkers will likely play an important future role in assessing progression of many neurological diseases inclusive of PD. In this paper, we derived structural biomarkers from diffusion MRI (dMRI), a structural modality that allows for non-invasive inference of neuronal fiber connectivity patterns. The structural biomarker we use is the ensemble average propagator (EAP), a probability density function fully characterizing the diffusion locally at a voxel level. To assess changes with respect to a normal anatomy, we construct an unbiased template brain map from the EAP fields of a control population. Use of an EAP captures both orientation and shape information of the diffusion process at each voxel in the dMRI data, and this feature can be a powerful representation to achieve enhanced PD brain mapping. This template brain map construction method is applicable to small animal models as well as to human brains. The differences between the control template brain map and novel patient data can then be assessed via a nonrigid warping algorithm that transforms the novel data into correspondence with the template brain map, thereby capturing the amount of elastic deformation needed to achieve this correspondence. We present the use of a manifold-valued feature called the Cauchy deformation tensor (CDT), which facilitates morphometric analysis and automated classification of a PD versus a control population. Finally, we present preliminary results of automated discrimination between a group of 22 controls and 46 PD patients using CDT. This method may be possibly applied to larger population sizes and other parkinsonian syndromes in the near future. PMID

  11. Reciprocal Benefits of Mass-Univariate and Multivariate Modeling in Brain Mapping: Applications to Event-Related Functional MRI, H2 15O-, and FDG-PET

    PubMed Central

    Habeck, Christian G.

    2006-01-01

    In brain mapping studies of sensory, cognitive, and motor operations, specific waveforms of dynamic neural activity are predicted based on theoretical models of human information processing. For example in event-related functional MRI (fMRI), the general linear model (GLM) is employed in mass-univariate analyses to identify the regions whose dynamic activity closely matches the expected waveforms. By comparison multivariate analyses based on PCA or ICA provide greater flexibility in detecting spatiotemporal properties of experimental data that may strongly support alternative neuroscientific explanations. We investigated conjoint multivariate and mass-univariate analyses that combine the capabilities to (1) verify activation of neural machinery we already understand and (2) discover reliable signatures of new neural machinery. We examined combinations of GLM and PCA that recover latent neural signals (waveforms and footprints) with greater accuracy than either method alone. Comparative results are illustrated with analyses of real fMRI data, adding to Monte Carlo simulation support. PMID:23165047

  12. Estimation of Directed Effective Connectivity from fMRI Functional Connectivity Hints at Asymmetries of Cortical Connectome

    PubMed Central

    Gilson, Matthieu; Moreno-Bote, Ruben; Ponce-Alvarez, Adrián; Ritter, Petra; Deco, Gustavo

    2016-01-01

    The brain exhibits complex spatio-temporal patterns of activity. This phenomenon is governed by an interplay between the internal neural dynamics of cortical areas and their connectivity. Uncovering this complex relationship has raised much interest, both for theory and the interpretation of experimental data (e.g., fMRI recordings) using dynamical models. Here we focus on the so-called inverse problem: the inference of network parameters in a cortical model to reproduce empirically observed activity. Although it has received a lot of interest, recovering directed connectivity for large networks has been rather unsuccessful so far. The present study specifically addresses this point for a noise-diffusion network model. We develop a Lyapunov optimization that iteratively tunes the network connectivity in order to reproduce second-order moments of the node activity, or functional connectivity. We show theoretically and numerically that the use of covariances with both zero and non-zero time shifts is the key to infer directed connectivity. The first main theoretical finding is that an accurate estimation of the underlying network connectivity requires that the time shift for covariances is matched with the time constant of the dynamical system. In addition to the network connectivity, we also adjust the intrinsic noise received by each network node. The framework is applied to experimental fMRI data recorded for subjects at rest. Diffusion-weighted MRI data provide an estimate of anatomical connections, which is incorporated to constrain the cortical model. The empirical covariance structure is reproduced faithfully, especially its temporal component (i.e., time-shifted covariances) in addition to the spatial component that is usually the focus of studies. We find that the cortical interactions, referred to as effective connectivity, in the tuned model are not reciprocal. In particular, hubs are either receptors or feeders: they do not exhibit both strong incoming

  13. Analysis of short single rest/activation epoch fMRI by self-organizing map neural network

    NASA Astrophysics Data System (ADS)

    Erberich, Stephan G.; Dietrich, Thomas; Kemeny, Stefan; Krings, Timo; Willmes, Klaus; Thron, Armin; Oberschelp, Walter

    2000-04-01

    Functional magnet resonance imaging (fMRI) has become a standard non invasive brain imaging technique delivering high spatial resolution. Brain activation is determined by magnetic susceptibility of the blood oxygen level (BOLD effect) during an activation task, e.g. motor, auditory and visual tasks. Usually box-car paradigms have 2 - 4 rest/activation epochs with at least an overall of 50 volumes per scan in the time domain. Statistical test based analysis methods need a large amount of repetitively acquired brain volumes to gain statistical power, like Student's t-test. The introduced technique based on a self-organizing neural network (SOM) makes use of the intrinsic features of the condition change between rest and activation epoch and demonstrated to differentiate between the conditions with less time points having only one rest and one activation epoch. The method reduces scan and analysis time and the probability of possible motion artifacts from the relaxation of the patients head. Functional magnet resonance imaging (fMRI) of patients for pre-surgical evaluation and volunteers were acquired with motor (hand clenching and finger tapping), sensory (ice application), auditory (phonological and semantic word recognition task) and visual paradigms (mental rotation). For imaging we used different BOLD contrast sensitive Gradient Echo Planar Imaging (GE-EPI) single-shot pulse sequences (TR 2000 and 4000, 64 X 64 and 128 X 128, 15 - 40 slices) on a Philips Gyroscan NT 1.5 Tesla MR imager. All paradigms were RARARA (R equals rest, A equals activation) with an epoch width of 11 time points each. We used the self-organizing neural network implementation described by T. Kohonen with a 4 X 2 2D neuron map. The presented time course vectors were clustered by similar features in the 2D neuron map. Three neural networks were trained and used for labeling with the time course vectors of one, two and all three on/off epochs. The results were also compared by using a

  14. Using voxel-based morphometry to map the structural changes associated with rapid conversion in MCI: a longitudinal MRI study.

    PubMed

    Chételat, G; Landeau, B; Eustache, F; Mézenge, F; Viader, F; de la Sayette, V; Desgranges, B; Baron, J-C

    2005-10-01

    Capturing the dynamics of gray matter (GM) atrophy in relation to the conversion from mild cognitive impairment (MCI) to clinically probable Alzheimer's disease (AD) would be of considerable interest. In this prospective study we have used a novel longitudinal voxel-based method to map the progression of GM loss in MCI patients over time and compared converters to non-converters. Eighteen amnestic MCI patients were followed-up for a predefined fixed period of 18 months and conversion was judged according to NINCDS-ADRDA criteria for probable AD. Each patient underwent a high-resolution T1-weighted volume MRI scan both at entry in the study and 18 months later. We used an optimal VBM protocol to compare baseline imaging data of converters to those of non-converters. Moreover, to map GM loss from baseline to follow-up assessment, we used a modified voxel-based morphometry (VBM) procedure specially designed for longitudinal studies. At the end of the follow-up period, seven patients had converted to probable AD. Areas of lower baseline GM value in converters mainly included the hippocampus, parahippocampal cortex, and lingual and fusiform gyri. Regions of significant GM loss over the 18-month follow-up period common to both converters and non-converters included the temporal neocortex, parahippocampal cortex, orbitofrontal and inferior parietal areas, and the left thalamus. However, there was significantly greater GM loss in converters relative to non-converters in the hippocampal area, inferior and middle temporal gyrus, posterior cingulate, and precuneus. This accelerated atrophy may result from both neurofibrillary tangles accumulation and parallel pathological processes such as functional alteration in the posterior cingulate. The ability to longitudinally assess GM changes in MCI offers new perspectives to better understand the pathological processes underlying AD and to monitor the effects of treatment on brain structure.

  15. Direct mapping of nuclear shell effects in the heaviest elements.

    PubMed

    Minaya Ramirez, E; Ackermann, D; Blaum, K; Block, M; Droese, C; Düllmann, Ch E; Dworschak, M; Eibach, M; Eliseev, S; Haettner, E; Herfurth, F; Heßberger, F P; Hofmann, S; Ketelaer, J; Marx, G; Mazzocco, M; Nesterenko, D; Novikov, Yu N; Plaß, W R; Rodríguez, D; Scheidenberger, C; Schweikhard, L; Thirolf, P G; Weber, C

    2012-09-01

    Quantum-mechanical shell effects are expected to strongly enhance nuclear binding on an "island of stability" of superheavy elements. The predicted center at proton number Z = 114, 120, or 126 and neutron number N = 184 has been substantiated by the recent synthesis of new elements up to Z = 118. However, the location of the center and the extension of the island of stability remain vague. High-precision mass spectrometry allows the direct measurement of nuclear binding energies and thus the determination of the strength of shell effects. Here, we present such measurements for nobelium and lawrencium isotopes, which also pin down the deformed shell gap at N = 152.

  16. Direct mapping of nuclear shell effects in the heaviest elements.

    PubMed

    Minaya Ramirez, E; Ackermann, D; Blaum, K; Block, M; Droese, C; Düllmann, Ch E; Dworschak, M; Eibach, M; Eliseev, S; Haettner, E; Herfurth, F; Heßberger, F P; Hofmann, S; Ketelaer, J; Marx, G; Mazzocco, M; Nesterenko, D; Novikov, Yu N; Plaß, W R; Rodríguez, D; Scheidenberger, C; Schweikhard, L; Thirolf, P G; Weber, C

    2012-09-01

    Quantum-mechanical shell effects are expected to strongly enhance nuclear binding on an "island of stability" of superheavy elements. The predicted center at proton number Z = 114, 120, or 126 and neutron number N = 184 has been substantiated by the recent synthesis of new elements up to Z = 118. However, the location of the center and the extension of the island of stability remain vague. High-precision mass spectrometry allows the direct measurement of nuclear binding energies and thus the determination of the strength of shell effects. Here, we present such measurements for nobelium and lawrencium isotopes, which also pin down the deformed shell gap at N = 152. PMID:22878498

  17. Three-dimensional MRI perfusion maps: a step beyond volumetric analysis in mental disorders

    PubMed Central

    Fabene, Paolo F; Farace, Paolo; Brambilla, Paolo; Andreone, Nicola; Cerini, Roberto; Pelizza, Luisa; Versace, Amelia; Rambaldelli, Gianluca; Birbaumer, Niels; Tansella, Michele; Sbarbati, Andrea

    2007-01-01

    A new type of magnetic resonance imaging analysis, based on fusion of three-dimensional reconstructions of time-to-peak parametric maps and high-resolution T1-weighted images, is proposed in order to evaluate the perfusion of selected volumes of interest. Because in recent years a wealth of data have suggested the crucial involvement of vascular alterations in mental diseases, we tested our new method on a restricted sample of schizophrenic patients and matched healthy controls. The perfusion of the whole brain was compared with that of the caudate nucleus by means of intrasubject analysis. As expected, owing to the encephalic vascular pattern, a significantly lower time-to-peak was observed in the caudate nucleus than in the whole brain in all healthy controls, indicating that the suggested method has enough sensitivity to detect subtle perfusion changes even in small volumes of interest. Interestingly, a less uniform pattern was observed in the schizophrenic patients. The latter finding needs to be replicated in an adequate number of subjects. In summary, the three-dimensional analysis method we propose has been shown to be a feasible tool for revealing subtle vascular changes both in normal subjects and in pathological conditions. PMID:17229290

  18. Detection and mapping of delays in early cortical folding derived from in utero MRI

    NASA Astrophysics Data System (ADS)

    Habas, Piotr A.; Rajagopalan, Vidya; Scott, Julia A.; Kim, Kio; Roosta, Ahmad; Rousseau, Francois; Barkovich, A. James; Glenn, Orit A.; Studholme, Colin

    2011-03-01

    Understanding human brain development in utero and detecting cortical abnormalities related to specific clinical conditions is an important area of research. In this paper, we describe and evaluate methodology for detection and mapping of delays in early cortical folding from population-based studies of fetal brain anatomies imaged in utero. We use a general linear modeling framework to describe spatiotemporal changes in curvature of the developing brain and explore the ability to detect and localize delays in cortical folding in the presence of uncertainty in estimation of the fetal age. We apply permutation testing to examine which regions of the brain surface provide the most statistical power to detect a given folding delay at a given developmental stage. The presented methodology is evaluated using MR scans of fetuses with normal brain development and gestational ages ranging from 20.57 to 27.86 weeks. This period is critical in early cortical folding and the formation of the primary and secondary sulci. Finally, we demonstrate a clinical application of the framework for detection and localization of folding delays in fetuses with isolated mild ventriculomegaly.

  19. Three-dimensional MRI perfusion maps: a step beyond volumetric analysis in mental disorders.

    PubMed

    Fabene, Paolo F; Farace, Paolo; Brambilla, Paolo; Andreone, Nicola; Cerini, Roberto; Pelizza, Luisa; Versace, Amelia; Rambaldelli, Gianluca; Birbaumer, Niels; Tansella, Michele; Sbarbati, Andrea

    2007-01-01

    A new type of magnetic resonance imaging analysis, based on fusion of three-dimensional reconstructions of time-to-peak parametric maps and high-resolution T1-weighted images, is proposed in order to evaluate the perfusion of selected volumes of interest. Because in recent years a wealth of data have suggested the crucial involvement of vascular alterations in mental diseases, we tested our new method on a restricted sample of schizophrenic patients and matched healthy controls. The perfusion of the whole brain was compared with that of the caudate nucleus by means of intrasubject analysis. As expected, owing to the encephalic vascular pattern, a significantly lower time-to-peak was observed in the caudate nucleus than in the whole brain in all healthy controls, indicating that the suggested method has enough sensitivity to detect subtle perfusion changes even in small volumes of interest. Interestingly, a less uniform pattern was observed in the schizophrenic patients. The latter finding needs to be replicated in an adequate number of subjects. In summary, the three-dimensional analysis method we propose has been shown to be a feasible tool for revealing subtle vascular changes both in normal subjects and in pathological conditions.

  20. 3D maps from multiple MRI illustrate changing atrophy patterns as subjects progress from mild cognitive impairment to Alzheimer's disease.

    PubMed

    Whitwell, Jennifer L; Przybelski, Scott A; Weigand, Stephen D; Knopman, David S; Boeve, Bradley F; Petersen, Ronald C; Jack, Clifford R

    2007-07-01

    Mild cognitive impairment (MCI), particularly the amnestic subtype (aMCI), is considered as a transitional stage between normal aging and a diagnosis of clinically probable Alzheimer's disease (AD). The aMCI construct is particularly useful as it provides an opportunity to assess a clinical stage which in most subjects represents prodromal AD. The aim of this study was to assess the progression of cerebral atrophy over multiple serial MRI during the period from aMCI to progression to AD. Thirty-three subjects were selected that fulfilled clinical criteria for aMCI and had three serial MRI scans: the first scan approximately 3 years before the diagnosis of AD, the second scan approximately 1 year before, and the third scan at the time of the diagnosis of AD. A group of 33 healthy controls were age and gender-matched to the study cohort. Voxel-based morphometry (VBM) was used to assess patterns of grey matter atrophy in the aMCI subjects at each time-point compared to the control group. Customized templates and prior probability maps were used to avoid normalization and segmentation bias. The pattern of grey matter loss in the aMCI subject scans that were 3 years before the diagnosis of AD was focused primarily on the medial temporal lobes, including the amygdala, anterior hippocampus and entorhinal cortex, with some additional involvement of the fusiform gyrus, compared to controls. The extent and magnitude of the cerebral atrophy further progressed by the time the subjects were 1 year before the diagnosis of AD. At this point atrophy in the temporal lobes spread to include the middle temporal gyrus, and extended into more posterior regions of the temporal lobe to include the entire extent of the hippocampus. The parietal lobe also started to become involved. By the time the subjects had progressed to a clinical diagnosis of AD the pattern of grey matter atrophy had become still more widespread with more severe involvement of the medial temporal lobes and the

  1. Heart MRI

    MedlinePlus

    Magnetic resonance imaging - cardiac; Magnetic resonance imaging - heart; Nuclear magnetic resonance - cardiac; NMR - cardiac; MRI of the heart; Cardiomyopathy - MRI; Heart failure - MRI; Congenital heart disease - MRI

  2. Mapping of human and macaque sensorimotor areas by integrating architectonic, transmitter receptor, MRI and PET data.

    PubMed Central

    Zilles, K; Schlaug, G; Matelli, M; Luppino, G; Schleicher, A; Qü, M; Dabringhaus, A; Seitz, R; Roland, P E

    1995-01-01

    The human and macaque sensorimotor cortex was subdivided into numerous areas by a correlative analysis based on cytoarchitectonics, myeloarchitecture and the distribution of transmitter receptors. Receptor densities and laminar distribution patterns differ not only between motor and somatosensory regions, but also between different areas within these regions of the cortex. Changes in receptor distribution often match architectonically defined borders. Receptor findings provide new criteria for a more detailed mapping in the human brain which cannot be achieved by cytoarchitectonic analysis alone. Morphological data on these areas were integrated with functional data from positron emission tomography (PET) on the basis of a recently developed computerised brain atlas. The central sulcus marks the border between (1) the agranular motor cortex with a generally low density of glutamatergic, muscarinic, GABAergic and serotoninergic receptors, and (2) the granular somatosensory cortex with higher densities of these receptors. Rostral to the primary motor cortex, 2 isocortical areas are found on the mesial cortex which probably represent the functionally defined supplementary motor areas (SMA) SMA-proper (caudally) and pre-SMA (rostrally). Below SMA-proper the areas 24d (macaque) and the caudal cingulate motor area cmc (human) are located in the cingulate sulcus. Both regions correspond to the 'posterior cingulate motor areas' of recent PET studies and to the posterior part of the agranular cingulate cortex of architectonic studies. Below pre-SMA the area 24c (macaque) and the rostral cingulate motor area cmr (human) are located in the cingulate sulcus; they correspond to the 'anterior cingulate motor areas' of recent PET observations and to the anterior part of the agranular cingulate cortex of architectonic studies. Homologous sensorimotor areas can be defined in both species on the basis of common architectonic features. Images Fig. 2 (cont.) Fig. 2 Fig. 8 Fig. 9 Fig

  3. Improved fidelity of brain microstructure mapping from single-shell diffusion MRI.

    PubMed

    Taquet, Maxime; Scherrer, Benoit; Boumal, Nicolas; Peters, Jurriaan M; Macq, Benoit; Warfield, Simon K

    2015-12-01

    Diffusion weighted imaging (DWI) is sensitive to alterations in the diffusion of water molecules caused by microstructural barriers. Different microstructural compartments are characterized by differences in DWI signal. Diffusion tensor imaging conflates the signal from these compartments into a single tensor, which poorly represents multiple white matter fascicles and extra-axonal space. Diffusion compartment imaging (DCI) models overcome this limitation by providing parametric representations for the signal contribution of each compartment, thereby improving the fidelity of brain microstructure mapping. However, current approaches fail to identify DCI model parameters from conventional single-shell DWI with the desired accuracy. It has been demonstrated that part of this inaccuracy is due to the ill-posedness of the estimation of DCI model parameters from conventional single-shell acquisitions. In this paper, we propose to regularize the estimation problem for single-shell DWI by learning a prior distribution of DCI model parameters from DWI acquired at multiple b-values in an external population of subjects. We demonstrate that this population-informed prior enables, for the first time, accurate estimation of DCI models from single-shell DWI typically acquired in clinical practice. We validated our approach on synthetic and in vivo data of healthy subjects and patients with autism spectrum disorder. We applied the approach to population studies of brain microstructure in autism and found that introducing a population-informed prior leads to reliable detection of group differences. Our algorithm enables novel investigation from large existing DWI datasets in normal development and in disease and injury. PMID:26529580

  4. Directing wayfinders with maps: the effects of gender, age, route complexity, and familiarity with the environment.

    PubMed

    Harrell, W A; Bowlby, J W; Hall-Hoffarth, D

    2000-04-01

    The participants were 360 Canadian undergraduates. After receiving written scenarios involving a campus visitor seeking direction to a nearby destination (simple route) or a distant destination (complex route), they drew maps to that destination. The authors varied the visitor's gender, age, and familiarity with campus. They analyzed the content of the students' maps in terms of cardial indicators (compass grid, correct north-south orientation), landmarks, labeled buildings, directional arrows, and supplemental written directions. The men tended to provide more cartographically complete maps than the women, though there were no gender differences in use of landmarks or labeled buildings. The men were significantly more inclined than the women to take visitor characteristics into account, providing more complete maps to visitors navigating complex routes, to newcomers, and to older visitors who were unfamiliar with the campus. The men had more confidence that their maps would successfully lead visitors to their destinations. Route complexity led to greater use of landmarks, labeled buildings, and cardinal indicators. The participants' self-reported familiarity with campus had little effect on their direction giving, except for a greater use of labeled buildings in maps.

  5. PreSurgMapp: a MATLAB Toolbox for Presurgical Mapping of Eloquent Functional Areas Based on Task-Related and Resting-State Functional MRI.

    PubMed

    Huang, Huiyuan; Ding, Zhongxiang; Mao, Dewang; Yuan, Jianhua; Zhu, Fangmei; Chen, Shuda; Xu, Yan; Lou, Lin; Feng, Xiaoyan; Qi, Le; Qiu, Wusi; Zhang, Han; Zang, Yu-Feng

    2016-10-01

    The main goal of brain tumor surgery is to maximize tumor resection while minimizing the risk of irreversible postoperative functional sequelae. Eloquent functional areas should be delineated preoperatively, particularly for patients with tumors near eloquent areas. Functional magnetic resonance imaging (fMRI) is a noninvasive technique that demonstrates great promise for presurgical planning. However, specialized data processing toolkits for presurgical planning remain lacking. Based on several functions in open-source software such as Statistical Parametric Mapping (SPM), Resting-State fMRI Data Analysis Toolkit (REST), Data Processing Assistant for Resting-State fMRI (DPARSF) and Multiple Independent Component Analysis (MICA), here, we introduce an open-source MATLAB toolbox named PreSurgMapp. This toolbox can reveal eloquent areas using comprehensive methods and various complementary fMRI modalities. For example, PreSurgMapp supports both model-based (general linear model, GLM, and seed correlation) and data-driven (independent component analysis, ICA) methods and processes both task-based and resting-state fMRI data. PreSurgMapp is designed for highly automatic and individualized functional mapping with a user-friendly graphical user interface (GUI) for time-saving pipeline processing. For example, sensorimotor and language-related components can be automatically identified without human input interference using an effective, accurate component identification algorithm using discriminability index. All the results generated can be further evaluated and compared by neuro-radiologists or neurosurgeons. This software has substantial value for clinical neuro-radiology and neuro-oncology, including application to patients with low- and high-grade brain tumors and those with epilepsy foci in the dominant language hemisphere who are planning to undergo a temporal lobectomy.

  6. PreSurgMapp: a MATLAB Toolbox for Presurgical Mapping of Eloquent Functional Areas Based on Task-Related and Resting-State Functional MRI.

    PubMed

    Huang, Huiyuan; Ding, Zhongxiang; Mao, Dewang; Yuan, Jianhua; Zhu, Fangmei; Chen, Shuda; Xu, Yan; Lou, Lin; Feng, Xiaoyan; Qi, Le; Qiu, Wusi; Zhang, Han; Zang, Yu-Feng

    2016-10-01

    The main goal of brain tumor surgery is to maximize tumor resection while minimizing the risk of irreversible postoperative functional sequelae. Eloquent functional areas should be delineated preoperatively, particularly for patients with tumors near eloquent areas. Functional magnetic resonance imaging (fMRI) is a noninvasive technique that demonstrates great promise for presurgical planning. However, specialized data processing toolkits for presurgical planning remain lacking. Based on several functions in open-source software such as Statistical Parametric Mapping (SPM), Resting-State fMRI Data Analysis Toolkit (REST), Data Processing Assistant for Resting-State fMRI (DPARSF) and Multiple Independent Component Analysis (MICA), here, we introduce an open-source MATLAB toolbox named PreSurgMapp. This toolbox can reveal eloquent areas using comprehensive methods and various complementary fMRI modalities. For example, PreSurgMapp supports both model-based (general linear model, GLM, and seed correlation) and data-driven (independent component analysis, ICA) methods and processes both task-based and resting-state fMRI data. PreSurgMapp is designed for highly automatic and individualized functional mapping with a user-friendly graphical user interface (GUI) for time-saving pipeline processing. For example, sensorimotor and language-related components can be automatically identified without human input interference using an effective, accurate component identification algorithm using discriminability index. All the results generated can be further evaluated and compared by neuro-radiologists or neurosurgeons. This software has substantial value for clinical neuro-radiology and neuro-oncology, including application to patients with low- and high-grade brain tumors and those with epilepsy foci in the dominant language hemisphere who are planning to undergo a temporal lobectomy. PMID:27221107

  7. SU-D-18C-05: Variable Bolus Arterial Spin Labeling MRI for Accurate Cerebral Blood Flow and Arterial Transit Time Mapping

    SciTech Connect

    Johnston, M; Jung, Y

    2014-06-01

    Purpose: Arterial spin labeling (ASL) is an MRI perfusion imaging method from which quantitative cerebral blood flow (CBF) maps can be calculated. Acquisition with variable post-labeling delays (PLD) and variable TRs allows for arterial transit time (ATT) mapping and leads to more accurate CBF quantification with a scan time saving of 48%. In addition, T1 and M0 maps can be obtained without a separate scan. In order to accurately estimate ATT and T1 of brain tissue from the ASL data, variable labeling durations were invented, entitled variable-bolus ASL. Methods: All images were collected on a healthy subject with a 3T Siemens Skyra scanner. Variable-bolus Psuedo-continuous ASL (PCASL) images were collected with 7 TI times ranging 100-4300ms in increments of 700ms with TR ranging 1000-5200ms. All boluses were 1600ms when the TI allowed, otherwise the bolus duration was 100ms shorter than the TI. All TI times were interleaved to reduce sensitivity to motion. Voxel-wise T1 and M0 maps were estimated using a linear least squares fitting routine from the average singal from each TI time. Then pairwise subtraction of each label/control pair and averaging for each TI time was performed. CBF and ATT maps were created using the standard model by Buxton et al. with a nonlinear fitting routine using the T1 tissue map. Results: CBF maps insensitive to ATT were produced along with ATT maps. Both maps show patterns and averages consistent with literature. The T1 map also shows typical T1 contrast. Conclusion: It has been demonstrated that variablebolus ASL produces CBF maps free from the errors due to ATT and tissue T1 variations and provides M0, T1, and ATT maps which have potential utility. This is accomplished with a single scan in a feasible scan time (under 6 minutes) with low sensivity to motion.

  8. Monitoring dynamic alterations in calcium homeostasis by T1-mapping manganese-enhanced MRI (MEMRI) in the early stage of small intestinal ischemia-reperfusion injury.

    PubMed

    Zhao, Da-wei; Zhang, Le-tian; Cheng, Hai-yun; Zhang, Yu-long; Min, Jia-yan; Xiao, Hua-liang; Wang, Yi

    2015-08-01

    Manganese-enhanced MRI studies have proven to be useful in monitoring physiological activities associated with calcium ions (Ca(2+)) due to the paramagnetic property of the manganese ion (Mn(2+)), which makes it an excellent probe of Ca(2+) . In this study, we developed a method in which a Mn(2+)-enhanced T1 -map MRI could enable the monitoring of Ca(2+) influx during the early stages of intestinal ischemia-reperfusion (I/R) injury. The Mn(2+) infusion protocol was optimized by obtaining dose-dependent and time-course wash-out curves using a Mn(2+)-enhanced T1-map MRI of rabbit abdomens following an intravenous infusion of 50 mmol/l MnCl2 (5-10 nmol/g body weight (BW)). In the rabbit model of intestinal I/R injury, T1 values were derived from the T1 maps in the intestinal wall region and revealed a relationship between the dose of the infused MnCl2 and the intestinal wall relaxation time. Significant Mn(2+) clearance was also observed over time in control animals after the infusion of Mn(2+) at a dose of 10 nmol/g BW. This technique was also shown to be sensitive enough to monitor variations in calcium ion homeostasis in vivo after small intestinal I/R injury. The T1 values of the intestinal I/R group were significantly lower (P < 0.05) than that of the control group at 5, 10, and 15 min after Mn(2+) infusion. Our data suggest that MnCl2 has the potential to be an MRI contrast agent that can be effectively used to monitor changes in intracellular Ca(2+) homeostasis during the early stages of intestinal I/R injury.

  9. Mapping site-specific endonuclease binding to DNA by direct imaging with AFM

    SciTech Connect

    Allison, D.P.; Thundat, T.; Doktycz, M.J.; Kerper, P.S.; Warmack, R.J.; Modrich, P.; Isfort, R.J.

    1995-12-31

    Physical mapping of DNA can be accomplished by direct AFM imaging of site specific proteins bound to DNA molecules. Using Gln-111, a mutant of EcoRI endonuclease with a specific affinity for EcoRI sites 1,000 times greater than wild type enzyme but with cleavage rate constants reduced by a factor of 10{sup 4}, the authors demonstrate site-specific mapping by direct AFM imaging. Images are presented showing specific-site binding of Gln-111 to plasmids having either one (pBS{sup +}) or two (pMP{sup 32}) EcoRI sites. Identification of the Gln-111/DNA complex is greatly enhanced by biotinylation of the complex followed by reaction with streptavidin gold prior to imaging. Image enhancement coupled with improvements in the preparation techniques for imaging large DNA molecules, such as lambda DNA (47 kb), has the potential to contribute to direct AFM restriction mapping of cosmid-sized genomic DNAs.

  10. Mapping site-specific endonuclease binding to DNA by direct imaging with atomic force microscopy (AFM)

    NASA Astrophysics Data System (ADS)

    Allison, David P.; Thundat, Thomas G.; Modrich, P.; Isfort, R. J.; Doktycz, Mitchel J.; Kerper, P. S.; Warmack, R. J.

    1995-04-01

    Physical mapping of DNA can be accomplished by direct AFM imaging of site specific proteins bound to DNA molecules. Using Gln-111, a mutant of EcoRI endonuclease with a specific affinity for EcoRI sites 1000 times greater than wild type enzyme but with cleavage rate constants reduced by a factor of 104, we demonstrate site-specific mapping by direct AFM imaging. Images are presented showing specific-site binding of Gln-111 to plasmids having either one (pBS+) or two (pMP32) EcoRI sites. Identification of the Gln-111/DNA complex is greatly enhanced by biotinylation of the complex followed by reaction with streptavidin gold prior to imaging. Image enhancement coupled with improvements in our preparation techniques for imaging large DNA molecules, such as lambda DNA (47 kb), has the potential to contribute to direct AFM restriction mapping of cosmid-sized genomic DNAs.

  11. Spatial averaging errors in creating hemispherical reflectance (albedo) maps from directional reflectance data

    NASA Technical Reports Server (NTRS)

    Kimes, D. S.; Kerber, A. G.; Sellers, P. J.

    1993-01-01

    Spatial averaging errors which may occur when creating hemispherical reflectance maps for different cover types from direct nadir technique to estimate the hemispherical reflectance are assessed by comparing the results with those obtained with a knowledge-based system called VEG (Kimes et al., 1991, 1992). It was found that hemispherical reflectance errors provided by using VEG are much less than those using the direct nadir techniques, depending on conditions. Suggestions are made concerning sampling and averaging strategies for creating hemispherical reflectance maps for photosynthetic, carbon cycle, and climate change studies.

  12. Direct evidence of intra- and interhemispheric corticomotor network degeneration in amyotrophic lateral sclerosis: an automated MRI structural connectivity study.

    PubMed

    Rose, Stephen; Pannek, Kerstin; Bell, Christopher; Baumann, Fusun; Hutchinson, Nicole; Coulthard, Alan; McCombe, Pamela; Henderson, Robert

    2012-02-01

    Although the pathogenesis of amyotrophic lateral sclerosis (ALS) is uncertain, there is mounting neuroimaging evidence to suggest a mechanism involving the degeneration of multiple white matter (WM) motor and extramotor neural networks. This insight has been achieved, in part, by using MRI Diffusion Tensor Imaging (DTI) and the voxelwise analysis of anisotropy indices, along with DTI tractography to determine which specific motor pathways are involved with ALS pathology. Automated MRI structural connectivity analyses, which probe WM connections linking various functionally discrete cortical regions, have the potential to provide novel information about degenerative processes within multiple white matter (WM) pathways. Our hypothesis is that measures of altered intra- and interhemispheric structural connectivity of the primary motor and somatosensory cortex will provide an improved assessment of corticomotor involvement in ALS. To test this hypothesis, we acquired High Angular Resolution Diffusion Imaging (HARDI) scans along with high resolution structural images (sMRI) on 15 patients with clinical evidence of upper and lower motor neuron involvement, and 20 matched control participants. Whole brain probabilistic tractography was applied to define specific WM pathways connecting discrete corticomotor targets generated from anatomical parcellation of sMRI of the brain. The integrity of these connections was interrogated by comparing the mean fractional anisotropy (FA) derived for each WM pathway. To assist in the interpretation of results, we measured the reproducibility of the FA summary measures over time (6months) in control participants. We also incorporated into our analysis pipeline the evaluation and replacement of outlier voxels due to head motion and physiological noise. When assessing corticomotor connectivity, we found a significant reduction in mean FA within a number of intra- and interhemispheric motor pathways in ALS patients. The abnormal

  13. Head MRI

    MedlinePlus

    ... the head; MRI - cranial; NMR - cranial; Cranial MRI; Brain MRI; MRI - brain; MRI - head ... the test, tell your provider if you have: Brain aneurysm clips An artificial heart valves Heart defibrillator ...

  14. Electron paramagnetic resonance oxygen mapping (EPROM): direct visualization of oxygen concentration in tissue.

    PubMed

    Velan, S S; Spencer, R G; Zweier, J L; Kuppusamy, P

    2000-06-01

    Tissue oxygen content is a central parameter in physiology but is difficult to measure. We report a novel procedure for spatial mapping of oxygen by electron paramagnetic resonance (EPR) utilizing a spectral-spatial imaging data set, in which an EPR spectrum is obtained from each image volume element. From this data set, spatial maps corresponding to local spin density and maximum EPR spectral line amplitude are generated. A map of local EPR spectral linewidth is then computed. Because linewidth directly correlates with oxygen concentration, the linewidth image provides a map of oxygenation. This method avoids a difficulty inherent in other oxygen content mapping techniques using EPR, that is, the unwanted influence of local spin probe density on the image. We provide simulation results and data from phantom studies demonstrating the validity of this method. We then apply the method to map oxygen content in rat tail tissue and vasculature. This method provides a new, widely applicable, approach to direct visualization of oxygen concentration in living tissue. Magn Reson Med 43:804-809, 2000.

  15. Mapping of spatial and temporal heterogeneity of plantar flexor muscle activity during isometric contraction: correlation of velocity-encoded MRI with EMG

    PubMed Central

    Csapo, Robert; Malis, Vadim; Sinha, Usha

    2015-01-01

    The aim of this study was to assess the correlation between contraction-associated muscle kinematics as measured by velocity-encoded phase-contrast (VE-PC) magnetic resonance imaging (MRI) and activity recorded via electromyography (EMG), and to construct a detailed three-dimensional (3-D) map of the contractile behavior of the triceps surae complex from the MRI data. Ten axial-plane VE-PC MRI slices of the triceps surae and EMG data were acquired during submaximal isometric contractions in 10 subjects. MRI images were analyzed to yield the degree of contraction-associated muscle displacement on a voxel-by-voxel basis and determine the heterogeneity of muscle movement within and between slices. Correlational analyses were performed to determine the agreement between EMG data and displacements. Pearson's coefficients demonstrated good agreement (0.84 < r < 0.88) between EMG data and displacements. Comparison between different slices in the gastrocnemius muscle revealed significant heterogeneity in displacement values both in-plane and along the cranio-caudal axis, with highest values in the mid-muscle regions. By contrast, no significant differences between muscle regions were found in the soleus muscle. Substantial differences among displacements were also observed within slices, with those in static areas being only 17–39% (maximum) of those in the most mobile muscle regions. The good agreement between EMG data and displacements suggests that VE-PC MRI may be used as a noninvasive, high-resolution technique for quantifying and modeling muscle activity over the entire 3-D volume of muscle groups. Application to the triceps surae complex revealed substantial heterogeneity of contraction-associated muscle motion both within slices and between different cranio-caudal positions. PMID:26112239

  16. Mapping of spatial and temporal heterogeneity of plantar flexor muscle activity during isometric contraction: correlation of velocity-encoded MRI with EMG.

    PubMed

    Csapo, Robert; Malis, Vadim; Sinha, Usha; Sinha, Shantanu

    2015-09-01

    The aim of this study was to assess the correlation between contraction-associated muscle kinematics as measured by velocity-encoded phase-contrast (VE-PC) magnetic resonance imaging (MRI) and activity recorded via electromyography (EMG), and to construct a detailed three-dimensional (3-D) map of the contractile behavior of the triceps surae complex from the MRI data. Ten axial-plane VE-PC MRI slices of the triceps surae and EMG data were acquired during submaximal isometric contractions in 10 subjects. MRI images were analyzed to yield the degree of contraction-associated muscle displacement on a voxel-by-voxel basis and determine the heterogeneity of muscle movement within and between slices. Correlational analyses were performed to determine the agreement between EMG data and displacements. Pearson's coefficients demonstrated good agreement (0.84 < r < 0.88) between EMG data and displacements. Comparison between different slices in the gastrocnemius muscle revealed significant heterogeneity in displacement values both in-plane and along the cranio-caudal axis, with highest values in the mid-muscle regions. By contrast, no significant differences between muscle regions were found in the soleus muscle. Substantial differences among displacements were also observed within slices, with those in static areas being only 17-39% (maximum) of those in the most mobile muscle regions. The good agreement between EMG data and displacements suggests that VE-PC MRI may be used as a noninvasive, high-resolution technique for quantifying and modeling muscle activity over the entire 3-D volume of muscle groups. Application to the triceps surae complex revealed substantial heterogeneity of contraction-associated muscle motion both within slices and between different cranio-caudal positions.

  17. A quantitative spatial comparison of high-density diffuse optical tomography and fMRI cortical mapping

    PubMed Central

    Eggebrecht, Adam T.; White, Brian R.; Ferradal, Silvina L.; Chen, Chunxiao; Zhan, Yuxuan; Snyder, Abraham Z.; Dehghani, Hamid; Culver, Joseph P.

    2012-01-01

    Functional neuroimaging commands a dominant role in current neuroscience research. However its use in bedside clinical and certain neuro-scientific studies has been limited because the current tools lack the combination of being non-invasive, non-ionizing and portable while maintaining moderate resolution and localization accuracy. Optical neuroimaging satisfies many of these requirements, but, until recent advances in high-density diffuse optical tomography (HD-DOT), has been hampered by limited resolution. While early results of HD-DOT have been promising, a quantitative voxel-wise comparison and validation of HD-DOT against the gold standard of functional magnetic resonance imaging (fMRI) has been lacking. Herein, we provide such an analysis within the visual cortex using matched visual stimulation protocols in a single group of subjects (n=5) during separate HD-DOT and fMRI scanning sessions. To attain the needed voxel-to-voxel co-registration between HD-DOT and fMRI image spaces, we implemented subject-specific head modeling that incorporated MRI anatomy, detailed segmentation, and alignment of source and detector positions. Comparisons of the visual responses found an average localization error between HD-DOT and fMRI of 4.4 +/− 1 mm, significantly less than the average distance between cortical gyri. This specificity demonstrates that HD-DOT has sufficient image quality to be useful as a surrogate for fMRI. PMID:22330315

  18. Direct dose mapping versus energy/mass transfer mapping for 4D dose accumulation: fundamental differences and dosimetric consequences

    NASA Astrophysics Data System (ADS)

    Li, Haisen S.; Zhong, Hualiang; Kim, Jinkoo; Glide-Hurst, Carri; Gulam, Misbah; Nurushev, Teamour S.; Chetty, Indrin J.

    2014-01-01

    The direct dose mapping (DDM) and energy/mass transfer (EMT) mapping are two essential algorithms for accumulating the dose from different anatomic phases to the reference phase when there is organ motion or tumor/tissue deformation during the delivery of radiation therapy. DDM is based on interpolation of the dose values from one dose grid to another and thus lacks rigor in defining the dose when there are multiple dose values mapped to one dose voxel in the reference phase due to tissue/tumor deformation. On the other hand, EMT counts the total energy and mass transferred to each voxel in the reference phase and calculates the dose by dividing the energy by mass. Therefore it is based on fundamentally sound physics principles. In this study, we implemented the two algorithms and integrated them within the Eclipse treatment planning system. We then compared the clinical dosimetric difference between the two algorithms for ten lung cancer patients receiving stereotactic radiosurgery treatment, by accumulating the delivered dose to the end-of-exhale (EE) phase. Specifically, the respiratory period was divided into ten phases and the dose to each phase was calculated and mapped to the EE phase and then accumulated. The displacement vector field generated by Demons-based registration of the source and reference images was used to transfer the dose and energy. The DDM and EMT algorithms produced noticeably different cumulative dose in the regions with sharp mass density variations and/or high dose gradients. For the planning target volume (PTV) and internal target volume (ITV) minimum dose, the difference was up to 11% and 4% respectively. This suggests that DDM might not be adequate for obtaining an accurate dose distribution of the cumulative plan, instead, EMT should be considered.

  19. Software Defined Radio (SDR) and Direct Digital Synthesizer (DDS) for NMR/MRI Instruments at Low-Field

    PubMed Central

    Asfour, Aktham; Raoof, Kosai; Yonnet, Jean-Paul

    2013-01-01

    A proof-of-concept of the use of a fully digital radiofrequency (RF) electronics for the design of dedicated Nuclear Magnetic Resonance (NMR) systems at low-field (0.1 T) is presented. This digital electronics is based on the use of three key elements: a Direct Digital Synthesizer (DDS) for pulse generation, a Software Defined Radio (SDR) for a digital receiving of NMR signals and a Digital Signal Processor (DSP) for system control and for the generation of the gradient signals (pulse programmer). The SDR includes a direct analog-to-digital conversion and a Digital Down Conversion (digital quadrature demodulation, decimation filtering, processing gain…). The various aspects of the concept and of the realization are addressed with some details. These include both hardware design and software considerations. One of the underlying ideas is to enable such NMR systems to “enjoy” from existing advanced technology that have been realized in other research areas, especially in telecommunication domain. Another goal is to make these systems easy to build and replicate so as to help research groups in realizing dedicated NMR desktops for a large palette of new applications. We also would like to give readers an idea of the current trends in this field. The performances of the developed electronics are discussed throughout the paper. First FID (Free Induction Decay) signals are also presented. Some development perspectives of our work in the area of low-field NMR/MRI will be finally addressed. PMID:24287540

  20. Software Defined Radio (SDR) and Direct Digital Synthesizer (DDS) for NMR/MRI instruments at low-field.

    PubMed

    Asfour, Aktham; Raoof, Kosai; Yonnet, Jean-Paul

    2013-01-01

    A proof-of-concept of the use of a fully digital radiofrequency (RF) electronics for the design of dedicated Nuclear Magnetic Resonance (NMR) systems at low-field (0.1 T) is presented. This digital electronics is based on the use of three key elements: a Direct Digital Synthesizer (DDS) for pulse generation, a Software Defined Radio (SDR) for a digital receiving of NMR signals and a Digital Signal Processor (DSP) for system control and for the generation of the gradient signals (pulse programmer). The SDR includes a direct analog-to-digital conversion and a Digital Down Conversion (digital quadrature demodulation, decimation filtering, processing gain…). The various aspects of the concept and of the realization are addressed with some details. These include both hardware design and software considerations. One of the underlying ideas is to enable such NMR systems to "enjoy" from existing advanced technology that have been realized in other research areas, especially in telecommunication domain. Another goal is to make these systems easy to build and replicate so as to help research groups in realizing dedicated NMR desktops for a large palette of new applications. We also would like to give readers an idea of the current trends in this field. The performances of the developed electronics are discussed throughout the paper. First FID (Free Induction Decay) signals are also presented. Some development perspectives of our work in the area of low-field NMR/MRI will be finally addressed. PMID:24287540

  1. Software Defined Radio (SDR) and Direct Digital Synthesizer (DDS) for NMR/MRI instruments at low-field.

    PubMed

    Asfour, Aktham; Raoof, Kosai; Yonnet, Jean-Paul

    2013-11-27

    A proof-of-concept of the use of a fully digital radiofrequency (RF) electronics for the design of dedicated Nuclear Magnetic Resonance (NMR) systems at low-field (0.1 T) is presented. This digital electronics is based on the use of three key elements: a Direct Digital Synthesizer (DDS) for pulse generation, a Software Defined Radio (SDR) for a digital receiving of NMR signals and a Digital Signal Processor (DSP) for system control and for the generation of the gradient signals (pulse programmer). The SDR includes a direct analog-to-digital conversion and a Digital Down Conversion (digital quadrature demodulation, decimation filtering, processing gain…). The various aspects of the concept and of the realization are addressed with some details. These include both hardware design and software considerations. One of the underlying ideas is to enable such NMR systems to "enjoy" from existing advanced technology that have been realized in other research areas, especially in telecommunication domain. Another goal is to make these systems easy to build and replicate so as to help research groups in realizing dedicated NMR desktops for a large palette of new applications. We also would like to give readers an idea of the current trends in this field. The performances of the developed electronics are discussed throughout the paper. First FID (Free Induction Decay) signals are also presented. Some development perspectives of our work in the area of low-field NMR/MRI will be finally addressed.

  2. Comparison of muscle fiber directions between different levator ani muscle subdivisions: in vivo MRI measurements in women

    PubMed Central

    Kim, Jinyong; Miller, Janis M.; Ashton-Miller, James A.; DeLancey, John O. L.

    2014-01-01

    Introduction and hypothesis This study describes a technique to quantify muscle fascicle directions in the levator ani (LA) and tests the null hypothesis that the in vivo fascicle directions for each LA subdivision subtend the same parasagittal angle relative to a horizontal reference axis. Methods Visible muscle fascicle direction in the each of the three LA muscle subdivisions, the pubovisceral (PVM; synonymous with pubococcygeal), puborectal (PRM), and iliococcygeal (ICM) muscles, as well as the external anal sphincter (EAS), were measured on 3-T sagittal MRI images in a convenience sample of 14 healthy women in whom muscle fascicles were visible. Mean ± standard deviation (SD) angle values relative to the horizontal were calculated for each muscle subdivision. Repeated measures ANOVA and post-hoc paired t tests were used to compare muscle groups. Results Pubovisceral muscle fiber inclination was 41±8.0°, PRM was −19±10.1°, ICM was 33±8.8°, and EAS was −43±6.4°. These fascicle directions were statistically different (p<0.001). Pairwise comparisons among levator subdivisions showed angle differences of 60° between PVM and PRM, and 52° between ICM and PRM. An 84° difference existed between PVM and EAS. The smallest angle difference between levator divisions was between PVM and ICM 8°. The difference between PRM and EAS was 24°. All pairwise comparisons were significant (p<0.001). Conclusions The null hypothesis that muscle fascicle inclinations are similar in the three subdivisions of the levator ani and the external anal sphincter was rejected. The largest difference in levator subdivision inclination, 60°, was found between the PVM and PRM. PMID:24832855

  3. Mapping

    ERIC Educational Resources Information Center

    Kinney, Douglas M.; McIntosh, Willard L.

    1978-01-01

    Geologic mapping in the United States increased by about one-quarter in the past year. Examinations of mapping trends were in the following categories: (1) Mapping at scales of 1:100, 000; (2) Metric-scale base maps; (3) International mapping, and (4) Planetary mapping. (MA)

  4. Spatial resolution limits for the localization of noise sources using direct sound mapping

    NASA Astrophysics Data System (ADS)

    Fernandez Comesaña, D.; Holland, K. R.; Fernandez-Grande, E.

    2016-08-01

    One of the main challenges arising from noise and vibration problems is how to identify the areas of a device, machine or structure that produce significant acoustic excitation, i.e. the localization of main noise sources. The direct visualization of sound, in particular sound intensity, has extensively been used for many years to locate sound sources. However, it is not yet well defined when two sources should be regarded as resolved by means of direct sound mapping. This paper derives the limits of the direct representation of sound pressure, particle velocity and sound intensity by exploring the relationship between spatial resolution, noise level and geometry. The proposed expressions are validated via simulations and experiments. It is shown that particle velocity mapping yields better results for identifying closely spaced sound sources than sound pressure or sound intensity, especially in the acoustic near-field.

  5. Review of language organisation in bilingual patients: what can we learn from direct brain mapping?

    PubMed

    Giussani, C; Roux, F-E; Lubrano, V; Gaini, S M; Bello, L

    2007-11-01

    Although the majority of people worldwide are bilingual, the brain representation of language in bilingual persons is still a matter of debate. Since the beginning of the studies conducted on bilinguals, most authors denied that learning a new language requires a new semantic processing or the involvement of new cortical areas. In this paper, we review neurosurgical studies using direct electrocortical or subcortical stimulation techniques for brain mapping in bilingual subjects and compare this data with that obtained from other brain mapping methods. The authors focused on the most controversial issue whether multiple languages are represented in common or distinct cerebral areas. Seven direct brain mapping studies from different teams focused on bilingualism and multilingualism. All these studies showed that even if cerebral representation of language in multilingual patients could be grossly located in the same cortical region, it was possible to individualise distinct language-specific areas by direct cortical stimulation in the dominant frontal and temporo-parietal regions. Task- and language-specific sites were also described, demonstrating an important specialisation of some cortical areas. Using subcortical stimulation, some authors were able to find specific white matter tracts for different languages. Finally, all authors recommend in bilingual patients who need brain mapping for neurosurgical purpose to test all languages in which the subjects are fluent.

  6. Mapping motion from 4D-MRI to 3D-CT for use in 4D dose calculations: A technical feasibility study

    SciTech Connect

    Boye, Dirk; Lomax, Tony; Knopf, Antje

    2013-06-15

    Purpose: Target sites affected by organ motion require a time resolved (4D) dose calculation. Typical 4D dose calculations use 4D-CT as a basis. Unfortunately, 4D-CT images have the disadvantage of being a 'snap-shot' of the motion during acquisition and of assuming regularity of breathing. In addition, 4D-CT acquisitions involve a substantial additional dose burden to the patient making many, repeated 4D-CT acquisitions undesirable. Here the authors test the feasibility of an alternative approach to generate patient specific 4D-CT data sets. Methods: In this approach motion information is extracted from 4D-MRI. Simulated 4D-CT data sets [which the authors call 4D-CT(MRI)] are created by warping extracted deformation fields to a static 3D-CT data set. The employment of 4D-MRI sequences for this has the advantage that no assumptions on breathing regularity are made, irregularities in breathing can be studied and, if necessary, many repeat imaging studies (and consequently simulated 4D-CT data sets) can be performed on patients and/or volunteers. The accuracy of 4D-CT(MRI)s has been validated by 4D proton dose calculations. Our 4D dose algorithm takes into account displacements as well as deformations on the originating 4D-CT/4D-CT(MRI) by calculating the dose of each pencil beam based on an individual time stamp of when that pencil beam is applied. According to corresponding displacement and density-variation-maps the position and the water equivalent range of the dose grid points is adjusted at each time instance. Results: 4D dose distributions, using 4D-CT(MRI) data sets as input were compared to results based on a reference conventional 4D-CT data set capturing similar motion characteristics. Almost identical 4D dose distributions could be achieved, even though scanned proton beams are very sensitive to small differences in the patient geometry. In addition, 4D dose calculations have been performed on the same patient, but using 4D-CT(MRI) data sets based on

  7. A posteriori model validation for the temporal order of directed functional connectivity maps.

    PubMed

    Beltz, Adriene M; Molenaar, Peter C M

    2015-01-01

    A posteriori model validation for the temporal order of neural directed functional connectivity maps is rare. This is striking because models that require sequential independence among residuals are regularly implemented. The aim of the current study was (a) to apply to directed functional connectivity maps of functional magnetic resonance imaging data an a posteriori model validation procedure (i.e., white noise tests of one-step-ahead prediction errors combined with decision criteria for revising the maps based upon Lagrange Multiplier tests), and (b) to demonstrate how the procedure applies to single-subject simulated, single-subject task-related, and multi-subject resting state data. Directed functional connectivity was determined by the unified structural equation model family of approaches in order to map contemporaneous and first order lagged connections among brain regions at the group- and individual-levels while incorporating external input, then white noise tests were run. Findings revealed that the validation procedure successfully detected unmodeled sequential dependencies among residuals and recovered higher order (greater than one) simulated connections, and that the procedure can accommodate task-related input. Findings also revealed that lags greater than one were present in resting state data: With a group-level network that contained only contemporaneous and first order connections, 44% of subjects required second order, individual-level connections in order to obtain maps with white noise residuals. Results have broad methodological relevance (e.g., temporal validation is necessary after directed functional connectivity analyses because the presence of unmodeled higher order sequential dependencies may bias parameter estimates) and substantive implications (e.g., higher order lags may be common in resting state data).

  8. A posteriori model validation for the temporal order of directed functional connectivity maps

    PubMed Central

    Beltz, Adriene M.; Molenaar, Peter C. M.

    2015-01-01

    A posteriori model validation for the temporal order of neural directed functional connectivity maps is rare. This is striking because models that require sequential independence among residuals are regularly implemented. The aim of the current study was (a) to apply to directed functional connectivity maps of functional magnetic resonance imaging data an a posteriori model validation procedure (i.e., white noise tests of one-step-ahead prediction errors combined with decision criteria for revising the maps based upon Lagrange Multiplier tests), and (b) to demonstrate how the procedure applies to single-subject simulated, single-subject task-related, and multi-subject resting state data. Directed functional connectivity was determined by the unified structural equation model family of approaches in order to map contemporaneous and first order lagged connections among brain regions at the group- and individual-levels while incorporating external input, then white noise tests were run. Findings revealed that the validation procedure successfully detected unmodeled sequential dependencies among residuals and recovered higher order (greater than one) simulated connections, and that the procedure can accommodate task-related input. Findings also revealed that lags greater than one were present in resting state data: With a group-level network that contained only contemporaneous and first order connections, 44% of subjects required second order, individual-level connections in order to obtain maps with white noise residuals. Results have broad methodological relevance (e.g., temporal validation is necessary after directed functional connectivity analyses because the presence of unmodeled higher order sequential dependencies may bias parameter estimates) and substantive implications (e.g., higher order lags may be common in resting state data). PMID:26379489

  9. Perceptual “Read-Out” of Conjoined Direction and Disparity Maps in Extrastriate Area MT

    PubMed Central

    2004-01-01

    Cortical neurons are frequently tuned to several stimulus dimensions, and many cortical areas contain intercalated maps of multiple variables. Relatively little is known about how information is “read out” of these multidimensional maps. For example, how does an organism extract information relevant to the task at hand from neurons that are also tuned to other, irrelevant stimulus dimensions? We addressed this question by employing microstimulation techniques to examine the contribution of disparity-tuned neurons in the middle temporal (MT) visual area to performance on a direction discrimination task. Most MT neurons are tuned to both binocular disparity and the direction of stimulus motion, and MT contains topographic maps of both parameters. We assessed the effect of microstimulation on direction judgments after first characterizing the disparity tuning of each stimulation site. Although the disparity of the stimulus was irrelevant to the required task, we found that microstimulation effects were strongly modulated by the disparity tuning of the stimulated neurons. For two of three monkeys, microstimulation of nondisparity-selective sites produced large biases in direction judgments, whereas stimulation of disparity-selective sites had little or no effect. The binocular disparity was optimized for each stimulation site, and our result could not be explained by variations in direction tuning, response strength, or any other tuning property that we examined. When microstimulation of a disparity-tuned site did affect direction judgments, the effects tended to be stronger at the preferred disparity of a stimulation site than at the nonpreferred disparity, indicating that monkeys can selectively monitor direction columns that are best tuned to an appropriate conjunction of parameters. We conclude that the contribution of neurons to behavior can depend strongly upon tuning to stimulus dimensions that appear to be irrelevant to the current task, and we suggest that

  10. Mind over chatter: plastic up-regulation of the fMRI salience network directly after EEG neurofeedback

    PubMed Central

    Ros, Tomas; Théberge, Jean; Frewen, Paul A.; Kluetsch, Rosemarie; Densmore, Maria; Calhoun, Vince D.; Lanius, Ruth A.

    2016-01-01

    Neurofeedback (NFB) involves a brain-computer interface that allows users to learn to voluntarily control their cortical oscillations, reflected in the electroencephalogram (EEG). Although NFB is being pioneered as a noninvasive tool for treating brain disorders, there is insufficient evidence on the mechanism of its impact on brain function. Furthermore, the dominant rhythm of the human brain is the alpha oscillation (8–12 Hz), yet its behavioral significance remains multifaceted and largely correlative. In this study with 34 healthy participants, we examined whether during the performance of an attentional task, the functional connectivity of distinct fMRI networks would be plastically altered after a 30-min session of voluntary reduction of alpha rhythm (n=17) versus a sham-feedback condition (n=17). We reveal that compared to sham-feedback, NFB induced an increase of connectivity within the salience network (dorsal anterior cingulate focus), which was detectable 30 minutes after termination of training. This increase in connectivity was negatively correlated with changes in 'on-task' mind-wandering as well as resting state alpha rhythm. Crucially, there was a causal dependence between alpha rhythm modulations during NFB and at subsequent resting state, not exhibited by the sham group. Our findings provide neurobehavioral evidence for a temporally direct, plastic impact of NFB on a key cognitive control network of the brain, suggesting a promising basis for its use to treat cognitive disorders under physiological conditions. PMID:23022326

  11. Globally conditioned causality in estimating directed brain-heart interactions through joint MRI and RR series analysis.

    PubMed

    Duggento, Andrea; Bianciardi, Marta; Wald, Lawrence L; Passamonti, Luca; Guerrisi, Maria; Barbieri, Riccardo; Toschi, Nicola

    2015-08-01

    We used 7T fMRI with simultaneous physiological signals acquisitions to investigate the causal interactions from resting state brain activity to autonomic nervous system (ANS) outflow as quantified through a probabilistic heartbeat model. Given the highly redundant nature of brain-derived signals, we compare the results of traditional bivariate Granger Causality (GC) to a globally conditioned approach which evaluates the additional influence of each brain region on ANS activity while factoring out effects concomitantly mediated by other brain regions. The bivariate approach results in an unrealistically large number of spurious causal brain-heart links. In contrast, using the globally conditioned approac, we demonstrate the existence of significant selective causal links between cortical/subcortical brain regions and ANS outflow for sympathetic and parasympathetic modulation as well as sympathovagal balance, with a prominent involvement of frontal, parietal, and cerebellar regions and Sensory Motor, Default Mode, Left and Right executive networks. Provided proper conditioning is employed to eliminate spurious causalities, 7T functional imaging coupled with physiological signal acquisition and GC analysis is able to quantify directed brain-heart interactions reflecting central modulation of ANS outflow.

  12. Mind over chatter: plastic up-regulation of the fMRI salience network directly after EEG neurofeedback.

    PubMed

    Ros, Tomas; Théberge, Jean; Frewen, Paul A; Kluetsch, Rosemarie; Densmore, Maria; Calhoun, Vince D; Lanius, Ruth A

    2013-01-15

    Neurofeedback (NFB) involves a brain-computer interface that allows users to learn to voluntarily control their cortical oscillations, reflected in the electroencephalogram (EEG). Although NFB is being pioneered as a noninvasive tool for treating brain disorders, there is insufficient evidence on the mechanism of its impact on brain function. Furthermore, the dominant rhythm of the human brain is the alpha oscillation (8-12 Hz), yet its behavioral significance remains multifaceted and largely correlative. In this study with 34 healthy participants, we examined whether during the performance of an attentional task, the functional connectivity of distinct fMRI networks would be plastically altered after a 30-min session of voluntary reduction of alpha rhythm (n=17) versus a sham-feedback condition (n=17). We reveal that compared to sham-feedback, NFB induced an increase of connectivity within regions of the salience network involved in intrinsic alertness (dorsal anterior cingulate), which was detectable 30 min after termination of training. The increase in salience network (default-mode network) connectivity was negatively (positively) correlated with changes in 'on task' mind-wandering as well as resting state alpha rhythm. Crucially, we observed a causal dependence between alpha rhythm synchronization during NFB and its subsequent change at resting state, not exhibited by the SHAM group. Our findings provide neurobehavioral evidence for the brain's exquisite functional plasticity, and for a temporally direct impact of NFB on a key cognitive control network, suggesting a promising basis for its use to treat cognitive disorders under physiological conditions.

  13. SILC: a new Planck internal linear combination CMB temperature map using directional wavelets

    NASA Astrophysics Data System (ADS)

    Rogers, Keir K.; Peiris, Hiranya V.; Leistedt, Boris; McEwen, Jason D.; Pontzen, Andrew

    2016-08-01

    We present new clean maps of the cosmic microwave background (CMB) temperature anisotropies (as measured by Planck) constructed with a novel internal linear combination (ILC) algorithm using directional, scale-discretized wavelets - scale-discretized, directional wavelet ILC or Scale-discretised, directional wavelet Internal Linear Combination (SILC). Directional wavelets, when convolved with signals on the sphere, can separate the anisotropic filamentary structures which are characteristic of both the CMB and foregrounds. Extending previous component separation methods, which use the frequency, spatial and harmonic signatures of foregrounds to separate them from the cosmological background signal, SILC can additionally use morphological information in the foregrounds and CMB to better localize the cleaning algorithm. We test the method on Planck data and simulations, demonstrating consistency with existing component separation algorithms, and discuss how to optimize the use of morphological information by varying the number of directional wavelets as a function of spatial scale. We find that combining the use of directional and axisymmetric wavelets depending on scale could yield higher quality CMB temperature maps. Our results set the stage for the application of SILC to polarization anisotropies through an extension to spin wavelets.

  14. On the Relationship Between fMRI and Theories of Cognition: The Arrow Points in Both Directions.

    PubMed

    Wixted, John T; Mickes, Laura

    2013-01-01

    In this article, we ask about the contribution of fMRI data to our understanding of theories of cognition and about the contribution of theories of cognition to our understanding of fMRI data. Experiments using fMRI can contribute to our understanding of cognition when they are designed to test the predictions of a particular cognitive theory. Although not all cognitive theories make clear predictions about patterns of activity in the brain fMRI experiments are often well suited to testing the predictions of those that do. However, many fMRI studies that are concerned with cognitive functional neuroanatomy are not designed to test predictions of cognitive theories but are instead designed to investigate the role played by different regions of the brain in cognitive activity. These fMRI studies do not shed light on cognitive theories but instead depend on cognitive theories to interpret the data-an interpretation that is only as valid as the cognitive theory on which it is based. These considerations suggest that the relationship between fMRI and theories of cognition is a two-way street.

  15. Wavelet Entropy and Directed Acyclic Graph Support Vector Machine for Detection of Patients with Unilateral Hearing Loss in MRI Scanning

    PubMed Central

    Wang, Shuihua; Yang, Ming; Du, Sidan; Yang, Jiquan; Liu, Bin; Gorriz, Juan M.; Ramírez, Javier; Yuan, Ti-Fei; Zhang, Yudong

    2016-01-01

    Highlights We develop computer-aided diagnosis system for unilateral hearing loss detection in structural magnetic resonance imaging.Wavelet entropy is introduced to extract image global features from brain images. Directed acyclic graph is employed to endow support vector machine an ability to handle multi-class problems.The developed computer-aided diagnosis system achieves an overall accuracy of 95.1% for this three-class problem of differentiating left-sided and right-sided hearing loss from healthy controls. Aim: Sensorineural hearing loss (SNHL) is correlated to many neurodegenerative disease. Now more and more computer vision based methods are using to detect it in an automatic way. Materials: We have in total 49 subjects, scanned by 3.0T MRI (Siemens Medical Solutions, Erlangen, Germany). The subjects contain 14 patients with right-sided hearing loss (RHL), 15 patients with left-sided hearing loss (LHL), and 20 healthy controls (HC). Method: We treat this as a three-class classification problem: RHL, LHL, and HC. Wavelet entropy (WE) was selected from the magnetic resonance images of each subjects, and then submitted to a directed acyclic graph support vector machine (DAG-SVM). Results: The 10 repetition results of 10-fold cross validation shows 3-level decomposition will yield an overall accuracy of 95.10% for this three-class classification problem, higher than feedforward neural network, decision tree, and naive Bayesian classifier. Conclusions: This computer-aided diagnosis system is promising. We hope this study can attract more computer vision method for detecting hearing loss. PMID:27807415

  16. MRI T1ρ and T2 mapping for the assessment of articular cartilage changes in patients with medial knee osteoarthritis after hemicallotasis osteotomy

    PubMed Central

    Nakamura, E.; Hirose, J.; Okamoto, N.; Yamabe, S.; Mizuta, H.

    2016-01-01

    Objectives The purpose of this study was to clarify the appearance of the reparative tissue on the articular surface and to analyse the properties of the reparative tissue after hemicallotasis osteotomy (HCO) using MRI T1ρ and T2 mapping. Methods Coronal T1ρ and T2 mapping and three-dimensional gradient-echo images were obtained from 20 subjects with medial knee osteoarthritis. We set the regions of interest (ROIs) on the full-thickness cartilage of the medial femoral condyle (MFC) and medial tibial plateau (MTP) of the knee and measured the cartilage thickness (mm) and T1ρ and T2 relaxation times (ms). Statistical analysis of time-dependent changes in the cartilage thickness and the T1ρ and T2 relaxation times was performed using one-way analysis of variance, and Scheffe’s test was employed for post hoc multiple comparison. Results The cartilage-like repair tissue appeared on the cartilage surface of the medial compartment post-operatively, and the cartilage thickness showed a significant increase between the pre-operative and one-year post-operative time points (MFC; p = 0.003, MTP; p < 0.001). The T1ρ values of the cartilage-like repair tissue showed no difference over time, however, the T2 values showed a significant decrease between the pre-operative and one-year post-operative time points (MFC; p = 0.004, MTP; p = 0.040). Conclusion This study clarified that the fibrocartilage-like repair tissue appeared on the articular surface of the medial compartment after HCO as evidenced by MRI T1ρ and T2 mapping. Cite this article: H. Nishioka, E. Nakamura, J. Hirose, N. Okamoto, S. Yamabe, H. Mizuta. MRI T1ρ and T2 mapping for the assessment of articular cartilage changes in patients with medial knee osteoarthritis after hemicallotasis osteotomy. Bone Joint Res 2016;5:294–300. DOI: 10.1302/2046-3758.57.BJR-2016-0057.R1. PMID:27421285

  17. Anomia produced by direct cortical stimulation of the pre-supplementary motor area in a patient undergoing preoperative language mapping.

    PubMed

    Rozanski, Verena Eveline; Peraud, Aurelia; Noachtar, Soheyl

    2015-06-01

    There is sparse data on the analysis of supplementary motor area in language function using direct cortical stimulation of the supplementary motor area. Here, we report a patient who experienced isolated anomia during stimulation of the anterior supplementary motor area and discuss the role of the supplementary motor area in speech production. The role of the pre-supplementary motor· area in word selection, observed in fMRI studies, can be confirmed by direct cortical stimulation.

  18. Comprehensive in vivo mapping of the human basal ganglia and thalamic connectome in individuals using 7T MRI.

    PubMed

    Lenglet, Christophe; Abosch, Aviva; Yacoub, Essa; De Martino, Federico; Sapiro, Guillermo; Harel, Noam

    2012-01-01

    Basal ganglia circuits are affected in neurological disorders such as Parkinson's disease (PD), essential tremor, dystonia and Tourette syndrome. Understanding the structural and functional connectivity of these circuits is critical for elucidating the mechanisms of the movement and neuropsychiatric disorders, and is vital for developing new therapeutic strategies such as deep brain stimulation (DBS). Knowledge about the connectivity of the human basal ganglia and thalamus has rapidly evolved over recent years through non-invasive imaging techniques, but has remained incomplete because of insufficient resolution and sensitivity of these techniques. Here, we present an imaging and computational protocol designed to generate a comprehensive in vivo and subject-specific, three-dimensional model of the structure and connections of the human basal ganglia. High-resolution structural and functional magnetic resonance images were acquired with a 7-Tesla magnet. Capitalizing on the enhanced signal-to-noise ratio (SNR) and enriched contrast obtained at high-field MRI, detailed structural and connectivity representations of the human basal ganglia and thalamus were achieved. This unique combination of multiple imaging modalities enabled the in-vivo visualization of the individual human basal ganglia and thalamic nuclei, the reconstruction of seven white-matter pathways and their connectivity probability that, to date, have only been reported in animal studies, histologically, or group-averaged MRI population studies. Also described are subject-specific parcellations of the basal ganglia and thalamus into sub-territories based on their distinct connectivity patterns. These anatomical connectivity findings are supported by functional connectivity data derived from resting-state functional MRI (R-fMRI). This work demonstrates new capabilities for studying basal ganglia circuitry, and opens new avenues of investigation into the movement and neuropsychiatric disorders, in

  19. Directed acyclic graph-based technology mapping of genetic circuit models.

    PubMed

    Roehner, Nicholas; Myers, Chris J

    2014-08-15

    As engineering foundations such as standards and abstraction begin to mature within synthetic biology, it is vital that genetic design automation (GDA) tools be developed to enable synthetic biologists to automatically select standardized DNA components from a library to meet the behavioral specification for a genetic circuit. To this end, we have developed a genetic technology mapping algorithm that builds on the directed acyclic graph (DAG) based mapping techniques originally used to select parts for digital electronic circuit designs and implemented it in our GDA tool, iBioSim. It is among the first genetic technology mapping algorithms to adapt techniques from electronic circuit design, in particular the use of a cost function to guide the search for an optimal solution, and perhaps that which makes the greatest use of standards for describing genetic function and structure to represent design specifications and component libraries. This paper demonstrates the use of our algorithm to map the specifications for three different genetic circuits against four randomly generated libraries of increasing size to evaluate its performance against both exhaustive search and greedy variants for finding optimal and near-optimal solutions.

  20. Effects of spin-lock field direction on the quantitative measurement of spin-lattice relaxation time constant in the rotating frame (T1ρ) in a clinical MRI system

    SciTech Connect

    Yee, Seonghwan; Gao, Jia-Hong

    2014-12-15

    Purpose: To investigate whether the direction of spin-lock field, either parallel or antiparallel to the rotating magnetization, has any effect on the spin-lock MRI signal and further on the quantitative measurement of T1ρ, in a clinical 3 T MRI system. Methods: The effects of inverted spin-lock field direction were investigated by acquiring a series of spin-lock MRI signals for an American College of Radiology MRI phantom, while the spin-lock field direction was switched between the parallel and antiparallel directions. The acquisition was performed for different spin-locking methods (i.e., for the single- and dual-field spin-locking methods) and for different levels of clinically feasible spin-lock field strength, ranging from 100 to 500 Hz, while the spin-lock duration was varied in the range from 0 to 100 ms. Results: When the spin-lock field was inverted into the antiparallel direction, the rate of MRI signal decay was altered and the T1ρ value, when compared to the value for the parallel field, was clearly different. Different degrees of such direction-dependency were observed for different spin-lock field strengths. In addition, the dependency was much smaller when the parallel and the antiparallel fields are mixed together in the dual-field method. Conclusions: The spin-lock field direction could impact the MRI signal and further the T1ρ measurement in a clinical MRI system.

  1. Multispectral X-ray Imagaing for Core Temperature and Density Maps Retrieval in Direct Drive Implosions

    SciTech Connect

    Tommasini, R; Koch, J A; Izumi, N; Welser, L A; Mancini, R C; Delettrez, J; Regan, S; Smalyuk, V

    2006-04-26

    We report on the experiments aimed at obtaining core temperature and density maps in direct drive implosions at the OMEGA Laser Facility using multi-monochromatic X-ray imagers. These instruments use an array of pinholes and a flat multilayer mirror to provide unique multi-spectral images distributed over a wide spectral range. Using Argon as a dopant in the DD-filled plastic shells produces emission images in the Ar He-b and Ly-b spectral regions. These images allow the retrieval of temperature and density maps of the plasma. We deployed three identical multi-monochromatic X-ray imagers in a quasi-orthogonal line-of-sight configuration to allow tomographic reconstruction of the structure of the imploding core.

  2. 3D image copyright protection based on cellular automata transform and direct smart pixel mapping

    NASA Astrophysics Data System (ADS)

    Li, Xiao-Wei; Kim, Seok-Tae; Lee, In-Kwon

    2014-10-01

    We propose a three-dimensional (3D) watermarking system with the direct smart pixel mapping algorithm to improve the resolution of the reconstructed 3D watermark plane images. The depth-converted elemental image array (EIA) is obtained through the computational pixel mapping method. In the watermark embedding process, the depth-converted EIA is first scrambled by using the Arnold transform, which is then embedded in the middle frequency of the cellular automata (CA) transform. Compared with conventional computational integral imaging reconstruction (CIIR) methods, this proposed scheme gives us a higher resolution of the reconstructed 3D plane images by using the quality-enhanced depth-converted EIA. The proposed method, which can obtain many transform planes for embedding watermark data, uses CA transforms with various gateway values. To prove the effectiveness of the proposed method, we present the results of our preliminary experiments.

  3. Directed isolation and mapping of microsatellites from swine Chromosome 1q telomeric region through microdissection and RH mapping.

    PubMed

    Sarker, N; Hawken, R J; Takahashi, S; Alexander, L J; Awata, T; Schook, L B; Yasue, H

    2001-07-01

    Several quantitative trait loci (QTLs) (vertebrate number, birth weight, age at puberty, growth rate, gestation length, and backfat depth) have been independently mapped to the distal region of swine Chromosome (SSC) 1q in several resource populations. In order to improve the map resolution and refine these QTLs more precisely on SSC1q, we have isolated and mapped additional microsatellites (ms), using chromosome microdissection and radiation hybrid (RH) mapping. Five copies of the telomeric region of SSC1q were microdissected from metaphase spreads and pooled. The chromosomal fragment DNA was randomly amplified by using degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR), enriched for ms, and subcloned into a PCR vector. Screening of subsequent clones with ms probes identified 23 unique ms sequences. Fifteen of these (65%) were subjected to radiation hybrid (RH) mapping by using the INRA-University of Minnesota porcine RH panel (IMpRH); and the remaining eight were not suited for the RH mapping. Twelve microsatellites were assigned to SSC1q telomeric region of IMpRH map (LOD >6), and three remain unlinked (LOD <6). Out of the 15 microsatellite markers, 9 were polymorphic in NIAI reference population based on the Meishan and Göttingen miniature pig. In summary, we have used microdissection and radiation hybrid mapping to clone and map 12 new microsatellites to the swine gene map to increase the resolution of SSC1q in the region of known QTLs.

  4. Combining self-organizing mapping and supervised affinity propagation clustering approach to investigate functional brain networks involved in motor imagery and execution with fMRI measurements

    PubMed Central

    Zhang, Jiang; Liu, Qi; Chen, Huafu; Yuan, Zhen; Huang, Jin; Deng, Lihua; Lu, Fengmei; Zhang, Junpeng; Wang, Yuqing; Wang, Mingwen; Chen, Liangyin

    2015-01-01

    Clustering analysis methods have been widely applied to identifying the functional brain networks of a multitask paradigm. However, the previously used clustering analysis techniques are computationally expensive and thus impractical for clinical applications. In this study a novel method, called SOM-SAPC that combines self-organizing mapping (SOM) and supervised affinity propagation clustering (SAPC), is proposed and implemented to identify the motor execution (ME) and motor imagery (MI) networks. In SOM-SAPC, SOM was first performed to process fMRI data and SAPC is further utilized for clustering the patterns of functional networks. As a result, SOM-SAPC is able to significantly reduce the computational cost for brain network analysis. Simulation and clinical tests involving ME and MI were conducted based on SOM-SAPC, and the analysis results indicated that functional brain networks were clearly identified with different response patterns and reduced computational cost. In particular, three activation clusters were clearly revealed, which include parts of the visual, ME and MI functional networks. These findings validated that SOM-SAPC is an effective and robust method to analyze the fMRI data with multitasks. PMID:26236217

  5. Combining self-organizing mapping and supervised affinity propagation clustering approach to investigate functional brain networks involved in motor imagery and execution with fMRI measurements.

    PubMed

    Zhang, Jiang; Liu, Qi; Chen, Huafu; Yuan, Zhen; Huang, Jin; Deng, Lihua; Lu, Fengmei; Zhang, Junpeng; Wang, Yuqing; Wang, Mingwen; Chen, Liangyin

    2015-01-01

    Clustering analysis methods have been widely applied to identifying the functional brain networks of a multitask paradigm. However, the previously used clustering analysis techniques are computationally expensive and thus impractical for clinical applications. In this study a novel method, called SOM-SAPC that combines self-organizing mapping (SOM) and supervised affinity propagation clustering (SAPC), is proposed and implemented to identify the motor execution (ME) and motor imagery (MI) networks. In SOM-SAPC, SOM was first performed to process fMRI data and SAPC is further utilized for clustering the patterns of functional networks. As a result, SOM-SAPC is able to significantly reduce the computational cost for brain network analysis. Simulation and clinical tests involving ME and MI were conducted based on SOM-SAPC, and the analysis results indicated that functional brain networks were clearly identified with different response patterns and reduced computational cost. In particular, three activation clusters were clearly revealed, which include parts of the visual, ME and MI functional networks. These findings validated that SOM-SAPC is an effective and robust method to analyze the fMRI data with multitasks. PMID:26236217

  6. FUNCTIONAL CARTILAGE MRI T2 MAPPING: EVALUATING THE EFFECT OF AGE AND TRAINING ON KNEE CARTILAGE RESPONSE TO RUNNING

    PubMed Central

    Mosher, Timothy J.; Liu, Yi; Torok, Collin M.

    2009-01-01

    Objective To characterize effects of age and physical activity level on cartilage thickness and T2 response immediately after running. Design Institutional review board approval was obtained and all subjects provided informed consent prior to study participation. Cartilage thickness and MRI T2 values of 22 marathon runners and 15 sedentary controls were compared before and after 30 minutes of running. Runner and control groups were stratified by age ≤ 45 and ≥ 46 years. Multi-echo (TR/TE 1500 ms/9 –109 ms) MR images obtained using a 3.0 T scanner were used to calculate thickness and T2 values from the central femoral and tibial cartilage. Baseline cartilage T2 values, and change in cartilage thickness and T2 values after running were compared between the four groups using 1-way ANOVA. Results After running MRI T2 values decreased in superficial femoral (2 ms to 4 ms) and tibial (1 ms to 3 ms) cartilage along with a decrease in cartilage thickness: (femoral: 4% to 8%, tibial: 0% to 12%). Smaller decrease in cartilage t2 values were observed in the middle zone of cartilage, and no change was observed in the deepest layer. There was no difference cartilage deformation or T2 response to running as a function of age or level of physical activity. Conclusions Running results in a measurable decrease in cartilage thickness and MRI T2 values of superficial cartilage consistent with greater compressibility of the superficial cartilage layer. Age and level of physical activity did not alter the T2 response to running. PMID:19948266

  7. Convergence of human brain mapping tools: neuronavigated TMS parameters and fMRI activity in the hand motor area.

    PubMed

    Sarfeld, Anna-Sophia; Diekhoff, Svenja; Wang, Ling E; Liuzzi, Gianpiero; Uludağ, Kamil; Eickhoff, Simon B; Fink, Gereon R; Grefkes, Christian

    2012-05-01

    Functional magnetic resonance imaging (fMRI) and transcranial magnetic stimulation (TMS) are well-established tools for investigating the human motor system in-vivo. We here studied the relationship between movement-related fMRI signal changes in the primary motor cortex (M1) and electrophysiological properties of the hand motor area assessed with neuronavigated TMS in 17 healthy subjects. The voxel showing the highest task-related BOLD response in the left hand motor area during right hand movements was identified for each individual subject. This fMRI peak voxel in M1 served as spatial target for coil positioning during neuronavigated TMS. We performed correlation analyses between TMS parameters, BOLD signal estimates and effective connectivity parameters of M1 assessed with dynamic causal modeling (DCM). The results showed a negative correlation between the movement-related BOLD signal in left M1 and resting as well as active motor threshold (MT) obtained for left M1. The DCM analysis revealed that higher excitability of left M1 was associated with a stronger coupling between left supplementary motor area (SMA) and M1. Furthermore, BOLD activity in left M1 correlated with ipsilateral silent period (ISP), i.e. the stronger the task-related BOLD response in left M1, the higher interhemispheric inhibition effects targeting right M1. DCM analyses revealed a positive correlation between the coupling of left SMA with left M1 and the duration of ISP. The data show that TMS parameters assessed for the hand area of M1 do not only reflect the intrinsic properties at the stimulation site but also interactions with remote areas in the human motor system.

  8. Spatial Mapping of Flow-Induced Molecular Alignment in a Noncrystalline Biopolymer Fluid Using Double Quantum Filtered (DQF) (23)Na MRI.

    PubMed

    Pavlovskaya, Galina E; Meersmann, Thomas

    2014-08-01

    Flow-induced molecular alignment was observed experimentally in a non-liquid-crystalline bioplymeric fluid during developed tubular flow. The fluid was comprised of rigid rods of the polysaccharide xanthan and exhibited shear-thinning behavior. Without a requirement for optical transparency or the need for an added tracer, (23)Na magic angle (MA) double quantum filtered (DQF) magnetic resonance imaging (MRI) enabled the mapping of the anisotropic molecular arrangement under flow conditions. A regional net molecular alignment was found in areas of high shear values in the vicinity of the tube wall. Furthermore, the xanthan molecules resumed random orientations after the cessation of flow. The observed flow-induced molecular alignment was correlated with the rheological properties of the fluid. The work demonstrates the ability of (23)Na MA DQF magnetic resonance to provide a valuable molecular-mechanical link. PMID:26277955

  9. Mapping.

    ERIC Educational Resources Information Center

    Kinney, Douglas M.; McIntosh, Willard L.

    1979-01-01

    The area of geological mapping in the United States in 1978 increased greatly over that reported in 1977; state geological maps were added for California, Idaho, Nevada, and Alaska last year. (Author/BB)

  10. Rapid geodesic mapping of brain functional connectivity: implementation of a dedicated co-processor in a field-programmable gate array (FPGA) and application to resting state functional MRI.

    PubMed

    Minati, Ludovico; Cercignani, Mara; Chan, Dennis

    2013-10-01

    Graph theory-based analyses of brain network topology can be used to model the spatiotemporal correlations in neural activity detected through fMRI, and such approaches have wide-ranging potential, from detection of alterations in preclinical Alzheimer's disease through to command identification in brain-machine interfaces. However, due to prohibitive computational costs, graph-based analyses to date have principally focused on measuring connection density rather than mapping the topological architecture in full by exhaustive shortest-path determination. This paper outlines a solution to this problem through parallel implementation of Dijkstra's algorithm in programmable logic. The processor design is optimized for large, sparse graphs and provided in full as synthesizable VHDL code. An acceleration factor between 15 and 18 is obtained on a representative resting-state fMRI dataset, and maps of Euclidean path length reveal the anticipated heterogeneous cortical involvement in long-range integrative processing. These results enable high-resolution geodesic connectivity mapping for resting-state fMRI in patient populations and real-time geodesic mapping to support identification of imagined actions for fMRI-based brain-machine interfaces. PMID:23746911

  11. Rapid geodesic mapping of brain functional connectivity: implementation of a dedicated co-processor in a field-programmable gate array (FPGA) and application to resting state functional MRI.

    PubMed

    Minati, Ludovico; Cercignani, Mara; Chan, Dennis

    2013-10-01

    Graph theory-based analyses of brain network topology can be used to model the spatiotemporal correlations in neural activity detected through fMRI, and such approaches have wide-ranging potential, from detection of alterations in preclinical Alzheimer's disease through to command identification in brain-machine interfaces. However, due to prohibitive computational costs, graph-based analyses to date have principally focused on measuring connection density rather than mapping the topological architecture in full by exhaustive shortest-path determination. This paper outlines a solution to this problem through parallel implementation of Dijkstra's algorithm in programmable logic. The processor design is optimized for large, sparse graphs and provided in full as synthesizable VHDL code. An acceleration factor between 15 and 18 is obtained on a representative resting-state fMRI dataset, and maps of Euclidean path length reveal the anticipated heterogeneous cortical involvement in long-range integrative processing. These results enable high-resolution geodesic connectivity mapping for resting-state fMRI in patient populations and real-time geodesic mapping to support identification of imagined actions for fMRI-based brain-machine interfaces.

  12. TGF-β activates Erk MAP kinase signalling through direct phosphorylation of ShcA

    PubMed Central

    Lee, Matt K; Pardoux, Cécile; Hall, Marie C; Lee, Pierre S; Warburton, David; Qing, Jing; Smith, Susan M; Derynck, Rik

    2007-01-01

    Erk1/Erk2 MAP kinases are key regulators of cell behaviour and their activation is generally associated with tyrosine kinase signalling. However, TGF-β stimulation also activates Erk MAP kinases through an undefined mechanism, albeit to a much lower level than receptor tyrosine kinase stimulation. We report that upon TGF-β stimulation, the activated TGF-β type I receptor (TβRI) recruits and directly phosphorylates ShcA proteins on tyrosine and serine. This dual phosphorylation results from an intrinsic TβRI tyrosine kinase activity that complements its well-defined serine-threonine kinase function. TGF-β-induced ShcA phosphorylation induces ShcA association with Grb2 and Sos, thereby initiating the well-characterised pathway linking receptor tyrosine kinases with Erk MAP kinases. We also found that TβRI is tyrosine phosphorylated in response to TGF-β. Thus, TβRI, like the TGF-β type II receptor, is a dual-specificity kinase. Recruitment of tyrosine kinase signalling pathways may account for aspects of TGF-β biology that are independent of Smad signalling. PMID:17673906

  13. Directional disorder of ciliary metachronal waves using two-dimensional correlation map.

    PubMed

    Yi, Won-Jin; Park, Kwang-Suk; Lee, Chul-Hee; Rhee, Chae-Seo; Nam, Sang-Won

    2002-03-01

    The interrelationship of cilia and the order of wave directions are important factors that determine the effectiveness of cilia to transport materials in mucociliary systems of the respiratory tract. The interrelationship of cilia and the directional disorder of ciliary metachronal wave were analyzed using digital microscopic images. The degree of synchronization between ciliary beats was determined by the correlation factor between two different spots. To find out the uniphase directions of beating cilia, principal axes of inertia were applied to the two-dimensional correlation map calculated from sequential ciliary images. The standard deviation of determined wave directions in a region of interest (ROI) was defined as a measure of metachronal wave disorder. The pooled mean of metachronal wave disorder was 23.4 +/- 8.79 degrees in ROIs of 8 microm x 8 microm and 25.4 +/- 6.46 degrees in 32 microm x 24 microm from the sphenoid sinus mucosa of five normal subjects. Our result shows that there is a considerable variation in metachronal wave directions of cilia beating on the epithelium.

  14. Investigation and direct mapping of the persistent spin helix in confined structures

    NASA Astrophysics Data System (ADS)

    Schwemmer, Markus; Weingartner, Matthias; Völkl, Roland; Oltscher, Martin; Schuh, Dieter; Bougeard, Dominique; Korn, Tobias; Schüller, Christian

    The spin-orbit field in GaAs-based quantum well (QW) structures typically consists of two different contributions: Dresselhaus and Rashba field. The geometry of the Dresselhaus field, which arises due to the bulk inversion asymmetry, is mostly determined by the growth direction of the quantum well. The Rashba field instead is caused by a structure inversion asymmetry, which can be controlled, e.g. by the modulation doping. For the specific case of a (001)-grown GaAs quantum well with equal strength of Dresselhaus and Rashba fields, the effective spin-orbit field is oriented along the in-plane [110] direction for all k values and the spin splitting for this direction vanishes. For optically injected spins, which are initially oriented perpendicular to the QW plane, a persistent spin helix (PSH) state forms. We use a femtosecond pulsed TiSa-Laser system combined with a magneto-optical Kerr effect microscope for time- and space-resolved mapping of the PSH. With this technique, we investigate the PSH behavior in confined structures, e.g., thin channels along the helix direction. Hence we find that lateral confinement increases the effective PSH lifetime drastically. In more complex structures, we observe that PSH formation is even stable under a forced direction change. Financial support by the DFG via SFB 689 and SPP 1285 is gratefully acknowledged.

  15. Mapping the Functional Network of Medial Prefrontal Cortex by Combining Optogenetics and fMRI in Awake Rats

    PubMed Central

    Liang, Zhifeng; Watson, Glenn D.R.; Alloway, Kevin D.; Lee, Gangchea; Neuberger, Thomas; Zhang, Nanyin

    2015-01-01

    The medial prefrontal cortex (mPFC) plays a critical role in multiple cognitive and limbic functions. Given its vital importance, investigating the function of individual mPFC circuits in animal models has provided critical insight into the neural basis underlying different behaviors and psychiatric conditions. However, our knowledge regarding the mPFC whole-brain network stays largely at the anatomical level, while the functional network of mPFC, which can be dynamic in different conditions or following manipulations, remains elusive especially in awake rodents. Here we combined optogenetic stimulation and functional magnetic resonance imaging (opto-fMRI) to reveal the network of brain regions functionally activated by mPFC outputs in awake rodents. Our data showed significant increases in blood-oxygenation-level dependent (BOLD) signals in prefrontal, striatal and limbic regions when mPFC was optically stimulated. This activation pattern was robust, reproducible, and did not depend on the stimulation period in awake rats. BOLD signals, however, were substantially reduced when animals were anesthetized. In addition, regional brain activation showing increased BOLD signals during mPFC stimulation was corroborated by electrophysiological recordings. These results expand the applicability of the opto-fMRI approach from sensorimotor processing to cognition-related networks in awake rodents. Importantly, it may help elucidate the circuit mechanisms underlying numerous mPFC-related functions and behaviors that need to be assessed in the awake state. PMID:26002727

  16. Non-invasive mapping of deep-tissue lymph nodes in live animals using a multimodal PET/MRI nanoparticle

    PubMed Central

    Thorek, Daniel L.J.; Ulmert, David; Diop, Ndeye-Fatou M.; Lupu, Mihaela E.; Doran, Michael G.; Huang, Ruimin; Abou, Diane S.; Larson, Steven M.; Grimm, Jan

    2014-01-01

    The invasion status of tumour-draining lymph nodes (LNs) is a critical indicator of cancer stage and is important for treatment planning. Clinicians currently use planar scintigraphy and single-photon emission computed tomography (SPECT) with 99mTc-radiocolloid to guide biopsy and resection of LNs. However, emerging multimodality approaches such as positron emission tomography combined with magnetic resonance imaging (PET/MRI) detect sites of disease with higher sensitivity and accuracy. Here we present a multimodal nanoparticle, 89Zr-ferumoxytol, for the enhanced detection of LNs with PET/MRI. For genuine translational potential, we leverage a clinical iron oxide formulation, altered with minimal modification for radiolabelling. Axillary drainage in naive mice and from healthy and tumour-bearing prostates was investigated. We demonstrate that 89Zr-ferumoxytol can be used for high-resolution tomographic studies of lymphatic drainage in preclinical disease models. This nanoparticle platform has significant translational potential to improve preoperative planning for nodal resection and tumour staging. PMID:24445347

  17. In vivo electric conductivity of cervical cancer patients based on B₁⁺ maps at 3T MRI.

    PubMed

    Balidemaj, E; de Boer, P; van Lier, A L H M W; Remis, R F; Stalpers, L J A; Westerveld, G H; Nederveen, A J; van den Berg, C A T; Crezee, J

    2016-02-21

    The in vivo electric conductivity (σ) values of tissue are essential for accurate electromagnetic simulations and specific absorption rate (SAR) assessment for applications such as thermal dose computations in hyperthermia. Currently used σ-values are mostly based on ex vivo measurements. In this study the conductivity of human muscle, bladder content and cervical tumors is acquired non-invasively in vivo using MRI. The conductivity of 20 cervical cancer patients was measured with the MR-based electric properties tomography method on a standard 3T MRI system. The average in vivo σ-value of muscle is 14% higher than currently used in human simulation models. The σ-value of bladder content is an order of magnitude higher than the value for bladder wall tissue that is used for the complete bladder in many models. Our findings are confirmed by various in vivo animal studies from the literature. In cervical tumors, the observed average conductivity was 13% higher than the literature value reported for cervical tissue. Considerable deviations were found for the electrical conductivity observed in this study and the commonly used values for SAR assessment, emphasizing the importance of acquiring in vivo conductivity for more accurate SAR assessment in various applications.

  18. Mapping the functional network of medial prefrontal cortex by combining optogenetics and fMRI in awake rats.

    PubMed

    Liang, Zhifeng; Watson, Glenn D R; Alloway, Kevin D; Lee, Gangchea; Neuberger, Thomas; Zhang, Nanyin

    2015-08-15

    The medial prefrontal cortex (mPFC) plays a critical role in multiple cognitive and limbic functions. Given its vital importance, investigating the function of individual mPFC circuits in animal models has provided critical insight into the neural basis underlying different behaviors and psychiatric conditions. However, our knowledge regarding the mPFC whole-brain network stays largely at the anatomical level, while the functional network of mPFC, which can be dynamic in different conditions or following manipulations, remains elusive especially in awake rodents. Here we combined optogenetic stimulation and functional magnetic resonance imaging (opto-fMRI) to reveal the network of brain regions functionally activated by mPFC outputs in awake rodents. Our data showed significant increases in blood-oxygenation-level dependent (BOLD) signals in prefrontal, striatal and limbic regions when mPFC was optically stimulated. This activation pattern was robust, reproducible, and did not depend on the stimulation period in awake rats. BOLD signals, however, were substantially reduced when animals were anesthetized. In addition, regional brain activation showing increased BOLD signals during mPFC stimulation was corroborated by electrophysiological recordings. These results expand the applicability of the opto-fMRI approach from sensorimotor processing to cognition-related networks in awake rodents. Importantly, it may help elucidate the circuit mechanisms underlying numerous mPFC-related functions and behaviors that need to be assessed in the awake state.

  19. In vivo electric conductivity of cervical cancer patients based on B_{1}^{+} maps at 3T MRI

    NASA Astrophysics Data System (ADS)

    Balidemaj, E.; de Boer, P.; van Lier, A. L. H. M. W.; Remis, R. F.; Stalpers, L. J. A.; Westerveld, G. H.; Nederveen, A. J.; van den Berg, C. A. T.; Crezee, J.

    2016-02-01

    The in vivo electric conductivity (σ) values of tissue are essential for accurate electromagnetic simulations and specific absorption rate (SAR) assessment for applications such as thermal dose computations in hyperthermia. Currently used σ-values are mostly based on ex vivo measurements. In this study the conductivity of human muscle, bladder content and cervical tumors is acquired non-invasively in vivo using MRI. The conductivity of 20 cervical cancer patients was measured with the MR-based electric properties tomography method on a standard 3T MRI system. The average in vivo σ-value of muscle is 14% higher than currently used in human simulation models. The σ-value of bladder content is an order of magnitude higher than the value for bladder wall tissue that is used for the complete bladder in many models. Our findings are confirmed by various in vivo animal studies from the literature. In cervical tumors, the observed average conductivity was 13% higher than the literature value reported for cervical tissue. Considerable deviations were found for the electrical conductivity observed in this study and the commonly used values for SAR assessment, emphasizing the importance of acquiring in vivo conductivity for more accurate SAR assessment in various applications.

  20. Neural network models for spatial data mining, map production, and cortical direction selectivity

    NASA Astrophysics Data System (ADS)

    Parsons, Olga

    A family of ARTMAP neural networks for incremental supervised learning has been developed over the last decade. The Sensor Exploitation Group of MIT Lincoln Laboratory (LL) has incorporated an early version of this network as the recognition engine of a hierarchical system for fusion and data mining of multiple registered geospatial images. The LL system has been successfully fielded, but it is limited to target vs. non-target identifications and does not produce whole maps. This dissertation expands the capabilities of the LL system so that it learns to identify arbitrarily many target classes at once and can thus produce a whole map. This new spatial data mining system is designed particularly to cope with the highly skewed class distributions of typical mapping problems. Specification of a consistent procedure and a benchmark testbed has permitted the evaluation of candidate recognition networks as well as pre- and post-processing and feature extraction options. The resulting default ARTMAP network and mapping methodology set a standard for a variety of related mapping problems and application domains. The second part of the dissertation investigates the development of cortical direction selectivity. The possible role of visual experience and oculomotor behavior in the maturation of cells in the primary visual cortex is studied. The responses of neurons in the thalamus and cortex of the cat are modeled when natural scenes are scanned by several types of eye movements. Inspired by the Hebbian-like synaptic plasticity, which is based upon correlations between cell activations, the second-order statistical structure of thalamo-cortical activity is examined. In the simulations, patterns of neural activity that lead to a correct refinement of cell responses are observed during visual fixation, when small ocular movements occur, but are not observed in the presence of large saccades. Simulations also replicate experiments in which kittens are reared under stroboscopic

  1. Automated mapping of hippocampal atrophy in 1-year repeat MRI data from 490 subjects with Alzheimer's disease, mild cognitive impairment, and elderly controls.

    PubMed

    Morra, Jonathan H; Tu, Zhuowen; Apostolova, Liana G; Green, Amity E; Avedissian, Christina; Madsen, Sarah K; Parikshak, Neelroop; Toga, Arthur W; Jack, Clifford R; Schuff, Norbert; Weiner, Michael W; Thompson, Paul M

    2009-03-01

    As one of the earliest structures to degenerate in Alzheimer's disease (AD), the hippocampus is the target of many studies of factors that influence rates of brain degeneration in the elderly. In one of the largest brain mapping studies to date, we mapped the 3D profile of hippocampal degeneration over time in 490 subjects scanned twice with brain MRI over a 1-year interval (980 scans). We examined baseline and 1-year follow-up scans of 97 AD subjects (49 males/48 females), 148 healthy control subjects (75 males/73 females), and 245 subjects with mild cognitive impairment (MCI; 160 males/85 females). We used our previously validated automated segmentation method, based on AdaBoost, to create 3D hippocampal surface models in all 980 scans. Hippocampal volume loss rates increased with worsening diagnosis (normal=0.66%/year; MCI=3.12%/year; AD=5.59%/year), and correlated with both baseline and interval changes in Mini-Mental State Examination (MMSE) scores and global and sum-of-boxes Clinical Dementia Rating scale (CDR) scores. Surface-based statistical maps visualized a selective profile of ongoing atrophy in all three diagnostic groups. Healthy controls carrying the ApoE4 gene atrophied faster than non-carriers, while more educated controls atrophied more slowly; converters from MCI to AD showed faster atrophy than non-converters. Hippocampal loss rates can be rapidly mapped, and they track cognitive decline closely enough to be used as surrogate markers of Alzheimer's disease in drug trials. They also reveal genetically greater atrophy in cognitively intact subjects.

  2. Acquiring concepts and features of novel words by two types of learning: direct mapping and inference.

    PubMed

    Chen, Shuang; Wang, Lin; Yang, Yufang

    2014-04-01

    This study examined the semantic representation of novel words learnt in two conditions: directly mapping a novel word to a concept (Direct mapping: DM) and inferring the concept from provided features (Inferred learning: IF). A condition where no definite concept could be inferred (No basic-level meaning: NM) served as a baseline. The semantic representation of the novel word was assessed via a semantic-relatedness judgment task. In this task, the learned novel word served as a prime, while the corresponding concept, an unlearned feature of the concept, and an unrelated word served as targets. ERP responses to the targets, primed by the novel words in the three learning conditions, were compared. For the corresponding concept, smaller N400s were elicited in the DM and IF conditions than in the NM condition, indicating that the concept could be obtained in both learning conditions. However, for the unlearned feature, the targets in the IF condition produced an N400 effect while in the DM condition elicited an LPC effect relative to the NM learning condition. No ERP difference was observed among the three learning conditions for the unrelated words. The results indicate that conditions of learning affect the semantic representation of novel word, and that the unlearned feature was only activated by the novel word in the IF learning condition.

  3. Functional MRI in human motor control studies and clinical applications.

    PubMed

    Toma, Keiichiro; Nakai, Toshiharu

    2002-07-01

    Functional magnetic resonance imaging (fMRI) has been a useful tool for the noninvasive mapping of brain function associated with various motor and cognitive tasks. Because fMRI is based on the blood oxygenation level dependent (BOLD) effect, it does not directly record neural activity. With the fMRI technique, distinguishing BOLD signals created by cortical projection neurons from those created by intracortical neurons appears to be difficult. Two major experimental designs are used in fMRI studies: block designs and event-related designs. Block-designed fMRI presupposes the steady state of regional cerebral blood flow and has been applied to examinations of brain activation caused by tasks requiring sustained or repetitive movements. By contrast, the more recently developed event-related fMRI with time resolution of a few seconds allows the mapping of brain activation associated with a single movement according to the transient aspects of the hemodynamic response. Increasing evidence suggests that multiple motor areas are engaged in a networked manner to execute various motor acts. In order to understand functional brain maps, it is important that one understands sequential and parallel organizations of anatomical connections between multiple motor areas. In fMRI studies of complex motor tasks, elementary parameters such as movement length, force, velocity, acceleration and frequency should be controlled, because inconsistency in those parameters may alter the extent and intensity of motor cortical activation, confounding interpretation of the findings obtained. In addition to initiation of movements, termination of movements plays an important role in the successful achievement of complex movements. Brain areas exclusively related to the termination of movements have been, for the first time, uncovered with an event-related fMRI technique. We propose the application of fMRI to the elucidation of the pathophysiology of movement disorders, particularly dystonia

  4. Mapping the reading circuitry for skilled deaf readers: an fMRI study of semantic and phonological processing.

    PubMed

    Emmorey, Karen; Weisberg, Jill; McCullough, Stephen; Petrich, Jennifer A F

    2013-08-01

    We examined word-level reading circuits in skilled deaf readers whose primary language is American Sign Language, and hearing readers matched for reading ability (college level). During fMRI scanning, participants performed a semantic decision (concrete concept?), a phonological decision (two syllables?), and a false-font control task (string underlined?). The groups performed equally well on the semantic task, but hearing readers performed better on the phonological task. Semantic processing engaged similar left frontotemporal language circuits in deaf and hearing readers. However, phonological processing elicited increased neural activity in deaf, relative to hearing readers, in the left precentral gyrus, suggesting greater reliance on articulatory phonological codes, and in bilateral parietal cortex, suggesting increased phonological processing effort. Deaf readers also showed stronger anterior-posterior functional segregation between semantic and phonological processes in left inferior prefrontal cortex. Finally, weaker phonological decoding ability did not alter activation in the visual word form area for deaf readers.

  5. The EU Physical Agents (EMF) Directive and its impact on MRI imaging in animal experiments: a submission by FRAME to the HSE.

    PubMed

    Hudson, Michelle

    2006-06-01

    The EU Physical Agents (EMF) Directive, Directive 2004/40/EC, which threatens to greatly restrict the use of magnetic resonance imaging (MRI) in both clinical and research situations, will come into force on 30 April 2008. This could severely affect experimental animal welfare and scientific progress, as well as patient care. FRAME made a submission to a Health and Safety Executive round-table discussion about the Directive, held in January 2006, detailing concerns about the implications that the legislation would have on implementing the Three Rs in animal-based research and testing, and the subsequent consequences for animal welfare and the quality of scientific output. The submission is reproduced here, with additional comments on the outcome of the meeting and recommendations for further research into the consequences of the Directive.

  6. Rupture Directivity Effect on the Probabilistic Seismic Hazard Maps in the Marmara Region, Turkey

    NASA Astrophysics Data System (ADS)

    Spagnuolo, E.; Akinci, A.; Herrero, A.; Pucci, S.

    2014-12-01

    In this study, we attempt to incorporate the rupture directivity effects into seismic hazard analysis in the Marmara region, Turkey. We introduce information about the fault segments by focusing on the fault rupture characteristics, near source directivity effects and its influence on the probabilistic seismic hazard analyses (PSHA) accounting for the azimuthal variations of the ground motion spatial distribution. An analytical model developed by Spudich and Chiou (2008) is used as a corrective factor that modifies four ground motion predictive equations (GMPEs) (Abrahamson & Silva 2008; Boore & Atkinson 2008; Campbell & Bozorgnia 2008; Chiou &Youngs 2008) and accounts for rupture related parameters that generally lump together into the term directivity effect. In this paper, we only use the relation calibrated for the Abrahamson & Silva (2008) and Boore & Atkinson (2008). In order to evaluate the impact of the rupture directivity effects to ground motion hazard in the near source we attempt to calculate the fault-based probabilistic seismic hazard maps (PSHA) of mean Peak Ground Acceleration (PGA) having 10% probability of exceedance in 50 years on rock site condition. Therefore the PSHMs for the Marmara region is produced incorporating detailed knowledge of active faulting and tectonic rates in earthquake recurrence models using the available database and the most innovative approaches. In order to test the impact of the corrective factor on seismic hazard we first considered its effect on a normal fault and on a strike slip fault as a function of magnitude. Seismic hazard is given in terms of Spectral Acceleration (SA) at seven different periods. We also report the percentage ratio between the seismic hazards computed with the directivity model and without it, over the seismic hazard resulting from the standard practice. Finally, we improve the seismic hazard maps in the near fault source incorporating the directivity effects in the ground motion prediction in

  7. MRI and low back pain

    MedlinePlus

    Backache - MRI; Low back pain - MRI; Lumbar pain - MRI; Back strain - MRI; Lumbar radiculopathy - MRI; Herniated intervertebral disk - MRI; Prolapsed intervertebral disk - MRI; Slipped disk - MRI; Ruptured ...

  8. Robust fluence map optimization via alternating direction method of multipliers with empirical parameter optimization

    NASA Astrophysics Data System (ADS)

    Gao, Hao

    2016-04-01

    For the treatment planning during intensity modulated radiation therapy (IMRT) or volumetric modulated arc therapy (VMAT), beam fluence maps can be first optimized via fluence map optimization (FMO) under the given dose prescriptions and constraints to conformally deliver the radiation dose to the targets while sparing the organs-at-risk, and then segmented into deliverable MLC apertures via leaf or arc sequencing algorithms. This work is to develop an efficient algorithm for FMO based on alternating direction method of multipliers (ADMM). Here we consider FMO with the least-square cost function and non-negative fluence constraints, and its solution algorithm is based on ADMM, which is efficient and simple-to-implement. In addition, an empirical method for optimizing the ADMM parameter is developed to improve the robustness of the ADMM algorithm. The ADMM based FMO solver was benchmarked with the quadratic programming method based on the interior-point (IP) method using the CORT dataset. The comparison results suggested the ADMM solver had a similar plan quality with slightly smaller total objective function value than IP. A simple-to-implement ADMM based FMO solver with empirical parameter optimization is proposed for IMRT or VMAT.

  9. Rapid exploration of configuration space with diffusion-map-directed molecular dynamics.

    PubMed

    Zheng, Wenwei; Rohrdanz, Mary A; Clementi, Cecilia

    2013-10-24

    The gap between the time scale of interesting behavior in macromolecular systems and that which our computational resources can afford often limits molecular dynamics (MD) from understanding experimental results and predicting what is inaccessible in experiments. In this paper, we introduce a new sampling scheme, named diffusion-map-directed MD (DM-d-MD), to rapidly explore molecular configuration space. The method uses a diffusion map to guide MD on the fly. DM-d-MD can be combined with other methods to reconstruct the equilibrium free energy, and here, we used umbrella sampling as an example. We present results from two systems: alanine dipeptide and alanine-12. In both systems, we gain tremendous speedup with respect to standard MD both in exploring the configuration space and reconstructing the equilibrium distribution. In particular, we obtain 3 orders of magnitude of speedup over standard MD in the exploration of the configurational space of alanine-12 at 300 K with DM-d-MD. The method is reaction coordinate free and minimally dependent on a priori knowledge of the system. We expect wide applications of DM-d-MD to other macromolecular systems in which equilibrium sampling is not affordable by standard MD.

  10. Mapping of top of permafrost using a direct current resistivity survey

    SciTech Connect

    Gilmore, T.J.; Clayton, E.A.

    1995-10-01

    Data from a direct current resistivity survey and geologic logs from boreholes were used to map the top of permafrost at a remote Air Force installation in Alaska. This study resulted from a remedial investigation that was conducted at Eielson Air Force base near Fairbanks, Alaska under the federal Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) regulations. The depth and continuity of the permafrost was important in determining the fate of petroleum contamination that was inadvertently discharged to the ground during earlier Air Force operations. The results indicate that the top of permafrost forms a highly irregular surface. In general, however, the top of permafrost forms a diagonal ridge at the center of the contour grid that is bordered on each side by troughs.

  11. Atom Probe Tomographic Mapping Directly Reveals the Atomic Distribution of Phosphorus in Resin Embedded Ferritin

    PubMed Central

    Perea, Daniel E.; Liu, Jia; Bartrand, Jonah; Dicken, Quinten; Thevuthasan, S. Theva; Browning, Nigel D.; Evans, James E.

    2016-01-01

    Here we report the atomic-scale analysis of biological interfaces within the ferritin protein using atom probe tomography that is facilitated by an advanced specimen preparation approach. Embedding ferritin in an organic polymer resin lacking nitrogen provided chemical contrast to visualise atomic distributions and distinguish the inorganic-organic interface of the ferrihydrite mineral core and protein shell, as well as the organic-organic interface between the ferritin protein shell and embedding resin. In addition, we definitively show the atomic-scale distribution of phosphorus as being at the surface of the ferrihydrite mineral with the distribution of sodium mapped within the protein shell environment with an enhanced distribution at the mineral/protein interface. The sample preparation method is robust and can be directly extended to further enhance the study of biological, organic and inorganic nanomaterials relevant to health, energy or the environment. PMID:26924804

  12. Methods of mapping from phase to sine amplitude in direct digital synthesis.

    PubMed

    Vankka, J

    1997-01-01

    There are many methods for performing functional mapping from phase to sine amplitude (e.g., ROM look-up, coarse/fine segmentation into multiple ROM's, Taylor series, CORDIC algorithm). The spectral purity of the conventional direct digital synthesizer (DDS) is also determined by the resolution of the values stored in the sine table ROM. Therefore, it is desirable to increase the resolution of the ROM. Unfortunately, larger ROM storage means higher power consumption, lower reliability, lower speed, and greatly increased costs. Different memory compression and algorithmic techniques and their effect on distortion and trade-offs are investigated in detail. A computer program has been created to simulate the effects of the memory compression and algorithmic techniques on the output spectrum of the DDS. For each memory compression and algorithmic technique, the worst case spurious response is calculated using the computer program. PMID:18244150

  13. A direct approach to generalised multiple mapping conditioning for selected turbulent diffusion flame cases

    NASA Astrophysics Data System (ADS)

    Sundaram, Brruntha; Klimenko, Alexander Yuri; Cleary, Matthew John; Ge, Yipeng

    2016-07-01

    This work presents a direct and transparent interpretation of two concepts for modelling turbulent combustion: generalised Multiple Mapping Conditioning (MMC) and sparse-Lagrangian Large Eddy Simulation (LES). The MMC approach is presented as a hybrid between the Probability Density Function (PDF) method and approaches based on conditioning (e.g. Conditional Moment Closure, flamelet, etc.). The sparse-Lagrangian approach, which allows for a dramatic reduction of computational cost, is viewed as an alternative interpretation of the Filtered Density Function (FDF) methods. This work presents simulations of several turbulent diffusion flame cases and discusses the universality of the localness parameter between these cases and the universality of sparse-Lagrangian FDF methods with MMC.

  14. In-vivo Imaging of Magnetic Fields Induced by Transcranial Direct Current Stimulation (tDCS) in Human Brain using MRI

    NASA Astrophysics Data System (ADS)

    Jog, Mayank V.; Smith, Robert X.; Jann, Kay; Dunn, Walter; Lafon, Belen; Truong, Dennis; Wu, Allan; Parra, Lucas; Bikson, Marom; Wang, Danny J. J.

    2016-10-01

    Transcranial direct current stimulation (tDCS) is an emerging non-invasive neuromodulation technique that applies mA currents at the scalp to modulate cortical excitability. Here, we present a novel magnetic resonance imaging (MRI) technique, which detects magnetic fields induced by tDCS currents. This technique is based on Ampere’s law and exploits the linear relationship between direct current and induced magnetic fields. Following validation on a phantom with a known path of electric current and induced magnetic field, the proposed MRI technique was applied to a human limb (to demonstrate in-vivo feasibility using simple biological tissue) and human heads (to demonstrate feasibility in standard tDCS applications). The results show that the proposed technique detects tDCS induced magnetic fields as small as a nanotesla at millimeter spatial resolution. Through measurements of magnetic fields linearly proportional to the applied tDCS current, our approach opens a new avenue for direct in-vivo visualization of tDCS target engagement.

  15. In-vivo Imaging of Magnetic Fields Induced by Transcranial Direct Current Stimulation (tDCS) in Human Brain using MRI

    PubMed Central

    Jog, Mayank V.; Smith, Robert X.; Jann, Kay; Dunn, Walter; Lafon, Belen; Truong, Dennis; Wu, Allan; Parra, Lucas; Bikson, Marom; Wang, Danny J. J.

    2016-01-01

    Transcranial direct current stimulation (tDCS) is an emerging non-invasive neuromodulation technique that applies mA currents at the scalp to modulate cortical excitability. Here, we present a novel magnetic resonance imaging (MRI) technique, which detects magnetic fields induced by tDCS currents. This technique is based on Ampere’s law and exploits the linear relationship between direct current and induced magnetic fields. Following validation on a phantom with a known path of electric current and induced magnetic field, the proposed MRI technique was applied to a human limb (to demonstrate in-vivo feasibility using simple biological tissue) and human heads (to demonstrate feasibility in standard tDCS applications). The results show that the proposed technique detects tDCS induced magnetic fields as small as a nanotesla at millimeter spatial resolution. Through measurements of magnetic fields linearly proportional to the applied tDCS current, our approach opens a new avenue for direct in-vivo visualization of tDCS target engagement. PMID:27698358

  16. Task-specific Aspects of Goal-directed Word Generation Identified via Simultaneous EEG-fMRI.

    PubMed

    Shapira-Lichter, Irit; Klovatch, Ilana; Nathan, Dana; Oren, Noga; Hendler, Talma

    2016-09-01

    Generating words according to a given rule relies on retrieval-related search and postretrieval control processes. Using fMRI, we recently characterized neural patterns of word generation in response to episodic, semantic, and phonemic cues by comparing free recall of wordlists, category fluency, and letter fluency [Shapira-Lichter, I., Oren, N., Jacob, Y., Gruberger, M., & Hendler, T. Portraying the unique contribution of the default mode network to internally driven mnemonic processes. Proceedings of the National Academy of Sciences, U.S.A., 110, 4950-4955, 2013]. Distinct selectivity for each condition was evident, representing discrete aspects of word generation-related memory retrieval. For example, the precuneus, implicated in processing spatiotemporal information, emerged as a key contributor to the episodic condition, which uniquely requires this information. Gamma band is known to play a central role in memory, and increased gamma power has been observed before word generation. Yet, gamma modulation in response to task demands has not been investigated. To capture the task-specific modulation of gamma power, we analyzed the EEG data recorded simultaneously with the aforementioned fMRI, focusing on the activity locked to and immediately preceding word articulation. Transient increases in gamma power were identified in a parietal electrode immediately before episodic and semantic word generation, however, within a different time frame relative to articulation. Gamma increases were followed by an alpha-theta decrease in the episodic condition, a gamma decrease in the semantic condition. This pattern indicates a task-specific modulation of the gamma signal corresponding to the specific demands of each word generation task. The gamma power and fMRI signal from the precuneus were correlated during the episodic condition, implying the existence of a common cognitive construct uniquely required for this task, possibly the reactivation or processing of

  17. Directly mapping the surface charge density of lipid bilayers under physiological conditions

    NASA Astrophysics Data System (ADS)

    Fuhs, Thomas; Klausen, Lasse Hyldgaard; Besenbacher, Flemming; Dong, Mingdong

    2015-03-01

    The surface charge density of lipid bilayers governs the cellular uptake of charged particles and guides cell-cell and cell-surface interactions. Direct probing of the potential requires sub nanometer distances as the electrostatic potential is screened by high physiological salt concentrations. This prevented direct measurement of the SCD under physiological conditions. In this study we investigate supported bilayers of lipid mixtures that form domains of distinct surface charges, submerged in 150mM NaCl. We use a scanning ion-conductance microscope (SICM) setup to measure the ionic current through a nanopipette as the pipette is scanned several nanometers above the sample. The charged headgroups of the lipids attract counter ions leading to a charge dependent enhancement of the ion concentration near the surface. This creates a measurable change of conductivity in the vicinity of the surface. As the dependency of the current on the SCD and pipette potential is non-trivial we characterized it using numerical solutions to Poisson and Nernst-Planck equations. Based on the simulation results we propose an imaging method. We confirm feasibility of the proposed method by experimentally mapping the local surface charge density of phase separated lipid bilayers.

  18. Mapping Dimensionality and Directionality of Electronic Behavior in CeCoIn5: the Normal State

    NASA Astrophysics Data System (ADS)

    Gyenis, Andras; Feldman, Benjamin E.; Randeria, Mallika T.; Peterson, Gabriel A.; Aynajian, Pegor; Bauer, Eric D.; Yazdani, Ali

    Materials made from alternating layers of different constituents can exhibit dramatic variability in their electronic properties depending on which layer is probed. This is evident in the heavy fermion compound CeCoIn5, where scanning tunneling microscopy (STM) has revealed preferential coupling to either light or heavy electron states depending on the surface termination. Here we report STM measurements of CeCoIn5 cleaved perpendicular to its basal plane that clearly shows the quasi-two-dimensional nature of the electronic behavior on a single (100) surface. We observe atomic scale modulation of tunneling into the light and heavy electron bands in the c-axis direction, with no variation visible along the basal planes in the b-axis direction. In addition, conductance maps reveal preferential scattering along the two-dimensional basal planes. Our measurements highlight the reduced effective dimensionality of electronic states in CeCoIn5, and underscore the potential insight that can be gained by imaging layered materials perpendicular to their c-axis.

  19. Direct Sensor Orientation of a Land-Based Mobile Mapping System

    PubMed Central

    Rau, Jiann-Yeou; Habib, Ayman F.; Kersting, Ana P.; Chiang, Kai-Wei; Bang, Ki-In; Tseng, Yi-Hsing; Li, Yu-Hua

    2011-01-01

    A land-based mobile mapping system (MMS) is flexible and useful for the acquisition of road environment geospatial information. It integrates a set of imaging sensors and a position and orientation system (POS). The positioning quality of such systems is highly dependent on the accuracy of the utilized POS. This limitation is the major drawback due to the elevated cost associated with high-end GPS/INS units, particularly the inertial system. The potential accuracy of the direct sensor orientation depends on the architecture and quality of the GPS/INS integration process as well as the validity of the system calibration (i.e., calibration of the individual sensors as well as the system mounting parameters). In this paper, a novel single-step procedure using integrated sensor orientation with relative orientation constraint for the estimation of the mounting parameters is introduced. A comparative analysis between the proposed single-step and the traditional two-step procedure is carried out. Moreover, the estimated mounting parameters using the different methods are used in a direct geo-referencing procedure to evaluate their performance and the feasibility of the implemented system. Experimental results show that the proposed system using single-step system calibration method can achieve high 3D positioning accuracy. PMID:22164015

  20. Implementing the effect of the rupture directivity on PSHA maps: Application to the Marmara Region (Turkey)

    NASA Astrophysics Data System (ADS)

    Herrero, Andre; Spagnuolo, Elena; Akinci, Aybige; Pucci, Stefano

    2016-04-01

    seismic potential of the Marmara region to derive a statistical distribution for nucleation position. Our results suggest that accounting for rupture related parameters in a PSHA using deterministic information from dynamic models is feasible and in particular, the use of a non-uniform statistical distribution for nucleation position has serious consequences on the hazard assessment. Since the directivity effect is conditional on the nucleation position the hazard map changes with the assumptions made. A worst case scenario (both the faults are rupturing towards the city of Istanbul) predicts up to 25% change than the standard formulation at 2 sec and increases with longer periods. The former result is heavily different if a deterministically based nucleation position is assumed.

  1. An fMRI investigation of analogical mapping in metaphor comprehension: the influence of context and individual cognitive capacities on processing demands.

    PubMed

    Prat, Chantel S; Mason, Robert A; Just, Marcel Adam

    2012-03-01

    This study used fMRI to investigate the neural correlates of analogical mapping during metaphor comprehension, with a focus on dynamic configuration of neural networks with changing processing demands and individual abilities. Participants with varying vocabulary sizes and working memory capacities read 3-sentence passages ending in nominal critical utterances of the form "X is a Y." Processing demands were manipulated by varying preceding contexts. Three figurative conditions manipulated difficulty by varying the extent to which preceding contexts mentioned relevant semantic features for relating the vehicle and topic of the critical utterance to one another. In the easy condition, supporting information was mentioned. In the neutral condition, no relevant information was mentioned. In the most difficult condition, opposite features were mentioned, resulting in an ironic interpretation of the critical utterance. A fourth, literal condition included context that supported a literal interpretation of the critical utterance. Activation in lateral and medial frontal regions increased with increasing contextual difficulty. Lower vocabulary readers also had greater activation across conditions in the right inferior frontal gyrus. In addition, volumetric analyses showed increased right temporo-parietal junction and superior medial frontal activation for all figurative conditions over the literal condition. The results from this experiment imply that the cortical regions are dynamically recruited in language comprehension as a function of the processing demands of a task. Individual differences in cognitive capacities were also associated with differences in recruitment and modulation of working memory and executive function regions, highlighting the overlapping computations in metaphor comprehension and general thinking and reasoning.

  2. Mapping the Dynamic Network Interactions Underpinning Cognition: A cTBS-fMRI Study of the Flexible Adaptive Neural System for Semantics

    PubMed Central

    Jung, JeYoung; Lambon Ralph, Matthew A.

    2016-01-01

    Higher cognitive function reflects the interaction of a network of multiple brain regions. Previous investigations have plotted out these networks using functional or structural connectivity approaches. While these map the topography of the regions involved, they do not explore the key aspect of this neuroscience principle—namely that the regions interact in a dynamic fashion. Here, we achieved this aim with respect to semantic memory. Although converging evidence implicates the anterior temporal lobes (ATLs), bilaterally, as a crucial component in semantic representation, the underlying neural interplay between the ATLs remains unclear. By combining continuous theta-burst stimulation (cTBS) with functional magnetic resonance imaging (fMRI), we perturbed the left ventrolateral ATL (vATL) and investigated acute changes in neural activity and effective connectivity of the semantic system. cTBS resulted in decreased activity at the target region and compensatory, increased activity at the contralateral vATL. In addition, there were task-specific increases in effective connectivity between the vATLs, reflecting an increased facilitatory intrinsic connectivity from the right to left vATL. Our results suggest that semantic representation is founded on a flexible, adaptive bilateral neural system and reveals an adaptive plasticity-based mechanism that might support functional recovery after unilateral damage in neurological patients. PMID:27242027

  3. Mapping the Multiple Graded Contributions of the Anterior Temporal Lobe Representational Hub to Abstract and Social Concepts: Evidence from Distortion-corrected fMRI

    PubMed Central

    Binney, Richard J.; Hoffman, Paul; Lambon Ralph, Matthew A.

    2016-01-01

    A growing body of recent convergent evidence indicates that the anterior temporal lobe (ATL) has connectivity-derived graded differences in semantic function: the ventrolateral region appears to be the transmodal, omni-category center-point of the hub whilst secondary contributions come from the peripheries of the hub in a manner that reflects their differential connectivity to different input/output modalities. One of the key challenges for this neurocognitive theory is how different types of concept, especially those with less reliance upon external sensory experience (such as abstract and social concepts), are coded across the graded ATL hub. We were able to answer this key question by using distortion-corrected fMRI to detect functional activations across the entire ATL region and thus to map the neural basis of social and psycholinguistically-matched abstract concepts. Both types of concept engaged a core left-hemisphere semantic network, including the ventrolateral ATL, prefrontal regions and posterior MTG. Additionally, we replicated previous findings of weaker differential activation of the superior and polar ATL for the processing of social stimuli, in addition to the stronger, omni-category activation observed in the vATL. These results are compatible with the view of the ATL as a graded transmodal substrate for the representation of coherent concepts. PMID:27600844

  4. Single-subject fMRI mapping at 7 T of the representation of fingertips in S1: a comparison of event-related and phase-encoding designs.

    PubMed

    Besle, Julien; Sánchez-Panchuelo, Rosa-Maria; Bowtell, Richard; Francis, Susan; Schluppeck, Denis

    2013-05-01

    A desirable goal of functional MRI (fMRI), both clinically and for basic research, is to produce detailed maps of cortical function in individual subjects. Single-subject mapping of the somatotopic hand representation in the human primary somatosensory cortex (S1) has been performed using both phase-encoding and block/event-related designs. Here, we review the theoretical strengths and limits of each method and empirically compare high-resolution (1.5 mm isotropic) somatotopic maps obtained using fMRI at ultrahigh magnetic field (7 T) with phase-encoding and event-related designs in six subjects in response to vibrotactile stimulation of the five fingertips. Results show that the phase-encoding design is more efficient than the event-related design for mapping fingertip-specific responses and in particular allows us to describe a new additional somatotopic representation of fingertips on the precentral gyrus. However, with sufficient data, both designs yield very similar fingertip-specific maps in S1, which confirms that the assumption of local representational continuity underlying phase-encoding designs is largely valid at the level of the fingertips in S1. In addition, it is shown that the event-related design allows the mapping of overlapping cortical representations that are difficult to estimate using the phase-encoding design. The event-related data show a complex pattern of overlapping cortical representations for different fingertips within S1 and demonstrate that regions of S1 responding to several adjacent fingertips can incorrectly be identified as responding preferentially to one fingertip in the phase-encoding data.

  5. Single-subject fMRI mapping at 7 T of the representation of fingertips in S1: a comparison of event-related and phase-encoding designs

    PubMed Central

    Sánchez-Panchuelo, Rosa-Maria; Bowtell, Richard; Francis, Susan; Schluppeck, Denis

    2013-01-01

    A desirable goal of functional MRI (fMRI), both clinically and for basic research, is to produce detailed maps of cortical function in individual subjects. Single-subject mapping of the somatotopic hand representation in the human primary somatosensory cortex (S1) has been performed using both phase-encoding and block/event-related designs. Here, we review the theoretical strengths and limits of each method and empirically compare high-resolution (1.5 mm isotropic) somatotopic maps obtained using fMRI at ultrahigh magnetic field (7 T) with phase-encoding and event-related designs in six subjects in response to vibrotactile stimulation of the five fingertips. Results show that the phase-encoding design is more efficient than the event-related design for mapping fingertip-specific responses and in particular allows us to describe a new additional somatotopic representation of fingertips on the precentral gyrus. However, with sufficient data, both designs yield very similar fingertip-specific maps in S1, which confirms that the assumption of local representational continuity underlying phase-encoding designs is largely valid at the level of the fingertips in S1. In addition, it is shown that the event-related design allows the mapping of overlapping cortical representations that are difficult to estimate using the phase-encoding design. The event-related data show a complex pattern of overlapping cortical representations for different fingertips within S1 and demonstrate that regions of S1 responding to several adjacent fingertips can incorrectly be identified as responding preferentially to one fingertip in the phase-encoding data. PMID:23427300

  6. Variance Decomposition of MRI-Based Covariance Maps Using Genetically-Informative Samples and Structural Equation Modeling

    PubMed Central

    Schmitt, J. Eric; Lenroot, Rhoshel; Ordaz, Sarah E.; Wallace, Gregory L.; Lerch, Jason P.; Evans, Alan C.; Prom, Elizabeth C.; Kendler, Kenneth S.; Neale, Michael C.; Giedd, Jay N.

    2010-01-01

    The role of genetics in driving intracortical relationships is an important question that has rarely been studied in humans. In particular, there are no extant high-resolution imaging studies on genetic covariance. In this article, we describe a novel method that combines classical quantitative genetic methodologies for variance decomposition with recently-developed semi-multivariate algorithms for high-resolution measurement of phenotypic covariance. Using these tools, we produced correlational maps of genetic and environmental (i.e. nongenetic) relationships between several regions of interest and the cortical surface in a large pediatric sample of 600 twins, siblings, and singletons. These analyses demonstrated high, fairly uniform, statistically significant genetic correlations between the entire cortex and global mean cortical thickness. In agreement with prior reports on phenotypic covariance using similar methods, we found mean cortical thickness was most strongly correlated with association cortices. However, the present study suggests that genetics plays a large role in global brain patterning of cortical thickness in this manner. Further, using specific gyri with known high heritabilities as seed regions, we found a consistent pattern of high bilateral genetic correlations between structural homologues, with environmental correlations more restricted to the same hemisphere as the seed region, suggesting that interhemispheric covariance is largely genetically mediated. These findings are consistent with the limited existing knowledge on the genetics of cortical variability as well as our prior multivariate studies on cortical gyri. PMID:18672072

  7. High-field (9.4 T) MRI of brain dysmyelination by quantitative mapping of magnetic susceptibility.

    PubMed

    Liu, Chunlei; Li, Wei; Johnson, G Allan; Wu, Bing

    2011-06-01

    The multilayered myelin sheath wrapping around nerve axons is essential for proper functioning of the central nervous system. Abnormal myelination leads to a wide range of neurological diseases and developmental disorders. Non-invasive imaging of myelin content is of great clinical importance. The present work demonstrated that loss of myelin in the central nervous system of the shiverer mouse results in a dramatic reduction of magnetic susceptibility in white matter axons. The reduction resulted in a near extinction of susceptibility contrast between gray and white matter. Quantitative magnetic susceptibility imaging and diffusion tensor imaging were conducted on a group of control and shiverer mice at 9.4 T. We measured the resonance frequency distribution of the whole brain for each mouse. Magnetic susceptibility maps were computed and compared between the two groups. It was shown that the susceptibility contrast between gray and white matter was reduced by 96% in the shiverer compared to the controls. Diffusion measurements further confirmed intact fiber pathways in the shiverer mice, ruling out the possibility of axonal injury and its potential contribution to the altered susceptibility. As an autosomal recessive mutation, shiverer is characterized by an almost total lack of central nervous system myelin. Our data provide new evidences indicating that myelin is the predominant source of susceptibility differences between deep gray and white matter observed in magnetic resonance imaging. More importantly, the present study suggests that quantitative magnetic susceptibility is a potential endogenous biomarker for myelination.

  8. High Resolution 13C MRI With Hyperpolarized Urea: In Vivo T2 Mapping and 15N Labeling Effects

    PubMed Central

    Reed, Galen D.; von Morze, Cornelius; Bok, Robert; Koelsch, Bertram L.; Van Criekinge, Mark; Smith, Kenneth J.; Shang, Hong; Larson, Peder E. Z.; Kurhanewicz, John; Vigneron, Daniel B.

    2014-01-01

    13C steady state free precession (SSFP) magnetic resonance imaging and effective spin-spin relaxation time (T2) mapping were performed using hyperpolarized [13C] urea and [13C, 15N2] urea injected intravenously in rats. 15N labeling gave large T2 increases both in solution and in vivo due to the elimination of a strong scalar relaxation pathway. The T2 increase was pronounced in the kidney, with [13C, 15N2] urea giving T2 values of 6.3±1.3 s in the cortex and medulla, and 11±2 s in the renal pelvis. The measured T2 in the aorta was 1.3±0.3 s. [13C] urea showed shortened T2 values in the kidney of 0.23±0.03 s compared to 0.28±0.03 s measured in the aorta. The enhanced T2 of [13C, 15N2] urea was utilized to generate large signal enhancement by SSFP acquisitions with flip angles approaching the fully refocused regime. Projection images at 0.94 mm in-plane resolution were acquired with both urea isotopes, with [13C, 15N2] urea giving a greater than four-fold increase in signal-to-noise ratio [13C] over urea. PMID:24235273

  9. Asymmetric friction of non-motor MAPs can lead to their directional motion in active microtubule networks

    PubMed Central

    Forth, Scott; Hsia, Kuo-Chiang; Shimamoto, Yuta; Kapoor, Tarun M.

    2014-01-01

    Summary Diverse cellular processes require microtubules to be organized into distinct structures, such as asters or bundles. Within these dynamic motifs, microtubule-associated proteins (MAPs) are frequently under load, but how force modulates these proteins’ function is poorly understood. Here, we combine optical-trapping with TIRF-based microscopy to measure the force-dependence of microtubule interaction for three non-motor MAPs (NuMA, PRC1, and EB1) required for cell division. We find that frictional forces increase non-linearly with MAP velocity across microtubules and depend on filament polarity, with NuMA’s friction being lower when moving towards minus-ends, EB1’s lower towards plus-ends, and PRC1 exhibiting no directional preference. Mathematical models predict, and experiments confirm, that MAPs with asymmetric friction can move directionally within active microtubule pairs they crosslink. Our findings reveal how non-motor MAPs can generate frictional resistance in dynamic cytoskeletal networks via micromechanical adaptations whose anisotropy may be optimized for MAP localization and function within cellular structures. PMID:24725408

  10. Efficient global fiber tracking on multi-dimensional diffusion direction maps

    NASA Astrophysics Data System (ADS)

    Klein, Jan; Köhler, Benjamin; Hahn, Horst K.

    2012-02-01

    Global fiber tracking algorithms have recently been proposed which were able to compute results of unprecedented quality. They account for avoiding accumulation errors by a global optimization process at the cost of a high computation time of several hours or even days. In this paper, we introduce a novel global fiber tracking algorithm which, for the first time, globally optimizes the underlying diffusion direction map obtained from DTI or HARDI data, instead of single fiber segments. As a consequence, the number of iterations in the optimization process can drastically be reduced by about three orders of magnitude. Furthermore, in contrast to all previous algorithms, the density of the tracked fibers can be adjusted after the optimization within a few seconds. We evaluated our method for diffusion-weighted images obtained from software phantoms, healthy volunteers, and tumor patients. We show that difficult fiber bundles, e.g., the visual pathways or tracts for different motor functions can be determined and separated in an excellent quality. Furthermore, crossing and kissing bundles are correctly resolved. On current standard hardware, a dense fiber tracking result of a whole brain can be determined in less than half an hour which is a strong improvement compared to previous work.

  11. Glioma localization and excision using direct electrical stimulation for language mapping during awake surgery

    PubMed Central

    LI, TIANDONG; BAI, HONGMIN; WANG, GUOLIANG; WANG, WEIMIN; LIN, JIAN; GAO, HAN; WANG, LIMIN; XIA, LIHUI; XIE, XUEMIN

    2015-01-01

    The aim of this study was to investigate the method and significance of the application of direct electrical stimulation (DES) to the brain mapping of language functions during glioma surgery. A retrospective analysis of clinical data was performed for 91 cases of brain functional area glioma surgery under DES from January 2003 until January 2012. Following cortical electrical stimulation, 88 patients exhibited seizures involving facial or hand movements and 91 cases experienced language disorders such as counting interruption, naming errors or anomia. The most commonly observed areas of counting interruption were distributed on the posterior part of the left anterior central gyrus (47.7%), the operculum of the left inferior frontal gyrus (24.4%) and the triangular part of the left inferior frontal gyrus (12.8%). Postoperative magnetic resonance imaging demonstrated that overall excision was achieved in 53 cases and sub-overall excision was performed in 31 cases. A total of 42 cases (46.2%) exhibited no postoperative neurological dysfunction, 39 cases (42.9%) exhibited brief language dysfunction, 27 cases (29.7%) experienced brief limb movement disorder, and one case appeared to have permanent neurological dysfunction. DES was indicated to be a reliable and noninvasive method for the intraoperative positioning of language areas, and was able to resect gliomas in the language area with maximal safety. PMID:26136923

  12. Identifying effective connectivity parameters in simulated fMRI: a direct comparison of switching linear dynamic system, stochastic dynamic causal, and multivariate autoregressive models

    PubMed Central

    Smith, Jason F.; Chen, Kewei; Pillai, Ajay S.; Horwitz, Barry

    2013-01-01

    The number and variety of connectivity estimation methods is likely to continue to grow over the coming decade. Comparisons between methods are necessary to prune this growth to only the most accurate and robust methods. However, the nature of connectivity is elusive with different methods potentially attempting to identify different aspects of connectivity. Commonalities of connectivity definitions across methods upon which base direct comparisons can be difficult to derive. Here, we explicitly define “effective connectivity” using a common set of observation and state equations that are appropriate for three connectivity methods: dynamic causal modeling (DCM), multivariate autoregressive modeling (MAR), and switching linear dynamic systems for fMRI (sLDSf). In addition while deriving this set, we show how many other popular functional and effective connectivity methods are actually simplifications of these equations. We discuss implications of these connections for the practice of using one method to simulate data for another method. After mathematically connecting the three effective connectivity methods, simulated fMRI data with varying numbers of regions and task conditions is generated from the common equation. This simulated data explicitly contains the type of the connectivity that the three models were intended to identify. Each method is applied to the simulated data sets and the accuracy of parameter identification is analyzed. All methods perform above chance levels at identifying correct connectivity parameters. The sLDSf method was superior in parameter estimation accuracy to both DCM and MAR for all types of comparisons. PMID:23717258

  13. MRI Scans

    MedlinePlus

    Magnetic resonance imaging (MRI) uses a large magnet and radio waves to look at organs and structures inside your body. Health care professionals use MRI scans to diagnose a variety of conditions, from torn ...

  14. Hide, Map and Seek: Assessing Students' Understanding of Location and Direction

    ERIC Educational Resources Information Center

    Bragg, Leicha

    2013-01-01

    In this article Leicha Bragg introduces an open-ended assessment task that gives students the opportunity to access skills and knowledge from the Measurement and Geometry strand. Students take on the roles of cartographer and map user to "hide, map and seek."

  15. An fMRI Investigation of Analogical Mapping in Metaphor Comprehension: The Influence of Context and Individual Cognitive Capacities on Processing Demands

    PubMed Central

    Prat, Chantel S.; Mason, Robert A.; Just, Marcel Adam

    2014-01-01

    This study used fMRI to investigate the neural correlates of analogical mapping during metaphor comprehension, with a focus on dynamic configuration of neural networks with changing processing demands and individual abilities. Participants with varying vocabulary sizes and working memory capacities read 3-sentence passages ending in nominal critical utterances of the form “X is a Y.” Processing demands were manipulated by varying preceding contexts. Three figurative conditions manipulated difficulty by varying the extent to which preceding contexts mentioned relevant semantic features for relating the vehicle and topic of the critical utterance to one another. In the easy condition, supporting information was mentioned. In the neutral condition, no relevant information was mentioned. In the most difficult condition, opposite features were mentioned, resulting in an ironic interpretation of the critical utterance. A fourth, literal condition included context that supported a literal interpretation of the critical utterance. Activation in lateral and medial frontal regions increased with increasing contextual difficulty. Lower vocabulary readers also had greater activation across conditions in the right inferior frontal gyrus. In addition, volumetric analyses showed increased right temporo-parietal junction and superior medial frontal activation for all figurative conditions over the literal condition. The results from this experiment imply that the cortical regions are dynamically recruited in language comprehension as a function of the processing demands of a task. Individual differences in cognitive capacities were also associated with differences in recruitment and modulation of working memory and executive function regions, highlighting the overlapping computations in metaphor comprehension and general thinking and reasoning. PMID:22122242

  16. Mapping Primary Gyrogenesis During Fetal Development in Primate Brains: High-Resolution in Utero Structural MRI of Fetal Brain Development in Pregnant Baboons

    PubMed Central

    Kochunov, Peter; Castro, Carlos; Davis, Duff; Dudley, Donald; Brewer, Jordan; Zhang, Yi; Kroenke, Christopher D.; Purdy, David; Fox, Peter T.; Simerly, Calvin; Schatten, Gerald

    2010-01-01

    The global and regional changes in the fetal cerebral cortex in primates were mapped during primary gyrification (PG; weeks 17–25 of 26 weeks total gestation). Studying pregnant baboons using high-resolution MRI in utero, measurements included cerebral volume, cortical surface area, gyrification index and length and depth of 10 primary cortical sulci. Seven normally developing fetuses were imaged in two animals longitudinally and sequentially. We compared these results to those on PG that from the ferret studies and analyzed them in the context of our recent studies of phylogenetics of cerebral gyrification. We observed that in both primates and non-primates, the cerebrum undergoes a very rapid transformation into the gyrencephalic state, subsequently accompanied by an accelerated growth in brain volume and cortical surface area. However, PG trends in baboons exhibited some critical differences from those observed in ferrets. For example, in baboons, the growth along the long (length) axis of cortical sulci was unrelated to the growth along the short (depth) axis and far outpaced it. Additionally, the correlation between the rate of growth along the short sulcal axis and heritability of sulcal depth was negative and approached significance (r = −0.60; p < 0.10), while the same trend for long axis was positive and not significant (p = 0.3; p = 0.40). These findings, in an animal that shares a highly orchestrated pattern of PG with humans, suggest that ontogenic processes that influence changes in sulcal length and depth are diverse and possibly driven by different factors in primates than in non-primates. PMID:20631812

  17. Quality assurance for diffusion tensor imaging using an ACR phantom: Comparative analysis with 6, 15, and 32 directions at 1.5T and 3.0T MRI systems

    NASA Astrophysics Data System (ADS)

    Lee, Jung-Hoon; Kim, Sang-Young; Lee, Do-Wan; Jung, Jin-Young; Song, Kyu-Ho; Choe, Bo-Young

    2014-07-01

    Although diffusion tensor imaging (DTI) has been widely used for the quantitative analyses of the integrity of white matter in the brain in clinical and research fields, quality assurance (QA) for DTI has not been fully established. Thus, we suggest a QA guideline for DTI using the American College of Radiology (ACR) Magnetic resonance imaging (MRI) head phantom. In this study, the geometric accuracy, slice-position accuracy, image intensity uniformity, percent signalghosting, low-contrast object detectability, image distortion, fractional anisotropy (FA), and apparent diffusion coefficient (ADC) were measured and evaluated in 1.5T and 3.0T MRI scanners equipped with an 8-channel SENSE head coil. The standard axial spin echo (SE) T1-weighted MR images and DTI with 6, 15 and 32 directions were obtained. Concerning geometric accuracy, image twisting in the three directions was observed due to the inhomogeneity of echo planar imaging (EPI). Image intensity uniformity was significantly lower for DTI than for the standard SE T1-weighted MR images. Percent signal ghosting was higher for images from 3.0T MRI than for images from 1.5T MRI. Low-contrast object detectability was visually identified and measured at a low contrasttonoise ratio (CNR) and a low signaltonoise ratio (SNR). Image distortion changed remarkably to the phaseencoding direction. The present study using the ACR MRI phantom suggests a QA method for DTI with high reproducibility and easy accessibility.

  18. SU-F-BRF-10: Deformable MRI to CT Validation Employing Same Day Planning MRI for Surrogate Analysis

    SciTech Connect

    Padgett, K; Stoyanova, R; Johnson, P; Dogan, N; Pollack, A; Piper, J; Javorek, A

    2014-06-15

    Purpose: To compare rigid and deformable registrations of the prostate in the multi-modality setting (diagnostic-MRI to planning-CT) by utilizing a planning-MRI as a surrogate. The surrogate allows for the direct quantitative analysis which can be difficult in the multi-modality domain where intensity mapping differs. Methods: For ten subjects, T2 fast-spin-echo images were acquired at two different time points, the first several weeks prior to planning (diagnostic-MRI) and the second on the same day in which the planning CT was collected (planning-MRI). Significant effort in patient positioning and bowel/bladder preparation was undertaken to minimize distortion of the prostate in all datasets. The diagnostic-MRI was deformed to the planning-CT utilizing a commercially available deformable registration algorithm synthesized from local registrations. The deformed MRI was then rigidly aligned to the planning MRI which was used as the surrogate for the planning-CT. Agreement between the two MRI datasets was scored using intensity based metrics including Pearson correlation and normalized mutual information, NMI. A local analysis was performed by looking only within the prostate, proximal seminal vesicles, penile bulb and combined areas. A similar method was used to assess a rigid registration between the diagnostic-MRI and planning-CT. Results: Utilizing the NMI, the deformable registrations were superior to the rigid registrations in 9 of 10 cases demonstrating a 15.94% improvement (p-value < 0.001) within the combined area. The Pearson correlation showed similar results with the deformable registration superior in the same number of cases and demonstrating a 6.97% improvement (p-value <0.011). Conclusion: Validating deformable multi-modality registrations using spatial intensity based metrics is difficult due to the inherent differences in intensity mapping. This population provides an ideal testing ground for MRI to CT deformable registrations by obviating the need

  19. Seismic Hazard Maps for Seattle, Washington, Incorporating 3D Sedimentary Basin Effects, Nonlinear Site Response, and Rupture Directivity

    USGS Publications Warehouse

    Frankel, Arthur D.; Stephenson, William J.; Carver, David L.; Williams, Robert A.; Odum, Jack K.; Rhea, Susan

    2007-01-01

    This report presents probabilistic seismic hazard maps for Seattle, Washington, based on over 500 3D simulations of ground motions from scenario earthquakes. These maps include 3D sedimentary basin effects and rupture directivity. Nonlinear site response for soft-soil sites of fill and alluvium was also applied in the maps. The report describes the methodology for incorporating source and site dependent amplification factors into a probabilistic seismic hazard calculation. 3D simulations were conducted for the various earthquake sources that can affect Seattle: Seattle fault zone, Cascadia subduction zone, South Whidbey Island fault, and background shallow and deep earthquakes. The maps presented in this document used essentially the same set of faults and distributed-earthquake sources as in the 2002 national seismic hazard maps. The 3D velocity model utilized in the simulations was validated by modeling the amplitudes and waveforms of observed seismograms from five earthquakes in the region, including the 2001 M6.8 Nisqually earthquake. The probabilistic seismic hazard maps presented here depict 1 Hz response spectral accelerations with 10%, 5%, and 2% probabilities of exceedance in 50 years. The maps are based on determinations of seismic hazard for 7236 sites with a spacing of 280 m. The maps show that the most hazardous locations for this frequency band (around 1 Hz) are soft-soil sites (fill and alluvium) within the Seattle basin and along the inferred trace of the frontal fault of the Seattle fault zone. The next highest hazard is typically found for soft-soil sites in the Duwamish Valley south of the Seattle basin. In general, stiff-soil sites in the Seattle basin exhibit higher hazard than stiff-soil sites outside the basin. Sites with shallow bedrock outside the Seattle basin have the lowest estimated hazard for this frequency band.

  20. Automatic search for fMRI connectivity mapping: an alternative to Granger causality testing using formal equivalences among SEM path modeling, VAR, and unified SEM.

    PubMed

    Gates, Kathleen M; Molenaar, Peter C M; Hillary, Frank G; Ram, Nilam; Rovine, Michael J

    2010-04-15

    Modeling the relationships among brain regions of interest (ROIs) carries unique potential to explicate how the brain orchestrates information processing. However, hurdles arise when using functional MRI data. Variation in ROI activity contains sequential dependencies and shared influences on synchronized activation. Consequently, both lagged and contemporaneous relationships must be considered for unbiased statistical parameter estimation. Identifying these relationships using a data-driven approach could guide theory-building regarding integrated processing. The present paper demonstrates how the unified SEM attends to both lagged and contemporaneous influences on ROI activity. Additionally, this paper offers an approach akin to Granger causality testing, Lagrange multiplier testing, for statistically identifying directional influence among ROIs and employs this approach using an automatic search procedure to arrive at the optimal model. Rationale for this equivalence is offered by explicating the formal relationships among path modeling, vector autoregression, and unified SEM. When applied to simulated data, biases in estimates which do not consider both lagged and contemporaneous paths become apparent. Finally, the use of unified SEM with the automatic search procedure is applied to an empirical data example.

  1. Prefrontal Transcranial Direct Current Stimulation Alters Activation and Connectivity in Cortical and Subcortical Reward Systems: A tDCS-fMRI Study

    PubMed Central

    Weber, Matthew J.; Messing, Samuel B.; Rao, Hengyi; Detre, John A.; Thompson-Schill, Sharon L.

    2014-01-01

    Transcranial direct current stimulation (tDCS) is a noninvasive brain stimulation technique used both experimentally and therapeutically to modulate regional brain function. However, few studies have directly measured the aftereffects of tDCS on brain activity or examined changes in task-related brain activity consequent to prefrontal tDCS. To investigate the neural effects of tDCS, we collected fMRI data from 22 human subjects, both at rest and while performing the Balloon Analog Risk Task (BART), before and after true or sham transcranial direct current stimulation. TDCS decreased resting blood perfusion in orbitofrontal cortex and the right caudate and increased task-related activity in the right dorsolateral prefrontal cortex (DLPFC) and anterior cingulate cortex (ACC) in response to losses but not wins or increasing risk. Network analysis showed that whole-brain connectivity of the right ACC correlated positively with the number of pumps subjects were willing to make on the BART, and that tDCS reduced connectivity between the right ACC and the rest of the brain. Whole-brain connectivity of the right DLPFC also correlated negatively with pumps on the BART, as prior literature would suggest. Our results suggest that tDCS can alter activation and connectivity in regions distal to the electrodes. PMID:24453107

  2. Nature or Nurture in Finger Counting: A Review on the Determinants of the Direction of Number–Finger Mapping

    PubMed Central

    Previtali, Paola; Rinaldi, Luca; Girelli, Luisa

    2011-01-01

    The spontaneous use of finger counting has been for long recognized as critical to the acquisition of number skills. Recently, the great interest on space–number associations shifted attention to the practice of finger counting itself, and specifically, to its spatial components. Besides general cross-cultural differences in mapping numbers onto fingers, contrasting results have been reported with regard to the directional features of this mapping. The key issue we address is to what extent directionality is culturally mediated, i.e., linked to the conventional reading–writing system direction, and/or biologically determined, i.e., linked to hand dominance. Although the preferred starting-hand for counting seems to depend on the surveyed population, even within the same population high inter-individual variability minimizes the role of cultural factors. Even if so far largely overlooked, handedness represents a sound candidate for shaping finger counting direction. Here we discuss adults and developmental evidence in support of this view and we reconsider the plausibility of multiple and coexistent number–space mapping in physical and representational space. PMID:22319502

  3. Molecular fMRI

    PubMed Central

    Bartelle, Benjamin B.; Barandov, Ali

    2016-01-01

    Comprehensive analysis of brain function depends on understanding the dynamics of diverse neural signaling processes over large tissue volumes in intact animals and humans. Most existing approaches to measuring brain signaling suffer from limited tissue penetration, poor resolution, or lack of specificity for well-defined neural events. Here we discuss a new brain activity mapping method that overcomes some of these problems by combining MRI with contrast agents sensitive to neural signaling. The goal of this “molecular fMRI” approach is to permit noninvasive whole-brain neuroimaging with specificity and resolution approaching current optical neuroimaging methods. In this article, we describe the context and need for molecular fMRI as well as the state of the technology today. We explain how major types of MRI probes work and how they can be sensitized to neurobiological processes, such as neurotransmitter release, calcium signaling, and gene expression changes. We comment both on past work in the field and on challenges and promising avenues for future development. SIGNIFICANCE STATEMENT Brain researchers currently have a choice between measuring neural activity using cellular-level recording techniques, such as electrophysiology and optical imaging, or whole-brain imaging methods, such as fMRI. Cellular level methods are precise but only address a small portion of mammalian brains; on the other hand, whole-brain neuroimaging techniques provide very little specificity for neural pathways or signaling components of interest. The molecular fMRI techniques we discuss have particular potential to combine the specificity of cellular-level measurements with the noninvasive whole-brain coverage of fMRI. On the other hand, molecular fMRI is only just getting off the ground. This article aims to offer a snapshot of the status and future prospects for development of molecular fMRI techniques. PMID:27076413

  4. A Concept-Mapping Strategy for Assessing Conceptual Change in a Student-Directed, Research-Based Geoscience Course

    NASA Astrophysics Data System (ADS)

    Rebich, S.

    2003-12-01

    The concept mapping technique has been proposed as a method for examining the evolving nature of students' conceptualizations of scientific concepts, and promises insight into a dimension of learning different from the one accessible through more conventional classroom testing techniques. The theory behind concept mapping is based on an assumption that knowledge acquisition is accomplished through "linking" of new information to an existing knowledge framework, and that meaningful (as opposed to arbitrary or verbatim) links allow for deeper understanding and conceptual change. Reflecting this theory, concept maps are constructed as a network of related concepts connected by labeled links that illustrate the relationship between the concepts. Two concepts connected by one such link make up a "proposition", the basic element of the concept map structure. In this paper, we examine the results of a pre- and post-test assessment program for an upper-division undergraduate geography course entitled "Mock Environmental Summit," which was part of a research project on assessment. Concept mapping was identified as a potentially powerful assessment tool for this course, as more conventional tools such as multiple-choice tests did not seem to provide a reliable indication of the learning students were experiencing as a result of the student-directed research, presentations, and discussions that make up a substantial portion of the course. The assessment program began at the beginning of the course with a one-hour training session during which students were introduced to the theory behind concept mapping, provided with instructions and guidance for constructing a concept map using the CMap software developed and maintained by the Institute for Human and Machine Cognition at the University of West Florida, and asked to collaboratively construct a concept map on a topic not related to the one to be assessed. This training session was followed by a 45-minute "pre-test" on the

  5. Direct optical mapping of transcription factor binding sites on field-stretched λ-DNA in nanofluidic devices

    PubMed Central

    Sriram, K. K.; Yeh, Jia-Wei; Lin, Yii-Lih; Chang, Yi-Ren; Chou, Chia-Fu

    2014-01-01

    Mapping transcription factor (TF) binding sites along a DNA backbone is crucial in understanding the regulatory circuits that control cellular processes. Here, we deployed a method adopting bioconjugation, nanofluidic confinement and fluorescence single molecule imaging for direct mapping of TF (RNA polymerase) binding sites on field-stretched single DNA molecules. Using this method, we have mapped out five of the TF binding sites of E. coli RNA polymerase to bacteriophage λ-DNA, where two promoter sites and three pseudo-promoter sites are identified with the corresponding binding frequency of 45% and 30%, respectively. Our method is quick, robust and capable of resolving protein-binding locations with high accuracy (∼ 300 bp), making our system a complementary platform to the methods currently practiced. It is advantageous in parallel analysis and less prone to false positive results over other single molecule mapping techniques such as optical tweezers, atomic force microscopy and molecular combing, and could potentially be extended to general mapping of protein–DNA interaction sites. PMID:24753422

  6. EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

    DOE PAGES

    Barad, Benjamin A.; Echols, Nathaniel; Wang, Ray Yu-Ruei; Cheng, Yifan; DiMaio, Frank; Adams, Paul D.; Fraser, James S.

    2015-08-17

    Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of validation metrics to independently assess map quality and model geometry. We report that EMRinger is a tool that assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. EMRinger (https://github.com/fraser-lab/EMRinger) will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM.

  7. Mapping Soil Salinity with ECa-Directed Soil Sampling: History, Protocols, Guidelines, Applications, and Future Research Trends

    NASA Astrophysics Data System (ADS)

    Corwin, Dennis

    2014-05-01

    Soil salinity is a spatially complex and dynamic property of soil that influences crop yields when the threshold salinity level is exceeded. Mapping soil salinity is necessary for soil classification, reclamation, crop selection, and site-specific irrigation management of salt-affected soils in the arid and semi-arid agricultural regions of the world. Because of its spatial and temporal heterogeneity soil salinity is difficult to map and monitor at field scales. There are various methods for characterizing soil salinity variability, but none of these approaches has been as extensively investigated and is as reliable and cost effective as apparent soil electrical conductivity (ECa) directed soil sampling. Geospatial measurements of ECa are well-suited for characterizing soil salinity spatial distribution because they are reliable, quick, and easy to take with GPS-based mobilized ECa measurement equipment. However, ECa is influenced by a variety of soil properties, which makes the measurement of soil salinity at field scale problematic. It is the goal of this presentation to provide an overview of the field-scale characterization of soil salinity distribution using ECa-directed soil sampling. A historical perspective, protocols and guidelines, strengths and limitations, applications, and future trends are presented for characterizing spatial and temporal variation in soil salinity using ECa-directed soil sampling. Land resource managers, farmers, extension specialists, soil classification specialists, and Natural Resource Conservation Service field staff are the beneficiaries of field-scale maps of soil salinity.

  8. Application of Direct Virtual Coil to Dynamic Contrast-Enhanced MRI and MR Angiography with Data-Driven Parallel Imaging

    PubMed Central

    Wang, Kang; Beatty, Philip J.; Nagle, Scott K.; Reeder, Scott B.; Holmes, James H.; Rahimi, Mahdi S.; Bell, Laura C.; Korosec, Frank R.; Brittain, Jean H.

    2013-01-01

    Purpose To demonstrate the feasibility of Direct Virtual Coil (DVC) in the setting of 4D dynamic imaging used in multiple clinical applications. Theory and Methods Three dynamic imaging applications were chosen: pulmonary perfusion, liver perfusion and peripheral MRA, with 18, 11 and 10 subjects respectively. After view-sharing, the k-space data were reconstructed twice: once with channel-by-channel (CBC) followed by sum-of-squares coil combination and once with DVC. Images reconstructed using CBC and DVC were compared and scored based on overall image quality by two experienced radiologists using a 5-point scale. Results The CBC and DVC showed similar image quality in image domain. Time course measurements also showed good agreement in the temporal domain. CBC and DVC images were scored as equivalent for all pulmonary perfusion cases, all liver perfusion cases, and 4 out of the 10 peripheral MRA cases. For the remaining 6 peripheral MRA cases, DVC were scored as slightly better (not clinically significant) than the CBC images by Radiologist A and as equivalent by Radiologist B. Conclusion For dynamic contrast-enhanced MR applications, it is clinically feasible to reduce image reconstruction time while maintaining image quality and time course measurement using the DVC technique. PMID:23441013

  9. Decoding the direction of imagined visual motion using 7 T ultra-high field fMRI

    PubMed Central

    Emmerling, Thomas C.; Zimmermann, Jan; Sorger, Bettina; Frost, Martin A.; Goebel, Rainer

    2016-01-01

    There is a long-standing debate about the neurocognitive implementation of mental imagery. One form of mental imagery is the imagery of visual motion, which is of interest due to its naturalistic and dynamic character. However, so far only the mere occurrence rather than the specific content of motion imagery was shown to be detectable. In the current study, the application of multi-voxel pattern analysis to high-resolution functional data of 12 subjects acquired with ultra-high field 7 T functional magnetic resonance imaging allowed us to show that imagery of visual motion can indeed activate the earliest levels of the visual hierarchy, but the extent thereof varies highly between subjects. Our approach enabled classification not only of complex imagery, but also of its actual contents, in that the direction of imagined motion out of four options was successfully identified in two thirds of the subjects and with accuracies of up to 91.3% in individual subjects. A searchlight analysis confirmed the local origin of decodable information in striate and extra-striate cortex. These high-accuracy findings not only shed new light on a central question in vision science on the constituents of mental imagery, but also show for the first time that the specific sub-categorical content of visual motion imagery is reliably decodable from brain imaging data on a single-subject level. PMID:26481673

  10. Vascular autorescaling of fMRI (VasA fMRI) improves sensitivity of population studies: A pilot study

    PubMed Central

    Kazan, Samira M.; Mohammadi, Siawoosh; Callaghan, Martina F.; Flandin, Guillaume; Huber, Laurentius; Leech, Robert; Kennerley, Aneurin; Windischberger, Christian; Weiskopf, Nikolaus

    2016-01-01

    The blood oxygenation level-dependent (BOLD) signal is widely used for functional magnetic resonance imaging (fMRI) of brain function in health and disease. The statistical power of fMRI group studies is significantly hampered by high inter-subject variance due to differences in baseline vascular physiology. Several methods have been proposed to account for physiological vascularization differences between subjects and hence improve the sensitivity in group studies. However, these methods require the acquisition of additional reference scans (such as a full resting-state fMRI session or ASL-based calibrated BOLD). We present a vascular autorescaling (VasA) method, which does not require any additional reference scans. VasA is based on the observation that slow oscillations (< 0.1 Hz) in arterial blood CO2 levels occur naturally due to changes in respiration patterns. These oscillations yield fMRI signal changes whose amplitudes reflect the blood oxygenation levels and underlying local vascularization and vascular responsivity. VasA estimates proxies of the amplitude of these CO2-driven oscillations directly from the residuals of task-related fMRI data without the need for reference scans. The estimates are used to scale the amplitude of task-related fMRI responses, to account for vascular differences. The VasA maps compared well to cerebrovascular reactivity (CVR) maps and cerebral blood volume maps based on vascular space occupancy (VASO) measurements in four volunteers, speaking to the physiological vascular basis of VasA. VasA was validated in a wide variety of tasks in 138 volunteers. VasA increased t-scores by up to 30% in specific brain areas such as the visual cortex. The number of activated voxels was increased by up to 200% in brain areas such as the orbital frontal cortex while still controlling the nominal false-positive rate. VasA fMRI outperformed previously proposed rescaling approaches based on resting-state fMRI data and can be readily applied to

  11. Gauging MRI

    NASA Astrophysics Data System (ADS)

    Herron, Ison; Goodman, Jeremy

    2009-11-01

    Axisymmetric stability of viscous resistive magnetized Couette flow is re-examined, with emphasis on flows that would be hydrodynamically stable according to Rayleigh's criterion: opposing gradients of angular velocity and specific angular momentum. A uniform axial magnetic field permeates the fluid. In this regime, magnetorotational instability (MRI) may occur. It is proved that MRI is suppressed, in fact no instability at all occurs, with insulating boundary conditions, when the magnetic resistivity is sufficiently large. This shows conclusively that small magnetic dissipation is a feature of this instability for all magnetic Prandtl numbers. A criterion is provided for the onset of MRI.

  12. Musculoskeletal MRI.

    PubMed

    Sage, Jaime E; Gavin, Patrick

    2016-05-01

    MRI has the unique ability to detect abnormal fluid content, and is therefore unparalleled in its role of detection, diagnosis, prognosis, treatment planning and follow-up evaluation of musculoskeletal disease. MRI in companion animals should be considered in the following circumstances: a definitive diagnosis cannot be made on radiographs; a patient is nonresponsive to medical or surgical therapy; prognostic information is desired; assessing surgical margins and traumatic and/or infectious joint and bone disease; ruling out subtle developmental or early aggressive bone lesions. The MRI features of common disorders affecting the shoulder, elbow, stifle, carpal, and tarsal joints are included in this chapter.

  13. Fast radio-frequency enforced steady state (FRESS) spin echo MRI for quantitative T2 mapping: minimizing the apparent repetition time (TR) dependence for fast T2 measurement.

    PubMed

    Cheung, Jerry S; Wang, Enfeng; Zhang, XiaoAn; Mandeville, Emiri; Lo, Eng H; Sorensen, A Gregory; Sun, Phillip Zhe

    2012-02-01

    Transverse relaxation time (T(2)) is a basic but very informative MRI parameter, widely used in imaging to examine a host of diseases, including multiple sclerosis, stroke, and tumor. However, short repetition time (TR) is often used to minimize scan time, which may introduce non-negligible errors in T(2) measurement. Specifically, due to the use of refocusing pulse, the steady state magnetization depends not only on TR but also on the TE. Hence, if the TE dependence is not properly accounted for, it may be mistaken as T(2)-induced signal attenuation, leading to non-negligible T(2) underestimation. Our study proposed a fast radio-frequency enforced steady state (FRESS) spin echo (SE) MRI sequence, which saturates the magnetization after the echo and ensures a TE-independent steady state. The proposed FRESS-SE MRI was evaluated with numerical simulation, implemented with echo planar imaging readout, and validated by both phantom and in vivo experiments. In summary, FRESS-SE T(2) MRI technique was developed for fast and accurate T(2) imaging, suitable for in vivo applications.

  14. Mapping membrane protein backbone dynamics: a comparison of site-directed spin labeling with NMR 15N-relaxation measurements.

    PubMed

    Lo, Ryan H; Kroncke, Brett M; Solomon, Tsega L; Columbus, Linda

    2014-10-01

    The ability to detect nanosecond backbone dynamics with site-directed spin labeling (SDSL) in soluble proteins has been well established. However, for membrane proteins, the nitroxide appears to have more interactions with the protein surface, potentially hindering the sensitivity to backbone motions. To determine whether membrane protein backbone dynamics could be mapped with SDSL, a nitroxide was introduced at 55 independent sites in a model polytopic membrane protein, TM0026. Electron paramagnetic resonance spectral parameters were compared with NMR (15)N-relaxation data. Sequential scans revealed backbone dynamics with the same trends observed for the R1 relaxation rate, suggesting that nitroxide dynamics remain coupled to the backbone on membrane proteins.

  15. Combined DTI Tractography and Functional MRI Study of the Language Connectome in Healthy Volunteers: Extensive Mapping of White Matter Fascicles and Cortical Activations.

    PubMed

    Vassal, François; Schneider, Fabien; Boutet, Claire; Jean, Betty; Sontheimer, Anna; Lemaire, Jean-Jacques

    2016-01-01

    Despite a better understanding of brain language organization into large-scale cortical networks, the underlying white matter (WM) connectivity is still not mastered. Here we combined diffusion tensor imaging (DTI) fiber tracking (FT) and language functional magnetic resonance imaging (fMRI) in twenty healthy subjects to gain new insights into the macroscopic structural connectivity of language. Eight putative WM fascicles for language were probed using a deterministic DTI-FT technique: the arcuate fascicle (AF), superior longitudinal fascicle (SLF), uncinate fascicle (UF), temporo-occipital fascicle, inferior fronto-occipital fascicle (IFOF), middle longitudinal fascicle (MdLF), frontal aslant fascicle and operculopremotor fascicle. Specific measurements (i.e. volume, length, fractional anisotropy) and precise cortical terminations were derived for each WM fascicle within both hemispheres. Connections between these WM fascicles and fMRI activations were studied to determine which WM fascicles are related to language. WM fascicle volumes showed asymmetries: leftward for the AF, temporoparietal segment of SLF and UF, and rightward for the frontoparietal segment of the SLF. The lateralization of the AF, IFOF and MdLF extended to differences in patterns of anatomical connections, which may relate to specific hemispheric abilities. The leftward asymmetry of the AF was correlated to the leftward asymmetry of fMRI activations, suggesting that the lateralization of the AF is a structural substrate of hemispheric language dominance. We found consistent connections between fMRI activations and terminations of the eight WM fascicles, providing a detailed description of the language connectome. WM fascicle terminations were also observed beyond fMRI-confirmed language areas and reached numerous cortical areas involved in different functional brain networks. These findings suggest that the reported WM fascicles are not exclusively involved in language and might be related to

  16. Combined DTI Tractography and Functional MRI Study of the Language Connectome in Healthy Volunteers: Extensive Mapping of White Matter Fascicles and Cortical Activations

    PubMed Central

    Schneider, Fabien; Boutet, Claire; Jean, Betty

    2016-01-01

    Despite a better understanding of brain language organization into large-scale cortical networks, the underlying white matter (WM) connectivity is still not mastered. Here we combined diffusion tensor imaging (DTI) fiber tracking (FT) and language functional magnetic resonance imaging (fMRI) in twenty healthy subjects to gain new insights into the macroscopic structural connectivity of language. Eight putative WM fascicles for language were probed using a deterministic DTI-FT technique: the arcuate fascicle (AF), superior longitudinal fascicle (SLF), uncinate fascicle (UF), temporo-occipital fascicle, inferior fronto-occipital fascicle (IFOF), middle longitudinal fascicle (MdLF), frontal aslant fascicle and operculopremotor fascicle. Specific measurements (i.e. volume, length, fractional anisotropy) and precise cortical terminations were derived for each WM fascicle within both hemispheres. Connections between these WM fascicles and fMRI activations were studied to determine which WM fascicles are related to language. WM fascicle volumes showed asymmetries: leftward for the AF, temporoparietal segment of SLF and UF, and rightward for the frontoparietal segment of the SLF. The lateralization of the AF, IFOF and MdLF extended to differences in patterns of anatomical connections, which may relate to specific hemispheric abilities. The leftward asymmetry of the AF was correlated to the leftward asymmetry of fMRI activations, suggesting that the lateralization of the AF is a structural substrate of hemispheric language dominance. We found consistent connections between fMRI activations and terminations of the eight WM fascicles, providing a detailed description of the language connectome. WM fascicle terminations were also observed beyond fMRI-confirmed language areas and reached numerous cortical areas involved in different functional brain networks. These findings suggest that the reported WM fascicles are not exclusively involved in language and might be related to

  17. Combined DTI Tractography and Functional MRI Study of the Language Connectome in Healthy Volunteers: Extensive Mapping of White Matter Fascicles and Cortical Activations.

    PubMed

    Vassal, François; Schneider, Fabien; Boutet, Claire; Jean, Betty; Sontheimer, Anna; Lemaire, Jean-Jacques

    2016-01-01

    Despite a better understanding of brain language organization into large-scale cortical networks, the underlying white matter (WM) connectivity is still not mastered. Here we combined diffusion tensor imaging (DTI) fiber tracking (FT) and language functional magnetic resonance imaging (fMRI) in twenty healthy subjects to gain new insights into the macroscopic structural connectivity of language. Eight putative WM fascicles for language were probed using a deterministic DTI-FT technique: the arcuate fascicle (AF), superior longitudinal fascicle (SLF), uncinate fascicle (UF), temporo-occipital fascicle, inferior fronto-occipital fascicle (IFOF), middle longitudinal fascicle (MdLF), frontal aslant fascicle and operculopremotor fascicle. Specific measurements (i.e. volume, length, fractional anisotropy) and precise cortical terminations were derived for each WM fascicle within both hemispheres. Connections between these WM fascicles and fMRI activations were studied to determine which WM fascicles are related to language. WM fascicle volumes showed asymmetries: leftward for the AF, temporoparietal segment of SLF and UF, and rightward for the frontoparietal segment of the SLF. The lateralization of the AF, IFOF and MdLF extended to differences in patterns of anatomical connections, which may relate to specific hemispheric abilities. The leftward asymmetry of the AF was correlated to the leftward asymmetry of fMRI activations, suggesting that the lateralization of the AF is a structural substrate of hemispheric language dominance. We found consistent connections between fMRI activations and terminations of the eight WM fascicles, providing a detailed description of the language connectome. WM fascicle terminations were also observed beyond fMRI-confirmed language areas and reached numerous cortical areas involved in different functional brain networks. These findings suggest that the reported WM fascicles are not exclusively involved in language and might be related to

  18. Direct mapping of local director field of nematic liquid crystals at the nanoscale

    PubMed Central

    Xia, Yu; Serra, Francesca; Kamien, Randall D.; Stebe, Kathleen J.; Yang, Shu

    2015-01-01

    Liquid crystals (LCs), owing to their anisotropy in molecular ordering, are of wide interest in both the display industry and soft matter as a route to more sophisticated optical objects, to direct phase separation, and to facilitate colloidal assemblies. However, it remains challenging to directly probe the molecular-scale organization of nonglassy nematic LC molecules without altering the LC directors. We design and synthesize a new type of nematic liquid crystal monomer (LCM) system with strong dipole–dipole interactions, resulting in a stable nematic phase and strong homeotropic anchoring on silica surfaces. Upon photopolymerization, the director field can be faithfully “locked,” allowing for direct visualization of the LC director field and defect structures by scanning electron microscopy (SEM) in real space with 100-nm resolution. Using this technique, we study the nematic textures in more complex LC/colloidal systems and calculate the extrapolation length of the LCM. PMID:26621729

  19. Direct mapping of local director field of nematic liquid crystals at the nanoscale.

    PubMed

    Xia, Yu; Serra, Francesca; Kamien, Randall D; Stebe, Kathleen J; Yang, Shu

    2015-12-15

    Liquid crystals (LCs), owing to their anisotropy in molecular ordering, are of wide interest in both the display industry and soft matter as a route to more sophisticated optical objects, to direct phase separation, and to facilitate colloidal assemblies. However, it remains challenging to directly probe the molecular-scale organization of nonglassy nematic LC molecules without altering the LC directors. We design and synthesize a new type of nematic liquid crystal monomer (LCM) system with strong dipole-dipole interactions, resulting in a stable nematic phase and strong homeotropic anchoring on silica surfaces. Upon photopolymerization, the director field can be faithfully "locked," allowing for direct visualization of the LC director field and defect structures by scanning electron microscopy (SEM) in real space with 100-nm resolution. Using this technique, we study the nematic textures in more complex LC/colloidal systems and calculate the extrapolation length of the LCM.

  20. Nonprofit health care services marketing: persuasive messages based on multidimensional concept mapping and direct magnitude estimation.

    PubMed

    Hall, Michael L

    2009-01-01

    Persuasive messages for marketing healthcare services in general and coordinated care in particular are more important now for providers, hospitals, and third-party payers than ever before. The combination of measurement-based information and creativity may be among the most critical factors in reaching markets or expanding markets. The research presented here provides an approach to marketing coordinated care services which allows healthcare managers to plan persuasive messages given the market conditions they face. Using market respondents' thinking about product attributes combined with distance measurement between pairs of product attributes, a conceptual marketing map is presented and applied to advertising, message copy, and delivery. The data reported here are representative of the potential caregivers for which the messages are intended. Results are described with implications for application to coordinated care services. Theory building and marketing practice are discussed in the light of findings and methodology.

  1. Structural MRI connectome in development: challenges of the changing brain

    PubMed Central

    Hess, C P; Xu, D; Barkovich, A J

    2014-01-01

    MRI connectomics is an emerging approach to study the brain as a network of interconnected brain regions. Understanding and mapping the development of the MRI connectome may offer new insights into the development of brain connectivity and plasticity, ultimately leading to improved understanding of normal development and to more effective diagnosis and treatment of developmental disorders. In this review, we describe the attempts made to date to map the whole-brain structural MRI connectome in the developing brain and pay a special attention to the challenges associated with the rapid changes that the brain is undergoing during maturation. The two main steps in constructing a structural brain network are (i) choosing connectivity measures that will serve as the network “edges” and (ii) finding an appropriate way to divide the brain into regions that will serve as the network “nodes”. We will discuss how these two steps are usually performed in developmental studies and the rationale behind different strategies. Changes in local and global network properties that have been described during maturation in neonates and children will be reviewed, along with differences in network topology between typically and atypically developing subjects, for example, owing to pre-mature birth or hypoxic ischaemic encephalopathy. Finally, future directions of connectomics will be discussed, addressing important steps necessary to advance the study of the structural MRI connectome in development. PMID:24827379

  2. fMRI analysis software tools: an evaluation framework

    NASA Astrophysics Data System (ADS)

    Pedoia, Valentina; Colli, Vittoria; Strocchi, Sabina; Vite, Cristina; Binaghi, Elisabetta; Conte, Leopoldo

    2011-03-01

    Performance comparison of functional Magnetic Resonance Imaging (fMRI) software tools is a very difficult task. In this paper, a framework for comparison of fMRI analysis results obtained with different software packages is proposed. An objective evaluation is possible only after pre-processing steps that normalize input data in a standard domain. Segmentation and registration algorithms are implemented in order to classify voxels belonging to brain or not, and to find the non rigid transformation that best aligns the volume under inspection with a standard one. Through the definitions of intersection and union of fuzzy logic an index was defined which quantify information overlap between Statistical Parametrical Maps (SPMs). Direct comparison between fMRI results can only highlight differences. In order to assess the best result, an index that represents the goodness of the activation detection is required. The transformation of the activation map in a standard domain allows the use of a functional Atlas for labeling the active voxels. For each functional area the Activation Weighted Index (AWI) that identifies the mean activation level of whole area was defined. By means of this brief, but comprehensive description, it is easy to find a metric for the objective evaluation of a fMRI analysis tools. Trough the first evaluation method the situations where the SPMs are inconsistent were identified. The result of AWI analysis suggest which tool has higher sensitivity and specificity. The proposed method seems a valid evaluation tool when applied to an adequate number of patients.

  3. Mapping Dimensionality and Directionality of Electronic Behavior in CeCoIn5: the Superconducting State

    NASA Astrophysics Data System (ADS)

    Feldman, Benjamin E.; Gyenis, Andras; Randeria, Mallika T.; Peterson, Gabriel A.; Aynajian, Pegor; Bauer, Eric D.; Yazdani, Ali

    Unconventional superconductors often exhibit anisotropic physical properties that arise from the directional dependence of their order parameters. A prime example is CeCoIn5, a heavy fermion d-wave superconductor with a rich low-temperature phase diagram consisting of competing and coexisting magnetic and superconducting orders. Here we present dilution refrigerator scanning tunneling microscopy of CeCoIn5 cleaved perpendicular to its basal plane. We study superconductivity on the (100) surface, whose normal vector points along the antinode of the superconducting energy gap. The gap magnitude is similar to that observed in the basal plane, with a key difference: it does not exhibit any suppression near step edges. Application of a magnetic field along the [100] direction leads to the formation of anisotropic vortices, and the vortex lattice undergoes a transition at high field before the superconducting state gives way to a pseudogap phase. Our measurements illustrate the directional dependence of the superconducting properties in CeCoIn5, and more generally, demonstrate the utility of imaging d-wave superconductors along their nodal and antinodal directions.

  4. Analysis of Contents, Contributors, and Research Directions: Mapping Publication Routes in the Journal

    ERIC Educational Resources Information Center

    English, Leona; D'souza, Mario; Chartrand, Leon

    2005-01-01

    A content analysis of the journal Religious Education: An Interfaith Journal of Spirituality, Growth and Transformation was conducted for a 10-year period between 1993?2002 (Volume 88, 1?Volume 97, 4). A total of 325 articles (277 authors) were analyzed into 3 primary research directions (theoretical, qualitative, and quantitative). Author…

  5. Longitudinally and circumferentially directed movements of the left ventricle studied by cardiovascular magnetic resonance phase contrast velocity mapping

    PubMed Central

    2010-01-01

    Objective Using high resolution cardiovascular magnetic resonance (CMR), we aimed to detect new details of left ventricular (LV) systolic and diastolic function, to explain the twisting and longitudinal movements of the left ventricle. Methods Using CMR phase contrast velocity mapping (also called Tissue Phase Mapping) regional wall motion patterns and longitudinally and circumferentially directed movements of the left ventricle were studied using a high temporal resolution technique in healthy male subjects (n = 14, age 23 ± 3 years). Results Previously undescribed systolic and diastolic motion patterns were obtained for left ventricular segments (based on the AHA segmental) and for basal, mid and apical segments. The summation of segmental motion results in a complex pattern of ventricular twisting and longitudinal motion in the normal human heart which underlies systolic and diastolic function. As viewed from the apex, the entire LV initially rotates in a counter-clockwise direction at the beginning of ventricular systole, followed by opposing clockwise rotation of the base and counter-clockwise rotation at the apex, resulting in ventricular torsion. Simultaneously, as the entire LV moves in an apical direction during systole, the base and apex move towards each other, with little net apical displacement. The reverse of these motion patterns occur in diastole. Conclusion Left ventricular function may be a consequence of the relative orientations and moments of torque of the sub-epicardial relative to the sub-endocardial myocyte layers, with influence from tethering of the heart to adjacent structures and the directional forces associated with blood flow. Understanding the complex mechanics of the left ventricle is vital to enable these techniques to be used for the evaluation of cardiac pathology. PMID:20716369

  6. Surface invasive cleavage assay on a maskless light-directed diamond DNA microarray for genome-wide human SNP mapping.

    PubMed

    Nie, Bei; Yang, Min; Fu, Weiling; Liang, Zhiqing

    2015-07-01

    The surface invasive cleavage assay, because of its innate accuracy and ability for self-signal amplification, provides a potential route for the mapping of hundreds of thousands of human SNP sites. However, its performance on a high density DNA array has not yet been established, due to the unusual "hairpin" probe design on the microarray and the lack of chemical stability of commercially available substrates. Here we present an applicable method to implement a nanocrystalline diamond thin film as an alternative substrate for fabricating an addressable DNA array using maskless light-directed photochemistry, producing the most chemically stable and biocompatible system for genetic analysis and enzymatic reactions. The surface invasive cleavage reaction, followed by degenerated primer ligation and post-rolling circle amplification is consecutively performed on the addressable diamond DNA array, accurately mapping SNP sites from PCR-amplified human genomic target DNA. Furthermore, a specially-designed DNA array containing dual probes in the same pixel is fabricated by following a reverse light-directed DNA synthesis protocol. This essentially enables us to decipher thousands of SNP alleles in a single-pot reaction by the simple addition of enzyme, target and reaction buffers.

  7. Curved reformat of the paediatric brain MRI into a 'flat-earth map' - standardised method for demonstrating cortical surface atrophy resulting from hypoxic-ischaemic encephalopathy.

    PubMed

    Simpson, Ewan; Andronikou, Savvas; Vedajallam, Schadie; Chacko, Anith; Thai, Ngoc Jade

    2016-09-01

    Hypoxic-ischaemic encephalopathy is optimally imaged with brain MRI in the neonatal period. However neuroimaging is often also performed later in childhood (e.g., when parents seek compensation in cases of alleged birth asphyxia). We describe a standardised technique for creating two curved reconstructions of the cortical surface to show the characteristic surface changes of hypoxic-ischaemic encephalopathy in children imaged after the neonatal period. The technique was applied for 10 cases of hypoxic-ischaemic encephalopathy and also for age-matched healthy children to assess the visibility of characteristic features of hypoxic-ischaemic encephalopathy. In the abnormal brains, fissural or sulcal widening was seen in all cases and ulegyria was identifiable in 7/10. These images could be used as a visual aid for communicating MRI findings to clinicians and other interested parties. PMID:27337989

  8. Curved reformat of the paediatric brain MRI into a 'flat-earth map' - standardised method for demonstrating cortical surface atrophy resulting from hypoxic-ischaemic encephalopathy.

    PubMed

    Simpson, Ewan; Andronikou, Savvas; Vedajallam, Schadie; Chacko, Anith; Thai, Ngoc Jade

    2016-09-01

    Hypoxic-ischaemic encephalopathy is optimally imaged with brain MRI in the neonatal period. However neuroimaging is often also performed later in childhood (e.g., when parents seek compensation in cases of alleged birth asphyxia). We describe a standardised technique for creating two curved reconstructions of the cortical surface to show the characteristic surface changes of hypoxic-ischaemic encephalopathy in children imaged after the neonatal period. The technique was applied for 10 cases of hypoxic-ischaemic encephalopathy and also for age-matched healthy children to assess the visibility of characteristic features of hypoxic-ischaemic encephalopathy. In the abnormal brains, fissural or sulcal widening was seen in all cases and ulegyria was identifiable in 7/10. These images could be used as a visual aid for communicating MRI findings to clinicians and other interested parties.

  9. Atom probe tomographic mapping directly reveals the atomic distribution of phosphorus in resin embedded ferritin

    DOE PAGES

    Perea, Daniel E.; Liu, Jia; Bartrand, Jonah A. G.; Dicken, Quinten G.; Thevuthasan, Suntharampillai Theva; Browning, Nigel D.; Evans, James E.

    2016-02-29

    In this study, we report the atomic-scale analysis of biological interfaces using atom probe tomography. Embedding the protein ferritin in an organic polymer resin lacking nitrogen provided chemical contrast to visualize atomic distributions and distinguish organic-organic and organic-inorganic interfaces. The sample preparation method can be directly extended to further enhance the study of biological, organic and inorganic nanomaterials relevant to health, energy or the environment.

  10. Three-Orthogonal-Direction Stress Mapping around a Fatigue-Crack Tip Using Neutron Diffraction

    NASA Astrophysics Data System (ADS)

    Huang, E.-Wen; Lee, Soo Yeol; Woo, Wanchuck; Lee, Kuan-Wei

    2012-08-01

    Quantitative determination of the stress fields around the crack tip is a challenging and important subject to understand the fatigue crack-growth mechanism. In the current study, we measured the distribution of residual stresses and the evolution of the stress fields around a fatigue crack tip subjected to the constant-amplitude cyclic loading in a 304L stainless steel compact-tension (CT) specimen. The three orthogonal stress components ( i.e., crack growth, crack opening, and through thickness) of the CT specimen were determined as a function of distance from the crack tip with 1-mm spatial resolution along the crack-propagation direction. In-situ neutron-diffraction results show that the enlarged tensile stresses were developed during loading along the through-thickness direction at a localized volume close to the crack tip, resulting in the lattice expansion in all three orthogonal directions during P max. The current study suggests that the atypical plane strainlike behavior observed at the midthickness position might be the reason for the mechanism of the faster crack-growth rate inside the interior than that near the surface.

  11. Map of autosomal recessive genetic disorders in Saudi Arabia: concepts and future directions.

    PubMed

    Al-Owain, Mohammed; Al-Zaidan, Hamad; Al-Hassnan, Zuhair

    2012-10-01

    Saudi Arabia has a population of 27.1 million. Prevalence of many autosomal recessive disorders is higher than in other known populations. This is attributable to the high rate of consanguineous marriages (56%), the tribal structure, and large family size. Founder mutations have been recognized in many autosomal recessive disorders, many of which are overrepresented within certain tribes. On the other hand, allelic heterogeneity is also observed among common and rare autosomal recessive conditions. With the adoption of more advanced molecular techniques in the country in recent years in conjunction with international collaboration, the mapping of various autosomal recessive disorders has increased dramatically. Different genetic concepts pertinent to this highly inbred population are discussed here. Addressing such genetic disorders at the national level will become a cornerstone of strategic health care initiatives in the 21st century. Current efforts are hampered by many socio-cultural and health care related factors. Education about genetic diseases, establishment of a "national registry" and mutational database, and enhanced healthcare access are crucial for success of any preventative campaign. PMID:22903695

  12. Mapping the crop row direction by using Formosat-2 panchromatic images.

    NASA Astrophysics Data System (ADS)

    Marais-Sicre, C.; Baup, F.; Fieuzal, R.

    2012-04-01

    The detection of crop row direction is a key factor for landscape analyses from satellite images. In optical and microwave frequency domains, Kimes and al, 1983 and Ulaby and al, 1984 shown the strong impact of the crop row orientation on the optical reflectance (Bidirectional reflectance distribution function) and on the radar backscattering coefficient (from L to X band). Consequently, it is particularly important to consider this parameter for remote sensing analyses but also in the physical and empirical approaches intended to the estimation of biophysical parameters (vegetation biomass, humidity, soil moisture content, tillage, runoff, erosion…) at the agricultural field scale. The studied area is located near Toulouse (South-west of France) in a region of alluvial plains and hills, which are mostly mixed farming and governed by a temperate climate with an annual rainfall of about 600mm per year. The region is composed of a wide variety of irrigated and non-irrigated crops (wheat, sunflower, corn, hemp…). Agricultural fields are strongly contrasted in terms of geometric forms, surface area (from 1ha to 50ha), type of soils, slopes... The remote sensing analyses are based on a time series of 13 panchromatic Formosat-2 images, acquired with a spatial resolution of 2 meters, and processed with a TOA (Top of Atmosphere) radiometric correction. Ground data are collected, the closest of satellite acquisitions, over 232 plots during the MCM'10 experiment (Multispectral Crop Monitoring, http://www.cesbio.ups-tlse.fr/us/mcm.html) conducted by the CESBIO laboratory in 2010. The proposed approach consists in estimating row direction, by using directional convolution filters and operators of mathematical morphology. First of all, one date capabilities is discussed, improved by multi-temporal analyses. Then, an original method is proposed for extrapolating the estimated row direction to the scene (over the Formosat-2 swath). Best results, obtained for multi

  13. Microscopic vision modeling method by direct mapping analysis for micro-gripping system with stereo light microscope.

    PubMed

    Wang, Yuezong; Zhao, Zhizhong; Wang, Junshuai

    2016-04-01

    We present a novel and high-precision microscopic vision modeling method, which can be used for 3D data reconstruction in micro-gripping system with stereo light microscope. This method consists of four parts: image distortion correction, disparity distortion correction, initial vision model and residual compensation model. First, the method of image distortion correction is proposed. Image data required by image distortion correction comes from stereo images of calibration sample. The geometric features of image distortions can be predicted though the shape deformation of lines constructed by grid points in stereo images. Linear and polynomial fitting methods are applied to correct image distortions. Second, shape deformation features of disparity distribution are discussed. The method of disparity distortion correction is proposed. Polynomial fitting method is applied to correct disparity distortion. Third, a microscopic vision model is derived, which consists of two models, i.e., initial vision model and residual compensation model. We derive initial vision model by the analysis of direct mapping relationship between object and image points. Residual compensation model is derived based on the residual analysis of initial vision model. The results show that with maximum reconstruction distance of 4.1mm in X direction, 2.9mm in Y direction and 2.25mm in Z direction, our model achieves a precision of 0.01mm in X and Y directions and 0.015mm in Z direction. Comparison of our model with traditional pinhole camera model shows that two kinds of models have a similar reconstruction precision of X coordinates. However, traditional pinhole camera model has a lower precision of Y and Z coordinates than our model. The method proposed in this paper is very helpful for the micro-gripping system based on SLM microscopic vision.

  14. Microscopic vision modeling method by direct mapping analysis for micro-gripping system with stereo light microscope.

    PubMed

    Wang, Yuezong; Zhao, Zhizhong; Wang, Junshuai

    2016-04-01

    We present a novel and high-precision microscopic vision modeling method, which can be used for 3D data reconstruction in micro-gripping system with stereo light microscope. This method consists of four parts: image distortion correction, disparity distortion correction, initial vision model and residual compensation model. First, the method of image distortion correction is proposed. Image data required by image distortion correction comes from stereo images of calibration sample. The geometric features of image distortions can be predicted though the shape deformation of lines constructed by grid points in stereo images. Linear and polynomial fitting methods are applied to correct image distortions. Second, shape deformation features of disparity distribution are discussed. The method of disparity distortion correction is proposed. Polynomial fitting method is applied to correct disparity distortion. Third, a microscopic vision model is derived, which consists of two models, i.e., initial vision model and residual compensation model. We derive initial vision model by the analysis of direct mapping relationship between object and image points. Residual compensation model is derived based on the residual analysis of initial vision model. The results show that with maximum reconstruction distance of 4.1mm in X direction, 2.9mm in Y direction and 2.25mm in Z direction, our model achieves a precision of 0.01mm in X and Y directions and 0.015mm in Z direction. Comparison of our model with traditional pinhole camera model shows that two kinds of models have a similar reconstruction precision of X coordinates. However, traditional pinhole camera model has a lower precision of Y and Z coordinates than our model. The method proposed in this paper is very helpful for the micro-gripping system based on SLM microscopic vision. PMID:26924646

  15. Functional Mapping of Protein-Protein Interactions in an Enzyme Complex by Directed Evolution

    PubMed Central

    Roderer, Kathrin; Neuenschwander, Martin; Codoni, Giosiana; Sasso, Severin; Gamper, Marianne; Kast, Peter

    2014-01-01

    The shikimate pathway enzyme chorismate mutase converts chorismate into prephenate, a precursor of Tyr and Phe. The intracellular chorismate mutase (MtCM) of Mycobacterium tuberculosis is poorly active on its own, but becomes >100-fold more efficient upon formation of a complex with the first enzyme of the shikimate pathway, 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase (MtDS). The crystal structure of the enzyme complex revealed involvement of C-terminal MtCM residues with the MtDS interface. Here we employed evolutionary strategies to probe the tolerance to substitution of the C-terminal MtCM residues from positions 84–90. Variants with randomized positions were subjected to stringent selection in vivo requiring productive interactions with MtDS for survival. Sequence patterns identified in active library members coincide with residue conservation in natural chorismate mutases of the AroQδ subclass to which MtCM belongs. An Arg-Gly dyad at positions 85 and 86, invariant in AroQδ sequences, was intolerant to mutation, whereas Leu88 and Gly89 exhibited a preference for small and hydrophobic residues in functional MtCM-MtDS complexes. In the absence of MtDS, selection under relaxed conditions identifies positions 84–86 as MtCM integrity determinants, suggesting that the more C-terminal residues function in the activation by MtDS. Several MtCM variants, purified using a novel plasmid-based T7 RNA polymerase gene expression system, showed that a diminished ability to physically interact with MtDS correlates with reduced activatability and feedback regulatory control by Tyr and Phe. Mapping critical protein-protein interaction sites by evolutionary strategies may pinpoint promising targets for drugs that interfere with the activity of protein complexes. PMID:25551646

  16. Evaluating the accuracy of a MODIS direct broadcast algorithm for mapping burned areas over Russia

    NASA Astrophysics Data System (ADS)

    Petkov, A.; Hao, W. M.; Nordgren, B.; Corley, R.; Urbanski, S. P.; Ponomarev, E. I.

    2012-12-01

    Emission inventories for open area biomass burning rely on burned area estimates as a key component. We have developed an automated algorithm based on MODerate resolution Imaging Spectroradiometer (MODIS) satellite instrument data for estimating burned area from biomass fires. The algorithm is based on active fire detections, burn scars from MODIS calibrated radiances (MOD02HKM), and MODIS land cover classification (MOD12Q1). Our burned area product combines active fires and burn scar detections using spatio-temporal criteria, and has a resolution of 500 x 500 meters. The algorithm has been used for smoke emission estimates over the western United States. We will present the assessed accuracy of our algorithm in different regions of Russia with intense wildfire activity by comparing our results with the burned area product from the Sukachev Institute of Forest (SIF) of the Russian Academy of Sciences in Krasnoyarsk, Russia, as well as burn scars extracted from Landsat imagery. Landsat burned area extraction was based on threshold classification using the Jenks Natural Breaks algorithm to the histogram for each singe scene Normalized Burn Ratio (NBR) image. The final evaluation consisted of a grid-based approach, where the burned area in each 3 km x 3 km grid cell was calculated and compared with the other two sources. A comparison between our burned area estimates and those from SIF showed strong correlation (R2=0.978), although our estimate is approximately 40% lower than the SIF burned areas. The linear fit between the burned area from Landsat scenes and our MODIS algorithm over 18,754 grid cells resulted with a slope of 0.998 and R2=0.7, indicating that our algorithm is suitable for mapping burned areas for fires in boreal forests and other ecosystems. The results of our burned area algorithm will be used for estimating emissions of trace gasses and aerosol particles (including black carbon) from biomass burning in Northern Eurasia for the period of 2002-2011.

  17. Internal Fiducial Markers and Susceptibility Effects in MRI-Simulation and Measurement of Spatial Accuracy

    SciTech Connect

    Jonsson, Joakim H.; Garpebring, Anders; Karlsson, Magnus G.; Nyholm, Tufve

    2012-04-01

    Background: It is well-known that magnetic resonance imaging (MRI) is preferable to computed tomography (CT) in radiotherapy target delineation. To benefit from this, there are two options available: transferring the MRI delineated target volume to the planning CT or performing the treatment planning directly on the MRI study. A precondition for excluding the CT study is the possibility to define internal structures visible on both the planning MRI and on the images used to position the patient at treatment. In prostate cancer radiotherapy, internal gold markers are commonly used, and they are visible on CT, MRI, x-ray, and portal images. The depiction of the markers in MRI are, however, dependent on their shape and orientation relative the main magnetic field because of susceptibility effects. In the present work, these effects are investigated and quantified using both simulations and phantom measurements. Methods and Materials: Software that simulated the magnetic field distortions around user defined geometries of variable susceptibilities was constructed. These magnetic field perturbation maps were then reconstructed to images that were evaluated. The simulation software was validated through phantom measurements of four commercially available gold markers of different shapes and one in-house gold marker. Results: Both simulations and phantom measurements revealed small position deviations of the imaged marker positions relative the actual marker positions (<1 mm). Conclusion: Cylindrical gold markers can be used as internal fiducial markers in MRI.

  18. Mapping the timecourse of goal-directed attention to location and colour in human vision.

    PubMed

    Adams, Rachel C; Chambers, Christopher D

    2012-03-01

    Goal-directed attention prioritises perception of task-relevant stimuli according to location, features, or onset time. In this study we compared the behavioural timecourse of goal-directed selection to locations and colours by varying the stimulus-onset asynchrony (SOA) between cue and target in a strategic cueing paradigm. Participants reported the presence or absence of a target following prior information regarding its location or colour. Results revealed that preparatory selection by colour is more effective at enhancing perceptual sensitivity than selection by location, even though both types of cue provided equivalent overall information. More detailed analysis revealed that this advantage arose due a limitation of spatial attention in maintaining a sufficiently broad focus (>2°) for target detection across multiple stimuli. In contrast, when target stimuli fell within 2° of the spatial attention spotlight, the strategic advantages and speed of spatial and colour attention were equated. Our findings are consistent with the conclusion that, under spatially optimal conditions, prior spatial and colour information are equally proficient at guiding top-down selection. When spatial locations are ambiguous, however, colour-based selection is the more efficient mechanism.

  19. Control over the strength of connections between modules: a double dissociation between stimulus format and task revealed by Granger causality mapping in fMRI

    PubMed Central

    Anderson, Britt; Soliman, Sherif; O’Malley, Shannon; Danckert, James; Besner, Derek

    2015-01-01

    Drawing on theoretical and computational work with the localist dual route reading model and results from behavioral studies, Besner et al. (2011) proposed that the ability to perform tasks that require overriding stimulus-specific defaults (e.g., semantics when naming Arabic numerals, and phonology when evaluating the parity of number words) necessitate the ability to modulate the strength of connections between cognitive modules for lexical representation, semantics, and phonology on a task- and stimulus-specific basis. We used functional magnetic resonance imaging to evaluate this account by assessing changes in functional connectivity while participants performed tasks that did and did not require such stimulus-task default overrides. The occipital region showing the greatest modulation of BOLD signal strength for the two stimulus types was used as the seed region for Granger causality mapping (GCM). Our GCM analysis revealed a region of rostromedial frontal cortex with a crossover interaction. When participants performed tasks that required overriding stimulus type defaults (i.e., parity judgments of number words and naming Arabic numerals) functional connectivity between the occipital region and rostromedial frontal cortex was present. Statistically significant functional connectivity was absent when the tasks were the default for the stimulus type (i.e., parity judgments of Arabic numerals and reading number words). This frontal region (BA 10) has previously been shown to be involved in goal-directed behavior and maintenance of a specific task set. We conclude that overriding stimulus-task defaults requires a modulation of connection strengths between cognitive modules and that the override mechanism predicted from cognitive theory is instantiated by frontal modulation of neural activity of brain regions specialized for sensory processing. PMID:25870571

  20. Portable MRI

    SciTech Connect

    Espy, Michelle A.

    2012-06-29

    This project proposes to: (1) provide the power of MRI to situations where it presently isn't available; (2) perform the engineering required to move from lab to a functional prototype; and (3) leverage significant existing infrastructure and capability in ultra-low field MRI. The reasons for doing this: (1) MRI is the most powerful tool for imaging soft-tissue (e.g. brain); (2) Billions don't have access due to cost or safety issues; (3) metal will heat/move in high magnetic fields; (4) Millions of cases of traumatic brain injury in US alone; (5) even more of non-traumatic brain injury; (6) (e.g. stroke, infection, chemical exposure); (7) Need for early diagnostic; (8) 'Signature' wound of recent conflicts; (9) 22% of injuries; (10) Implications for post-traumatic stress disorder; and (11) chronic traumatic encephalopathy.

  1. Efficient new ribozyme mimics: direct mapping of molecular design principles from small molecules to macromolecular, biomimetic catalysts.

    PubMed

    Putnam, W C; Daniher, A T; Trawick, B N; Bashkin, J K

    2001-05-15

    Dramatic improvements in ribozyme mimics have been achieved by employing the principles of small molecule catalysis to the design of macromolecular, biomimetic reagents. Ribozyme mimics derived from the ligand 2,9-dimethylphenanthroline (neocuproine) show at least 30-fold improvements in efficiency at sequence-specific RNA cleavage when compared with analogous o-phenanthroline- and terpyridine-derived reagents. The suppression of hydroxide-bridged dimers and the greater activation of coordinated water by Cu(II) neocuproine (compared with the o-phenanthroline and terpyridine complexes) better allow Cu(II) to reach its catalytic potential as a biomimetic RNA cleavage agent. This work demonstrates the direct mapping of molecular design principles from small-molecule cleavage to macromolecular cleavage events, generating enhanced biomimetic, sequence-specific RNA cleavage agents.

  2. Direct Mapping of Magnetic and Structural Profiles of Electric Field Moderated Oxygen Migration

    NASA Astrophysics Data System (ADS)

    Gilbert, Dustin A.; Grutter, Alexander J.; Kirby, Brian J.; Borchers, Julie A.; Maranville, Brian B.; Arenholz, Elke; Liu, Kai

    Recent studies on metal/oxide heterostructures have demonstrated control of interfacial magnetic anisotropy and saturation magnetization in ultrathin (5 ML) Co films through electric-field controlled oxygen migration. This approach presents a promising route to realizing next-generation, ultralow power sensor and data-storage technologies. Here we demonstrate magnetoelectric coupling moderated by electrically-driven oxygen migration in much thicker AlOx(1 um)/GdOx(2 nm)/Co (15 nm) heterostructures. Using polarized neutron reflectometry, we present direct, quantitative depth profiling of the magnetization and oxygen concentration in these systems. Electro-thermal conditioning moves oxygen from AlOx and GdOx base-layers throughout the entire thickness of the 15 nm Co layer, resulting in a suppressed magnetization. Switching the electric field polarity semi-reversibly ejects oxygen preferentially from the GdOX/Co interface, partially recovering the magnetization and establishing a practical limit to this approach. First order reversal curve diagrams show that the conditioned samples exhibit two distinct magnetic phases, while the as-grown samples are single phase, suggesting that the treatments alters the Co film microstructure. X-ray spectroscopy confirms the oxidation states of the Co and Gd, and suggest that the GdOX acts to transmit oxygen but does not source or sink it.

  3. Direct Mapping of Charge Distribution during Lithiation of Ge Nanowires Using Off-Axis Electron Holography.

    PubMed

    Gan, Zhaofeng; Gu, Meng; Tang, Jianshi; Wang, Chiu-Yen; He, Yang; Wang, Kang L; Wang, Chongmin; Smith, David J; McCartney, Martha R

    2016-06-01

    The successful operation of rechargeable batteries relies on reliable insertion/extraction of ions into/from the electrodes. The battery performance and the response of the electrodes to such ion insertion and extraction are directly related to the spatial distribution of the charge and its dynamic evolution. However, it remains unclear how charge is distributed in the electrodes during normal battery operation. In this work, we have used off-axis electron holography to measure charge distribution during lithium ion insertion into a Ge nanowire (NW) under dynamic operating conditions. We discovered that the surface region of the Ge core is negatively charged during the core-shell lithiation of the Ge NW, which is counterbalanced by positive charge on the inner surface of the lithiated LixGe shell. The remainder of the lithiated LixGe shell is free from net charge, consistent with its metallic characteristics. The present work provides a vivid picture of charge distribution and dynamic evolution during Ge NW lithiation and should form the basis for tackling the response of these and related materials under real electrochemical conditions. PMID:27192608

  4. High-Pressure EPR and Site-Directed Spin Labeling for Mapping Molecular Flexibility in Proteins.

    PubMed

    Lerch, Michael T; Yang, Zhongyu; Altenbach, Christian; Hubbell, Wayne L

    2015-01-01

    High hydrostatic pressure is a powerful probe of protein conformational flexibility. Pressurization reveals regions of elevated compressibility, and thus flexibility, within individual conformational states, but also shifts conformational equilibria such that "invisible" excited states become accessible for spectroscopic characterization. The central aim of this chapter is to describe recently developed instrumentation and methodologies that enable high-pressure site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) experiments on proteins and to demonstrate the information content of these experiments by highlighting specific recent applications. A brief introduction to the thermodynamics of proteins under pressure is presented first, followed by a discussion of the principles underlying SDSL-EPR detection of pressure effects in proteins, and the suitability of SDSL-EPR for this purpose in terms of timescale and ability to characterize conformational heterogeneity. Instrumentation and practical considerations for variable-pressure continuous wave EPR and pressure-resolved double electron-electron resonance (PR DEER) experiments are reviewed, and finally illustrations of data analysis using recent applications are presented. Although high-pressure SDSL-EPR is in its infancy, the recent applications presented highlight the considerable potential of the method to (1) identify compressible (flexible) regions in a folded protein; (2) determine thermodynamic parameters that relate conformational states in equilibrium; (3) populate and characterize excited states of proteins undetected at atmospheric pressure; (4) reveal the structural heterogeneity of conformational ensembles and provide distance constraints on the global structure of pressure-populated states with PR DEER.

  5. Presurgical language mapping in epilepsy: Using fMRI of reading to identify functional reorganization in a patient with long-standing temporal lobe epilepsy.

    PubMed

    Gould, Layla; Mickleborough, Marla J S; Wu, Adam; Tellez, Jose; Ekstrand, Chelsea; Lorentz, Eric; Ellchuk, Tasha; Babyn, Paul; Borowsky, Ron

    2016-01-01

    We report a 55-year-old, right-handed patient with intractable left temporal lobe epilepsy, who previously had a partial left temporal lobectomy. The patient could talk during seizures, suggesting that he might have language dominance in the right hemisphere. Presurgical fMRI localization of language processing including reading of exception and regular words, pseudohomophones, and dual meaning words confirmed the clinical hypothesis of right language dominance, with only small amounts of activation near the planned surgical resection and, thus, minimal eloquent cortex to avoid during surgery. Postoperatively, the patient was rendered seizure-free without speech deficits. PMID:27330987

  6. Chemiluminescence system for direct determination and mapping of ultra-trace metal impurities on a silicon wafer.

    PubMed

    Kim, Romertta; Sung, Y I; Lee, J S; Lim, H B

    2010-11-01

    A highly sensitive chemiluminescence (CL) system which consumed low sample and reagent volumes in the microlitre range was developed for direct determination and mapping of ultra-trace metal contaminants on solid surfaces, such as silicon wafers or flat display panels. The analytical result of the system was confirmed with ICP-MS. The system was composed of a scanner, sensor and a wafer moving stage. The scanner, with a scanning tip made of 0.03'' i.d. PTFE tubing, was used to collect metal impurities on the wafer surface with 5 μL of scanning solution. A coaxial sensing head of about 13 mm o.d. and 110 mm height was designed both to inject a luminescent reagent of luminol-H(2)O(2) mixture and to collect the luminescence light resulting from the reaction with metal ions of Co(2+), Fe(2+), Cu(2+), and Ni(2+). Due to the almost zero background, an extremely low limit of detection of 20.8 pg/mL for Co(2+) in 1% hydrofluoric acid (HF) was obtained from the calibration curve. In order to map the spatial distribution of the impurities, 11 cross sections of a Co-contaminated wafer were selected and scanned individually with a diluted HF solution. A contaminant level of 1.45-7.11 × 10(11) atoms cm(-2) was obtained for each section with an average of 4.21 × 10(11) atoms cm(-2), which was similar to the analytical result of 5.48 × 10(11) atoms cm(-2) obtained from vapor phase deposition-inductively coupled plasma-mass spectrometry (VPD-ICP-MS). Although this CL system does not have selectivity for each specific metal ion, its high sensitivity facilitates the monitoring and mapping of metal impurities of Co, Fe, Cu, etc. on the wafer directly and it can be used as an on-line inspection sensor for the first time in the semiconductor industry.

  7. Quantitative MRI techniques of cartilage composition

    PubMed Central

    Matzat, Stephen J.; van Tiel, Jasper; Gold, Garry E.

    2013-01-01

    Due to aging populations and increasing rates of obesity in the developed world, the prevalence of osteoarthritis (OA) is continually increasing. Decreasing the societal and patient burden of this disease motivates research in prevention, early detection of OA, and novel treatment strategies against OA. One key facet of this effort is the need to track the degradation of tissues within joints, especially cartilage. Currently, conventional imaging techniques provide accurate means to detect morphological deterioration of cartilage in the later stages of OA, but these methods are not sensitive to the subtle biochemical changes during early disease stages. Novel quantitative techniques with magnetic resonance imaging (MRI) provide direct and indirect assessments of cartilage composition, and thus allow for earlier detection and tracking of OA. This review describes the most prominent quantitative MRI techniques to date—dGEMRIC, T2 mapping, T1rho mapping, and sodium imaging. Other, less-validated methods for quantifying cartilage composition are also described—Ultrashort echo time (UTE), gagCEST, and diffusion-weighted imaging (DWI). For each technique, this article discusses the proposed biochemical correlates, as well its advantages and limitations for clinical and research use. The article concludes with a detailed discussion of how the field of quantitative MRI has progressed to provide information regarding two specific patient populations through clinical research—patients with anterior cruciate ligament rupture and patients with impingement in the hip. While quantitative imaging techniques continue to rapidly evolve, specific challenges for each technique as well as challenges to clinical applications remain. PMID:23833729

  8. Mapping methane sources and emissions over California from direct airborne flux and VOC source tracer measurements

    NASA Astrophysics Data System (ADS)

    Guha, A.; Misztal, P. K.; Peischl, J.; Karl, T.; Jonsson, H. H.; Woods, R. K.; Ryerson, T. B.; Goldstein, A. H.

    2013-12-01

    Quantifying the contributions of methane (CH4) emissions from anthropogenic sources in the Central Valley of California is important for validation of the statewide greenhouse gas (GHG) inventory and subsequent AB32 law implementation. The state GHG inventory is largely based on activity data and emission factor based estimates. The 'bottom-up' emission factors for CH4 have large uncertainties and there is a lack of adequate 'top-down' measurements to characterize emission rates. Emissions from non-CO2 GHG sources display spatial heterogeneity and temporal variability, and are thus, often, poorly characterized. The Central Valley of California is an agricultural and industry intensive region with large concentration of dairies and livestock operations, active oil and gas fields and refining operations, as well as rice cultivation all of which are known CH4 sources. In order to gain a better perspective of the spatial distribution of major CH4 sources in California, airborne measurements were conducted aboard a Twin Otter aircraft for the CABERNET (California Airborne BVOC Emissions Research in Natural Ecosystems Transects) campaign, where the driving research goal was to understand the spatial distribution of biogenic VOC emissions. The campaign took place in June 2011 and encompassed over forty hours of low-altitude and mixed layer airborne CH4 and CO2 measurements alongside coincident VOC measurements. Transects during eight unique flights covered much of the Central Valley and its eastern edge, the Sacramento-San Joaquin delta and the coastal range. We report direct quantification of CH4 fluxes using real-time airborne Eddy Covariance measurements. CH4 and CO2 were measured at 1-Hz data rate using an instrument based on Cavity Ring Down Spectroscopy (CRDS) along with specific VOCs (like isoprene, methanol, acetone etc.) measured at 10-Hz using Proton Transfer Reaction Mass Spectrometer - Eddy Covariance (PTRMS-EC) flux system. Spatially resolved eddy covariance

  9. Robust isotropic super-resolution by maximizing a Laplace posterior for MRI volumes

    NASA Astrophysics Data System (ADS)

    Han, Xian-Hua; Iwamoto, Yutaro; Shiino, Akihiko; Chen, Yen-Wei

    2014-03-01

    Magnetic resonance imaging can only acquire volume data with finite resolution due to various factors. In particular, the resolution in one direction (such as the slice direction) is much lower than others (such as the in-plane direction), yielding un-realistic visualizations. This study explores to reconstruct MRI isotropic resolution volumes from three orthogonal scans. This proposed super- resolution reconstruction is formulated as a maximum a posterior (MAP) problem, which relies on the generation model of the acquired scans from the unknown high-resolution volumes. Generally, the deviation ensemble of the reconstructed high-resolution (HR) volume from the available LR ones in the MAP is represented as a Gaussian distribution, which usually results in some noise and artifacts in the reconstructed HR volume. Therefore, this paper investigates a robust super-resolution by formulating the deviation set as a Laplace distribution, which assumes sparsity in the deviation ensemble based on the possible insight of the appeared large values only around some unexpected regions. In addition, in order to achieve reliable HR MRI volume, we integrates the priors such as bilateral total variation (BTV) and non-local mean (NLM) into the proposed MAP framework for suppressing artifacts and enriching visual detail. We validate the proposed robust SR strategy using MRI mouse data with high-definition resolution in two direction and low-resolution in one direction, which are imaged in three orthogonal scans: axial, coronal and sagittal planes. Experiments verifies that the proposed strategy can achieve much better HR MRI volumes than the conventional MAP method even with very high-magnification factor: 10.

  10. The application of MRI and MRS in psychiatry and performance evaluation of magnetic field homogeneity in MRI

    NASA Astrophysics Data System (ADS)

    Chen, Hua Hsuan

    Magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) is a safe non-invasive tool to study the physiological mechanisms of the human brain. MRS has the capability to provide the information regarding neurochemicals in brains of patients with neuropsychiatric disorders. Therefore, to produce measurable and interpretable information in MRI and MRS, a quality control (QC) program is required. Magnetic field homogeneity (MFH) is an important factor for QC when the volume sizes and neurochemical levels are quantified. Poor main (B0) MFH leads to artifacts, signal losses and broadened line widths. The American College of Radiology's (ACR) MRI QC manual mandates annual checks of MFH, suggesting tests using spectral line widths (FWHM) and phase-difference (Deltaϕ) maps. A new method, dubbed the bandwidth-difference (DeltaBW) method, is proposed along with a prototype phantom for determining MFH. The DeltaBW method is compared with standard methods and has also been tested in different model MRI systems from various manufacturers. Direct comparisons of the data obtained using the DeltaBW method demonstrated good agreement with data obtained using the linewidth method and the frequency map data provided by one MRI system manufacturer. As a result, the DeltaBW method produces measurements of MFH at various Diameter Sphere Volume (DSV) values that can be obtained from a single set of phantom images. The conclusion of the study is that the accuracy of DeltaBW B0 homogeneity measurements of MFH is comparable to the other methods tested while the ease of measurement in practical clinical setting is considerably improved.

  11. Battlefield MRI

    SciTech Connect

    Espy, Michelle

    2015-06-01

    Magnetic Resonance Imaging is the best method for non-invasive imaging of soft tissue anatomy, saving countless lives each year. It is regarded as the gold standard for diagnosis of mild to moderate traumatic brain injuries. Furthermore, conventional MRI relies on very high, fixed strength magnetic fields (> 1.5 T) with parts-per-million homogeneity, which requires very large and expensive magnets.

  12. Balanced Steady State Free Precession for Arterial Spin Labeling MRI: Initial Experience for Blood Flow Mapping in Human Brain, Retina, and Kidney

    PubMed Central

    Park, Sung-Hong; Wang, Danny J.J.; Duong, Timothy Q.

    2013-01-01

    We implemented pseudo-continuous ASL (pCASL) with 2D and 3D balanced steady state free precession (bSSFP) readout for mapping blood flow in the human brain, retina, and kidney, free of distortion and signal dropout, which are typically observed in the most commonly used echo-planar imaging acquisition. High resolution functional brain imaging in the human visual cortex was feasible with 3D bSSFP pCASL. Blood flow of the human retina could be imaged with pCASL and bSSFP in conjunction with a phase cycling approach to suppress the banding artifacts associated with bSSFP. Furthermore, bSSFP based pCASL enabled us to map renal blood flow within a single breath hold. Control and test-retest experiments suggested that the measured blood flow values in retina and kidney were reliable. Because there is no specific imaging tool for mapping human retina blood flow and the standard contrast agent technique for mapping renal blood flow can cause problems for patients with kidney dysfunction, bSSFP based pCASL may provide a useful tool for the diagnosis of retinal and renal diseases and can complement existing imaging techniques. PMID:23664680

  13. Interpolation of vector fields from human cardiac DT-MRI.

    PubMed

    Yang, F; Zhu, Y M; Rapacchi, S; Luo, J H; Robini, M; Croisille, P

    2011-03-01

    There has recently been increased interest in developing tensor data processing methods for the new medical imaging modality referred to as diffusion tensor magnetic resonance imaging (DT-MRI). This paper proposes a method for interpolating the primary vector fields from human cardiac DT-MRI, with the particularity of achieving interpolation and denoising simultaneously. The method consists of localizing the noise-corrupted vectors using the local statistical properties of vector fields, removing the noise-corrupted vectors and reconstructing them by using the thin plate spline (TPS) model, and finally applying global TPS interpolation to increase the resolution in the spatial domain. Experiments on 17 human hearts show that the proposed method allows us to obtain higher resolution while reducing noise, preserving details and improving direction coherence (DC) of vector fields as well as fiber tracking. Moreover, the proposed method perfectly reconstructs azimuth and elevation angle maps. PMID:21317482

  14. Three-dimensional quantitative assessment of ablation margins based on registration of pre- and post-procedural MRI and distance map

    PubMed Central

    Tani, Soichiro; Tatli, Servet; Hata, Nobuhiko; Garcia-Rojas, Xavier; Olubiyi, Olutayo I.; Silverman, Stuart G.; Tokuda, Junichi

    2016-01-01

    Purpose Contrast-enhanced MR images are widely used to confirm the adequacy of ablation margin after liver ablation for early prediction of local recurrence. However, quantitative assessment of the ablation margin by comparing pre- and post-procedural images remains challenging. We developed and tested a novel method for three-dimensional quantitative assessment of ablation margin based on non-rigid image registration and 3D distance map. Methods Our method was tested with pre- and post-procedural MR images acquired in 21 patients who underwent image-guided percutaneous liver ablation. The two images were co-registered using non-rigid intensity-based registration. After the tumor and ablation volumes were segmented, target volume coverage, percent of tumor coverage, and Dice Similarity Coefficient were calculated as metrics representing overall adequacy of ablation. In addition, 3D distance map around the tumor was computed and superimposed on the ablation volume to identify the area with insufficient margins. For patients with local recurrences, the follow-up images were registered to the post-procedural image. Three-D minimum distance between the recurrence and the areas with insufficient margins were quantified. Results The percent tumor coverage for all non-recurrent cases was 100%. Five cases had tumor recurrences, and the 3D distance map revealed insufficient tumor coverage or a 0-millimeter margin. It also showed that two recurrences were remote to the insufficient margin. Conclusions Non-rigid registration and 3D distance map allows us to quantitatively evaluate the adequacy of the ablation margin after percutaneous liver ablation. The method may be useful to predict local recurrences immediately following ablation procedure. PMID:27038962

  15. Functional near-infrared spectroscopy maps cortical plasticity underlying altered motor performance induced by transcranial direct current stimulation

    PubMed Central

    Hodics, Timea; Hervey, Nathan; Kondraske, George; Stowe, Ann M.; Alexandrakis, George

    2013-01-01

    Abstract. Transcranial direct current stimulation (tDCS) of the human sensorimotor cortex during physical rehabilitation induces plasticity in the injured brain that improves motor performance. Bi-hemispheric tDCS is a noninvasive technique that modulates cortical activation by delivering weak current through a pair of anodal–cathodal (excitation–suppression) electrodes, placed on the scalp and centered over the primary motor cortex of each hemisphere. To quantify tDCS-induced plasticity during motor performance, sensorimotor cortical activity was mapped during an event-related, wrist flexion task by functional near-infrared spectroscopy (fNIRS) before, during, and after applying both possible bi-hemispheric tDCS montages in eight healthy adults. Additionally, torque applied to a lever device during isometric wrist flexion and surface electromyography measurements of major muscle group activity in both arms were acquired concurrently with fNIRS. This multiparameter approach found that hemispheric suppression contralateral to wrist flexion changed resting-state connectivity from intra-hemispheric to inter-hemispheric and increased flexion speed (p<0.05). Conversely, exciting this hemisphere increased opposing muscle output resulting in a decrease in speed but an increase in accuracy (p<0.05 for both). The findings of this work suggest that tDCS with fNIRS and concurrent multimotor measurements can provide insights into how neuroplasticity changes muscle output, which could find future use in guiding motor rehabilitation. PMID:24193947

  16. Automatic detection of motion blur in intravital video microscopy image sequences via directional statistics of log-Gabor energy maps.

    PubMed

    Ferrari, Ricardo J; Pinto, Carlos H Villa; da Silva, Bruno C Gregório; Bernardes, Danielle; Carvalho-Tavares, Juliana

    2015-02-01

    Intravital microscopy is an important experimental tool for the study of cellular and molecular mechanisms of the leukocyte-endothelial interactions in the microcirculation of various tissues and in different inflammatory conditions of in vivo specimens. However, due to the limited control over the conditions of the image acquisition, motion blur and artifacts, resulting mainly from the heartbeat and respiratory movements of the in vivo specimen, will very often be present. This problem can significantly undermine the results of either visual or computerized analysis of the acquired video images. Since only a fraction of the total number of images are usually corrupted by severe motion blur, it is necessary to have a procedure to automatically identify such images in the video for either further restoration or removal. This paper proposes a new technique for the detection of motion blur in intravital video microscopy based on directional statistics of local energy maps computed using a bank of 2D log-Gabor filters. Quantitative assessment using both artificially corrupted images and real microscopy data were conducted to test the effectiveness of the proposed method. Results showed an area under the receiver operating characteristic curve (AUC) of 0.95 (AUC = 0.95; 95 % CI 0.93-0.97) when tested on 329 video images visually ranked by four observers.

  17. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

    PubMed Central

    Hahn, Christoph; Bachmann, Lutz; Chevreux, Bastien

    2013-01-01

    We present an in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (NGS) data—mitochondrial baiting and iterative mapping (MITObim). The method is straightforward even if only (i) distantly related mitochondrial genomes or (ii) mitochondrial barcode sequences are available as starting-reference sequences or seeds, respectively. We demonstrate the efficiency of the approach in case studies using real NGS data sets of the two monogenean ectoparasites species Gyrodactylus thymalli and Gyrodactylus derjavinoides including their respective teleost hosts European grayling (Thymallus thymallus) and Rainbow trout (Oncorhynchus mykiss). MITObim appeared superior to existing tools in terms of accuracy, runtime and memory requirements and fully automatically recovered mitochondrial genomes exceeding 99.5% accuracy from total genomic DNA derived NGS data sets in <24 h using a standard desktop computer. The approach overcomes the limitations of traditional strategies for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information at hand and represents a fast and highly efficient in silico alternative to laborious conventional strategies relying on initial long-range PCR. We furthermore demonstrate the applicability of MITObim for metagenomic/pooled data sets using simulated data. MITObim is an easy to use tool even for biologists with modest bioinformatics experience. The software is made available as open source pipeline under the MIT license at https://github.com/chrishah/MITObim. PMID:23661685

  18. Elastic Model Transitions: a Hybrid Approach Utilizing Quadratic Inequality Constrained Least Squares (LSQI) and Direct Shape Mapping (DSM)

    NASA Technical Reports Server (NTRS)

    Jurenko, Robert J.; Bush, T. Jason; Ottander, John A.

    2014-01-01

    A method for transitioning linear time invariant (LTI) models in time varying simulation is proposed that utilizes both quadratically constrained least squares (LSQI) and Direct Shape Mapping (DSM) algorithms to determine physical displacements. This approach is applicable to the simulation of the elastic behavior of launch vehicles and other structures that utilize multiple LTI finite element model (FEM) derived mode sets that are propagated throughout time. The time invariant nature of the elastic data for discrete segments of the launch vehicle trajectory presents a problem of how to properly transition between models while preserving motion across the transition. In addition, energy may vary between flex models when using a truncated mode set. The LSQI-DSM algorithm can accommodate significant changes in energy between FEM models and carries elastic motion across FEM model transitions. Compared with previous approaches, the LSQI-DSM algorithm shows improvements ranging from a significant reduction to a complete removal of transients across FEM model transitions as well as maintaining elastic motion from the prior state.

  19. Novel Imaging of Prostate Cancer with MRI, MRI/US, and PET.

    PubMed

    Koo, Phillip J; Kwak, Jennifer J; Pokharel, Sajal; Choyke, Peter L

    2015-12-01

    Imaging of prostate cancer presents many challenges to the imaging community. There has been much progress in this space in large part due to MRI and PET radiopharmaceuticals. Though MRI has been focused on the evaluation of local disease and PET on the detection of metastatic disease, these two areas do converge and will be complementary especially with the growth of new PET/MRI technologies. In this review article, we review novel MRI, MRI/US, and PET radiopharmaceuticals which will offer insight into the future direction of imaging in prostate cancer.

  20. Novel Imaging of Prostate Cancer with MRI, MRI/US, and PET.

    PubMed

    Koo, Phillip J; Kwak, Jennifer J; Pokharel, Sajal; Choyke, Peter L

    2015-12-01

    Imaging of prostate cancer presents many challenges to the imaging community. There has been much progress in this space in large part due to MRI and PET radiopharmaceuticals. Though MRI has been focused on the evaluation of local disease and PET on the detection of metastatic disease, these two areas do converge and will be complementary especially with the growth of new PET/MRI technologies. In this review article, we review novel MRI, MRI/US, and PET radiopharmaceuticals which will offer insight into the future direction of imaging in prostate cancer. PMID:26462919

  1. Mapping the spatiotemporal dynamics of processing task-relevant and task-irrelevant sound feature changes using concurrent EEG-fMRI.

    PubMed

    Puschmann, Sebastian; Huster, René J; Thiel, Christiane M

    2016-10-01

    The cortical processing of changes in auditory input involves auditory sensory regions as well as different frontoparietal brain networks. The spatiotemporal dynamics of the activation spread across these networks has, however, not been investigated in detail so far. We here approached this issue using concurrent functional magnetic resonance imaging (fMRI) and electroencephalography (EEG), providing us with simultaneous information on both the spatial and temporal patterns of change-related activity. We applied an auditory stimulus categorization task with switching categorization rules, allowing to analyze change-related responses as a function of the changing sound feature (pitch or duration) and the task relevance of the change. Our data show the successive progression of change-related activity from regions involved in early change detection to the ventral and dorsal attention networks, and finally the central executive network. While early change detection was found to recruit feature-specific networks involving auditory sensory but also frontal and parietal brain regions, the later spread of activity across the frontoparietal attention and executive networks was largely independent of the changing sound feature, suggesting the existence of a general feature-independent processing pathway of change-related information. Task relevance did not modulate early auditory sensory processing, but was mainly found to affect processing in frontal brain regions. Hum Brain Mapp 37:3400-3416, 2016. © 2016 Wiley Periodicals, Inc.

  2. Mapping the spatiotemporal dynamics of processing task-relevant and task-irrelevant sound feature changes using concurrent EEG-fMRI.

    PubMed

    Puschmann, Sebastian; Huster, René J; Thiel, Christiane M

    2016-10-01

    The cortical processing of changes in auditory input involves auditory sensory regions as well as different frontoparietal brain networks. The spatiotemporal dynamics of the activation spread across these networks has, however, not been investigated in detail so far. We here approached this issue using concurrent functional magnetic resonance imaging (fMRI) and electroencephalography (EEG), providing us with simultaneous information on both the spatial and temporal patterns of change-related activity. We applied an auditory stimulus categorization task with switching categorization rules, allowing to analyze change-related responses as a function of the changing sound feature (pitch or duration) and the task relevance of the change. Our data show the successive progression of change-related activity from regions involved in early change detection to the ventral and dorsal attention networks, and finally the central executive network. While early change detection was found to recruit feature-specific networks involving auditory sensory but also frontal and parietal brain regions, the later spread of activity across the frontoparietal attention and executive networks was largely independent of the changing sound feature, suggesting the existence of a general feature-independent processing pathway of change-related information. Task relevance did not modulate early auditory sensory processing, but was mainly found to affect processing in frontal brain regions. Hum Brain Mapp 37:3400-3416, 2016. © 2016 Wiley Periodicals, Inc. PMID:27280466

  3. Elastic Model Transitions: A Hybrid Approach Utilizing Quadratic Inequality Constrained Least Squares (LSQI) and Direct Shape Mapping (DSM)

    NASA Technical Reports Server (NTRS)

    Hannan, Mike R.; Jurenko, Robert J.; Bush, Jason; Ottander, John

    2014-01-01

    A method for transitioning linear time invariant (LTI) models in time varying simulation is proposed that utilizes a hybrid approach for determining physical displacements by augmenting the original quadratically constrained least squares (LSQI) algorithm with Direct Shape Mapping (DSM) and modifying the energy constraints. The approach presented is applicable to simulation of the elastic behavior of launch vehicles and other structures that utilize discrete LTI finite element model (FEM) derived mode sets (eigenvalues and eigenvectors) that are propagated throughout time. The time invariant nature of the elastic data presents a problem of how to properly transition elastic states from the prior to the new model while preserving motion across the transition and ensuring there is no truncation or excitation of the system. A previous approach utilizes a LSQI algorithm with an energy constraint to effect smooth transitions between eigenvector sets with no requirement that the models be of similar dimension or have any correlation. This approach assumes energy is conserved across the transition, which results in significant non-physical transients due to changing quasi-steady state energy between mode sets, a phenomenon seen when utilizing a truncated mode set. The computational burden of simulating a full mode set is significant so a subset of modes is often selected to reduce run time. As a result of this truncation, energy between mode sets may not be constant and solutions across transitions could produce non-physical transients. In an effort to abate these transients an improved methodology was developed based on the aforementioned approach, but this new approach can handle significant changes in energy across mode set transitions. It is proposed that physical velocities due to elastic behavior be solved for using the LSQI algorithm, but solve for displacements using a two-step process that independently addresses the quasi-steady-state and non

  4. Pelvis MRI scan

    MedlinePlus

    MRI - pelvis; MRI - hips; Pelvic MRI with prostate probe; Magnetic resonance imaging - pelvis ... care provider if you are afraid of close spaces (have claustrophobia). You may be given a medicine ...

  5. Breast MRI scan

    MedlinePlus

    MRI - breast; Magnetic resonance imaging - breast; Breast cancer - MRI; Breast cancer screening - MRI ... the same breast or the other breast after breast cancer has been diagnosed Distinguish between scar tissue and ...

  6. Evidence for an anterior-posterior differentiation in the human hippocampal formation revealed by meta-analytic parcellation of fMRI coordinate maps: Focus on the subiculum

    PubMed Central

    Chase, Henry W.; Clos, Mareike; Dibble, Sofia; Fox, Peter; Grace, Anthony A.; Phillips, Mary L.; Eickhoff, Simon B.

    2015-01-01

    Previous studies, predominantly in experimental animals, have suggested the presence of a differentiation of function across the hippocampal formation. In rodents, ventral regions are thought to be involved in emotional behavior while dorsal regions mediate cognitive or spatial processes. Using a combination of modeling the co-occurrence of significant activations across thousands of neuroimaging experiments and subsequent data-driven clustering of these data we were able to provide evidence of distinct subregions within a region corresponding to the human subiculum, a critical hub within the hippocampal formation. This connectivity-based model consists of a bilateral anterior region, as well as separate posterior and intermediate regions on each hemisphere. Functional connectivity assessed both by meta-analytic and resting fMRI approaches revealed that more anterior regions were more strongly connected to the default mode network, and more posterior regions were more strongly connected to ‘task positive’ regions. In addition, our analysis revealed that the anterior subregion was functionally connected to the ventral striatum, midbrain and amygdala, a circuit that is central to models of stress and motivated behavior. Analysis of a behavioral taxonomy provided evidence for a role for each subregion in mnemonic processing, as well as implication of the anterior subregion in emotional and visual processing and the right posterior subregion in reward processing. These findings lend support to models which posit anterior-posterior differentiation of function within the human hippocampal formation and complement other early steps toward a comparative (cross-species) model of the region. PMID:25776219

  7. Between-hand difference in ipsilateral deactivation is associated with hand lateralization: fMRI mapping of 284 volunteers balanced for handedness

    PubMed Central

    Tzourio-Mazoyer, N.; Petit, L.; Zago, L.; Crivello, F.; Vinuesa, N.; Joliot, M.; Jobard, G.; Mellet, E.; Mazoyer, B.

    2015-01-01

    In right-handers (RH), an increase in the pace of dominant hand movement results in increased ipsilateral deactivation of the primary motor cortex (M1). By contrast, an increase in non-dominant hand movement frequency is associated with reduced ipsilateral deactivation. This pattern suggests that inhibitory processes support right hand dominance in right-handers and raises the issues of whether this phenomenon also supports left hand preference in left-handers (LH), and/or whether it relates to asymmetry of manual ability in either group. Thanks to the BIL&GIN, a database dedicated to the investigation of hemispheric specialization (HS), we studied the variation in M1 activity during right and left finger tapping tasks (FTT) in a sample of 284 healthy participants balanced for handedness. An M1 fMRI localizer was defined for each participant as an 8 mm diameter sphere centered on the motor activation peak. RH exhibited significantly larger deactivation of the ipsilateral M1 when moving their dominant hand than their non-dominant hand. In contrast, LH exhibited comparable ipsilateral M1 deactivation during either hand movement, reflecting a bilateral cortical specialization. This pattern is likely related to left-handers’ good performances with their right hand and consequent lower asymmetry in manual ability compared with RH. Finally, inter-individual analyses over the whole sample demonstrated that the larger the difference in manual skill across hands, the larger the difference in ipsilateral deactivation. Overall, we propose that difference in ipsilateral deactivation is a marker of difference in manual ability asymmetry reflecting differences in the strength of transcallosal inhibition when a given hand is moving. PMID:25705184

  8. Volume transfer constant (K(trans)) maps from dynamic contrast enhanced MRI as potential guidance for MR-guided high intensity focused ultrasound treatment of hypervascular uterine fibroids.

    PubMed

    Liu, Jing; Keserci, Bilgin; Yang, Xuedong; Wei, Juan; Rong, Rong; Zhu, Ying; Wang, Xiaoying

    2014-11-01

    Higher perfusion of uterine fibroids at baseline is recognized as cause for poor efficacy of MR-guided high intensity focused ultrasound (HIFU) ablation, and higher acoustic power has been suggested for the treatment of high-perfused areas inside uterine fibroids. However, considering the heterogeneously vascular distribution inside the uterine fibroids especially with hyper vascularity, it is not easy to choose the correct therapy acoustic power for every part inside fibroids. In our study, we presented two cases of fibroids with hyper vascularity, to show the differences between them with different outcomes. Selecting higher therapy acoustic powers to ablate high-perfused areas efficiently inside fibroids might help achieving good ablation results. Volume transfer constant (K(trans)) maps from dynamic contrast-enhanced (DCE) imaging at baseline helps visualizing perfusion state inside the fibroids and locating areas with higher-perfusion. In addition, with the help of K(trans) maps, appropriate therapy acoustic power could be selected by the result of initial test and therapy sonications at different areas with significantly different perfusion state inside fibroids.

  9. Impact of the MLC on the MRI field distortion of a prototype MRI-linac

    SciTech Connect

    Kolling, Stefan; Keall, Paul; Oborn, Brad

    2013-12-15

    Purpose: To cope with intrafraction tumor motion, integrated MRI-linac systems for real-time image guidance are currently under development. The multileaf collimator (MLC) is a key component in every state-of-the-art radiotherapy treatment system, allowing for accurate field shaping and tumor tracking. This work quantifies the magnetic impact of a widely used MLC on the MRI field homogeneity for such a modality.Methods: The finite element method was employed to model a MRI-linac assembly comprised of a 1.0 T split-bore MRI magnet and the key ferromagnetic components of a Varian Millennium 120 MLC, namely, the leaves and motors. Full 3D magnetic field maps of the system were generated. From these field maps, the peak-to-peak distortion within the MRI imaging volume was evaluated over a 30 cm diameter sphere volume (DSV) around the isocenter and compared to a maximum preshim inhomogeneity of 300 μT. Five parametric studies were performed: (1) The source-to-isocenter distance (SID) was varied from 100 to 200 cm, to span the range of a compact system to that with lower magnetic coupling. (2) The MLC model was changed from leaves only to leaves with motors, to determine the contribution to the total distortion caused by MLC leaves and motors separately. (3) The system was configured in the inline or perpendicular orientation, i.e., the linac treatment beam was oriented parallel or perpendicular to the magnetic field direction. (4) The treatment field size was varied from 0 × 0 to 20×20 cm{sup 2}, to span the range of clinical treatment fields. (5) The coil currents were scaled linearly to produce magnetic field strengths B{sub 0} of 0.5, 1.0, and 1.5 T, to estimate how the MLC impact changes with B{sub 0}.Results: (1) The MLC-induced MRI field distortion fell continuously with increasing SID. (2) MLC leaves and motors were found to contribute to the distortion in approximately equal measure. (3) Due to faster falloff of the fringe field, the field

  10. Fast computation of voxel-level brain connectivity maps from resting-state functional MRI using l₁-norm as approximation of Pearson's temporal correlation: proof-of-concept and example vector hardware implementation.

    PubMed

    Minati, Ludovico; Zacà, Domenico; D'Incerti, Ludovico; Jovicich, Jorge

    2014-09-01

    An outstanding issue in graph-based analysis of resting-state functional MRI is choice of network nodes. Individual consideration of entire brain voxels may represent a less biased approach than parcellating the cortex according to pre-determined atlases, but entails establishing connectedness for 1(9)-1(11) links, with often prohibitive computational cost. Using a representative Human Connectome Project dataset, we show that, following appropriate time-series normalization, it may be possible to accelerate connectivity determination replacing Pearson correlation with l1-norm. Even though the adjacency matrices derived from correlation coefficients and l1-norms are not identical, their similarity is high. Further, we describe and provide in full an example vector hardware implementation of l1-norm on an array of 4096 zero instruction-set processors. Calculation times <1000 s are attainable, removing the major deterrent to voxel-based resting-sate network mapping and revealing fine-grained node degree heterogeneity. L1-norm should be given consideration as a substitute for correlation in very high-density resting-state functional connectivity analyses. PMID:25023958

  11. A novel local thresholding algorithm for trabecular bone volume fraction mapping in the limited spatial resolution regime of in vivo MRI.

    PubMed

    Vasilic, Branimir; Wehrli, Felix W

    2005-12-01

    Recent advances in micro-magnetic resonance imaging have shown the possibility of in vivo assessment of trabecular bone architecture. However, the small feature size and relatively low signal-to-noise ratio (SNR) achievable in vivo cause the intensity histogram to be unimodal. The critical first step in the processing of these images is the extraction of bone volume fraction for each voxel. Here, we propose a local threshold algorithm (LTA) that determines the marrow intensity value in the neighborhood of each voxel based on nearest-neighbor statistics. Using the local marrow intensities we threshold the image and scale the intensities of voxels partially occupied by bone to produce a marrow volume fraction map of the trabecular bone region. We show that structural parameters derived with the LTA are highly correlated with those obtained with the previously published histogram deconvolution algorithm (HDA) and that the LTA is robust to image noise corruption. The LTA is found to correctly identify trabeculae with a significantly higher reliability than HDA. Finally, we demonstrate that the LTA is superior in preserving connectivity by showing for 75 in vivo images that the genus of the trabecular bone surface is always higher than when processed with the HDA.

  12. Google Maps: You Are Here

    ERIC Educational Resources Information Center

    Jacobsen, Mikael

    2008-01-01

    Librarians use online mapping services such as Google Maps, MapQuest, Yahoo Maps, and others to check traffic conditions, find local businesses, and provide directions. However, few libraries are using one of Google Maps most outstanding applications, My Maps, for the creation of enhanced and interactive multimedia maps. My Maps is a simple and…

  13. A study-specific fMRI normalization approach that operates directly on high resolution functional EPI data at 7 Tesla.

    PubMed

    Grabner, Günther; Poser, Benedikt A; Fujimoto, Kyoko; Polimeni, Jonathan R; Wald, Lawrence L; Trattnig, Siegfried; Toni, Ivan; Barth, Markus

    2014-10-15

    Due to the availability of ultra-high field scanners and novel imaging methods, high resolution, whole brain functional MR imaging (fMRI) has become increasingly feasible. However, it is common to use extensive spatial smoothing to account for inter-subject anatomical variation when pooling over subjects. This reduces the spatial details of group level functional activation considerably, even when the original data was acquired with high resolution. In our study we used an accelerated 3D EPI sequence at 7 Tesla to acquire whole brain fMRI data with an isotropic spatial resolution of 1.1mm which shows clear gray/white matter contrast due to the stronger T1 weighting of 3D EPI. To benefit from the high spatial resolution on the group level, we develop a study specific, high resolution anatomical template which is facilitated by the good anatomical contrast that is present in the average functional EPI images. Different template generations with increasing accuracy were created by using a hierarchical linear and stepwise non-linear registration approach. As the template is based on the functional data themselves no additional co-registration step with the usual T1-weighted anatomical data is necessary which eliminates a potential source of misalignment. To test the improvement of functional localization and spatial details we performed a group level analysis of a finger tapping experiment in eight subjects. The most accurate template shows better spatial localization--such as a separation of somatosensory and motor areas and of single digit activation--compared to the simple linear registration. The number of activated voxels is increased by a factor of 1.2, 2.5, and 3.1 for somatosensory, supplementary motor area, and dentate nucleus, respectively, for the functional contrast between left versus right hand. Similarly, the number of activated voxels is increased 1.4- and 2.4-fold for right little versus right index finger and left little versus left index finger

  14. Estimating Motion From MRI Data

    PubMed Central

    OZTURK, CENGIZHAN; DERBYSHIRE, J. ANDREW; MCVEIGH, ELLIOT R.

    2007-01-01

    Invited Paper Magnetic resonance imaging (MRI) is an ideal imaging modality to measure blood flow and tissue motion. It provides excellent contrast between soft tissues, and images can be acquired at positions and orientations freely defined by the user. From a temporal sequence of MR images, boundaries and edges of tissues can be tracked by image processing techniques. Additionally, MRI permits the source of the image signal to be manipulated. For example, temporary magnetic tags displaying a pattern of variable brightness may be placed in the object using MR saturation techniques, giving the user a known pattern to detect for motion tracking. The MRI signal is a modulated complex quantity, being derived from a rotating magnetic field in the form of an induced current. Well-defined patterns can also be introduced into the phase of the magnetization, and could be thought of as generalized tags. If the phase of each pixel is preserved during image reconstruction, relative phase shifts can be used to directly encode displacement, velocity and acceleration. New methods for modeling motion fields from MRI have now found application in cardiovascular and other soft tissue imaging. In this review, we shall describe the methods used for encoding, imaging, and modeling motion fields with MRI. PMID:18958181

  15. Occupational exposure in MRI

    PubMed Central

    Mcrobbie, D W

    2012-01-01

    This article reviews occupational exposure in clinical MRI; it specifically considers units of exposure, basic physical interactions, health effects, guideline limits, dosimetry, results of exposure surveys, calculation of induced fields and the status of the European Physical Agents Directive. Electromagnetic field exposure in MRI from the static field B0, imaging gradients and radiofrequency transmission fields induces electric fields and currents in tissue, which are responsible for various acute sensory effects. The underlying theory and its application to the formulation of incident and induced field limits are presented. The recent International Commission on Non-Ionizing Radiation Protection (ICNIRP) Bundesministerium für Arbeit und Soziales and Institute of Electrical and Electronics Engineers limits for incident field exposure are interpreted in a manner applicable to MRI. Field measurements show that exposure from movement within the B0 fringe field can exceed ICNIRP reference levels within 0.5 m of the bore entrance. Rate of change of field dB/dt from the imaging gradients is unlikely to exceed the new limits, although incident field limits can be exceeded for radiofrequency (RF) exposure within 0.2–0.5 m of the bore entrance. Dosimetric surveys of routine clinical practice show that staff are exposed to peak values of 42±24% of B0, with time-averaged exposures of 5.2±2.8 mT for magnets in the range 0.6–4 T. Exposure to time-varying fields arising from movement within the B0 fringe resulted in peak dB/dt of approximately 2 T s−1. Modelling of induced electric fields from the imaging gradients shows that ICNIRP-induced field limits are unlikely to be exceeded in most situations; however, movement through the static field may still present a problem. The likely application of the limits is discussed with respect to the reformulation of the European Union (EU) directive and its possible implications for MRI. PMID:22457400

  16. Absolute Temperature Monitoring Using RF Radiometry in the MRI Scanner.

    PubMed

    El-Sharkawy, Abdel-Monem M; Sotiriadis, Paul P; Bottomley, Paul A; Atalar, Ergin

    2006-11-01

    Temperature detection using microwave radiometry has proven value for noninvasively measuring the absolute temperature of tissues inside the body. However, current clinical radiometers operate in the gigahertz range, which limits their depth of penetration. We have designed and built a noninvasive radiometer which operates at radio frequencies (64 MHz) with ∼100-kHz bandwidth, using an external RF loop coil as a thermal detector. The core of the radiometer is an accurate impedance measurement and automatic matching circuit of 0.05 Ω accuracy to compensate for any load variations. The radiometer permits temperature measurements with accuracy of ±0.1°K, over a tested physiological range of 28° C-40° C in saline phantoms whose electric properties match those of tissue. Because 1.5 T magnetic resonance imaging (MRI) scanners also operate at 64 MHz, we demonstrate the feasibility of integrating our radiometer with an MRI scanner to monitor RF power deposition and temperature dosimetry, obtaining coarse, spatially resolved, absolute thermal maps in the physiological range. We conclude that RF radiometry offers promise as a direct, noninvasive method of monitoring tissue heating during MRI studies and thereby providing an independent means of verifying patient-safe operation. Other potential applications include titration of hyper- and hypo-therapies. PMID:18026562

  17. Effect of direct eye contact in PTSD related to interpersonal trauma: an fMRI study of activation of an innate alarm system

    PubMed Central

    Steuwe, Carolin; Daniels, Judith K.; Frewen, Paul A.; Densmore, Maria; Pannasch, Sebastian; Beblo, Thomas; Reiss, Jeffrey; Lanius, Ruth A.

    2014-01-01

    In healthy individuals, direct eye contact initially leads to activation of a fast subcortical pathway, which then modulates a cortical route eliciting social cognitive processes. The aim of this study was to gain insight into the neurobiological effects of direct eye-to-eye contact using a virtual reality paradigm in individuals with posttraumatic stress disorder (PTSD) related to prolonged childhood abuse. We examined 16 healthy comparison subjects and 16 patients with a primary diagnosis of PTSD using a virtual reality functional magnetic resonance imaging paradigm involving direct vs averted gaze (happy, sad, neutral) as developed by Schrammel et al. in 2009. Irrespective of the displayed emotion, controls exhibited an increased blood oxygenation level-dependent response during direct vs averted gaze within the dorsomedial prefrontal cortex, left temporoparietal junction and right temporal pole. Under the same conditions, individuals with PTSD showed increased activation within the superior colliculus (SC)/periaqueductal gray (PAG) and locus coeruleus. Our findings suggest that healthy controls react to the exposure of direct gaze with an activation of a cortical route that enhances evaluative ‘top–down’ processes underlying social interactions. In individuals with PTSD, however, direct gaze leads to sustained activation of a subcortical route of eye-contact processing, an innate alarm system involving the SC and the underlying circuits of the PAG. PMID:22977200

  18. High-resolution direct microstimulation mapping of spinal cord motor pathways during resection of an intramedullary tumor.

    PubMed

    Gandhi, Ravi; Curtis, Corinne M; Cohen-Gadol, Aaron A

    2015-02-01

    Despite the use of advanced microsurgical techniques, resection of intramedullary tumors may result in significant postoperative deficits because of the vicinity or invasion of important functional tracts. Intraoperative monitoring of somatosensory evoked potentials and transcranial electrical motor evoked potentials has been used previously to limit such complications. Electromyography offers an opportunity for the surgeon to map the eloquent tissue associated with the tumor using intraoperative motor fiber stimulation. Similar to the use of cortical simulation in the resection of supratentorial gliomas, this technique can potentially advance the safety of intramedullary spinal cord tumor resection. The authors describe the use of intraoperative motor fiber tract stimulation to map the corticospinal tracts associated with an intramedullary tumor. This technique led to protection of these tracts during resection of the tumor. PMID:25431960

  19. [Incidence and causes of early end in awake surgery for language mapping not directly related to eloquence].

    PubMed

    Villalba, Gloria; Pacreu, Susana; Fernández-Candil, Juan Luis; León, Alba; Serrano, Laura; Conesa, Gerardo

    2016-01-01

    The incidence and causes that may lead to an early end (unfinished cortical/subcortical mapping) of awake surgery for language mapping are little known. A study was conducted on 41 patients with brain glioma located in the language area that had awake surgery under conscious sedation. Surgery was ended early in 6 patients. The causes were: tonic-clonic seizure (1), lack of cooperation due to fatigue/sleep (4), whether or not word articulation was involved, a decreased level of consciousness for ammonia encephalopathy that required endotracheal intubation (1). There are causes that could be expected and in some cases avoided. Tumour size, preoperative aphasia, valproate treatment, and type of anaesthesia used are variables to consider to avoid failure in awake surgery for language mapping. With these results, the following measures are proposed: l) If the tumour is large, perform surgery in two times to avoid fatigue, 2) if patient has a preoperative aphasia, do not use sedation during surgery to ensure that sleepiness does not cause worse word articulation, 3) if the patient is on valproate treatment, it is necessary to rule out the pre-operative symptoms that are not due to ammonia encephalopathy.

  20. [Incidence and causes of early end in awake surgery for language mapping not directly related to eloquence].

    PubMed

    Villalba, Gloria; Pacreu, Susana; Fernández-Candil, Juan Luis; León, Alba; Serrano, Laura; Conesa, Gerardo

    2016-01-01

    The incidence and causes that may lead to an early end (unfinished cortical/subcortical mapping) of awake surgery for language mapping are little known. A study was conducted on 41 patients with brain glioma located in the language area that had awake surgery under conscious sedation. Surgery was ended early in 6 patients. The causes were: tonic-clonic seizure (1), lack of cooperation due to fatigue/sleep (4), whether or not word articulation was involved, a decreased level of consciousness for ammonia encephalopathy that required endotracheal intubation (1). There are causes that could be expected and in some cases avoided. Tumour size, preoperative aphasia, valproate treatment, and type of anaesthesia used are variables to consider to avoid failure in awake surgery for language mapping. With these results, the following measures are proposed: l) If the tumour is large, perform surgery in two times to avoid fatigue, 2) if patient has a preoperative aphasia, do not use sedation during surgery to ensure that sleepiness does not cause worse word articulation, 3) if the patient is on valproate treatment, it is necessary to rule out the pre-operative symptoms that are not due to ammonia encephalopathy. PMID:26260205

  1. A Combined fMRI and DTI Examination of Functional Language Lateralization and Arcuate Fasciculus Structure: Effects of Degree versus Direction of Hand Preference

    ERIC Educational Resources Information Center

    Propper, Ruthe E.; O'Donnell, Lauren J.; Whalen, Stephen; Tie, Yanmei; Norton, Isaiah H.; Suarez, Ralph O.; Zollei, Lilla; Radmanesh, Alireza; Golby, Alexandra J.

    2010-01-01

    The present study examined the relationship between hand preference degree and direction, functional language lateralization in Broca's and Wernicke's areas, and structural measures of the arcuate fasciculus. Results revealed an effect of degree of hand preference on arcuate fasciculus structure, such that consistently-handed individuals,…

  2. Fast fMRI can detect oscillatory neural activity in humans

    PubMed Central

    Lewis, Laura D.; Setsompop, Kawin; Rosen, Bruce R.; Polimeni, Jonathan R.

    2016-01-01

    Oscillatory neural dynamics play an important role in the coordination of large-scale brain networks. High-level cognitive processes depend on dynamics evolving over hundreds of milliseconds, so measuring neural activity in this frequency range is important for cognitive neuroscience. However, current noninvasive neuroimaging methods are not able to precisely localize oscillatory neural activity above 0.2 Hz. Electroencephalography and magnetoencephalography have limited spatial resolution, whereas fMRI has limited temporal resolution because it measures vascular responses rather than directly recording neural activity. We hypothesized that the recent development of fast fMRI techniques, combined with the extra sensitivity afforded by ultra-high-field systems, could enable precise localization of neural oscillations. We tested whether fMRI can detect neural oscillations using human visual cortex as a model system. We detected small oscillatory fMRI signals in response to stimuli oscillating at up to 0.75 Hz within single scan sessions, and these responses were an order of magnitude larger than predicted by canonical linear models. Simultaneous EEG–fMRI and simulations based on a biophysical model of the hemodynamic response to neuronal activity suggested that the blood oxygen level-dependent response becomes faster for rapidly varying stimuli, enabling the detection of higher frequencies than expected. Accounting for phase delays across voxels further improved detection, demonstrating that identifying vascular delays will be of increasing importance with higher-frequency activity. These results challenge the assumption that the hemodynamic response is slow, and demonstrate that fMRI has the potential to map neural oscillations directly throughout the brain. PMID:27729529

  3. 4D flow imaging with MRI

    PubMed Central

    Stankovic, Zoran; Allen, Bradley D.; Garcia, Julio; Jarvis, Kelly B.

    2014-01-01

    Magnetic resonance imaging (MRI) has become an important tool for the clinical evaluation of patients with cardiovascular disease. Since its introduction in the late 1980s, 2-dimensional phase contrast MRI (2D PC-MRI) has become a routine part of standard-of-care cardiac MRI for the assessment of regional blood flow in the heart and great vessels. More recently, time-resolved PC-MRI with velocity encoding along all three flow directions and three-dimensional (3D) anatomic coverage (also termed ‘4D flow MRI’) has been developed and applied for the evaluation of cardiovascular hemodynamics in multiple regions of the human body. 4D flow MRI allows for the comprehensive evaluation of complex blood flow patterns by 3D blood flow visualization and flexible retrospective quantification of flow parameters. Recent technical developments, including the utilization of advanced parallel imaging techniques such as k-t GRAPPA, have resulted in reasonable overall scan times, e.g., 8-12 minutes for 4D flow MRI of the aorta and 10-20 minutes for whole heart coverage. As a result, the application of 4D flow MRI in a clinical setting has become more feasible, as documented by an increased number of recent reports on the utility of the technique for the assessment of cardiac and vascular hemodynamics in patient studies. A number of studies have demonstrated the potential of 4D flow MRI to provide an improved assessment of hemodynamics which might aid in the diagnosis and therapeutic management of cardiovascular diseases. The purpose of this review is to describe the methods used for 4D flow MRI acquisition, post-processing and data analysis. In addition, the article provides an overview of the clinical applications of 4D flow MRI and includes a review of applications in the heart, thoracic aorta and hepatic system. PMID:24834414

  4. Benthic habitat mapping on the Basque continental shelf (SE Bay of Biscay) and its application to the European Marine Strategy Framework Directive

    NASA Astrophysics Data System (ADS)

    Galparsoro, Ibon; Rodríguez, José Germán; Menchaca, Iratxe; Quincoces, Iñaki; Garmendia, Joxe Mikel; Borja, Ángel

    2015-06-01

    Benthic habitats on the Basque continental shelf were mapped based on multibeam echosounder surveys, grab sampling, video surveys and oceanographic monitoring. A total area of 2302 km2 was classified according to the European Nature Information System (EUNIS) hierarchical classification. Almost 50% of the area corresponded to rock and other hard substrata and the other 50% corresponded to soft bottoms. The biotic composition of several areas was significantly different from the EUNIS habitat classes described previously; therefore, we propose a total of 13 new classes. The habitat mapping has contributed to improving the knowledge and application of several criteria and indicators used to assess environmental status in the European Marine Strategy Framework Directive in relation to the biological diversity descriptors, such as non-indigenous species and seafloor integrity. It is also useful for other descriptors and for developing the sampling design.

  5. MRI-conditional pacemakers: current perspectives

    PubMed Central

    Ferreira, António M; Costa, Francisco; Tralhão, António; Marques, Hugo; Cardim, Nuno; Adragão, Pedro

    2014-01-01

    Use of both magnetic resonance imaging (MRI) and pacing devices has undergone remarkable growth in recent years, and it is estimated that the majority of patients with pacemakers will need an MRI during their lifetime. These investigations will generally be denied due to the potentially dangerous interactions between cardiac devices and the magnetic fields and radio frequency energy used in MRI. Despite the increasing reports of uneventful scanning in selected patients with conventional pacemakers under close surveillance, MRI is still contraindicated in those circumstances and cannot be considered a routine procedure. These limitations prompted a series of modifications in generator and lead engineering, designed to minimize interactions that could compromise device function and patient safety. The resulting MRI-conditional pacemakers were first introduced in 2008 and the clinical experience gathered so far supports their safety in the MRI environment if certain conditions are fulfilled. With this technology, new questions and controversies arise regarding patient selection, clinical impact, and cost-effectiveness. In this review, we discuss the potential risks of MRI in patients with electronic cardiac devices and present updated information regarding the features of MRI-conditional pacemakers and the clinical experience with currently available models. Finally, we provide some guidance on how to scan patients who have these devices and discuss future directions in the field. PMID:24851058

  6. Simplified correction of B1 inhomogeneity for chemical exchange saturation transfer (CEST) MRI measurement with surface transceiver coil

    NASA Astrophysics Data System (ADS)

    Sun, Phillip Z.; Zhou, Iris Y.; Igarashi, Takahiro; Guo, Yingkun; Xiao, Gang; Wu, Renhua

    2015-03-01

    Chemical exchange saturation transfer (CEST) MRI is sensitive to dilute exchangeable protons and local properties such as pH and temperate, yet its susceptibility to field inhomogeneity limits its in vivo applications. Particularly, CEST measurement varies with RF irradiation power, the dependence of which is complex due to concomitant direct RF saturation (RF spillover) effect. Because the volume transmitters provide relatively homogeneous RF field, they have been conventionally used for CEST imaging despite of their elevated specific absorption rate (SAR) and relatively low sensitivity than surface coils. To address this limitation, we developed an efficient B1 inhomogeneity correction algorithm that enables CEST MRI using surface transceiver coils. This is built on recent work that showed the inverse CEST asymmetry analysis (CESTRind) is not susceptible to confounding RF spillover effect. We here postulated that the linear relationship between RF power level and CESTRind can be extended for correcting B1 inhomogeneity induced CEST MRI artifacts. Briefly, we prepared a tissue-like Creatine gel pH phantom and collected multiparametric MRI including relaxation, field map and CEST MRI under multiple RF power levels, using a conventional surface transceiver coil. The raw CEST images showed substantial heterogeneity due to B1 inhomogeneity, with pH contrast to noise ratio (CNR) being 8.8. In comparison, pH MRI CNR of the fieldinhomogeneity corrected CEST MRI was found to be 17.2, substantially higher than that without correction. To summarize, our study validated an efficient field inhomogeneity correction that enables sensitive CEST MRI with surface transceiver, promising for in vivo translation.

  7. Getting an MRI

    MedlinePlus

    ... Help White House Lunch Recipes Getting an MRI (Video) KidsHealth > For Kids > Getting an MRI (Video) A A A en español Obtención de una resonancia magnética, RM (video) An MRI (magnetic resonance imaging) scan creates detailed ...

  8. Phage display revisited: Epitope mapping of a monoclonal antibody directed against Neisseria meningitidis adhesin A using the PROFILER technology.

    PubMed

    Cariccio, Veronica Lanza; Domina, Maria; Benfatto, Salvatore; Venza, Mario; Venza, Isabella; Faleri, Agnese; Bruttini, Marco; Bartolini, Erika; Giuliani, Marzia Monica; Santini, Laura; Brunelli, Brunella; Norais, Nathalie; Borgogni, Erica; Midiri, Angelina; Galbo, Roberta; Romeo, Letizia; Biondo, Carmelo; Masignani, Vega; Teti, Giuseppe; Felici, Franco; Beninati, Concetta

    2016-01-01

    There is a strong need for rapid and reliable epitope mapping methods that can keep pace with the isolation of increasingly larger numbers of mAbs. We describe here the identification of a conformational epitope using Phage-based Representation OF ImmunoLigand Epitope Repertoire (PROFILER), a recently developed high-throughput method based on deep sequencing of antigen-specific lambda phage-displayed libraries. A novel bactericidal monoclonal antibody (mAb 9F11) raised against Neisseria meningitidis adhesin A (NadA), an important component of the Bexsero(®) anti-meningococcal vaccine, was used to evaluate the technique in comparison with other epitope mapping methods. The PROFILER technology readily identified NadA fragments that were capable of fully recapitulating the reactivity of the entire antigen against mAb 9F11. Further analysis of these fragments using mutagenesis and hydrogen-deuterium exchange mass-spectrometry allowed us to identify the binding site of mAb 9F11 (A250-D274) and an adjoining sequence (V275-H312) that was also required for the full functional reconstitution of the epitope. These data suggest that, by virtue of its ability to detect a great variety of immunoreactive antigen fragments in phage-displayed libraries, the PROFILER technology can rapidly and reliably identify epitope-containing regions and provide, in addition, useful clues for the functional characterization of conformational mAb epitopes. PMID:26963435

  9. MRI of Heterogeneous Hydrogenation Reactions Using Parahydrogen Polarization

    SciTech Connect

    Burt, Scott Russell

    2008-01-01

    The power of magnetic resonance imaging (MRI) is its ability to image the internal structure of optically opaque samples and provide detailed maps of a variety of important parameters, such as density, diffusion, velocity and temperature. However, one of the fundamental limitations of this technique is its inherent low sensitivity. For example, the low signal to noise ratio (SNR) is particularly problematic for imaging gases in porous materials due to the low density of the gas and the large volume occluded by the porous material. This is unfortunate, as many industrially relevant chemical reactions take place at gas-surface interfaces in porous media, such as packed catalyst beds. Because of this severe SNR problem, many techniques have been developed to directly increase the signal strength. These techniques work by manipulating the nuclear spin populations to produce polarized} (i.e., non-equilibrium) states with resulting signal strengths that are orders of magnitude larger than those available at thermal equilibrium. This dissertation is concerned with an extension of a polarization technique based on the properties of parahydrogen. Specifically, I report on the novel use of heterogeneous catalysis to produce parahydrogen induced polarization and applications of this new technique to gas phase MRI and the characterization of micro-reactors. First, I provide an overview of nuclear magnetic resonance (NMR) and how parahydrogen is used to improve the SNR of the NMR signal. I then present experimental results demonstrating that it is possible to use heterogeneous catalysis to produce parahydrogen-induced polarization. These results are extended to imaging void spaces using a parahydrogen polarized gas. In the second half of this dissertation, I demonstrate the use of parahydrogen-polarized gas-phase MRI for characterizing catalytic microreactors. Specifically, I show how the improved SNR allows one to map parameters important for characterizing the heat and mass

  10. Differences in fMRI intersubject correlation while viewing unedited and edited videos of dance performance.

    PubMed

    Herbec, Aleksandra; Kauppi, Jukka-Pekka; Jola, Corinne; Tohka, Jussi; Pollick, Frank E

    2015-10-01

    Intersubject correlation (ISC) analysis of functional magnetic resonance imaging (fMRI) data provides insight into how continuous streams of sensory stimulation are processed by groups of observers. Although edited movies are frequently used as stimuli in ISC studies, there has been little direct examination of the effect of edits on the resulting ISC maps. In this study we showed 16 observers two audiovisual movie versions of the same dance. In one experimental condition there was a continuous view from a single camera (Unedited condition) and in the other condition there were views from different cameras (Edited condition) that provided close up views of the feet or face and upper body. We computed ISC maps for each condition, as well as created a map that showed the difference between the conditions. The results from the Unedited and Edited maps largely overlapped in the occipital and temporal cortices, although more voxels were found for the Edited map. The difference map revealed greater ISC for the Edited condition in the Postcentral Gyrus, Lingual Gyrus, Precentral Gyrus and Medial Frontal Gyrus, while the Unedited condition showed greater ISC in only the Superior Temporal Gyrus. These findings suggest that the visual changes associated with editing provide a source of correlation in maps obtained from edited film, and highlight the utility of using maps to evaluate the difference in ISC between conditions.

  11. Direct mapping of 19F in 19FDG-6P in brain tissue at subcellular resolution using soft X-ray fluorescence

    NASA Astrophysics Data System (ADS)

    Poitry-Yamate, C.; Gianoncelli, A.; Kourousias, G.; Kaulich, B.; Lepore, M.; Gruetter, R.; Kiskinova, M.

    2013-10-01

    Low energy x-ray fluorescence (LEXRF) detection was optimized for imaging cerebral glucose metabolism by mapping the fluorine LEXRF signal of 19F in 19FDG, trapped as intracellular 19F-deoxyglucose-6-phosphate (19FDG-6P) at 1μm spatial resolution from 3μm thick brain slices. 19FDG metabolism was evaluated in brain structures closely resembling the general cerebral cytoarchitecture following formalin fixation of brain slices and their inclusion in an epon matrix. 2-dimensional distribution maps of 19FDG-6P were placed in a cytoarchitectural and morphological context by simultaneous LEXRF mapping of N and O, and scanning transmission x-ray (STXM) imaging. A disproportionately high uptake and metabolism of glucose was found in neuropil relative to intracellular domains of the cell body of hypothalamic neurons, showing directly that neurons, like glial cells, also metabolize glucose. As 19F-deoxyglucose-6P is structurally identical to 18F-deoxyglucose-6P, LEXRF of subcellular 19F provides a link to in vivo 18FDG PET, forming a novel basis for understanding the physiological mechanisms underlying the 18FDG PET image, and the contribution of neurons and glia to the PET signal.

  12. In-Situ Phase Mapping and Direct Observations of Phase Transformations During Arc Welding of 1045 Steel

    SciTech Connect

    Elmer, J; Palmer, T

    2005-09-13

    In-situ Spatially Resolved X-Ray Diffraction (SRXRD) experiments were performed during gas tungsten arc (GTA) welding of AISI 1045 C-Mn steel. Ferrite ({alpha}) and austenite ({gamma}) phases were identified and quantified in the weld heat-affected zone (HAZ) from the real time x-ray diffraction data. The results were compiled along with weld temperatures calculated using a coupled thermal fluids weld model to create a phase map of the HAZ. This map shows the {alpha} {yields} {gamma} transformation taking place during weld heating and the reverse {gamma} {yields} {alpha} transformation taking place during weld cooling. Superheating is required to complete the {alpha} {yields} {gamma} phase transformation, and the amount of superheat above the A3 temperature was shown to vary with distance from the centerline of the weld. Superheat values as high as 250 C above the A3 temperature were observed at heating rates of 80 C/s. The SRXRD experiments also revealed details about the {gamma} phase not observable by conventional techniques, showing that {gamma} is present with two distinct lattice parameters as a result of inhomogeneous distribution of carbon and manganese in the starting pearlitic/ferritic microstructure. During cooling, the reverse {gamma} {yields} {alpha} phase transformation was shown to depend on the HAZ location. In the fine grained region of the HAZ, at distances greater than 2 mm from the fusion line, the {gamma} {yields} {alpha} transformation begins near the A3 temperature and ends near the A1 temperature. In this region of the HAZ where the cooling rates are below 40 C/s, the transformation occurs by nucleation and growth of pearlite. For HAZ locations closer to the fusion line, undercoolings of 200 C or more below the A1 temperature are required to complete the {gamma} {yields} {alpha} transformation. In this region of the HAZ, grain growth coupled with cooling rates in excess of 50 C/s causes the transformation to occur by a bainitic mechanism.

  13. Identifying Neural Drivers with Functional MRI: An Electrophysiological Validation

    PubMed Central

    David, Olivier; Guillemain, Isabelle; Saillet, Sandrine; Reyt, Sebastien; Deransart, Colin; Segebarth, Christoph; Depaulis, Antoine

    2008-01-01

    Whether functional magnetic resonance imaging (fMRI) allows the identification of neural drivers remains an open question of particular importance to refine physiological and neuropsychological models of the brain, and/or to understand neurophysiopathology. Here, in a rat model of absence epilepsy showing spontaneous spike-and-wave discharges originating from the first somatosensory cortex (S1BF), we performed simultaneous electroencephalographic (EEG) and fMRI measurements, and subsequent intracerebral EEG (iEEG) recordings in regions strongly activated in fMRI (S1BF, thalamus, and striatum). fMRI connectivity was determined from fMRI time series directly and from hidden state variables using a measure of Granger causality and Dynamic Causal Modelling that relates synaptic activity to fMRI. fMRI connectivity was compared to directed functional coupling estimated from iEEG using asymmetry in generalised synchronisation metrics. The neural driver of spike-and-wave discharges was estimated in S1BF from iEEG, and from fMRI only when hemodynamic effects were explicitly removed. Functional connectivity analysis applied directly on fMRI signals failed because hemodynamics varied between regions, rendering temporal precedence irrelevant. This paper provides the first experimental substantiation of the theoretical possibility to improve interregional coupling estimation from hidden neural states of fMRI. As such, it has important implications for future studies on brain connectivity using functional neuroimaging. PMID:19108604

  14. Direct ¹³C-detected NMR experiments for mapping and characterization of hydrogen bonds in RNA.

    PubMed

    Fürtig, Boris; Schnieders, Robbin; Richter, Christian; Zetzsche, Heidi; Keyhani, Sara; Helmling, Christina; Kovacs, Helena; Schwalbe, Harald

    2016-03-01

    In RNA secondary structure determination, it is essential to determine whether a nucleotide is base-paired and not. Base-pairing of nucleotides is mediated by hydrogen bonds. The NMR characterization of hydrogen bonds relies on experiments correlating the NMR resonances of exchangeable protons and can be best performed for structured parts of the RNA, where labile hydrogen atoms are protected from solvent exchange. Functionally important regions in RNA, however, frequently reveal increased dynamic disorder which often leads to NMR signals of exchangeable protons that are broadened beyond (1)H detection. Here, we develop (13)C direct detected experiments to observe all nucleotides in RNA irrespective of whether they are involved in hydrogen bonds or not. Exploiting the self-decoupling of scalar couplings due to the exchange process, the hydrogen bonding behavior of the hydrogen bond donor of each individual nucleotide can be determined. Furthermore, the adaption of HNN-COSY experiments for (13)C direct detection allows correlations of donor-acceptor pairs and the localization of hydrogen-bond acceptor nucleotides. The proposed (13)C direct detected experiments therefore provide information about molecular sites not amenable by conventional proton-detected methods. Such information makes the RNA secondary structure determination by NMR more accurate and helps to validate secondary structure predictions based on bioinformatics.

  15. An MRI-based attenuation correction method for combined PET/MRI applications

    NASA Astrophysics Data System (ADS)

    Fei, Baowei; Yang, Xiaofeng; Wang, Hesheng

    2009-02-01

    We are developing MRI-based attenuation correction methods for PET images. PET has high sensitivity but relatively low resolution and little anatomic details. MRI can provide excellent anatomical structures with high resolution and high soft tissue contrast. MRI can be used to delineate tumor boundaries and to provide an anatomic reference for PET, thereby improving quantitation of PET data. Combined PET/MRI can offer metabolic, functional and anatomic information and thus can provide a powerful tool to study the mechanism of a variety of diseases. Accurate attenuation correction represents an essential component for the reconstruction of artifact-free, quantitative PET images. Unfortunately, the present design of hybrid PET/MRI does not offer measured attenuation correction using a transmission scan. This problem may be solved by deriving attenuation maps from corresponding anatomic MR images. Our approach combines image registration, classification, and attenuation correction in a single scheme. MR images and the preliminary reconstruction of PET data are first registered using our automatic registration method. MRI images are then classified into different tissue types using our multiscale fuzzy C-mean classification method. The voxels of classified tissue types are assigned theoretical tissue-dependent attenuation coefficients to generate attenuation correction factors. Corrected PET emission data are then reconstructed using a threedimensional filtered back projection method and an order subset expectation maximization method. Results from simulated images and phantom data demonstrated that our attenuation correction method can improve PET data quantitation and it can be particularly useful for combined PET/MRI applications.

  16. MRI and MRS of human brain tumors.

    PubMed

    Hou, Bob L; Hu, Jiani

    2009-01-01

    The purpose of this chapter is to provide an introduction to magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) of human brain tumors, including the primary applications and basic terminology involved. Readers who wish to know more about this broad subject should seek out the referenced books (1. Tofts (2003) Quantitative MRI of the brain. Measuring changes caused by disease. Wiley; Bradley and Stark (1999) 2. Magnetic resonance imaging, 3rd Edition. Mosby Inc; Brown and Semelka (2003) 3. MRI basic principles and applications, 3rd Edition. Wiley-Liss) or reviews (4. Top Magn Reson Imaging 17:127-36, 2006; 5. JMRI 24:709-724, 2006; 6. Am J Neuroradiol 27:1404-1411, 2006).MRI is the most popular means of diagnosing human brain tumors. The inherent difference in the magnetic resonance (MR) properties of water between normal tissues and tumors results in contrast differences on the image that provide the basis for distinguishing tumors from normal tissues. In contrast to MRI, which provides spatial maps or images using water signals of the tissues, proton MRS detects signals of tissue metabolites. MRS can complement MRI because the observed MRS peaks can be linked to inherent differences in biochemical profiles between normal tissues and tumors.The goal of MRI and MRS is to characterize brain tumors, including tumor core, edge, edema, volume, types, and grade. The commonly used brain tumor MRI protocol includes T2-weighted images and T1-weighted images taken both before and after the injection of a contrast agent (typically gadolinium: Gd). The commonly used MRS technique is either point-resolved spectroscopy (PRESS) or stimulated echo acquisition mode (STEAM).

  17. Developing high-resolution carbon-13 and silicon-29 MRI of solids in sedimentary rocks

    NASA Astrophysics Data System (ADS)

    Blum, Robert; Barrett, Sean; Viswanathan, Ravinath; Song, Yi-Qiao

    2014-03-01

    Mapping pore structure and flow properties of sedimentary rock is directly relevant to current challenges in geophysics like carbon sequestration and oil/gas exploration. Such applications require detailed information about both structure and composition of porous rocks. However, existing scanning methods tend to be limited to gathering one or the other type of information. MRI could be used to measure both composition and structure simultaneously, but conventional MRI in such systems, which targets the proton signal of interstitial fluid, is severely limited by signal losses due to magnetic susceptibility inhomogeneity. Our lab has recently made advances in obtaining high spatial resolution (sub-400 μm)3 three-dimensional 31P MRI of bone through use of the quadratic echo line-narrowing sequence (1). In this talk, we describe our current work applying these methods to sedimentary rock, targeting the isotopes 13C and 29Si. We describe the results of characterization of limestone and shale samples, and we discuss our progress with producing MRI of these systems. (1) M. Frey, et al. PNAS 109: 5190 (2012)

  18. Fast interactive exploration of 4D MRI flow data

    NASA Astrophysics Data System (ADS)

    Hennemuth, A.; Friman, O.; Schumann, C.; Bock, J.; Drexl, J.; Huellebrand, M.; Markl, M.; Peitgen, H.-O.

    2011-03-01

    1- or 2-directional MRI blood flow mapping sequences are an integral part of standard MR protocols for diagnosis and therapy control in heart diseases. Recent progress in rapid MRI has made it possible to acquire volumetric, 3-directional cine images in reasonable scan time. In addition to flow and velocity measurements relative to arbitrarily oriented image planes, the analysis of 3-dimensional trajectories enables the visualization of flow patterns, local features of flow trajectories or possible paths into specific regions. The anatomical and functional information allows for advanced hemodynamic analysis in different application areas like stroke risk assessment, congenital and acquired heart disease, aneurysms or abdominal collaterals and cranial blood flow. The complexity of the 4D MRI flow datasets and the flow related image analysis tasks makes the development of fast comprehensive data exploration software for advanced flow analysis a challenging task. Most existing tools address only individual aspects of the analysis pipeline such as pre-processing, quantification or visualization, or are difficult to use for clinicians. The goal of the presented work is to provide a software solution that supports the whole image analysis pipeline and enables data exploration with fast intuitive interaction and visualization methods. The implemented methods facilitate the segmentation and inspection of different vascular systems. Arbitrary 2- or 3-dimensional regions for quantitative analysis and particle tracing can be defined interactively. Synchronized views of animated 3D path lines, 2D velocity or flow overlays and flow curves offer a detailed insight into local hemodynamics. The application of the analysis pipeline is shown for 6 cases from clinical practice, illustrating the usefulness for different clinical questions. Initial user tests show that the software is intuitive to learn and even inexperienced users achieve good results within reasonable processing

  19. Characterizing brain anatomical connections using diffusion weighted MRI and graph theory.

    PubMed

    Iturria-Medina, Y; Canales-Rodríguez, E J; Melie-García, L; Valdés-Hernández, P A; Martínez-Montes, E; Alemán-Gómez, Y; Sánchez-Bornot, J M

    2007-07-01

    A new methodology based on Diffusion Weighted Magnetic Resonance Imaging (DW-MRI) and Graph Theory is presented for characterizing the anatomical connections between brain gray matter areas. In a first step, brain voxels are modeled as nodes of a non-directed graph in which the weight of an arc linking two neighbor nodes is assumed to be proportional to the probability of being connected by nervous fibers. This probability is estimated by means of probabilistic tissue segmentation and intravoxel white matter orientational distribution function, obtained from anatomical MRI and DW-MRI, respectively. A new tractography algorithm for finding white matter routes is also introduced. This algorithm solves the most probable path problem between any two nodes, leading to the assessment of probabilistic brain anatomical connection maps. In a second step, for assessing anatomical connectivity between K gray matter structures, the previous graph is redefined as a K+1 partite graph by partitioning the initial nodes set in K non-overlapped gray matter subsets and one subset clustering the remaining nodes. Three different measures are proposed for quantifying anatomical connections between any pair of gray matter subsets: Anatomical Connection Strength (ACS), Anatomical Connection Density (ACD) and Anatomical Connection Probability (ACP). This methodology was applied to both artificial and actual human data. Results show that nervous fiber pathways between some regions of interest were reconstructed correctly. Additionally, mean connectivity maps of ACS, ACD and ACP between 71 gray matter structures for five healthy subjects are presented.

  20. MRI brain imaging.

    PubMed

    Skinner, Sarah

    2013-11-01

    General practitioners (GPs) are expected to be allowed to request MRI scans for adults for selected clinically appropriate indications from November 2013 as part of the expansion of Medicare-funded MRI services announced by the Federal Government in 2011. This article aims to give a brief overview of MRI brain imaging relevant to GPs, which will facilitate explanation of scan findings and management planning with their patients. Basic imaging techniques, common findings and terminology are presented using some illustrative case examples.

  1. Current Role of fMRI in diagnosis of movement disorders

    PubMed Central

    Hallett, Mark

    2016-01-01

    The emergence of functional magnetic resonance techniques for the purpose of brain mapping serves as a valuable tool for understanding both normal physiology and the dysfunction taking place in disorders of the brain. This article provides an overview of fMRI methods and their applications in the study of neurological movement disorders. We then review the current neuroimaging literature regarding Parkinsonisms, Dystonia, Essential Tremor, and Huntington’s disease, including discussion of current methodological limitations and future directions for this exciting field. PMID:19959022

  2. Dynamic contrast-enhanced MRI for prostate cancer localization.

    PubMed

    Jackson, A S N; Reinsberg, S A; Sohaib, S A; Charles-Edwards, E M; Jhavar, S; Christmas, T J; Thompson, A C; Bailey, M J; Corbishley, C M; Fisher, C; Leach, M O; Dearnaley, D P

    2009-02-01

    Radiotherapy dose escalation improves tumour control in prostate cancer but with increased toxicity. Boosting focal tumour only may allow dose escalation with acceptable toxicity. Intensity-modulated radiotherapy can deliver this, but visualization of the tumour remains limiting. CT or conventional MRI techniques are poor at localizing tumour, but dynamic contrast-enhanced MRI (DCE-MRI) may be superior. 18 patients with prostate cancer had T(2) weighted (T2W) and DCE-MRI prior to prostatectomy. The prostate was sectioned meticulously so as to achieve accurate correlation between imaging and pathology. The accuracy of DCE-MRI for cancer detection was calculated by a pixel-by-pixel correlation of quantitative DCE-MRI parameter maps and pathology. In addition, a radiologist interpreted the DCE-MRI and T2W images. The location of tumour on imaging was compared with histology, and the accuracy of DCE-MRI and T2W images was then compared. Pixel-by-pixel comparison of quantitative parameter maps showed a significant difference between the benign peripheral zone and tumour for the parameters K(trans), v(e) and k(ep). Calculation of areas under the receiver operating characteristic curve showed that the pharmacokinetic parameters were only "fair" discriminators between cancer and benign gland. Interpretation of DCE-MRI and T2W images by a radiologist showed DCE-MRI to be more sensitive than T2W images for tumour localization (50% vs 21%; p = 0.006) and similarly specific (85% vs 81%; p = 0.593). The superior sensitivity of DCE-MRI compared with T2W images, together with its high specificity, is arguably sufficient for its use in guiding radiotherapy boosts in prostate cancer.

  3. Development, Calibration and Evaluation of a Portable and Direct Georeferenced Laser Scanning System for Kinematic 3D Mapping

    NASA Astrophysics Data System (ADS)

    Heinz, Erik; Eling, Christian; Wieland, Markus; Klingbeil, Lasse; Kuhlmann, Heiner

    2015-12-01

    In recent years, kinematic laser scanning has become increasingly popular because it offers many benefits compared to static laser scanning. The advantages include both saving of time in the georeferencing and a more favorable scanning geometry. Often mobile laser scanning systems are installed on wheeled platforms, which may not reach all parts of the object. Hence, there is an interest in the development of portable systems, which remain operational even in inaccessible areas. The development of such a portable laser scanning system is presented in this paper. It consists of a lightweight direct georeferencing unit for the position and attitude determination and a small low-cost 2D laser scanner. This setup provides advantages over existing portable systems that employ heavy and expensive 3D laser scanners in a profiling mode. A special emphasis is placed on the system calibration, i. e. the determination of the transformation between the coordinate frames of the direct georeferencing unit and the 2D laser scanner. To this end, a calibration field is used, which consists of differently orientated georeferenced planar surfaces, leading to estimates for the lever arms and boresight angles with an accuracy of mm and one-tenth of a degree. Finally, point clouds of the mobile laser scanning system are compared with georeferenced point clouds of a high-precision 3D laser scanner. Accordingly, the accuracy of the system is in the order of cm to dm. This is in good agreement with the expected accuracy, which has been derived from the error propagation of previously estimated variance components.

  4. Mapping protein conformational heterogeneity under pressure with site-directed spin labeling and double electron-electron resonance.

    PubMed

    Lerch, Michael T; Yang, Zhongyu; Brooks, Evan K; Hubbell, Wayne L

    2014-04-01

    The dominance of a single native state for most proteins under ambient conditions belies the functional importance of higher-energy conformational states (excited states), which often are too sparsely populated to allow spectroscopic investigation. Application of high hydrostatic pressure increases the population of excited states for study, but structural characterization is not trivial because of the multiplicity of states in the ensemble and rapid (microsecond to millisecond) exchange between them. Site-directed spin labeling in combination with double electron-electron resonance (DEER) provides long-range (20-80 Å) distance distributions with angstrom-level resolution and thus is ideally suited to resolve conformational heterogeneity in an excited state populated under high pressure. DEER currently is performed at cryogenic temperatures. Therefore, a method was developed for rapidly freezing spin-labeled proteins under pressure to kinetically trap the high-pressure conformational ensemble for subsequent DEER data collection at atmospheric pressure. The methodology was evaluated using seven doubly-labeled mutants of myoglobin designed to monitor selected interhelical distances. For holomyoglobin, the distance distributions are narrow and relatively insensitive to pressure. In apomyoglobin, on the other hand, the distributions reveal a striking conformational heterogeneity involving specific helices in the pressure range of 0-3 kbar, where a molten globule state is formed. The data directly reveal the amplitude of helical fluctuations, information unique to the DEER method that complements previous rate determinations. Comparison of the distance distributions for pressure- and pH-populated molten globules shows them to be remarkably similar despite a lower helical content in the latter. PMID:24707053

  5. Epitope Mapping of a Monoclonal Antibody Directed against Neisserial Heparin Binding Antigen Using Next Generation Sequencing of Antigen-Specific Libraries.

    PubMed

    Domina, Maria; Lanza Cariccio, Veronica; Benfatto, Salvatore; Venza, Mario; Venza, Isabella; Donnarumma, Danilo; Bartolini, Erika; Borgogni, Erica; Bruttini, Marco; Santini, Laura; Midiri, Angelina; Galbo, Roberta; Romeo, Letizia; Patanè, Francesco; Biondo, Carmelo; Norais, Nathalie; Masignani, Vega; Teti, Giuseppe; Felici, Franco; Beninati, Concetta

    2016-01-01

    We explore here the potential of a newly described technology, which is named PROFILER and is based on next generation sequencing of gene-specific lambda phage-displayed libraries, to rapidly and accurately map monoclonal antibody (mAb) epitopes. For this purpose, we used a novel mAb (designated 31E10/E7) directed against Neisserial Heparin-Binding Antigen (NHBA), a component of the anti-group B meningococcus Bexsero® vaccine. An NHBA phage-displayed library was affinity-selected with mAb 31E10/E7, followed by massive sequencing of the inserts present in antibody-selected phage pools. Insert analysis identified an amino acid stretch (D91-A128) in the N-terminal domain, which was shared by all of the mAb-enriched fragments. Moreover, a recombinant fragment encompassing this sequence could recapitulate the immunoreactivity of the entire NHBA molecule against mAb 31E10/E7. These results were confirmed using a panel of overlapping recombinant fragments derived from the NHBA vaccine variant and a set of chemically synthetized peptides covering the 10 most frequent antigenic variants. Furthermore, hydrogen-deuterium exchange mass-spectrometry analysis of the NHBA-mAb 31E10/E7 complex was also compatible with mapping of the epitope to the D91-A128 region. Collectively, these results indicate that the PROFILER technology can reliably identify epitope-containing antigenic fragments and requires considerably less work, time and reagents than other epitope mapping methods. PMID:27508302

  6. Epitope Mapping of a Monoclonal Antibody Directed against Neisserial Heparin Binding Antigen Using Next Generation Sequencing of Antigen-Specific Libraries

    PubMed Central

    Domina, Maria; Lanza Cariccio, Veronica; Benfatto, Salvatore; Venza, Mario; Venza, Isabella; Donnarumma, Danilo; Bartolini, Erika; Borgogni, Erica; Bruttini, Marco; Santini, Laura; Midiri, Angelina; Galbo, Roberta; Romeo, Letizia; Patanè, Francesco; Biondo, Carmelo; Norais, Nathalie; Masignani, Vega; Teti, Giuseppe; Felici, Franco; Beninati, Concetta

    2016-01-01

    We explore here the potential of a newly described technology, which is named PROFILER and is based on next generation sequencing of gene-specific lambda phage-displayed libraries, to rapidly and accurately map monoclonal antibody (mAb) epitopes. For this purpose, we used a novel mAb (designated 31E10/E7) directed against Neisserial Heparin-Binding Antigen (NHBA), a component of the anti-group B meningococcus Bexsero® vaccine. An NHBA phage-displayed library was affinity-selected with mAb 31E10/E7, followed by massive sequencing of the inserts present in antibody-selected phage pools. Insert analysis identified an amino acid stretch (D91-A128) in the N-terminal domain, which was shared by all of the mAb-enriched fragments. Moreover, a recombinant fragment encompassing this sequence could recapitulate the immunoreactivity of the entire NHBA molecule against mAb 31E10/E7. These results were confirmed using a panel of overlapping recombinant fragments derived from the NHBA vaccine variant and a set of chemically synthetized peptides covering the 10 most frequent antigenic variants. Furthermore, hydrogen-deuterium exchange mass-spectrometry analysis of the NHBA-mAb 31E10/E7 complex was also compatible with mapping of the epitope to the D91-A128 region. Collectively, these results indicate that the PROFILER technology can reliably identify epitope-containing antigenic fragments and requires considerably less work, time and reagents than other epitope mapping methods. PMID:27508302

  7. Correction of MRI-induced geometric distortions in whole-body small animal PET-MRI

    SciTech Connect

    Frohwein, Lynn J. Schäfers, Klaus P.; Hoerr, Verena; Faber, Cornelius

    2015-07-15

    Purpose: The fusion of positron emission tomography (PET) and magnetic resonance imaging (MRI) data can be a challenging task in whole-body PET-MRI. The quality of the registration between these two modalities in large field-of-views (FOV) is often degraded by geometric distortions of the MRI data. The distortions at the edges of large FOVs mainly originate from MRI gradient nonlinearities. This work describes a method to measure and correct for these kind of geometric distortions in small animal MRI scanners to improve the registration accuracy of PET and MRI data. Methods: The authors have developed a geometric phantom which allows the measurement of geometric distortions in all spatial axes via control points. These control points are detected semiautomatically in both PET and MRI data with a subpixel accuracy. The spatial transformation between PET and MRI data is determined with these control points via 3D thin-plate splines (3D TPS). The transformation derived from the 3D TPS is finally applied to real MRI mouse data, which were acquired with the same scan parameters used in the phantom data acquisitions. Additionally, the influence of the phantom material on the homogeneity of the magnetic field is determined via field mapping. Results: The spatial shift according to the magnetic field homogeneity caused by the phantom material was determined to a mean of 0.1 mm. The results of the correction show that distortion with a maximum error of 4 mm could be reduced to less than 1 mm with the proposed correction method. Furthermore, the control point-based registration of PET and MRI data showed improved congruence after correction. Conclusions: The developed phantom has been shown to have no considerable negative effect on the homogeneity of the magnetic field. The proposed method yields an appropriate correction of the measured MRI distortion and is able to improve the PET and MRI registration. Furthermore, the method is applicable to whole-body small animal

  8. Optical display of magnified, real and orthoscopic 3-D object images by moving-direct-pixel-mapping in the scalable integral-imaging system

    NASA Astrophysics Data System (ADS)

    Zhang, Miao; Piao, Yongri; Kim, Eun-Soo

    2011-10-01

    In this paper, we proposed a novel approach for reconstruction of the magnified, real and orthoscopic three-dimensional (3-D) object images by using the moving-direct-pixel-mapping (MDPM) method in the MALT(moving-array-lenslet-technique)-based scalable integral-imaging system. In the proposed system, multiple sets of elemental image arrays (EIAs) are captured with the MALT, and these picked-up EIAs are computationally transformed into the depth-converted ones by using the proposed MDPM method. Then, these depth-converted EIAs are combined and interlaced together to form an enlarged EIA, from which a magnified, real and orthoscopic 3-D object images can be optically displayed without any degradation of resolution. Good experimental results finally confirmed the feasibility of the proposed method.

  9. Resolution-Enhanced Magnification of a Far Three-Dimensional Object Image by Using the Moving-Direct-Pixel-Mapping Method in Scalable Integral-Imaging System

    NASA Astrophysics Data System (ADS)

    Piao, Yongri; Zhang, Miao; Kim, Eun-Soo

    2012-02-01

    In this paper, we propose an effective approach for resolution-enhanced magnification of a far three-dimensional (3D) object image by employing the moving-direct-pixel-mapping (MDPM) method in the scalable integral imaging system. In the proposed method, a set of elemental image arrays (EIAs) are picked up from a far 3D object with the moving-array-lenslet technique (MALT) and computationally transformed into a new set of EIAs by using the MDPM method, which looks like the EIAs virtually picked up from a close object. These newly transformed EIAs then are interlaced together to form an enlarged EIA, from which resolution-enhanced magnification of a far 3D object image can be achieved. Good experimental results confirm the feasibility of the proposed method.

  10. Directional mapping of DNA nicking in ejaculated and cauda epididymidal spermatozoa of the short-beaked echidna (Tachyglossus aculeatus: Monotremata).

    PubMed

    Johnston, S D; López-Fernández, C; Gosálbez, A; Holt, W V; Gosálvez, J

    2009-01-01

    Prototherian spermatozoa are unique amongst the Mammalia in terms of their filiform morphology, tandem arrangement of chromosomes and formation of sperm bundles. In the present study, we provide observations of echidna spermatozoa and note that the superstructure of the bundle is engineered around the shape of the individual sperm head and that this in turn may be a consequence of the unusual circumferential and helicoidal condensation of the DNA during spermiogenesis. Frozen-thawed ejaculated echidna spermatozoa were incubated and examined for the presence of non-typical DNA conformation by means of in situ labelling of DNA breaks using Klenow polymerase and via alkaline single-cell comet assays for detection of fragmented DNA. Both techniques successfully revealed the presence of what appeared to be directional DNA nicking, co-localised with the presence of highly sensitive alkali sites along the length of the sperm nucleus. It was not possible to define whether these alternative DNA configurations were associated with a failure of the sperm nucleus to condense appropriately during spermiogenesis or were evidence of DNA fragmentation following post-thaw incubation or a sequential structural chromatin rearrangement necessary for fertilisation.

  11. Bakuchiol suppresses proliferation of skin cancer cells by directly targeting Hck, Blk, and p38 MAP kinase

    PubMed Central

    Lee, Younghyun; Yang, Hee; Heo, Yong-Seok; Bode, Ann M.; Lee, Ki Won; Dong, Zigang

    2016-01-01

    Bakuchiol is a meroterpene present in the medicinal plant Psoralea corylifolia, which has been traditionally used in China, India, Japan and Korea for the treatment of premature ejaculation, knee pain, alopecia spermatorrhea, enuresis, backache, pollakiuria, vitiligo, callus, and psoriasis. Here, we report the chemopreventive properties of bakuchiol, which acts by inhibiting epidermal growth factor (EGF)-induced neoplastic cell transformation. Bakuchiol also decreased viability and inhibited anchorage-independent growth of A431 human epithelial carcinoma cells. Bakuchiol reduced A431 xenograft tumor growth in an in vivo mouse model. Using kinase profiling, we identified Hck, Blk and p38 mitogen activated protein kinase (MAPK) as targets of bakuchiol, which directly bound to each kinase in an ATP-competitive manner. Bakuchiol also inhibited EGF-induced signaling pathways downstream of Hck, Blk and p38 MAPK, including the MEK/ERKs, p38 MAPK/MSK1 and AKT/p70S6K pathways. This report is the first mechanistic study identifying molecular targets for the anticancer activity of bakuchiol and our findings indicate that bakuchiol exhibits potent anticancer activity by targeting Hck, Blk and p38 MAPK. PMID:26910280

  12. The Ste5 scaffold directs mating signaling by catalytically unlocking the Fus3 MAP kinase for activation.

    PubMed

    Good, Matthew; Tang, Grace; Singleton, Julie; Reményi, Attila; Lim, Wendell A

    2009-03-20

    The scaffold protein Ste5 is required to properly direct signaling through the yeast mating pathway to the mitogen-activated protein kinase (MAPK), Fus3. Scaffolds are thought to function by tethering kinase and substrate in proximity. We find, however, that the previously identified Fus3-binding site on Ste5 is not required for signaling, suggesting an alternative mechanism controls Fus3's activation by the MAPKK Ste7. Reconstituting MAPK signaling in vitro, we find that Fus3 is an intrinsically poor substrate for Ste7, although the related filamentation MAPK, Kss1, is an excellent substrate. We identify and structurally characterize a domain in Ste5 that catalytically unlocks Fus3 for phosphorylation by Ste7. This domain selectively increases the k(cat) of Ste7-->Fus3 phosphorylation but has no effect on Ste7-->Kss1 phosphorylation. The dual requirement for both Ste7 and this Ste5 domain in Fus3 activation explains why Fus3 is selectively activated by the mating pathway and not by other pathways that also utilize Ste7. PMID:19303851

  13. Directional mapping of DNA nicking in ejaculated and cauda epididymidal spermatozoa of the short-beaked echidna (Tachyglossus aculeatus: Monotremata).

    PubMed

    Johnston, S D; López-Fernández, C; Gosálbez, A; Holt, W V; Gosálvez, J

    2009-01-01

    Prototherian spermatozoa are unique amongst the Mammalia in terms of their filiform morphology, tandem arrangement of chromosomes and formation of sperm bundles. In the present study, we provide observations of echidna spermatozoa and note that the superstructure of the bundle is engineered around the shape of the individual sperm head and that this in turn may be a consequence of the unusual circumferential and helicoidal condensation of the DNA during spermiogenesis. Frozen-thawed ejaculated echidna spermatozoa were incubated and examined for the presence of non-typical DNA conformation by means of in situ labelling of DNA breaks using Klenow polymerase and via alkaline single-cell comet assays for detection of fragmented DNA. Both techniques successfully revealed the presence of what appeared to be directional DNA nicking, co-localised with the presence of highly sensitive alkali sites along the length of the sperm nucleus. It was not possible to define whether these alternative DNA configurations were associated with a failure of the sperm nucleus to condense appropriately during spermiogenesis or were evidence of DNA fragmentation following post-thaw incubation or a sequential structural chromatin rearrangement necessary for fertilisation. PMID:19874725

  14. Biparametric versus multiparametric MRI in the diagnosis of prostate cancer

    PubMed Central

    Logager, Vibeke; Baslev, Ingerd; Møller, Jakob M; Hansen, Rasmus Hvass; Thomsen, Henrik S

    2016-01-01

    Background Since multiparametric magnetic resonance imaging (mp-MRI) of the prostate exceeds 30 min, minimizing the evaluation time of significant (Gleason scores > 6) prostate cancer (PCa) would be beneficial. A reduced protocol might be sufficient for the diagnosis. Purpose To study whether a short unenhanced biparametric MRI (bp-MRI) matches mp-MRI in detecting significant PCa. Material and Methods A total of 204 men (median age, 65 years; mean ± SD, 64.1; range 45–75 years; median serum PSA level, 14 ng/mL; range, 2.2–120 ng/mL; median prostate volume, 60 mL; range, 23–263 mL) fulfilled the criteria for being enrolled. They underwent mp-MRI and prostate biopsy from January through June 2014. Of the included patients, 9.3% underwent prostatectomy, 90.7% had TRUS-bx, and 10.8 had MRI-targeted TRUS-bx. Two radiologists separately assessed the mp-MRI examination (T2-weighted [T2W] imaging, diffusion-weighted imaging [DWI], apparent diffusion coefficient map [ADC-map] and dynamic contrast-enhanced imaging [DCE]). Two months later, the bp-MRI version (T2W imaging, DWI, and ADC-map) was evaluated. Results Reader 1: Assessing mp-MRI: 0 false negatives, sensitivity of 1, and specificity 0.04. Assessing bp-MRI: four false negatives, sensitivity of 0.94, and specificity 0.15. Reader 2: Assessing mp-MRI: five false negatives, sensitivity of 0.93, and specificity 0.16. Assessing bp-MRI: three false negatives, sensitivity of 0.96, and specificity 0.15. Intra-reader agreement Cohen’s Kappa (κ) was 0.87 for reader 1 (95% confidence interval [CI], 0.83–0.92) and 0.84 for reader 2 (95% CI 0.78–0.89). Conclusion Bp-MRI is as good as mp-MRI at detecting PCa. A large prospective study seems to be strongly warranted. PMID:27583170

  15. High-resolution mapping of the HyHEL-10 epitope of chicken lysozyme by site-directed mutagenesis

    SciTech Connect

    Kam-Morgan, L.N.; Taylor, M.G.; Kirsch, J.F. ); Smith-Gill, S.J. ); Wilson, A.C.

    1993-05-01

    The complex formed between hen egg white lysozyme (HEL) and the monoclonal antibody HyHEL-10 Fab fragment has an interface composed of van der Waals interactions, hydrogen bonds, and a single ion pair. The antibody overlaps part of the active site cleft. Putative critical residues within the epitope region of HEL, identified from the x-ray crystallographic structure of the complex, were replaced by site-directed mutagenesis to probe their relative importance in determining affinity of the antibody for HEL. Twenty single mutations of HEL at three contact residues (Arg-21[sub HEL], Asp-101[sub HEL], and Gly-102[sub HEL]) and at a partially buried residue (Asn-19[sub HEL]) in the epitope were made, and the effects on the free energies of dissociation were measured. A correlation between increased amino acid side-chain volume and reduced affinity for HELs with mutations at position 101 was observed. The D101G[sub HEL] mutant is bound to HyHEL-10 as tightly as wild-type enzyme, but the [delta][delta]G[sub dissoc] is increased by about 2.2 kcal (9.2 kJ)/mol for the larger residues in this position. HEL variants with lysine or histidine replacements for arginine at position 21 are bound 1.4-2.7 times more tightly than those with neutral or negatively charged amino acids in this position. These exhibit 1/40 the affinity for HyHEL-10 Fab compared with wild type. There is no side-chain volume correlation with [delta][delta]G[sub dissoc] at position 21. Although Gly-102[sub HEL] and Asn-19[sub HEL] are in the epitope, replacements at these positions have no effect on the affinity of HEL for the antibody. 34 refs., 2 figs., 3 tabs.

  16. CEST MRI reporter genes.

    PubMed

    Liu, Guanshu; Bulte, Jeff W M; Gilad, Assaf A

    2011-01-01

    In recent years, several reporter genes have been developed that can serve as a beacon for non-invasive magnetic resonance imaging (MRI). Here, we provide a brief summary of recent advances in MRI reporter gene technology, as well as detailed "hands-on" protocols for cloning, expression, and imaging of reporter genes based on chemical exchange saturation transfer (CEST).

  17. Transition from Collisionless to Collisional MRI

    SciTech Connect

    Prateek Sharma; Gregory W. Hammett; Eliot Quataert

    2003-07-24

    Recent calculations by Quataert et al. (2002) found that the growth rates of the magnetorotational instability (MRI) in a collisionless plasma can differ significantly from those calculated using MHD. This can be important in hot accretion flows around compact objects. In this paper, we study the transition from the collisionless kinetic regime to the collisional MHD regime, mapping out the dependence of the MRI growth rate on collisionality. A kinetic closure scheme for a magnetized plasma is used that includes the effect of collisions via a BGK operator. The transition to MHD occurs as the mean free path becomes short compared to the parallel wavelength 2*/k(sub)||. In the weak magnetic field regime where the Alfven and MRI frequencies w are small compared to the sound wave frequency k(sub)||c(sub)0, the dynamics are still effectively collisionless even if omega << v, so long as the collision frequency v << k(sub)||c(sub)0; for an accretion flow this requires n less than or approximately equal to *(square root of b). The low collisionality regime not only modifies the MRI growth rate, but also introduces collisionless Landau or Barnes damping of long wavelength modes, which may be important for the nonlinear saturation of the MRI.

  18. Current Status of Hybrid PET/MRI in Oncologic Imaging

    PubMed Central

    Rosenkrantz, Andrew B.; Friedman, Kent; Chandarana, Hersh; Melsaether, Amy; Moy, Linda; Ding, Yu-Shin; Jhaveri, Komal; Beltran, Luis; Jain, Rajan

    2016-01-01

    OBJECTIVE This review article explores recent advancements in PET/MRI for clinical oncologic imaging. CONCLUSION Radiologists should understand the technical considerations that have made PET/MRI feasible within clinical workflows, the role of PET tracers for imaging various molecular targets in oncology, and advantages of hybrid PET/MRI compared with PET/CT. To facilitate this understanding, we discuss clinical examples (including gliomas, breast cancer, bone metastases, prostate cancer, bladder cancer, gynecologic malignancy, and lymphoma) as well as future directions, challenges, and areas for continued technical optimization for PET/MRI. PMID:26491894

  19. Advanced flow MRI: emerging techniques and applications.

    PubMed

    Markl, M; Schnell, S; Wu, C; Bollache, E; Jarvis, K; Barker, A J; Robinson, J D; Rigsby, C K

    2016-08-01

    Magnetic resonance imaging (MRI) techniques provide non-invasive and non-ionising methods for the highly accurate anatomical depiction of the heart and vessels throughout the cardiac cycle. In addition, the intrinsic sensitivity of MRI to motion offers the unique ability to acquire spatially registered blood flow simultaneously with the morphological data, within a single measurement. In clinical routine, flow MRI is typically accomplished using methods that resolve two spatial dimensions in individual planes and encode the time-resolved velocity in one principal direction, typically oriented perpendicular to the two-dimensional (2D) section. This review describes recently developed advanced MRI flow techniques, which allow for more comprehensive evaluation of blood flow characteristics, such as real-time flow imaging, 2D multiple-venc phase contrast MRI, four-dimensional (4D) flow MRI, quantification of complex haemodynamic properties, and highly accelerated flow imaging. Emerging techniques and novel applications are explored. In addition, applications of these new techniques for the improved evaluation of cardiovascular (aorta, pulmonary arteries, congenital heart disease, atrial fibrillation, coronary arteries) as well as cerebrovascular disease (intra-cranial arteries and veins) are presented. PMID:26944696

  20. Modeling Neuronal Current MRI Signal with Human Neuron

    PubMed Central

    Luo, Qingfei; Jiang, Xia; Chen, Bin; Zhu, Yi; Gao, Jia-Hong

    2010-01-01

    Up to date, no consensus has been achieved regarding the possibility of detecting neuronal currents by MRI (ncMRI) in human brain. To evaluate the detectability of ncMRI, an effective way is to simulate ncMRI signal with the realistic neuronal geometry and electrophysiological processes. Unfortunately, previous realistic ncMRI models are based on rat and monkey neurons. The species difference in neuronal morphology and physiology would prevent these models from simulating the ncMRI signal accurately in human subjects. The aim of the present study is to bridge this gap by establishing a realistic ncMRI model specifically for human cerebral cortex. In this model, the ncMRI signal was simulated using anatomically reconstructed human pyramidal neurons and their biophysical properties. The modeling results showed that the amplitude of ncMRI signal significantly depends on the density of synchronously firing neurons and imaging conditions such as position of imaging voxel, direction of main magnetic field (B0) relative to the cortical surface and echo time. The results indicated that physiologically-evoked ncMRI signal is too weak to be detected (magnitude/phase change ≤ -1.4×10−6/0.02°), but the phase signal induced by spontaneous activity may reach a detectable level (up to 0.2°) in favorable conditions. PMID:21254209

  1. MRI-Safe Robot for Endorectal Prostate Biopsy

    PubMed Central

    Stoianovici, Dan; Kim, Chunwoo; Srimathveeravalli, Govindarajan; Sebrecht, Peter; Petrisor, Doru; Coleman, Jonathan; Solomon, Stephen B.; Hricak, Hedvig

    2014-01-01

    This paper reports the development of an MRI-Safe robot for direct (interventional) MRI-guided endorectal prostate biopsy. The robot is constructed of nonmagnetic and electrically nonconductive materials, and is electricity free, using pneumatic actuation and optical sensors. Targeting biopsy lesions of MRI abnormality presents substantial clinical potential for the management of prostate cancer. The paper describes MRI-Safe requirements, presents the kinematic architecture, design and construction of the robot, and a comprehensive set of preclinical tests for MRI compatibility and needle targeting accuracy. The robot has a compact and simple 3 degree-of-freedom (DoF) structure, two for orienting a needle-guide and one to preset the depth of needle insertion. The actual insertion is performed manually through the guide and up to the preset depth. To reduce the complexity and size of the robot next to the patient, the depth setting DoF is remote. Experimental results show that the robot is safe to use in any MRI environment (MRI-Safe). Comprehensive MRI tests show that the presence and motion of the robot in the MRI scanner cause virtually no image deterioration or signal to noise ratio (SNR) change. Robot’s accuracy in bench test, CT-guided in-vitro, MRI-guided in-vitro and animal tests are 0.37mm, 1.10mm, 2.09mm, and 2.58mm respectively. These values are acceptable for clinical use. PMID:25378897

  2. Subcortical mapping of calculation processing in the right parietal lobe.

    PubMed

    Della Puppa, Alessandro; De Pellegrin, Serena; Lazzarini, Anna; Gioffrè, Giorgio; Rustemi, Oriela; Cagnin, Annachiara; Scienza, Renato; Semenza, Carlo

    2015-05-01

    Preservation of calculation processing in brain surgery is crucial for patients' quality of life. Over the last decade, surgical electrostimulation was used to identify and preserve the cortical areas involved in such processing. Conversely, subcortical connectivity among different areas implicated in this function remains unclear, and the role of surgery in this domain has not been explored so far. The authors present the first 2 cases in which the subcortical functional sites involved in calculation were identified during right parietal lobe surgery. Two patients affected by a glioma located in the right parietal lobe underwent surgery with the aid of MRI neuronavigation. No calculation deficits were detected during preoperative assessment. Cortical and subcortical mapping were performed using a bipolar stimulator. The current intensity was determined by progressively increasing the amplitude by 0.5-mA increments (from a baseline of 1 mA) until a sensorimotor response was elicited. Then, addition and multiplication calculation tasks were administered. Corticectomy was performed according to both the MRI neuronavigation data and the functional findings obtained through cortical mapping. Direct subcortical electrostimulation was repeatedly performed during tumor resection. Subcortical functional sites for multiplication and addition were detected in both patients. Electrostimulation interfered with calculation processing during cortical mapping as well. Functional sites were spared during tumor removal. The postoperative course was uneventful, and calculation processing was preserved. Postoperative MRI showed complete resection of the tumor. The present preliminary study shows for the first time how functional mapping can be a promising method to intraoperatively identify the subcortical functional sites involved in calculation processing. This report therefore supports direct electrical stimulation as a promising tool to improve the current knowledge on

  3. Anemia rather than hypertension contributes to cerebral hyperperfusion in young adults undergoing hemodialysis: A phase contrast MRI study

    PubMed Central

    Zheng, Gang; Wen, Jiqiu; Yu, Wenkui; Li, Xue; Zhang, Zhe; Chen, Huijuan; Kong, Xiang; Luo, Song; Jiang, Xiaolu; Liu, Ya; Zhang, Zongjun; Zhang, Long Jiang; Lu, Guang Ming

    2016-01-01

    Cerebral hyperperfusion, anemia and hypertension are common in patients with end-stage renal disease (ESRD). Young ESRD adults might afford a better hemodynamic tolerance; however, their cerebral vascular disorders are often overlooked. This phase-contrast MRI study investigated relationships between cerebral blood flow (CBF), anemia and hypertension in young adults undergoing hemodialysis (HD). Blood flows, velocities, and cross-sectional areas of bilateral internal carotid arteries and vertebral arteries were quantified on phase maps in 33 patients and 27 healthy controls. Cerebral oxygen delivery (COD) and vascular resistance were (CVR) were computed based on CBF, hemoglobin and mean arterial pressure (MAP). We found strong correlations among hemoglobin, MAP and CBF. Hemoglobin rather than MAP was directly related to CBF. COD was negatively related to MAP, while CVR was positively related to hemoglobin. The cross-sectional areas of arteries were increased which were directly associated with hemoglobin rather than MAP. HD patients were of elevated CBF, decreased COD and unchanged CVR. Although elevated CBF compensated anemia-induced hypoxia, COD of these patients was still lower. Anemia directly contributed to elevated CBF and hypertension affected CBF through anemia. Unaffected CVR of young patients probably indicated that they could maintain basic functions of cerebral circulation under multiple risk factors. PMID:26923866

  4. Anemia rather than hypertension contributes to cerebral hyperperfusion in young adults undergoing hemodialysis: A phase contrast MRI study.

    PubMed

    Zheng, Gang; Wen, Jiqiu; Yu, Wenkui; Li, Xue; Zhang, Zhe; Chen, Huijuan; Kong, Xiang; Luo, Song; Jiang, Xiaolu; Liu, Ya; Zhang, Zongjun; Zhang, Long Jiang; Lu, Guang Ming

    2016-01-01

    Cerebral hyperperfusion, anemia and hypertension are common in patients with end-stage renal disease (ESRD). Young ESRD adults might afford a better hemodynamic tolerance; however, their cerebral vascular disorders are often overlooked. This phase-contrast MRI study investigated relationships between cerebral blood flow (CBF), anemia and hypertension in young adults undergoing hemodialysis (HD). Blood flows, velocities, and cross-sectional areas of bilateral internal carotid arteries and vertebral arteries were quantified on phase maps in 33 patients and 27 healthy controls. Cerebral oxygen delivery (COD) and vascular resistance were (CVR) were computed based on CBF, hemoglobin and mean arterial pressure (MAP). We found strong correlations among hemoglobin, MAP and CBF. Hemoglobin rather than MAP was directly related to CBF. COD was negatively related to MAP, while CVR was positively related to hemoglobin. The cross-sectional areas of arteries were increased which were directly associated with hemoglobin rather than MAP. HD patients were of elevated CBF, decreased COD and unchanged CVR. Although elevated CBF compensated anemia-induced hypoxia, COD of these patients was still lower. Anemia directly contributed to elevated CBF and hypertension affected CBF through anemia. Unaffected CVR of young patients probably indicated that they could maintain basic functions of cerebral circulation under multiple risk factors. PMID:26923866

  5. 19F MRI for quantitative in vivo cell tracking

    PubMed Central

    Srinivas, Mangala; Heerschap, Arend; Ahrens, Eric T.; Figdor, Carl G.; de Vries, I. Jolanda M.

    2010-01-01

    Cellular therapy, including stem cell transplants and dendritic cell vaccines, is typically monitored for dosage optimization, accurate delivery and localization using non-invasive imaging, of which magnetic resonance imaging (MRI) is a key modality. 19F MRI retains the advantages of MRI as an imaging modality, while allowing direct detection of labelled cells for unambiguous identification and quantification, unlike typical metal-based contrast agents. Recent developments in 19F MRI-based in vivo cell quantification, the existing clinical use of 19F compounds and current explosive interest in cellular therapeutics have brought 19F imaging technology closer to clinical application. We review the application of 19F MRI to cell tracking, discussing intracellular 19F labels, cell labelling and in vivo quantification, as well as the potential clinical use of 19F MRI. PMID:20427096

  6. Towards motion insensitive EEG-fMRI: Correcting motion-induced voltages and gradient artefact instability in EEG using an fMRI prospective motion correction (PMC) system.

    PubMed

    Maziero, Danilo; Velasco, Tonicarlo R; Hunt, Nigel; Payne, Edwin; Lemieux, Louis; Salmon, Carlos E G; Carmichael, David W

    2016-09-01

    The simultaneous acquisition of electroencephalography and functional magnetic resonance imaging (EEG-fMRI) is a multimodal technique extensively applied for mapping the human brain. However, the quality of EEG data obtained within the MRI environment is strongly affected by subject motion due to the induction of voltages in addition to artefacts caused by the scanning gradients and the heartbeat. This has limited its application in populations such as paediatric patients or to study epileptic seizure onset. Recent work has used a Moiré-phase grating and a MR-compatible camera to prospectively update image acquisition and improve fMRI quality (prospective motion correction: PMC). In this study, we use this technology to retrospectively reduce the spurious voltages induced by motion in the EEG data acquired inside the MRI scanner, with and without fMRI acquisitions. This was achieved by modelling induced voltages from the tracking system motion parameters; position and angles, their first derivative (velocities) and the velocity squared. This model was used to remove the voltages related to the detected motion via a linear regression. Since EEG quality during fMRI relies on a temporally stable gradient artefact (GA) template (calculated from averaging EEG epochs matched to scan volume or slice acquisition), this was evaluated in sessions both with and without motion contamination, and with and without PMC. We demonstrate that our approach is capable of significantly reducing motion-related artefact with a magnitude of up to 10mm of translation, 6° of rotation and velocities of 50mm/s, while preserving physiological information. We also demonstrate that the EEG-GA variance is not increased by the gradient direction changes associated with PMC. Provided a scan slice-based GA template is used (rather than a scan volume GA template) we demonstrate that EEG variance during motion can be supressed towards levels found when subjects are still. In summary, we show that

  7. Functional connectomics from resting-state fMRI

    PubMed Central

    Smith, Stephen M; Vidaurre, Diego; Beckmann, Christian F; Glasser, Matthew F; Jenkinson, Mark; Miller, Karla L; Nichols, Thomas E; Robinson, Emma; Salimi-Khorshidi, Gholamreza; Woolrich, Mark W; Barch, Deanna M; Uğurbil, Kamil; Van Essen, David C

    2014-01-01

    Spontaneous fluctuations in activity in different parts of the brain can be used to study functional brain networks. We review the use of resting-state functional MRI for the purpose of mapping the macroscopic functional connectome. After describing MRI acquisition and image processing methods commonly used to generate data in a form amenable to connectomics network analysis, we discuss different approaches for estimating network structure from that data. Finally, we describe new possibilities resulting from the high-quality rfMRI data being generated by the Human Connectome Project, and highlight some upcoming challenges in functional connectomics. PMID:24238796

  8. Shell stability and conditions analyzed using a new method of extracting shell areal density maps from spectrally resolved images of direct-drive inertial confinement fusion implosions

    DOE PAGES

    Johns, H. M.; Mancini, R. C.; Nagayama, T.; Mayes, D. C.; Tommasini, R.; Smalyuk, V. A.; Regan, S. P.; Delettrez, J. A.

    2016-01-25

    In warm target direct-drive ICF implosion experiments performed at the OMEGA laser facility, plastic microballoons doped with a titanium tracer layer in the shell and filled with deuterium gas were imploded using a low-adiabat shaped laser pulse. Continuum radiation emitted in the core is transmitted through the tracer layer and the resulting spectrum recorded with a gated multi-monochromatic x-ray imager (MMI). Titanium K-shell line absorption spectra observed in the data are due to transitions in L-shell titanium ions driven by the backlighting continuum. The MMI data consist of an array of spectrally resolved images of the implosion. These 2-D space-resolvedmore » titanium spectral features constrain the plasma conditions and areal density of the titanium doped region of the shell. The MMI data were processed to obtain narrow-band images and space resolved spectra of titanium spectral features. Shell areal density maps, ρL(x,y), extracted using a new method using both narrow-band images and space resolved spectra are confirmed to be consistent within uncertainties. We report plasma conditions in the titanium-doped region of electron temperature (Te) = 400±28eV, electron number density (Ne) = 8.5x1024±2.5x1024 cm-3, and average areal density <ρR> = 86±7mg/cm2. Fourier analysis of areal density maps reveals shell modulations caused by hydrodynamic instability growth near the fuel-shell interface in the deceleration phase. We observe significant structure in modes l = 2-9, dominated by l = 2. We extract a target breakup fraction of 7.1±1.5% from our Fourier analysis. A new method for estimating mix width is evaluated against existing literature and our target breakup fraction. We estimate a mix width of 10.5±1μm.« less

  9. Mapping the conformational epitope of a neutralizing antibody (AcV1) directed against the AcMNPV GP64 protein

    SciTech Connect

    Zhou Jian; Blissard, Gary W. . E-mail: gwb1@cornell.edu

    2006-09-01

    The envelope glycoprotein GP64 of Autographa californica nucleopolyhedrovirus (AcMNPV) is necessary and sufficient for the acid-induced membrane fusion activity that is required for fusion of the budded virus (BV) envelope and the endosome membrane during virus entry. Infectivity of the budded virus (BV) is neutralized by AcV1, a monoclonal antibody (MAb) directed against GP64. Prior studies indicated that AcV1 recognizes a conformational epitope and does not inhibit virus attachment to the cell, but instead inhibits entry at a step following virus attachment. We found that AcV1 recognition of GP64 was lost upon exposure of GP64 to low pH (pH 4.5) and restored by returning GP64 to pH 6.2. In addition, the AcV1 epitope was lost upon denaturation of GP64 in SDS, but the AcV1 epitope was restored by refolding the protein in the absence of SDS. Using truncated GP64 proteins expressed in insect cells, we mapped the AcV1 epitope to a 24 amino acid region in the central variable domain of GP64. When sequences within the mapped AcV1 epitope were substituted with a c-Myc epitope and the resulting construct was used to replace wt GP64 in recombinant AcMNPV viruses, the modified GP64 protein appeared to function normally. However, an anti-c-Myc monoclonal antibody did not neutralize infectivity of those viruses. Because binding of the c-Myc MAb to the same site in the GP64 sequence did not result in neutralization, these studies suggest that AcV1 neutralization may result from a specific structural constraint caused by AcV1 binding and not simply by steric hindrance caused by antibody binding at this position in GP64.

  10. Shell stability and conditions analyzed using a new method of extracting shell areal density maps from spectrally resolved images of direct-drive inertial confinement fusion implosions

    NASA Astrophysics Data System (ADS)

    Johns, H. M.; Mancini, R. C.; Nagayama, T.; Mayes, D. C.; Tommasini, R.; Smalyuk, V. A.; Regan, S. P.; Delettrez, J. A.

    2016-01-01

    In warm target direct-drive inertial confinement fusion implosion experiments performed at the OMEGA laser facility, plastic micro-balloons doped with a titanium tracer layer in the shell and filled with deuterium gas were imploded using a low-adiabat shaped laser pulse. Continuum radiation emitted in the core is transmitted through the tracer layer and the resulting spectrum recorded with a gated multi-monochromatic x-ray imager (MMI). Titanium K-shell line absorption spectra observed in the data are due to transitions in L-shell titanium ions driven by the backlighting continuum. The MMI data consist of an array of spectrally resolved images of the implosion. These 2-D space-resolved titanium spectral features constrain the plasma conditions and areal density of the titanium doped region of the shell. The MMI data were processed to obtain narrow-band images and space resolved spectra of titanium spectral features. Shell areal density maps, ρL(x,y), extracted using a new method using both narrow-band images and space resolved spectra are confirmed to be consistent within uncertainties. We report plasma conditions in the titanium-doped region of electron temperature (Te) = 400 ± 28 eV, electron number density (Ne) = 8.5 × 1024 ± 2.5 × 1024 cm-3, and average areal density <ρR> = 86 ± 7 mg/cm2. Fourier analysis of areal density maps reveals shell modulations caused by hydrodynamic instability growth near the fuel-shell interface in the deceleration phase. We observe significant structure in modes l = 2-9, dominated by l = 2. We extract a target breakup fraction of 7.1 ± 1.5% from our Fourier analysis. A new method for estimating mix width is evaluated against existing literature and our target breakup fraction. We estimate a mix width of 10.5 ± 1 μm.

  11. MicroRNA-148b enhances proliferation and apoptosis in human renal cancer cells via directly targeting MAP3K9.

    PubMed

    Nie, Fang; Liu, Tianming; Zhong, Liang; Yang, Xianggui; Liu, Yunhong; Xia, Hongwei; Liu, Xiaoqiang; Wang, Xiaoyan; Liu, Zhicheng; Zhou, Li; Mao, Zhaomin; Zhou, Qin; Chen, Tingmei

    2016-01-01

    Increasing evidence revealed that miRNAs, the vital regulators of gene expression, are involved in various cellular processes, including cell growth, differentiation, apoptosis and progression. In addition, miRNAs act as oncogenes and/or tumor suppressors. The present study aimed to verify the potential roles of miR148b in human renal cancer cells. miR‑148b was found to be downregulated in human renal cancel tissues and human renal cancer cell lines. Functional studies demonstrated that plasmid‑mediated overexpression of miR‑148b promoted cell proliferation, increased the S‑phase population of the cell cycle and enhanced apoptosis in the 786‑O and OS‑RC‑2 renal cancer cell lines, while it did not appear to affect the total number of viable cells according to a Cell Counting Kit‑8 assay. Subsequently, a luciferase reporter assay verified that miR148b directly targeted mitogen‑activated protein kinase (MAPK) kinase kinase 9 (MAP3K9), an upstream activator of MAPK kinase/c‑Jun N‑terminal kinase (JNK) signaling, suppressing the protein but not the mRNA levels. Furthermore, western blot analysis indicated that overexpression of miR148b in renal cancer cells inhibited MAPK/JNK signaling by decreasing the expression of phosphorylated (p)JNK. In addition, overexpression of MAP3K9 and pJNK was detected in clinical renal cell carcinoma specimens compared with that in their normal adjacent tissues. The present study therefore suggested that miR‑148b exerts an oncogenic function by enhancing the proliferation and apoptosis of renal cancer cells by inhibiting the MAPK/JNK pathway.

  12. Quantitative Susceptibility Mapping: Contrast Mechanisms and Clinical Applications

    PubMed Central

    Liu, Chunlei; Wei, Hongjiang; Gong, Nan-Jie; Cronin, Matthew; Dibb, Russel; Decker, Kyle

    2016-01-01

    Quantitative susceptibility mapping (QSM) is a recently developed MRI technique for quantifying the spatial distribution of magnetic susceptibility within biological tissues. It first uses the frequency shift in the MRI signal to map the magnetic field profile within the tissue. The resulting field map is then used to determine the spatial distribution of the underlying magnetic susceptibility by solving an inverse problem. The solution is achieved by deconvolving the field map with a dipole field, under the assumption that the magnetic field is a result of the superposition of the dipole fields generated by all voxels and that each voxel has its unique magnetic susceptibility. QSM provides improved contrast to noise ratio for certain tissues and structures compared to its magnitude counterpart. More importantly, magnetic susceptibility is a direct reflection of the molecular composition and cellular architecture of the tissue. Consequently, by quantifying magnetic susceptibility, QSM is becoming a quantitative imaging approach for characterizing normal and pathological tissue properties. This article reviews the mechanism generating susceptibility contrast within tissues and some associated applications. PMID:26844301

  13. Electrical tissue property imaging using MRI at dc and Larmor frequency

    NASA Astrophysics Data System (ADS)

    Seo, Jin Keun; Kim, Dong-Hyun; Lee, Joonsung; In Kwon, Oh; Sajib, Saurav Z. K.; Woo, Eung Je

    2012-08-01

    Cross-sectional imaging of conductivity and permittivity distributions inside the human body has been actively investigated in impedance imaging areas such as electrical impedance tomography (EIT) and magnetic induction tomography (MIT). Since the conductivity and permittivity values exhibit frequency-dependent changes, it is worthwhile to perform spectroscopic imaging from almost dc to hundreds of MHz. To probe the human body, we may inject current using surface electrodes or induce current using external coils. In EIT and MIT, measured data are only available on the boundary or exterior of the body unless we invasively place sensors inside the body. Their image reconstruction problems are nonlinear and ill-posed to result in images with a relatively low spatial resolution. Noting that an MRI scanner can noninvasively measure magnetic fields inside the human body, electrical tissue property imaging methods using MRI have lately been proposed. Magnetic resonance EIT (MREIT) performs conductivity imaging at dc or below 1 kHz by externally injecting current into the human body and measuring induced internal magnetic flux density data using an MRI scanner. Magnetic resonance electrical property tomography (MREPT) produces both conductivity and permittivity images at the Larmor frequency of an MRI scanner based on B1-mapping techniques. Since internal data are only available in MREIT and MREPT, we may formulate well-posed inverse problems for image reconstructions. To develop related imaging techniques, we should clearly understand the basic principles of MREIT and MREPT, which are based on coupled physics of bioelectromagnetism and MRI as well as associated mathematical methods. In this paper, we describe the physical principles of MREIT and MREPT in a unified way and associate measurable quantities with the conductivity and permittivity. Clarifying the key relations among them, we examine existing image reconstruction algorithms to reveal their capabilities and

  14. Atlas-guided generation of pseudo-CT images for MRI-only and hybrid PET–MRI-guided radiotherapy treatment planning

    NASA Astrophysics Data System (ADS)

    Arabi, Hossein; Koutsouvelis, Nikolaos; Rouzaud, Michel; Miralbell, Raymond; Zaidi, Habib

    2016-09-01

    Magnetic resonance imaging (MRI)-guided attenuation correction (AC) of positron emission tomography (PET) data and/or radiation therapy (RT) treatment planning is challenged by the lack of a direct link between MRI voxel intensities and electron density. Therefore, even if this is not a trivial task, a pseudo-computed tomography (CT) image must be predicted from MRI alone. In this work, we propose a two-step (segmentation and fusion) atlas-based algorithm focusing on bone tissue identification to create a pseudo-CT image from conventional MRI sequences and evaluate its performance against the conventional MRI segmentation technique and a recently proposed multi-atlas approach. The clinical studies consisted of pelvic CT, PET and MRI scans of 12 patients with loco-regionally advanced rectal disease. In the first step, bone segmentation of the target image is optimized through local weighted atlas voting. The obtained bone map is then used to assess the quality of deformed atlases to perform voxel-wise weighted atlas fusion. To evaluate the performance of the method, a leave-one-out cross-validation (LOOCV) scheme was devised to find optimal parameters for the model. Geometric evaluation of the produced pseudo-CT images and quantitative analysis of the accuracy of PET AC were performed. Moreover, a dosimetric evaluation of volumetric modulated arc therapy photon treatment plans calculated using the different pseudo-CT images was carried out and compared to those produced using CT images serving as references. The pseudo-CT images produced using the proposed method exhibit bone identification accuracy of 0.89 based on the Dice similarity metric compared to 0.75 achieved by the other atlas-based method. The superior bone extraction resulted in a mean standard uptake value bias of  ‑1.5  ±  5.0% (mean  ±  SD) in bony structures compared to  ‑19.9  ±  11.8% and  ‑8.1  ±  8.2% achieved by MRI segmentation-based (water

  15. Atlas-guided generation of pseudo-CT images for MRI-only and hybrid PET-MRI-guided radiotherapy treatment planning.

    PubMed

    Arabi, Hossein; Koutsouvelis, Nikolaos; Rouzaud, Michel; Miralbell, Raymond; Zaidi, Habib

    2016-09-01

    Magnetic resonance imaging (MRI)-guided attenuation correction (AC) of positron emission tomography (PET) data and/or radiation therapy (RT) treatment planning is challenged by the lack of a direct link between MRI voxel intensities and electron density. Therefore, even if this is not a trivial task, a pseudo-computed tomography (CT) image must be predicted from MRI alone. In this work, we propose a two-step (segmentation and fusion) atlas-based algorithm focusing on bone tissue identification to create a pseudo-CT image from conventional MRI sequences and evaluate its performance against the conventional MRI segmentation technique and a recently proposed multi-atlas approach. The clinical studies consisted of pelvic CT, PET and MRI scans of 12 patients with loco-regionally advanced rectal disease. In the first step, bone segmentation of the target image is optimized through local weighted atlas voting. The obtained bone map is then used to assess the quality of deformed atlases to perform voxel-wise weighted atlas fusion. To evaluate the performance of the method, a leave-one-out cross-validation (LOOCV) scheme was devised to find optimal parameters for the model. Geometric evaluation of the produced pseudo-CT images and quantitative analysis of the accuracy of PET AC were performed. Moreover, a dosimetric evaluation of volumetric modulated arc therapy photon treatment plans calculated using the different pseudo-CT images was carried out and compared to those produced using CT images serving as references. The pseudo-CT images produced using the proposed method exhibit bone identification accuracy of 0.89 based on the Dice similarity metric compared to 0.75 achieved by the other atlas-based method. The superior bone extraction resulted in a mean standard uptake value bias of  -1.5  ±  5.0% (mean  ±  SD) in bony structures compared to  -19.9  ±  11.8% and  -8.1  ±  8.2% achieved by MRI segmentation-based (water

  16. Atlas-guided generation of pseudo-CT images for MRI-only and hybrid PET-MRI-guided radiotherapy treatment planning

    NASA Astrophysics Data System (ADS)

    Arabi, Hossein; Koutsouvelis, Nikolaos; Rouzaud, Michel; Miralbell, Raymond; Zaidi, Habib

    2016-09-01

    Magnetic resonance imaging (MRI)-guided attenuation correction (AC) of positron emission tomography (PET) data and/or radiation therapy (RT) treatment planning is challenged by the lack of a direct link between MRI voxel intensities and electron density. Therefore, even if this is not a trivial task, a pseudo-computed tomography (CT) image must be predicted from MRI alone. In this work, we propose a two-step (segmentation and fusion) atlas-based algorithm focusing on bone tissue identification to create a pseudo-CT image from conventional MRI sequences and evaluate its performance against the conventional MRI segmentation technique and a recently proposed multi-atlas approach. The clinical studies consisted of pelvic CT, PET and MRI scans of 12 patients with loco-regionally advanced rectal disease. In the first step, bone segmentation of the target image is optimized through local weighted atlas voting. The obtained bone map is then used to assess the quality of deformed atlases to perform voxel-wise weighted atlas fusion. To evaluate the performance of the method, a leave-one-out cross-validation (LOOCV) scheme was devised to find optimal parameters for the model. Geometric evaluation of the produced pseudo-CT images and quantitative analysis of the accuracy of PET AC were performed. Moreover, a dosimetric evaluation of volumetric modulated arc therapy photon treatment plans calculated using the different pseudo-CT images was carried out and compared to those produced using CT images serving as references. The pseudo-CT images produced using the proposed method exhibit bone identification accuracy of 0.89 based on the Dice similarity metric compared to 0.75 achieved by the other atlas-based method. The superior bone extraction resulted in a mean standard uptake value bias of  -1.5  ±  5.0% (mean  ±  SD) in bony structures compared to  -19.9  ±  11.8% and  -8.1  ±  8.2% achieved by MRI segmentation-based (water

  17. Atlas-guided generation of pseudo-CT images for MRI-only and hybrid PET-MRI-guided radiotherapy treatment planning.

    PubMed

    Arabi, Hossein; Koutsouvelis, Nikolaos; Rouzaud, Michel; Miralbell, Raymond; Zaidi, Habib

    2016-09-01

    Magnetic resonance imaging (MRI)-guided attenuation correction (AC) of positron emission tomography (PET) data and/or radiation therapy (RT) treatment planning is challenged by the lack of a direct link between MRI voxel intensities and electron density. Therefore, even if this is not a trivial task, a pseudo-computed tomography (CT) image must be predicted from MRI alone. In this work, we propose a two-step (segmentation and fusion) atlas-based algorithm focusing on bone tissue identification to create a pseudo-CT image from conventional MRI sequences and evaluate its performance against the conventional MRI segmentation technique and a recently proposed multi-atlas approach. The clinical studies consisted of pelvic CT, PET and MRI scans of 12 patients with loco-regionally advanced rectal disease. In the first step, bone segmentation of the target image is optimized through local weighted atlas voting. The obtained bone map is then used to assess the quality of deformed atlases to perform voxel-wise weighted atlas fusion. To evaluate the performance of the method, a leave-one-out cross-validation (LOOCV) scheme was devised to find optimal parameters for the model. Geometric evaluation of the produced pseudo-CT images and quantitative analysis of the accuracy of PET AC were performed. Moreover, a dosimetric evaluation of volumetric modulated arc therapy photon treatment plans calculated using the different pseudo-CT images was carried out and compared to those produced using CT images serving as references. The pseudo-CT images produced using the proposed method exhibit bone identification accuracy of 0.89 based on the Dice similarity metric compared to 0.75 achieved by the other atlas-based method. The superior bone extraction resulted in a mean standard uptake value bias of  -1.5  ±  5.0% (mean  ±  SD) in bony structures compared to  -19.9  ±  11.8% and  -8.1  ±  8.2% achieved by MRI segmentation-based (water

  18. Myelin and iron concentration in the human brain: a quantitative study of MRI contrast.

    PubMed

    Stüber, Carsten; Morawski, Markus; Schäfer, Andreas; Labadie, Christian; Wähnert, Miriam; Leuze, Christoph; Streicher, Markus; Barapatre, Nirav; Reimann, Katja; Geyer, Stefan; Spemann, Daniel; Turner, Robert

    2014-06-01

    During the last five years ultra-high-field magnetic resonance imaging (MRI) has enabled an unprecedented view of living human brain. Brain tissue contrast in most MRI sequences is known to reflect mainly the spatial distributions of myelin and iron. These distributions have been shown to overlap significantly in many brain regions, especially in the cortex. It is of increasing interest to distinguish and identify cortical areas by their appearance in MRI, which has been shown to be feasible in vivo. Parcellation can benefit greatly from quantification of the independent contributions of iron and myelin to MRI contrast. Recent studies using susceptibility mapping claim to allow such a separation of the effects of myelin and iron in MRI. We show, using post-mortem human brain tissue, that this goal can be achieved. After MRI scanning of the block with appropriate T1 mapping and T2* weighted sequences, we section the block and apply a novel technique, proton induced X-ray emission (PIXE), to spatially map iron, phosphorus and sulfur elemental concentrations, simultaneously with 1μm spatial resolution. Because most brain phosphorus is located in myelin phospholipids, a calibration step utilizing element maps of sulfur enables semi-quantitative ex vivo mapping of myelin concentration. Combining results for iron and myelin concentration in a linear model, we have accurately modeled MRI tissue contrasts. Conversely, iron and myelin concentrations can now be estimated from appropriate MRI measurements in post-mortem brain samples. PMID:24607447

  19. Accuracy of MRI-based Magnetic Susceptibility Measurements

    NASA Astrophysics Data System (ADS)

    Russek, Stephen; Erdevig, Hannah; Keenan, Kathryn; Stupic, Karl

    Magnetic Resonance Imaging (MRI) is increasingly used to map tissue susceptibility to identify microbleeds associated with brain injury and pathologic iron deposits associated with neurologic diseases such as Parkinson's and Alzheimer's disease. Field distortions with a resolution of a few parts per billion can be measured using MRI phase maps. The field distortion map can be inverted to obtain a quantitative susceptibility map. To determine the accuracy of MRI-based susceptibility measurements, a set of phantoms with paramagnetic salts and nano-iron gels were fabricated. The shapes and orientations of features were varied. Measured susceptibility of 1.0 mM GdCl3 solution in water as a function of temperature agreed well with the theoretical predictions, assuming Gd+3 is spin 7/2. The MRI susceptibility measurements were compared with SQUID magnetometry. The paramagnetic susceptibility sits on top of the much larger diamagnetic susceptibility of water (-9.04 x 10-6), which leads to errors in the SQUID measurements. To extract out the paramagnetic contribution using standard magnetometry, measurements must be made down to low temperature (2K). MRI-based susceptometry is shown to be as or more accurate than standard magnetometry and susceptometry techniques.

  20. MRI Zooms in on Microscopic Flow

    SciTech Connect

    2010-01-01

    MRI images of water flow through a constricted microfluidic channel with the XZ axis on the left and the YZ axis on the right. Note that fast moving components directly aligned with the constricted region emerge at the detector first, followed by components that are not aligned with the constriction.

  1. MRI Scanners Guide Therapy to Tumors.

    PubMed

    2015-11-01

    A new study shows that MRI scanners can direct magnetically labeled macrophages bearing an oncolytic virus toward primary and metastatic tumors in mice. Researchers hope this approach, called magnetic resonance targeting, can be scaled for use in humans, to improve the delivery of cell-based cancer therapy. PMID:26370155

  2. Pharmacological MRI (phMRI) of the Human Central Nervous System.

    PubMed

    Lanfermann, H; Schindler, C; Jordan, J; Krug, N; Raab, P

    2015-10-01

    Pharmacological magnetic resonance imaging (phMRI) of the central nervous system (CNS) addresses the increasing demands in the biopharma industry for new methods that can accurately predict, as early as possible, whether novel CNS agents will be effective and safe. Imaging of physiological and molecular-level function can provide a more direct measure of a drug mechanism of action, enabling more predictive measures of drug activity. The availability of phMRI of the nervous system within the professional infrastructure of the Clinical Research Center (CRC) Hannover as proof of concept center ensures that advances in basic science progress swiftly into benefits for patients. Advanced standardized MRI techniques including quantitative MRI, kurtosis determination, functional MRI, and spectroscopic imaging of the entire brain are necessary for phMRI. As a result, MR scanners will evolve into high-precision measuring instruments for assessment of desirable and undesirable effects of drugs as the basic precondition for individually tailored therapy. The CRC's Imaging Unit with high-end large-scale equipment will allow the following unique opportunities: for example, identification of MR-based biomarkers to assess the effect of drugs (surrogate parameters), establishment of normal levels and reference ranges for MRI-based biomarkers, evaluation of the most relevant MRI sequences for drug monitoring in outpatient care. Another very important prerequisite for phMRI is the MHH Core Facility as the scientific and operational study unit of the CRC partner Hannover Medical School. This unit is responsible for the study coordination, conduction, complete study logistics, administration, and application of the quality assurance system based on required industry standards.

  3. Leg MRI scan

    MedlinePlus

    ... resonance imaging) scan of the leg uses strong magnets to create pictures of the leg. This may ... in your eyes) Because the MRI contains strong magnets, metal objects are not allowed into the room ...

  4. Shoulder MRI scan

    MedlinePlus

    ... an imaging test that uses energy from powerful magnets and to create pictures of the shoulder area. ... in your eyes) Because the MRI contains strong magnets, metal objects are not allowed in the room ...

  5. MRI (Magnetic Resonance Imaging)

    MedlinePlus

    ... some MRI exams, intravenous (IV) drugs, such as gadolinium-based contrast agents (GBCAs) are used to change the contrast of the MR image. Gadolinium-based contrast agents are rare earth metals that ...

  6. MRI of the Breast

    MedlinePlus

    ... as a supplemental tool to breast screening with mammography or ultrasound. It may be used to screen ... following diagnosis, or further evaluate abnormalities seen on mammography. Breast MRI does not use ionizing radiation, and ...

  7. Abdominal MRI scan

    MedlinePlus

    Nuclear magnetic resonance - abdomen; NMR - abdomen; Magnetic resonance imaging - abdomen; MRI of the abdomen ... used to look at: Blood flow in the abdomen Blood vessels in the abdomen The cause of ...

  8. MRI of the Chest

    MedlinePlus

    ... magnetic field of the MRI unit, metal and electronic items are not allowed in the exam room. ... tell the technologist if you have medical or electronic devices in your body. These objects may interfere ...

  9. Lumbar MRI scan

    MedlinePlus

    ... may need a lumbar MRI if you have: Low back pain that does not get better after treatment Leg ... spine Injury or trauma to the lower spine Low back pain and a history or signs of cancer Multiple ...

  10. Knee MRI scan

    MedlinePlus

    ... have been no reported side effects from the magnetic fields and radio waves. The most common type of ... health care provider before the test. The strong magnetic fields created during an MRI can cause heart pacemakers ...

  11. Cervical MRI scan

    MedlinePlus

    ... have been no reported side effects from the magnetic fields and radio waves. The most common type of ... tell your provider before the test. The strong magnetic fields created during an MRI can cause heart pacemakers ...

  12. Arm MRI scan

    MedlinePlus

    ... have been no reported side effects from the magnetic fields and radio waves. The most common type of ... tell your provider before the test The strong magnetic fields created during an MRI can cause heart pacemakers ...

  13. Multimodal description of whole brain connectivity: A comparison of resting state MEG, fMRI, and DWI.

    PubMed

    Garcés, Pilar; Pereda, Ernesto; Hernández-Tamames, Juan A; Del-Pozo, Francisco; Maestú, Fernando; Pineda-Pardo, José Ángel

    2016-01-01

    Structural and functional connectivity (SC and FC) have received much attention over the last decade, as they offer unique insight into the coordination of brain functioning. They are often assessed independently with three imaging modalities: SC using diffusion-weighted imaging (DWI), FC using functional magnetic resonance imaging (fMRI), and magnetoencephalography/electroencephalography (MEG/EEG). DWI provides information about white matter organization, allowing the reconstruction of fiber bundles. fMRI uses blood-oxygenation level-dependent (BOLD) contrast to indirectly map neuronal activation. MEG and EEG are direct measures of neuronal activity, as they are sensitive to the synchronous inputs in pyramidal neurons. Seminal studies have targeted either the electrophysiological substrate of BOLD or the anatomical basis of FC. However, multimodal comparisons have been scarcely performed, and the relation between SC, fMRI-FC, and MEG-FC is still unclear. Here we present a systematic comparison of SC, resting state fMRI-FC, and MEG-FC between cortical regions, by evaluating their similarities at three different scales: global network, node, and hub distribution. We obtained strong similarities between the three modalities, especially for the following pairwise combinations: SC and fMRI-FC; SC and MEG-FC at theta, alpha, beta and gamma bands; and fMRI-FC and MEG-FC in alpha and beta. Furthermore, highest node similarity was found for regions of the default mode network and primary motor cortex, which also presented the highest hubness score. Distance was partially responsible for these similarities since it biased all three connectivity estimates, but not the unique contributor, since similarities remained after controlling for distance.

  14. Liver response to hemorrhagic shock and subsequent resuscitation: MRI analysis.

    PubMed

    Matot, Idit; Cohen, Keren; Pappo, Orit; Barash, Hila; Abramovitch, Rinat

    2008-01-01

    The liver is a target for injury in low flow states. Markers of liver injury are either invasive or not rapidly responding. Magnetic resonance imaging (MRI) may offer a noninvasive alternative to evaluate liver injury due to reduced perfusion. Recently, we reported an MRI method (functional MRI [fMRI]) that enables us to follow liver perfusion by changing the enrichment of inspired gas (air, air-5% carbon dioxide, 95% oxygen-5% carbon dioxide). Rats were subjected to hemorrhagic shock (HS) (bleeding to a MAP of 25 mmHg) and randomized to no resuscitation or resuscitation with Ringer lactate (RL) or adrenaline infusion targeted to a MAP of 50 mmHg or baseline. Significantly decreased fMRI responses to hyperoxia and hypercapnia were observed immediately after HS. Liver enzymes levels, liver histology, and apoptosis assessments were normal immediately after hemorrhage, however, showed significant changes after 6 h. Functional MRI revealed that adrenaline, but not RL infusion, significantly (P < 0.01) improved liver perfusion. Similarly, liver injury, as assessed by liver enzyme levels, liver histology, and apoptosis, was attenuated to a greater extent with adrenaline resuscitation. No significant differences in liver perfusion and injury were noted between resuscitation to low (50 mmHg) versus high (baseline) MAP. This study shows that fMRI enables early assessment of changes in liver perfusion, resulting in liver injury or recovery, and therefore, it may be considered as a noninvasive, rapidly responding tool for following liver outcome subsequent to hemorrhage and resuscitation. Using fMRI, we showed that adrenaline may be preferable to RL as an initial measure to attenuate liver injury after HS.

  15. Optogenetic Functional MRI

    PubMed Central

    Lin, Peter; Fang, Zhongnan; Liu, Jia; Lee, Jin Hyung

    2016-01-01

    The investigation of the functional connectivity of precise neural circuits across the entire intact brain can be achieved through optogenetic functional magnetic resonance imaging (ofMRI), which is a novel technique that combines the relatively high spatial resolution of high-field fMRI with the precision of optogenetic stimulation. Fiber optics that enable delivery of specific wavelengths of light deep into the brain in vivo are implanted into regions of interest in order to specifically stimulate targeted cell types that have been genetically induced to express light-sensitive trans-membrane conductance channels, called opsins. fMRI is used to provide a non-invasive method of determining the brain's global dynamic response to optogenetic stimulation of specific neural circuits through measurement of the blood-oxygen-level-dependent (BOLD) signal, which provides an indirect measurement of neuronal activity. This protocol describes the construction of fiber optic implants, the implantation surgeries, the imaging with photostimulation and the data analysis required to successfully perform ofMRI. In summary, the precise stimulation and whole-brain monitoring ability of ofMRI are crucial factors in making ofMRI a powerful tool for the study of the connectomics of the brain in both healthy and diseased states. PMID:27167840

  16. Sodium and T1rho MRI for molecular and diagnostic imaging of articular cartilage.

    PubMed

    Borthakur, Arijitt; Mellon, Eric; Niyogi, Sampreet; Witschey, Walter; Kneeland, J Bruce; Reddy, Ravinder

    2006-11-01

    In this article, both sodium magnetic resonance (MR) and T1rho relaxation mapping aimed at measuring molecular changes in cartilage for the diagnostic imaging of osteoarthritis are reviewed. First, an introduction to structure of cartilage, its degeneration in osteoarthritis (OA) and an outline of diagnostic imaging methods in quantifying molecular changes and early diagnostic aspects of cartilage degeneration are described. The sodium MRI section begins with a brief overview of the theory of sodium NMR of biological tissues and is followed by a section on multiple quantum filters that can be used to quantify both bi-exponential relaxation and residual quadrupolar interaction. Specifically, (i) the rationale behind the use of sodium MRI in quantifying proteoglycan (PG) changes, (ii) validation studies using biochemical assays, (iii) studies on human OA specimens, (iv) results on animal models and (v) clinical imaging protocols are reviewed. Results demonstrating the feasibility of quantifying PG in OA patients and comparison with that in healthy subjects are also presented. The section concludes with the discussion of advantages and potential issues with sodium MRI and the impact of new technological advancements (e.g. ultra-high field scanners and parallel imaging methods). In the theory section on T1rho, a brief description of (i) principles of measuring T1rho relaxation, (ii) pulse sequences for computing T1rho relaxation maps, (iii) issues regarding radio frequency power deposition, (iv) mechanisms that contribute to T1rho in biological tissues and (v) effects of exchange and dipolar interaction on T1rho dispersion are discussed. Correlation of T1rho relaxation rate with macromolecular content and biomechanical properties in cartilage specimens subjected to trypsin and cytokine-induced glycosaminoglycan depletion and validation against biochemical assay and histopathology are presented. Experimental T1rho data from osteoarthritic specimens, animal models

  17. "MRI Stealth" robot for prostate interventions.

    PubMed

    Stoianovici, Dan; Song, Danny; Petrisor, Doru; Ursu, Daniel; Mazilu, Dumitru; Muntener, Michael; Mutener, Michael; Schar, Michael; Patriciu, Alexandru

    2007-01-01

    The paper reports an important achievement in MRI instrumentation, a pneumatic, fully actuated robot located within the scanner alongside the patient and operating under remote control based on the images. Previous MRI robots commonly used piezoelectric actuation limiting their compatibility. Pneumatics is an ideal choice for MRI compatibility because it is decoupled from electromagnetism, but pneumatic actuators were hardly controllable. This achievement was possible due to a recent technology breakthrough, the invention of a new type of pneumatic motor, PneuStep 1, designed for the robot reported here with uncompromised MRI compatibility, high-precision, and medical safety. MrBot is one of the "MRI stealth" robots today (the second is described in this issue by Zangos et al.). Both of these systems are also multi-imager compatible, being able to operate with the imager of choice or cross-imaging modalities. For MRI compatibility the robot is exclusively constructed of nonmagnetic and dielectric materials such as plastics, ceramics, crystals, rubbers and is electricity free. Light-based encoding is used for feedback, so that all electric components are distally located outside the imager's room. MRI robots are modern, digital medical instruments in line with advanced imaging equipment and methods. These allow for accessing patients within closed bore scanners and performing interventions under direct (in scanner) imaging feedback. MRI robots could allow e.g. to biopsy small lesions imaged with cutting edge cancer imaging methods, or precisely deploy localized therapy at cancer foci. Our robot is the first to show the feasibility of fully automated in-scanner interventions. It is customized for the prostate and operates transperineally for needle interventions. It can accommodate various needle drivers for different percutaneous procedures such as biopsy, thermal ablations, or brachytherapy. The first needle driver is customized for fully automated low

  18. "MRI Stealth" robot for prostate interventions.

    PubMed

    Stoianovici, Dan; Song, Danny; Petrisor, Doru; Ursu, Daniel; Mazilu, Dumitru; Muntener, Michael; Mutener, Michael; Schar, Michael; Patriciu, Alexandru

    2007-01-01

    The paper reports an important achievement in MRI instrumentation, a pneumatic, fully actuated robot located within the scanner alongside the patient and operating under remote control based on the images. Previous MRI robots commonly used piezoelectric actuation limiting their compatibility. Pneumatics is an ideal choice for MRI compatibility because it is decoupled from electromagnetism, but pneumatic actuators were hardly controllable. This achievement was possible due to a recent technology breakthrough, the invention of a new type of pneumatic motor, PneuStep 1, designed for the robot reported here with uncompromised MRI compatibility, high-precision, and medical safety. MrBot is one of the "MRI stealth" robots today (the second is described in this issue by Zangos et al.). Both of these systems are also multi-imager compatible, being able to operate with the imager of choice or cross-imaging modalities. For MRI compatibility the robot is exclusively constructed of nonmagnetic and dielectric materials such as plastics, ceramics, crystals, rubbers and is electricity free. Light-based encoding is used for feedback, so that all electric components are distally located outside the imager's room. MRI robots are modern, digital medical instruments in line with advanced imaging equipment and methods. These allow for accessing patients within closed bore scanners and performing interventions under direct (in scanner) imaging feedback. MRI robots could allow e.g. to biopsy small lesions imaged with cutting edge cancer imaging methods, or precisely deploy localized therapy at cancer foci. Our robot is the first to show the feasibility of fully automated in-scanner interventions. It is customized for the prostate and operates transperineally for needle interventions. It can accommodate various needle drivers for different percutaneous procedures such as biopsy, thermal ablations, or brachytherapy. The first needle driver is customized for fully automated low

  19. Quantitative DNA fiber mapping

    DOEpatents

    Gray, Joe W.; Weier, Heinz-Ulrich G.

    1998-01-01

    The present invention relates generally to the DNA mapping and sequencing technologies. In particular, the present invention provides enhanced methods and compositions for the physical mapping and positional cloning of genomic DNA. The present invention also provides a useful analytical technique to directly map cloned DNA sequences onto individual stretched DNA molecules.

  20. Anisotropic conductivity tensor imaging in MREIT using directional diffusion rate of water molecules.

    PubMed

    Kwon, Oh In; Jeong, Woo Chul; Sajib, Saurav Z K; Kim, Hyung Joong; Woo, Eung Je

    2014-06-21

    Magnetic resonance electrical impedance tomography (MREIT) is an emerging method to visualize electrical conductivity and/or current density images at low frequencies (below 1 KHz). Injecting currents into an imaging object, one component of the induced magnetic flux density is acquired using an MRI scanner for isotropic conductivity image reconstructions. Diffusion tensor MRI (DT-MRI) measures the intrinsic three-dimensional diffusion property of water molecules within a tissue. It characterizes the anisotropic water transport by the effective diffusion tensor. Combining the DT-MRI and MREIT techniques, we propose a novel direct method for absolute conductivity tensor image reconstructions based on a linear relationship between the water diffusion tensor and the electrical conductivity tensor. We first recover the projected current density, which is the best approximation of the internal current density one can obtain from the measured single component of the induced magnetic flux density. This enables us to estimate a scale factor between the diffusion tensor and the conductivity tensor. Combining these values at all pixels with the acquired diffusion tensor map, we can quantitatively recover the anisotropic conductivity tensor map. From numerical simulations and experimental verifications using a biological tissue phantom, we found that the new method overcomes the limitations of each method and successfully reconstructs both the direction and magnitude of the conductivity tensor for both the anisotropic and isotropic regions.

  1. MO-C-17A-08: Evaluation of Lung Deformation Using Three Dimensional Strain Maps

    SciTech Connect

    Cui, T; Huang, Q; Miller, W; Zhong, X; Yin, F; Cai, J

    2014-06-15

    Purpose: To develop a systematic approach to generate three dimensional (3D) strain maps of lung using the displacement vector field (DVF) during the respiratory deformation, and to demonstrate its application in evaluating deformable image registration (DIR). Methods: A DVF based strain tensor at each voxel of interest (VOI) was calculated from the relative displacements between the VOI and each of the six nearest neighbors. The maximum and minimum stretches of a VOI can be determined by the principal strains (E{sub 1}, E{sub 2} and E{sub 3}), which are the eigenvalues and the corresponding strain tensors. Two healthy volunteers enrolled in this study under IRB-approved protocol, each was scanned using 3D Hyperpolarized He-3 tagging-MRI and 3D proton-MRI with TrueFISP sequence at the endof- inhalation (EOI) and the end-of-exhalation (EOE) phases. 3D DVFs of tagging- and proton-MRI were obtained by the direct measurements of the tagging grid trajectory and by the DIR method implemented in commercial software. Results: 3D strain maps were successfully generated for all DVFs. The principal strain E1s were calculated as 0.43±0.05 and 0.17±0.25 for tagging-MRI and proton-MRI, respectively. The large values of E{sub 1} indicate the predominant lung motion in the superior-inferior (SI) direction. Given that the DVFs from the tagging images are considered as the ground truth, the discrepancies in the DIR-based strain maps suggest the inaccuracy of the DIR algorithm. In the E{sub 1} maps of tagging-MRI for subject 1, the fissures were distinguishable by the larger values (0.49±0.02) from the adjacent tissues (0.41±0.03) due to the larger relative displacement between the lung lobes. Conclusion: We have successfully developed a methodology to generate DVF-based 3D strain maps of lung. It can potentially enable us to better understand the pulmonary biomechanics and to evaluate and improve the DIR algorithms for the lung deformation. We are currently studying more

  2. MRI in patients with inflammatory bowel disease

    PubMed Central

    Gee, Michael S.; Harisinghani, Mukesh G.

    2011-01-01

    Inflammatory bowel disease (IBD) affects approximately 1.4 million people in North America and, because of its typical early age of onset and episodic disease course, IBD patients often undergo numerous imaging studies over the course of their lifetimes. CT has become the standard imaging modality for assessment of IBD patients because of its widespread availability, rapid image acquisition, and ability to evaluate intraluminal and extraluminal disease. However, repetitive CT imaging has been associated with a significant ionizing radiation risk to patients, making MRI an appealing alternative IBD imaging modality. Pelvic MRI is currently the imaging gold standard for detecting perianal disease, while recent studies indicate that MRI bowel-directed techniques (enteroclysis, enterography, colonography) can accurately evaluate bowel inflammation in IBD. With recent technical innovations leading to faster and higher resolution body MRI, the role of MRI in IBD evaluation is likely to continue to expand. Future applications include surveillance imaging, detection of mural fibrosis, and early assessment of therapy response. PMID:21512607

  3. Unmixing concurrent EEG-fMRI with parallel independent component analysis

    PubMed Central

    Eichele, Tom; Calhoun, Vince D.; Moosmann, Matthias; Specht, Karsten; Jongsma, Marijtje L.A.; Quian Quiroga, Rodrigo; Nordby, Helge; Hugdahl, Kenneth

    2008-01-01

    Concurrent event-related EEG-fMRI recordings pick up volume-conducted and hemodynamically convoluted signals from latent neural sources that are spatially and temporally mixed across the brain, i.e. the observed data in both modalities represent multiple, simultaneously active, regionally overlapping neuronal mass responses. This mixing process decreases the sensitivity of voxel-by-voxel prediction of hemodynamic activation by the EEG when multiple sources contribute to either the predictor and/or the response variables. In order to address this problem, we used independent component analysis (ICA) to recover maps from the fMRI and timecourses from the EEG, and matched these components across the modalities by correlating their trial-to-trial modulation. The analysis was implemented as a group-level ICA that extracts a single set of components from the data and directly allows for population inferences about consistently expressed function-relevant spatiotemporal responses. We illustrate the utility of this method by extracting a previously undetected but relevant EEG-fMRI component from a concurrent auditory target detection experiment. PMID:17688963

  4. Brain responses to facial attractiveness induced by facial proportions: evidence from an fMRI study

    PubMed Central

    Shen, Hui; Chau, Desmond K. P.; Su, Jianpo; Zeng, Ling-Li; Jiang, Weixiong; He, Jufang; Fan, Jintu; Hu, Dewen

    2016-01-01

    Brain responses to facial attractiveness induced by facial proportions are investigated by using functional magnetic resonance imaging (fMRI), in 41 young adults (22 males and 19 females). The subjects underwent fMRI while they were presented with computer-generated, yet realistic face images, which had varying facial proportions, but the same neutral facial expression, baldhead and skin tone, as stimuli. Statistical parametric mapping with parametric modulation was used to explore the brain regions with the response modulated by facial attractiveness ratings (ARs). The results showed significant linear effects of the ARs in the caudate nucleus and the orbitofrontal cortex for all of the subjects, and a non-linear response profile in the right amygdala for only the male subjects. Furthermore, canonical correlation analysis was used to learn the most relevant facial ratios that were best correlated with facial attractiveness. A regression model on the fMRI-derived facial ratio components demonstrated a strong linear relationship between the visually assessed mean ARs and the predictive ARs. Overall, this study provided, for the first time, direct neurophysiologic evidence of the effects of facial ratios on facial attractiveness and suggested that there are notable gender differences in perceiving facial attractiveness as induced by facial proportions. PMID:27779211

  5. Mapping with the Masses: Google Map Maker

    NASA Astrophysics Data System (ADS)

    Pfund, J.

    2008-12-01

    After some 15,000 years of map making, which saw the innovations of cardinal directions, map projections for a spherical earth, and GIS analysis, many parts of the world still appear as the "Dark Continent" on modern maps. Google Map Maker intends to shine a light on these areas by tapping into the power of the GeoWeb. Google Map Maker is a website which allows you to collaborate with others on one unified map to add, edit, locate, describe, and moderate map features, such as roads, cities, businesses, parks, schools and more, for certain regions of the world using Google Maps imagery. In this session, we will show some examples of how people are mapping with this powerful tool as well as what they are doing with the data. With Google Map Maker, you can become a citizen cartographer and join the global network of users helping to improve the quality of maps and local information in your region of interest. You are invited to map the world with us!

  6. Tissue-Point Motion Tracking in the Tongue from Cine-MRI and Tagged-MRI

    PubMed Central

    Woo, Jonghye; Stone, Maureen; Suo, Yuanming; Murano, Emi Z.; Prince, Jerry L.

    2015-01-01

    Purpose Accurate tissue motion tracking within the tongue can help to diagnose and treat vocal tract related disorders, evaluate speech quality before and after surgery, and conduct various scientific studies. We have compared tissue tracking results from four widely used deformable registration (DR) methods applied to Cine-MRI with harmonic phase (HARP)-based tracking applied to tagged-MRI. Method Ten subjects repeated the words “a geese” multiple times while sagittal images of the head were collected at 26 Hz, first in a tagged-MRI data set, and then in a Cine-MRI data set. HARP tracked the motion of eight specified tissue points in the tagged data set. Four DR methods including diffeomorphic demons and free-form deformations based on cubic B-spline with three different similarity measures were used to track the same eight points in the Cine-MRI data set. Individual points were tracked and length changes of several muscles were calculated using the DR and HARP based tracking methods. Results Results showed that the DR tracking errors were non-systematic and varied in direction, amount, and timing across speakers and within speakers. Comparison of HARP and DR tracking with manual tracking showed better tracking results for HARP except at the tongue surface, where mistracking caused greater errors in HARP than DR. Conclusions Tissue point tracking using DR tracking methods contain non-systematic tracking errors within and across subjects, making it less successful than tagged-MRI tracking within the tongue. However, HARP sometimes mistracks points at the tongue surface of tagged MRI due to its limited bandpass filter and tag pattern fading, so that DR has better success measuring surface tissue points on Cine-MRI than HARP does. Therefore a hybrid method is being explored. PMID:24686470

  7. MRI of nasopharyngeal adenoid hypertrophy.

    PubMed

    Surov, Alexey; Ryl, Ina; Bartel-Friedrich, Sylvia; Wienke, Andreas; Kösling, Sabrina

    2016-10-01

    Nasopharyngeal adenoid hypertrophy (NAH) is a typical benign lesion. Due to involution, nasopharyngeal lymphatic tissue usually is not found in adults beyond the 30th to 40th year of life. However, occasionally NAH has been recognized after the 50th or 60th year. The aim of this study is to identify the frequency of NAH and to analyze its MRI findings in different age groups. From 2007 to 2011, 6693 MR investigations of the head were performed at our institution. MRI was obtained with a 1.5 T MRI device. NAH was identified in 18.0% of the patients. The frequency of NAH varied from 60.3% to 1.0% in the different age groups. The mean size of NAH was 23.2 ± 4.5 mm in cranio-caudal, 31.1 ± 5.2 mm in left-right, and 14.2 ± 4.1 mm in the anterior-posterior direction. The left-right and cranio-caudal sizes of NAH were largest in the 0-9 age group and decreased with age. On T1-w images most lesions (95.4%) were hypointense in comparison to the adjacent musculature. On T2-w fat-saturated images 82.4% of the lesions were hyperintense. After intravenous administration of contrast medium most lesions showed a slight enhancement (58.6%). Moderate enhancement was seen in 32.4% and a marked enhancement was identified in 9.0%. In the 0-9 age group most lesions showed a slight enhancement. Cysts within NAH were identified in 433 cases (35.9%). The frequency of cysts increased continuously with age, namely from 10.9% to 65.2%.

  8. Triaxial fiber optic magnetic field sensor for MRI applications

    NASA Astrophysics Data System (ADS)

    Filograno, Massimo L.; Pisco, Marco; Catalano, Angelo; Forte, Ernesto; Aiello, Marco; Soricelli, Andrea; Davino, Daniele; Visone, Ciro; Cutolo, Antonello; Cusano, Andrea

    2016-05-01

    In this paper, we report a fiber-optic triaxial magnetic field sensor, based on Fiber Bragg Gratings (FBGs) integrated with giant magnetostrictive material, the Terfenol-D. The realized sensor has been designed and engineered for Magnetic Resonance Imaging (MRI) applications. A full magneto-optical characterization of the triaxial sensing probe has been carried out, providing the complex relationship among the FBGs wavelength shift and the applied magnetostatic field vector. Finally, the developed fiber optic sensors have been arranged in a sensor network composed of 20 triaxial sensors for mapping the magnetic field distribution in a MRI-room at a diagnostic center in Naples (SDN), equipped with Positron emission tomography/magnetic resonance (PET/MR) instrumentation. Experimental results reveal that the proposed sensor network can be efficiently used in MRI centers for performing quality assurance tests, paving the way for novel integrated tools to measure the magnetic dose accumulated day by day by MRI operators.

  9. Improving Bladder Cancer Imaging Using 3T Functional Dynamic Contrast-Enhanced MRI

    PubMed Central

    Nguyen, Huyen T.; Pohar, Kamal S.; Jia, Guang; Shah, Zarine K.; Mortazavi, Amir; Zynger, Debra L.; Wei, Lai; Clark, Daniel; Yang, Xiangyu; Knopp, Michael V.

    2015-01-01

    Objectives To assess the capability of T2-weighted MRI (T2W-MRI) and the additional diagnostic value of Dynamic Contrast-Enhanced MRI (DCE-MRI) using multi-transmit 3T in the localization of bladder cancer. Materials and Methods This prospective study was approved by the local Institutional Review Board. Thirty–six patients were included in the study and provided informed consent. MRI scans were performed with T2W-MRI and DCE-MRI on a 3T multi-transmit system. Two observers (with 12 and 25 years of experience) independently interpreted T2W-MRI prior to DCE-MRI data (maps of pharmacokinetic parameters) to localize bladder tumors. The pathological examination of cystectomy bladder specimens was used as a reference gold standard. The McNemar test was performed to evaluate the differences in sensitivity, specificity, and accuracy. Kappa scores were calculated to assess interobserver agreement. Results The sensitivity, specificity, and accuracy of the localization with T2W-MRI alone were 81% (29/36), 63% (5/8) and 77% (34/44) for observer 1, and 72% (26/36), 63% (5/8), and 70% (31/44) for observer 2. With additional DCE-MRI available, these values were 92% (33/36), 75% (6/8), and 89% (39/44) for observer 1, and 92% (33/36), 63% (5/8), and 86% (38/44) for observer 2. DCE-MRI significantly (P < 0.01) improved the sensitivity and accuracy for observer 2. For the twenty-three patients treated with chemotherapy, DCE-MRI also significantly (P < 0.02) improved the sensitivity and accuracy of bladder cancer localization with T2W-MRI alone for observer 2. Kappa scores were 0.63 for T2W-MRI alone, and 0.78 for additional DCE-MRI. Out of seven sub-centimeter malignant tumors, four (57%) were identified on T2W images and six (86%) on DCE maps. Out of eleven malignant tumors within the bladder wall thickening, six (55%) were found on T2W images and ten (91%) on DCE maps. Conclusions Compared to conventional T2W-MRI alone, the addition of DCE-MRI improved interobserver agreement as

  10. Nonaxisymmetric modes of MRI in dissipative Keplerian disks

    NASA Astrophysics Data System (ADS)

    Kitchatinov, L. L.; Rüdiger, G.

    2010-04-01

    Aims: Deviations from the axial symmetry are necessary to maintain self-sustained MRI-turbulence by a dynamo mechanism. We define the parameter region where the nonaxisymmetric MRI modes are excited and study their geometries and growth rates. Methods: The linear eigenvalue problem for global nonaxisymmetric modes of standard-MRI in Keplerian disks is solved numerically with allowance for finite diffusion. Results: For small magnetic Prandtl numbers the microscopic viscosity completely drops out of the analysis so that the stability maps and the growth rates expressed in terms of the magnetic Reynolds number Rm and the Lundquist number S do not depend on the magnetic Prandtl number Pm. The minimum magnetic field for the onset of nonaxisymmetric MRI grows with the rotation rate. For a given S all nonaxisymmetric modes disappear for a sufficiently large Rm. This is a consequence of the radial fine-structure of the nonaxisymmetric modes resulting from the winding effect of differential rotation. It is this fine-structure which also provides serious resolution problems for the numerical simulation of MRI at large Rm. Conclusions: For weak magnetic fields slightly above the critical value for the onset of MRI only axisymmetric modes are unstable. Nonaxisymmetric modes need stronger fields and not too large Rm. If Pm is small its real value does not play any role in MRI.

  11. Polarized noble gas MRI

    SciTech Connect

    Brookeman, James R.; Mugler, John P. III; Lange, Eduard E. de; Knight-Scott, Jack; Maier, Therese; Bogorad, Paul; Driehuys, Bastiaan; Cates, Gordon; Happer, William; Daniel, Thomas M.; Truwit, Jonathon D.

    1998-01-20

    The development of convenient methods to polarize liter quantities of the noble gases helium-3 and xenon-129 has provided the opportunity for a new MRI method to visualize the internal air spaces of the human lung. These spaces are usually poorly seen with hydrogen-based MRI, because of the limited water content of the lung and the low thermal polarization of the water protons achieved in conventional magnets. In addition, xenon, which has a relatively high solubility and a sufficiently persistent polarization level in blood and biological tissue, offers the prospect of providing perfusion images of the lung, brain and other organs.

  12. Extension of dVCA model and its application in estimating fMRI components

    NASA Astrophysics Data System (ADS)

    Zhang, Gaoyan; Zhang, Jiacai; Yao, Li; Zhao, Xiaojie

    2010-03-01

    General linear model (GLM) and independent component analysis (ICA) are widely used methods in the community of functional magnetic resonance imaging (fMRI) data analysis. GLM and ICA are all assuming that fMRI components are location locked. Here we extend the Differentially variable component analysis (dVCA) and introduce it into fMRI data to analyze the transient changes during fMRI experiments which are ignored in GLM and ICA. We apply the extended dVCA to model fMRI images as the linear combination of ongoing activity and multiple fMRI components. We test our extended dVCA method on simulated images that mimicked the fMRI slice images containing two components, and employ the iterative maximum a posteriori (MAP) solution succeed to estimate each component's time-invariant spatial patterns, and its time-variant amplitude scaling factors and location shifts. The extended dVCA algorithm also identify two fMRI components that reflect the fact of hemispheric asymmetry for motor area in another test with fMRI data acquired with the block design task of right/left hand finger tapping alternately. This work demonstrates that our extended dVCA method is robustness to detect the variability of the fMRI components that maybe existent during the fMRI experiments.

  13. MRI of the brain (image)

    MedlinePlus

    An MRI (magnetic resonance imaging) of the brain creates a detailed image of the complex structures in the brain. An MRI can give a three-dimensional depiction of the brain, making location of problems such ...

  14. Co-registration of high resolution MRI sub-volumes in non-human primates

    NASA Astrophysics Data System (ADS)

    Lecoeur, Jérémy; Wang, Feng; Chen, Li Min; Li, Rui; Avison, Malcom J.; Dawant, Benoit M.

    2011-03-01

    Dynamic structural and functional remodeling of the Central Nervous System occurs throughout the lifespan of the organism from the molecular to the systems level. MRI offers several advantages to observe this phenomenon: it is non-invasive and non-destructive, the contrast can be tuned to interrogate different tissue properties and imaging resolution can range from cortical columns to whole brain networks in the same session. To measure these changes reliably, functional maps generated over time with high resolution fMRI need to be registered accurately. This article presents a new method for registering automatically thin cortical MR volumes that are aligned with the functional maps. These acquisitions focus on the primary somato-sensory cortex, a region in the anterior parietal part of the brain, responsible for fine touch and proprioception. Currently, these slabs are acquired in approximately the same orientation from acquisition to acquisition and then registered by hand. Because they only cover a small portion of the cortex, their direct automatic registration is difficult. To address this issue, we propose a method relying on an intermediate image, acquired with a surface coil that covers a larger portion of the head to which the slabs can be registered. Because images acquired with surface coils suffer from severe intensity attenuation artifact, we also propose a method to register these. The results from data sets obtained with three squirrel monkeys show a registration accuracy of thirty micrometers.

  15. Multi-modal image registration: matching MRI with histology

    NASA Astrophysics Data System (ADS)

    Alic, Lejla; Haeck, Joost C.; Klein, Stefan; Bol, Karin; van Tiel, Sandra T.; Wielopolski, Piotr A.; Bijster, Magda; Niessen, Wiro J.; Bernsen, Monique; Veenland, Jifke F.; de Jong, Marion

    2010-03-01

    Spatial correspondence between histology and multi sequence MRI can provide information about the capabilities of non-invasive imaging to characterize cancerous tissue. However, shrinkage and deformation occurring during the excision of the tumor and the histological processing complicate the co registration of MR images with histological sections. This work proposes a methodology to establish a detailed 3D relation between histology sections and in vivo MRI tumor data. The key features of the methodology are a very dense histological sampling (up to 100 histology slices per tumor), mutual information based non-rigid B-spline registration, the utilization of the whole 3D data sets, and the exploitation of an intermediate ex vivo MRI. In this proof of concept paper, the methodology was applied to one tumor. We found that, after registration, the visual alignment of tumor borders and internal structures was fairly accurate. Utilizing the intermediate ex vivo MRI, it was possible to account for changes caused by the excision of the tumor: we observed a tumor expansion of 20%. Also the effects of fixation, dehydration and histological sectioning could be determined: 26% shrinkage of the tumor was found. The annotation of viable tissue, performed in histology and transformed to the in vivo MRI, matched clearly with high intensity regions in MRI. With this methodology, histological annotation can be directly related to the corresponding in vivo MRI. This is a vital step for the evaluation of the feasibility of multi-spectral MRI to depict histological groundtruth.

  16. Map reading tools for map libraries.

    USGS Publications Warehouse

    Greenberg, G.L.

    1982-01-01

    Engineers, navigators and military strategists employ a broad array of mechanical devices to facilitate map use. A larger number of map users such as educators, students, tourists, journalists, historians, politicians, economists and librarians are unaware of the available variety of tools which can be used with maps to increase the speed and efficiency of their application and interpretation. This paper identifies map reading tools such as coordinate readers, protractors, dividers, planimeters, and symbol-templets according to a functional classification. Particularly, arrays of tools are suggested for use in determining position, direction, distance, area and form (perimeter-shape-pattern-relief). -from Author

  17. microRNA-206 impairs c-Myc-driven cancer in a synthetic lethal manner by directly inhibiting MAP3K13

    PubMed Central

    Han, Han; Chen, Yuxing; Cheng, Li; Prochownik, Edward V.; Li, Youjun

    2016-01-01

    c-Myc (Myc) is one of the most frequently dysregulated oncogenic transcription factors in human cancer. By functionally screening a microRNA (miR) library, we identified miR-206 as being a synthetic lethal in Myc over-expressing human cancer cells. miR-206 inhibited MAP3K13, which resulted in Myc protein de-stabilization, and an inhibition of anchorage-independent growth and in vivo tumorigenesis by Myc over-expressing human cancer cells. Eliminating MAP3K13 by shRNA recapitulated the effects caused by miR-206, thus supporting the idea that miR-206's effect on Myc was mediated through MAP3K13. Conversely, enforced expression of MAP3K13 stabilized Myc by promoting its N-terminal phosphorylation and enhancing its transcriptional activity. Gene expression analyses of breast cancers expressing high levels of Myc indicated that low miR-206 expression and high MAP3K13 expression correlated with poor patient survival. The critical link between miR-206 and MAP3K13 in the development of Myc over-expressing human cancers suggests potential points of therapeutic intervention for this molecular sub-category. PMID:26918941

  18. Simultaneous EEG-fMRI reveals brain networks underlying recognition memory ERP old/new effects.

    PubMed

    Hoppstädter, Michael; Baeuchl, Christian; Diener, Carsten; Flor, Herta; Meyer, Patric

    2015-08-01

    The mapping of event-related potentials (ERP) on functional magnetic resonance imaging (fMRI) data remains difficult as scalp electroencephalography (EEG) is assumed to be largely insensitive to deep brain structures. Simultaneous recordings of EEG and fMRI might be helpful in reconciling surface ERPs with hemodynamic activations in medial temporal lobe structures related to recognition memory. EEG and imaging studies provide evidence for two independent processes underlying recognition memory, namely recollection and familiarity. Recollection reflects the conscious retrieval of contextual information about a specific episode, while familiarity refers to an acontextual feeling of knowing. Both processes were related to two spatiotemporally different ERP effects, namely the early mid-frontal old/new effect (familiarity) and the late parietal old new effect (recollection). We conducted an exploratory simultaneous EEG-fMRI study using a recognition memory paradigm to investigate which brain activations are modulated in relation to the ERP old/new effects. To this end we examined 17 participants in a yes/no recognition task with word stimuli. Single-trial amplitudes of ERP old/new effects were related to the hemodynamic signal in an EEG-informed fMRI analysis for a subset of 12 subjects. FMRI activation in the right dorsolateral prefrontal cortex and the right intraparietal sulcus was associated with the amplitude of the early frontal old/new effect (350-550ms), and activation in the right posterior hippocampus, parahippocampal cortex and retrosplenial cortex was associated with the amplitude of the late parietal old new effect (580-750ms). These results provide the first direct link between electrophysiological and hemodynamic correlates of familiarity and recollection. Moreover, these findings in healthy subjects complement data from intracranial ERP recordings in epilepsy patients and lesion studies in hypoxia patients. PMID:25988228

  19. Convex-Optimization-Based Compartmental Pharmacokinetic Analysis for Prostate Tumor Characterization Using DCE-MRI.

    PubMed

    Ambikapathi, ArulMurugan; Chan, Tsung-Han; Lin, Chia-Hsiang; Yang, Fei-Shih; Chi, Chong-Yung; Wang, Yue

    2016-04-01

    Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a powerful imaging modality to study the pharmacokinetics in a suspected cancer/tumor tissue. The pharmacokinetic (PK) analysis of prostate cancer includes the estimation of time activity curves (TACs), and thereby, the corresponding kinetic parameters (KPs), and plays a pivotal role in diagnosis and prognosis of prostate cancer. In this paper, we endeavor to develop a blind source separation algorithm, namely convex-optimization-based KPs estimation (COKE) algorithm for PK analysis based on compartmental modeling of DCE-MRI data, for effective prostate tumor detection and its quantification. The COKE algorithm first identifies the best three representative pixels in the DCE-MRI data, corresponding to the plasma, fast-flow, and slow-flow TACs, respectively. The estimation accuracy of the flux rate constants (FRCs) of the fast-flow and slow-flow TACs directly affects the estimation accuracy of the KPs that provide the cancer and normal tissue distribution maps in the prostate region. The COKE algorithm wisely exploits the matrix structure (Toeplitz, lower triangular, and exponential decay) of the original nonconvex FRCs estimation problem, and reformulates it into two convex optimization problems that can reliably estimate the FRCs. After estimation of the FRCs, the KPs can be effectively estimated by solving a pixel-wise constrained curve-fitting (convex) problem. Simulation results demonstrate the efficacy of the proposed COKE algorithm. The COKE algorithm is also evaluated with DCE-MRI data of four different patients with prostate cancer and the obtained results are consistent with clinical observations. PMID:26292336

  20. Convex-Optimization-Based Compartmental Pharmacokinetic Analysis for Prostate Tumor Characterization Using DCE-MRI.

    PubMed

    Ambikapathi, ArulMurugan; Chan, Tsung-Han; Lin, Chia-Hsiang; Yang, Fei-Shih; Chi, Chong-Yung; Wang, Yue

    2016-04-01

    Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a powerful imaging modality to study the pharmacokinetics in a suspected cancer/tumor tissue. The pharmacokinetic (PK) analysis of prostate cancer includes the estimation of time activity curves (TACs), and thereby, the corresponding kinetic parameters (KPs), and plays a pivotal role in diagnosis and prognosis of prostate cancer. In this paper, we endeavor to develop a blind source separation algorithm, namely convex-optimization-based KPs estimation (COKE) algorithm for PK analysis based on compartmental modeling of DCE-MRI data, for effective prostate tumor detection and its quantification. The COKE algorithm first identifies the best three representative pixels in the DCE-MRI data, corresponding to the plasma, fast-flow, and slow-flow TACs, respectively. The estimation accuracy of the flux rate constants (FRCs) of the fast-flow and slow-flow TACs directly affects the estimation accuracy of the KPs that provide the cancer and normal tissue distribution maps in the prostate region. The COKE algorithm wisely exploits the matrix structure (Toeplitz, lower triangular, and exponential decay) of the original nonconvex FRCs estimation problem, and reformulates it into two convex optimization problems that can reliably estimate the FRCs. After estimation of the FRCs, the KPs can be effectively estimated by solving a pixel-wise constrained curve-fitting (convex) problem. Simulation results demonstrate the efficacy of the proposed COKE algorithm. The COKE algorithm is also evaluated with DCE-MRI data of four different patients with prostate cancer and the obtained results are consistent with clinical observations.

  1. MRI in decompression illness.

    PubMed

    Hierholzer, J; Tempka, A; Stroszczynski, C; Amodio, F; Hosten, N; Haas, J; Felix, R

    2000-05-01

    We report a case of decompression illness in which the patient developed paraparesis during scuba diving after rapid ascent. MRI of the spine revealed a focal intramedullary lesion consistent with the symptoms. The pathophysiological and radiological aspects of spinal decompression illness are discussed.

  2. Background and Mathematical Analysis of Diffusion MRI Methods.

    PubMed

    Ozcan, Alpay; Wong, Kenneth H; Larson-Prior, Linda; Cho, Zang-Hee; Mun, Seong K

    2012-03-01

    The addition of a pair of magnetic field gradient pulses had initially provided the measurement of spin motion with nuclear magnetic resonance (NMR) techniques. In the adaptation of DW-NMR techniques to magnetic resonance imaging (MRI), the taxonomy of mathematical models is divided in two categories: model matching and spectral methods. In this review, the methods are summarized starting from early diffusion weighted (DW) NMR models followed up with their adaptation to DW MRI. Finally, a newly introduced Fourier analysis based unifying theory, so-called Complete Fourier Direct MRI, is included to explain the mechanisms of existing methods.

  3. PCA-based groupwise image registration for quantitative MRI.

    PubMed

    Huizinga, W; Poot, D H J; Guyader, J-M; Klaassen, R; Coolen, B F; van Kranenburg, M; van Geuns, R J M; Uitterdijk, A; Polfliet, M; Vandemeulebroucke, J; Leemans, A; Niessen, W J; Klein, S

    2016-04-01

    Quantitative magnetic resonance imaging (qMRI) is a technique for estimating quantitative tissue properties, such as the T1 and T2 relaxation times, apparent diffusion coefficient (ADC), and various perfusion measures. This estimation is achieved by acquiring multiple images with different acquisition parameters (or at multiple time points after injection of a contrast agent) and by fitting a qMRI signal model to the image intensities. Image registration is often necessary to compensate for misalignments due to subject motion and/or geometric distortions caused by the acquisition. However, large differences in image appearance make accurate image registration challenging. In this work, we propose a groupwise image registration method for compensating misalignment in qMRI. The groupwise formulation of the method eliminates the requirement of choosing a reference image, thus avoiding a registration bias. The method minimizes a cost function that is based on principal component analysis (PCA), exploiting the fact that intensity changes in qMRI can be described by a low-dimensional signal model, but not requiring knowledge on the specific acquisition model. The method was evaluated on 4D CT data of the lungs, and both real and synthetic images of five different qMRI applications: T1 mapping in a porcine heart, combined T1 and T2 mapping in carotid arteries, ADC mapping in the abdomen, diffusion tensor mapping in the brain, and dynamic contrast-enhanced mapping in the abdomen. Each application is based on a different acquisition model. The method is compared to a mutual information-based pairwise registration method and four other state-of-the-art groupwise registration methods. Registration accuracy is evaluated in terms of the precision of the estimated qMRI parameters, overlap of segmented structures, distance between corresponding landmarks, and smoothness of the deformation. In all qMRI applications the proposed method performed better than or equally well as

  4. PCA-based groupwise image registration for quantitative MRI.

    PubMed

    Huizinga, W; Poot, D H J; Guyader, J-M; Klaassen, R; Coolen, B F; van Kranenburg, M; van Geuns, R J M; Uitterdijk, A; Polfliet, M; Vandemeulebroucke, J; Leemans, A; Niessen, W J; Klein, S

    2016-04-01

    Quantitative magnetic resonance imaging (qMRI) is a technique for estimating quantitative tissue properties, such as the T1 and T2 relaxation times, apparent diffusion coefficient (ADC), and various perfusion measures. This estimation is achieved by acquiring multiple images with different acquisition parameters (or at multiple time points after injection of a contrast agent) and by fitting a qMRI signal model to the image intensities. Image registration is often necessary to compensate for misalignments due to subject motion and/or geometric distortions caused by the acquisition. However, large differences in image appearance make accurate image registration challenging. In this work, we propose a groupwise image registration method for compensating misalignment in qMRI. The groupwise formulation of the method eliminates the requirement of choosing a reference image, thus avoiding a registration bias. The method minimizes a cost function that is based on principal component analysis (PCA), exploiting the fact that intensity changes in qMRI can be described by a low-dimensional signal model, but not requiring knowledge on the specific acquisition model. The method was evaluated on 4D CT data of the lungs, and both real and synthetic images of five different qMRI applications: T1 mapping in a porcine heart, combined T1 and T2 mapping in carotid arteries, ADC mapping in the abdomen, diffusion tensor mapping in the brain, and dynamic contrast-enhanced mapping in the abdomen. Each application is based on a different acquisition model. The method is compared to a mutual information-based pairwise registration method and four other state-of-the-art groupwise registration methods. Registration accuracy is evaluated in terms of the precision of the estimated qMRI parameters, overlap of segmented structures, distance between corresponding landmarks, and smoothness of the deformation. In all qMRI applications the proposed method performed better than or equally well as

  5. Virtual Electrophysiologic Study in a Three-dimensional Cardiac MRI Model of Porcine Myocardial Infarction

    PubMed Central

    Ng, Jason; Jacobson, Jason T; Ng, Justin K; Gordon, David; Lee, Daniel C; Carr, James C.; Goldberger, Jeffrey J

    2012-01-01

    Objective This study sought to test the hypothesis that “virtual” electrophysiologic studies (EPS) on an anatomic platform generated by 3D MRI reconstruction of the left ventricle (LV) can reproduce the reentrant circuits of induced ventricular tachycardia (VT) in a porcine model of myocardial infarction (MI). Background Delayed-enhancement MRI has been used to characterize MI and “gray zones”, which are thought to reflect heterogeneous regions of viable and non-viable myocytes. Methods MI by coronary artery occlusion was induced in eight pigs. After a recovery period, 3D cardiac MRIs were obtained from each pig in-vivo. Normal areas, gray zones, and infarct cores were classified based on voxel intensity. In the computer model, gray zones were assigned slower conduction and longer action potential durations than those for normal myocardium. Virtual EPS was performed and was compared to results of actual in vivo programmed stimulation and non-contact mapping. Results The LV volumes ranged from 97.8 to 166.2 cm3 with 4.9 to 17.5% of voxels classified as infarct zones. Six of the seven pigs that developed VT during actual EPS were also inducible with virtual EPS. Four of the six pigs that had simulated VT had reentrant circuits that approximated the circuits seen with non-contact mapping, while the remaining two had similar circuits but propagating in opposite directions. Conclusions This initial study demonstrates the feasibility of applying a mathematical model to MRI reconstructions of the LV to predict VT circuits. Virtual EPS may be helpful to plan catheter ablation strategies or to identify patients who are at risk for future episodes of VT. PMID:22633654

  6. Threats to ultra-high-field MRI

    NASA Astrophysics Data System (ADS)

    Le Bihan, Denis

    2009-08-01

    In 2004 the European Commission (EC) adopted a directive restricting occupational exposure to electromagnetic fields. This directive (2004/40/CE), which examines the possible health risks of the electromagnetic fields from mobile phones, Wi-Fi, Bluetooth and other devices, concluded that upper limits on radiation and applied electromagnetic fields are necessary to prevent workers from suffering any undue acute health effects. But although not initially intended, the biggest impact of the directive could be on magnetic resonance imaging (MRI), which is used in hospitals worldwide to produce images of unrivalled quality of the brain and other soft tissues.

  7. MR Scanner Systems Should Be Adequately Characterized in Diffusion-MRI of the Breast

    PubMed Central

    Giannelli, Marco; Sghedoni, Roberto; Iacconi, Chiara; Iori, Mauro; Traino, Antonio Claudio; Guerrisi, Maria; Mascalchi, Mario; Toschi, Nicola; Diciotti, Stefano

    2014-01-01

    Breast imaging represents a relatively recent and promising field of application of quantitative diffusion-MRI techniques. In view of the importance of guaranteeing and assessing its reliability in clinical as well as research settings, the aim of this study was to specifically characterize how the main MR scanner system-related factors affect quantitative measurements in diffusion-MRI of the breast. In particular, phantom acquisitions were performed on three 1.5 T MR scanner systems by different manufacturers, all equipped with a dedicated multi-channel breast coil as well as acquisition sequences for diffusion-MRI of the breast. We assessed the accuracy, inter-scan and inter-scanner reproducibility of the mean apparent diffusion coefficient measured along the main orthogonal directions () as well as of diffusion-tensor imaging (DTI)-derived mean diffusivity (MD) measurements. Additionally, we estimated spatial non-uniformity of (NU) and MD (NUMD) maps. We showed that the signal-to-noise ratio as well as overall calibration of high strength diffusion gradients system in typical acquisition sequences for diffusion-MRI of the breast varied across MR scanner systems, introducing systematic bias in the measurements of diffusion indices. While and MD values were not appreciably different from each other, they substantially varied across MR scanner systems. The mean of the accuracies of measured and MD was in the range [−2.3%,11.9%], and the mean of the coefficients of variation for and MD measurements across MR scanner systems was 6.8%. The coefficient of variation for repeated measurements of both and MD was < 1%, while NU and NUMD values were <4%. Our results highlight that MR scanner system-related factors can substantially affect quantitative diffusion-MRI of the breast. Therefore, a specific quality control program for assessing and monitoring the performance of MR scanner systems for diffusion-MRI of the breast is

  8. Technical Note: MRI only prostate radiotherapy planning using the statistical decomposition algorithm

    SciTech Connect

    Siversson, Carl; Nordström, Fredrik; Nilsson, Terese; Nyholm, Tufve; Jonsson, Joakim; Gunnlaugsson, Adalsteinn; Olsson, Lars E.

    2015-10-15

    Purpose: In order to enable a magnetic resonance imaging (MRI) only workflow in radiotherapy treatment planning, methods are required for generating Hounsfield unit (HU) maps (i.e., synthetic computed tomography, sCT) for dose calculations, directly from MRI. The Statistical Decomposition Algorithm (SDA) is a method for automatically generating sCT images from a single MR image volume, based on automatic tissue classification in combination with a model trained using a multimodal template material. This study compares dose calculations between sCT generated by the SDA and conventional CT in the male pelvic region. Methods: The study comprised ten prostate cancer patients, for whom a 3D T2 weighted MRI and a conventional planning CT were acquired. For each patient, sCT images were generated from the acquired MRI using the SDA. In order to decouple the effect of variations in patient geometry between imaging modalities from the effect of uncertainties in the SDA, the conventional CT was nonrigidly registered to the MRI to assure that their geometries were well aligned. For each patient, a volumetric modulated arc therapy plan was created for the registered CT (rCT) and recalculated for both the sCT and the conventional CT. The results were evaluated using several methods, including mean average error (MAE), a set of dose-volume histogram parameters, and a restrictive gamma criterion (2% local dose/1 mm). Results: The MAE within the body contour was 36.5 ± 4.1 (1 s.d.) HU between sCT and rCT. Average mean absorbed dose difference to target was 0.0% ± 0.2% (1 s.d.) between sCT and rCT, whereas it was −0.3% ± 0.3% (1 s.d.) between CT and rCT. The average gamma pass rate was 99.9% for sCT vs rCT, whereas it was 90.3% for CT vs rCT. Conclusions: The SDA enables a highly accurate MRI only workflow in prostate radiotherapy planning. The dosimetric uncertainties originating from the SDA appear negligible and are notably lower than the uncertainties

  9. Co-Registration of MEG and ULF MRI using a 7 channel low-Tc SQUID system

    SciTech Connect

    Magnelind, Per E; Sandin, Jan H; Volegov, Petr L; Matlashov, Andrei N; Owens, Tuba; Gomez, John J; Espy, Michelle A

    2010-01-01

    In human brain imaging, e.g. pre-surgical mapping, it is highly desired to obtain images with high spatial and temporal resolution. However, no single imaging device is capable of producing both a high spatial resolution anatomical image and a high temporal resolution functional image. During the last couple of years significant efforts have been directed towards magnetic resonance imaging (MRI) in fields comparable to the Earth's field, i.e. microtesla fields, or lower fields. The fields in this range are called ultra-low fields (ULF). Interestingly, the idea of magnetic resonance at microtesla fields is more than 50 years old. In ULF MR it is essential to use pre-polarization to increase the signal-to-noise ratio of the signal from the precessing spins, since the magnetization from the measurement field alone is very small. Even with the present level of prepolarization the ULF images are not as highly resolved as their high-field counterparts. By using a 7 channel system equipped with low transition temperature (T{sub c}) Superconducting QUantum Interference Devices (SQUIDs) to perform both ULF MRI and magnetoencephalography (MEG), it is possible to coregister a lower resolution ULF MR image and an MEG image obtained during one run. Thereby, the MEG data is aligned to the ULF MR image after performing a calibration run with a phantom. The ULF MR image can then be used to align the MEG data onto a high-field MR image. Recently, our group presented the first brain images obtained by ULF MRI. The MR imaging was combined with an MEG session performed a posteriori. The subject's head was moved in between the MRI run and the MEG run and no reference coils were used to quantify the translation. The main reason for the translation of the head was to improve the coverage of the auditory evoked response. In this paper, we report interleaved ULF MRI and MEG measurements co-registered in the same system.

  10. A review of MRI evaluation of demyelination in cuprizone murine model

    SciTech Connect

    Krutenkova, E. Pan, E.; Khodanovich, M.

    2015-11-17

    The cuprizone mouse model of non-autoimmune demyelination reproduces some phenomena of multiple sclerosis and is appropriate for validation and specification of a new method of non-invasive diagnostics. In the review new data which are collected using the new MRI method are compared with one or more conventional MRI tools. Also the paper reviewed the validation of MRI approaches using histological or immunohistochemical methods. Luxol fast blue histological staining and myelin basic protein immunostaining is widespread. To improve the accuracy of non-invasive conventional MRI, multimodal scanning could be applied. The new quantitative MRI method of fast mapping of the macromolecular proton fraction is a reliable biomarker of myelin in the brain and can be used for research of demyelination in animals. To date, a validation of MPF method on the CPZ mouse model of demyelination is not performed, although this method is probably the best way to evaluate demyelination using MRI.

  11. A review of MRI evaluation of demyelination in cuprizone murine model

    NASA Astrophysics Data System (ADS)

    Krutenkova, E.; Pan, E.; Khodanovich, M.

    2015-11-01

    The cuprizone mouse model of non-autoimmune demyelination reproduces some phenomena of multiple sclerosis and is appropriate for validation and specification of a new method of non-invasive diagnostics. In the review new data which are collected using the new MRI method are compared with one or more conventional MRI tools. Also the paper reviewed the validation of MRI approaches using histological or immunohistochemical methods. Luxol fast blue histological staining and myelin basic protein immunostaining is widespread. To improve the accuracy of non-invasive conventional MRI, multimodal scanning could be applied. The new quantitative MRI method of fast mapping of the macromolecular proton fraction is a reliable biomarker of myelin in the brain and can be used for research of demyelination in animals. To date, a validation of MPF method on the CPZ mouse model of demyelination is not performed, although this method is probably the best way to evaluate demyelination using MRI.

  12. Electrophysiological correlates of the BOLD signal for EEG-informed fMRI

    PubMed Central

    Murta, Teresa; Leite, Marco; Carmichael, David W; Figueiredo, Patrícia; Lemieux, Louis

    2015-01-01

    Electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) are important tools in cognitive and clinical neuroscience. Combined EEG–fMRI has been shown to help to characterise brain networks involved in epileptic activity, as well as in different sensory, motor and cognitive functions. A good understanding of the electrophysiological correlates of the blood oxygen level-dependent (BOLD) signal is necessary to interpret fMRI maps, particularly when obtained in combination with EEG. We review the current understanding of electrophysiological–haemodynamic correlates, during different types of brain activity. We start by describing the basic mechanisms underlying EEG and BOLD signals and proceed by reviewing EEG-informed fMRI studies using fMRI to map specific EEG phenomena over the entire brain (EEG–fMRI mapping), or exploring a range of EEG-derived quantities to determine which best explain colocalised BOLD fluctuations (local EEG–fMRI coupling). While reviewing studies of different forms of brain activity (epileptic and nonepileptic spontaneous activity; cognitive, sensory and motor functions), a significant attention is given to epilepsy because the investigation of its haemodynamic correlates is the most common application of EEG-informed fMRI. Our review is focused on EEG-informed fMRI, an asymmetric approach of data integration. We give special attention to the invasiveness of electrophysiological measurements and the simultaneity of multimodal acquisitions because these methodological aspects determine the nature of the conclusions that can be drawn from EEG-informed fMRI studies. We emphasise the advantages of, and need for, simultaneous intracranial EEG–fMRI studies in humans, which recently became available and hold great potential to improve our understanding of the electrophysiological correlates of BOLD fluctuations. PMID:25277370

  13. Linking contemporary high resolution magnetic resonance imaging to the von Economo legacy: A study on the comparison of MRI cortical thickness and histological measurements of cortical structure.

    PubMed

    Scholtens, Lianne H; de Reus, Marcel A; van den Heuvel, Martijn P

    2015-08-01

    The cerebral cortex is a distinctive part of the mammalian nervous system, displaying a spatial variety in cyto-, chemico-, and myelinoarchitecture. As part of a rich history of histological findings, pioneering anatomists von Economo and Koskinas provided detailed mappings on the cellular structure of the human cortex, reporting on quantitative aspects of cytoarchitecture of cortical areas. Current day investigations into the structure of human cortex have embraced technological advances in Magnetic Resonance Imaging (MRI) to assess macroscale thickness and organization of the cortical mantle in vivo. However, direct comparisons between current day MRI estimates and the quantitative measurements of early anatomists have been limited. Here, we report on a simple, but nevertheless important cross-analysis between the histological reports of von Economo and Koskinas on variation in thickness of the cortical mantle and MRI derived measurements of cortical thickness. We translated the von Economo cortical atlas to a subdivision of the commonly used Desikan-Killiany atlas (as part of the FreeSurfer Software package and a commonly used parcellation atlas in studies examining MRI cortical thickness). Next, values of "width of the cortical mantle" as provided by the measurements of von Economo and Koskinas were correlated to cortical thickness measurements derived from high-resolution anatomical MRI T1 data of 200+ subjects of the Human Connectome Project (HCP). Cross-correlation revealed a significant association between group-averaged MRI measurements of cortical thickness and histological recordings (r = 0.54, P < 0.001). Further validating such a correlation, we manually segmented the von Economo parcellation atlas on the standardized Colin27 brain dataset and applied the obtained three-dimensional von Economo segmentation atlas to the T1 data of each of the HCP subjects. Highly consistent with our findings for the mapping to the Desikan-Killiany regions, cross

  14. Use of affinity-directed liquid chromatography-mass spectrometry to map the epitopes of a factor VIII inhibitor antibody fraction

    PubMed Central

    Griffiths, Amy E.; Wang, Wensheng; Hagen, Fred K.; Fay, Philip J.

    2011-01-01

    Summary Background Neutralizing factor (F) VIII antibodies develop in ~30% of individuals with hemophilia A and show specificity to multiple sites in the FVIII protein. Methods Reactive epitopes to an immobilized IgG fraction prepared from a high-titer, FVIII inhibitor plasma were determined following immuno-precipitation (IP) of tryptic and chymotryptic peptides derived from digests of the A1 and A2 subunits of FVIIIa and FVIII light chain. Peptides were detected and identified using highly sensitive liquid chromatography-mass spectrometry (LC-MS). Results Coverage maps of the A1 subunit, A2 subunit and light chain represented 79%, 69% and 90%, respectively, of the protein sequences. Dot blots indicated that the inhibitor IgG reacted with epitopes contained within each subunit of FVIIIa. IP coupled with LC-MS identified 19 peptides representing epitopes from all FVIII A and C domains. The majority of peptides (10) were derived from the A2 domain. Three peptides mapped to the C2 domain, while two mapped to the A1 and A3 domains, and single peptides mapped to the a1 segment and C1 domain. Epitopes were typically defined by peptide sequences of <12 residues. Conclusions IP coupled with LC-MS identified extensive antibody reactivity at high resolution over the entire functional FVIII molecule and yielded sequence lengths of less than 15 residues. A number of the peptides identified mapped to known sequences involved in functionally important protein-protein and protein-membrane interactions. PMID:21668738

  15. Direct cDNA selection with DNA microdissected from mouse chromosome 16: isolation of novel clones and construction of a partial transcription map of the C3-C4 region.

    PubMed

    Wei, J; Hodes, M E; Wang, Y; Feng, Y; Ghetti, B; Dlouhy, S R

    1996-08-01

    A group of cDNA segments was selected by direct hybridization of mouse cerebellar cDNAs against genomic DNA pools generated by microdissection of the mouse chromosome 16 (MMU16) C3-C4 region. After elimination of repetitive sequences and adjustment for redundancy among clones, 34 novel cDNA fragments were isolated. The MMU16 origin of clones was confirmed by genetic linkage mapping. Reverse transcription PCR indicated that approximately 68% of the cDNAs represent transcripts that are expressed in adult mouse cerebellum. Northern blotting showed that some of these are predominantly or solely expressed in brain. This work demonstrates that DNA microdissected from banded MMU16 can be used for direct cDNA selection, thus enabling construction of a new, region-specific partial transcription map. This selected cDNA library should be a useful reagent for further molecular neurobiological studies.

  16. Human brain functional MRI and DTI visualization with virtual reality.

    PubMed

    Chen, Bin; Moreland, John; Zhang, Jingyu

    2011-12-01

    Magnetic resonance diffusion tensor imaging (DTI) and functional MRI (fMRI) are two active research areas in neuroimaging. DTI is sensitive to the anisotropic diffusion of water exerted by its macromolecular environment and has been shown useful in characterizing structures of ordered tissues such as the brain white matter, myocardium, and cartilage. The diffusion tensor provides two new types of information of water diffusion: the magnitude and the spatial orientation of water diffusivity inside the tissue. This information has been used for white matter fiber tracking to review physical neuronal pathways inside the brain. Functional MRI measures brain activations using the hemodynamic response. The statistically derived activation map corresponds to human brain functional activities caused by neuronal activities. The combination of these two methods provides a new way to understand human brain from the anatomical neuronal fiber connectivity to functional activities between different brain regions. In this study, virtual reality (VR) based MR DTI and fMRI visualization with high resolution anatomical image segmentation and registration, ROI definition and neuronal white matter fiber tractography visualization and fMRI activation map integration is proposed. Rationale and methods for producing and distributing stereoscopic videos are also discussed. PMID:23256049

  17. BOLD matches neuronal activity at the mm scale: a combined 7T fMRI and ECoG study in human sensorimotor cortex.

    PubMed

    Siero, Jeroen C W; Hermes, Dora; Hoogduin, Hans; Luijten, Peter R; Ramsey, Nick F; Petridou, Natalia

    2014-11-01

    High resolution BOLD fMRI has the potential to map activation patterns of small neuronal populations at the scale of cortical columns. However, BOLD fMRI does not measure neuronal activity, but only a correlate thereof, since it measures blood dynamics. To confirm that BOLD activation maps reflect neuronal population activity patterns, a direct comparison with neuro-electrophysiological data from the same cortical patch is necessary. Here, we compare BOLD activation patterns obtained with fMRI at 7 T to electrophysiological patterns obtained with implanted high density electrocorticography (ECoG) grids in the same patch of human sensorimotor cortex, and with similar resolution (1.5mm). We used high spatially sampled high-frequency broadband (HFB) power from ECoG, which reflects local neuronal population activity. The spatial distribution of 7 T BOLD activation matched the spatial distribution of ECoG HFB-power changes in the covered patch of sensorimotor cortex. BOLD fMRI activation foci were located within 1-3mm of the HFB-power ECoG foci. Both methods distinguished individual finger movement activation within a 1cm cortical patch, revealing a topographical medial to lateral layout for the little finger to index to thumb. These findings demonstrate that the BOLD signal at 7 T is strongly correlated with the underlying electrophysiology, and is capable of discriminating patterns of neuronal population activity at a millimeter scale. The results further indicate the utility of 7 T fMRI for investigation of intra-area organization of function and network dynamics.

  18. The relationship between MEG and fMRI.

    PubMed

    Hall, Emma L; Robson, Siân E; Morris, Peter G; Brookes, Matthew J

    2014-11-15

    In recent years functional neuroimaging techniques such as fMRI, MEG, EEG and PET have provided researchers with a wealth of information on human brain function. However none of these modalities can measure directly either the neuro-electrical or neuro-chemical processes that mediate brain function. This means that metrics directly reflecting brain 'activity' must be inferred from other metrics (e.g. magnetic fields (MEG) or haemodynamics (fMRI)). To overcome this limitation, many studies seek to combine multiple complementary modalities and an excellent example of this is the combination of MEG (which has high temporal resolution) with fMRI (which has high spatial resolution). However, the full potential of multi-modal approaches can only be truly realised in cases where the relationship between metrics is known. In this paper, we explore the relationship between measurements made using fMRI and MEG. We describe the origins of the two signals as well as their relationship to electrophysiology. We review multiple studies that have attempted to characterise the spatial relationship between fMRI and MEG, and we also describe studies that exploit the rich information content of MEG to explore differing relationships between MEG and fMRI across neural oscillatory frequency bands. Monitoring the brain at "rest" has become of significant recent interest to the neuroimaging community and we review recent evidence comparing MEG and fMRI metrics of functional connectivity. A brief discussion of the use of magnetic resonance spectroscopy (MRS) to probe the relationship between MEG/fMRI and neurochemistry is also given. Finally, we highlight future areas of interest and offer some recommendations for the parallel use of fMRI and MEG.

  19. Mapping the semantic structure of cognitive neuroscience.

    PubMed

    Beam, Elizabeth; Appelbaum, L Gregory; Jack, Jordynn; Moody, James; Huettel, Scott A

    2014-09-01

    Cognitive neuroscience, as a discipline, links the biological systems studied by neuroscience to the processing constructs studied by psychology. By mapping these relations throughout the literature of cognitive neuroscience, we visualize the semantic structure of the discipline and point to directions for future research that will advance its integrative goal. For this purpose, network text analyses were applied to an exhaustive corpus of abstracts collected from five major journals over a 30-month period, including every study that used fMRI to investigate psychological processes. From this, we generate network maps that illustrate the relationships among psychological and anatomical terms, along with centrality statistics that guide inferences about network structure. Three terms--prefrontal cortex, amygdala, and anterior cingulate cortex--dominate the network structure with their high frequency in the literature and the density of their connections with other neuroanatomical terms. From network statistics, we identify terms that are understudied compared with their importance in the network (e.g., insula and thalamus), are underspecified in the language of the discipline (e.g., terms associated with executive function), or are imperfectly integrated with other concepts (e.g., subdisciplines like decision neuroscience that are disconnected from the main network). Taking these results as the basis for prescriptive recommendations, we conclude that semantic analyses provide useful guidance for cognitive neuroscience as a discipline, both by illustrating systematic biases in the conduct and presentation of research and by identifying directions that may be most productive for future research.

  20. A proposal for PET/MRI attenuation correction with μ-values measured using a fixed-position radiation source and MRI segmentation

    NASA Astrophysics Data System (ADS)

    Kawaguchi, Hiroshi; Hirano, Yoshiyuki; Yoshida, Eiji; Kershaw, Jeff; Shiraishi, Takahiro; Suga, Mikio; Ikoma, Yoko; Obata, Takayuki; Ito, Hiroshi; Yamaya, Taiga

    2014-01-01

    Several MRI-based attenuation correction methods have been reported for PET/MRI; these methods are expected to make efficient use of high-quality anatomical MRIs and reduce the radiation dose for PET/MRI scanning. The accuracy of the attenuation map (μ-map) from an MRI depends on the accuracy of tissue segmentation and the attenuation coefficients to be assigned (μ-values). In this study, we proposed an MRI-based μ-value estimation method with a non-rotational radiation source to construct a suitable μ-map for PET/MRI. The proposed method uses an accurately segmented tissue map, the partial path length of each tissue, and detected intensities of attenuated radiation from a fixed-position (rather than a rotating) radiation source to obtain the μ-map. We estimated the partial path length from a virtual blank scan of fixed-point radiation with the same scanner geometry using the known tissue map from MRI. The μ-values of every tissue were estimated by inverting a linear relationship involving the partial path lengths and measured radioactivity intensity. Validation of the proposed method was performed by calculating a fixed- point data set based upon real a real transmission scan. The root-mean-square error between the μ-values derived from a conventional transmission scan and those obtained with our proposed method were 2.4±1.4%, 17.4±9.1% and 6.6±4.3% for brain, bone and soft tissue other than brain, respectively. Although the error estimates for bone and soft tissue are not insignificant, the method we propose is able to estimate the brain μ-value accurately and it is this factor that most strongly affects the quantitative value of PET images because of the large volumetric ratio of the brain.

  1. Tissue characterization in cerebral ischemia using multiparameter MRI

    NASA Astrophysics Data System (ADS)

    Soltanian-Zadeh, Hamid; Hammoud, Rabih; Jacobs, Michael A.; Patel, Suresh C.; Mitsias, Panayiotis D.; Pasnoor, Mamatha; Knight, Robert; Zheng, Zhang G.; Lu, Mei; Chopp, Michael

    2001-05-01

    After pre-processing and segmentation, the proposed method scores tissue regions between 1 and N. Score 1 is assigned to normal white matter and score N to CSF. Lesion zones are assigned a score based on their relative levels of similarities to white matter and CSF. To evaluate the method, 15 rats were imaged by a 7T MRI system at one of the three time points (acute, sub-acute, chronic) after MCA occlusion. Then, they were sacrificed and their brains were sliced and prepared for histological studies. MRI of 2 or 3 slices of each rat brain, using 2 DWI (b equals 400, b equals 800), 1 PDWI, 1 T2WI, and 1 T1WI, was used and an MRI score between 1 and 100 (N equals 100) was found for each region. Segmented regions were mapped onto the histology images and were scored by an experienced pathologist, from 1 to 10. MRI scores were validated using histology scores. To this end, correlation coefficients between the two scores (MRI and histology) were found. The results showed excellent correlations between MRI and histology scores at different time points.

  2. The physics of functional magnetic resonance imaging (fMRI)

    NASA Astrophysics Data System (ADS)

    Buxton, Richard B.

    2013-09-01

    Functional magnetic resonance imaging (fMRI) is a methodology for detecting dynamic patterns of activity in the working human brain. Although the initial discoveries that led to fMRI are only about 20 years old, this new field has revolutionized the study of brain function. The ability to detect changes in brain activity has a biophysical basis in the magnetic properties of deoxyhemoglobin, and a physiological basis in the way blood flow increases more than oxygen metabolism when local neural activity increases. These effects translate to a subtle increase in the local magnetic resonance signal, the blood oxygenation level dependent (BOLD) effect, when neural activity increases. With current techniques, this pattern of activation can be measured with resolution approaching 1 mm3 spatially and 1 s temporally. This review focuses on the physical basis of the BOLD effect, the imaging methods used to measure it, the possible origins of the physiological effects that produce a mismatch of blood flow and oxygen metabolism during neural activation, and the mathematical models that have been developed to understand the measured signals. An overarching theme is the growing field of quantitative fMRI, in which other MRI methods are combined with BOLD methods and analyzed within a theoretical modeling framework to derive quantitative estimates of oxygen metabolism and other physiological variables. That goal is the current challenge for fMRI: to move fMRI from a mapping tool to a quantitative probe of brain physiology.

  3. The physics of functional magnetic resonance imaging (fMRI)

    PubMed Central

    Buxton, Richard B

    2015-01-01

    Functional magnetic resonance imaging (fMRI) is a methodology for detecting dynamic patterns of activity in the working human brain. Although the initial discoveries that led to fMRI are only about 20 years old, this new field has revolutionized the study of brain function. The ability to detect changes in brain activity has a biophysical basis in the magnetic properties of deoxyhemoglobin, and a physiological basis in the way blood flow increases more than oxygen metabolism when local neural activity increases. These effects translate to a subtle increase in the local magnetic resonance signal, the blood oxygenation level dependent (BOLD) effect, when neural activity increases. With current techniques, this pattern of activation can be measured with resolution approaching 1 mm3 spatially and 1 s temporally. This review focuses on the physical basis of the BOLD effect, the imaging methods used to measure it, the possible origins of the physiological effects that produce a mismatch of blood flow and oxygen metabolism during neural activation, and the mathematical models that have been developed to understand the measured signals. An overarching theme is the growing field of quantitative fMRI, in which other MRI methods are combined with BOLD methods and analyzed within a theoretical modeling framework to derive quantitative estimates of oxygen metabolism and other physiological variables. That goal is the current challenge for fMRI: to move fMRI from a mapping tool to a quantitative probe of brain physiology. PMID:24006360

  4. Eosinophilic granuloma: MRI manifestations.

    PubMed

    Beltran, J; Aparisi, F; Bonmati, L M; Rosenberg, Z S; Present, D; Steiner, G C

    1993-01-01

    The appearance on magnetic resonance imaging (MRI) of 16 cases of pathologically proven eosinophilic granuloma were reviewed retrospectively and correlated with the radiographic appearance of the lesion. The most common MR appearance (ten cases) was a focal lesion, surrounded by an extensive, ill-defined bone marrow and soft tissue reaction with low signal intensity on T1-weighted images and high signal intensity on T2-weighted images, considered to represent bone marrow and soft tissue edema (the flare phenomenon). The MRI manifestations of eosinophilic granuloma, especially during the early stages, are nonspecific, and may stimulate an aggressive lesion such as osteomyelitis or Ewings sarcoma, or other benign bone tumors such as osteoid osteoma or chondroblastoma. PMID:8480200

  5. MRI of the penis.

    PubMed

    Kirkham, A

    2012-11-01

    MRI of the penis is an expensive test that is not always superior to clinical examination or ultrasound. However, it shows many of the important structures, and in particular the combination of tumescence from intracavernosal alprostadil, and high-resolution T(2) sequences show the glans, corpora and the tunica albuginea well. In this paper we summarise the radiological anatomy and discuss the indications for MRI. For penile cancer, it may be useful in cases where the local stage is not apparent clinically. In priapism, it is an emerging technique for assessing corporal viability, and in fracture it can in most cases make the diagnosis and locate the injury. In some cases of penile fibrosis and Peyronie's disease, it may aid surgical planning, and in complex pelvic fracture may replace or augment conventional urethrography. It is an excellent investigation for the malfunctioning penile prosthesis.

  6. Structural and functional correlates of visual field asymmetry in the human brain by diffusion kurtosis MRI and functional MRI.

    PubMed

    O'Connell, Caitlin; Ho, Leon C; Murphy, Matthew C; Conner, Ian P; Wollstein, Gadi; Cham, Rakie; Chan, Kevin C

    2016-11-01

    Human visual performance has been observed to show superiority in localized regions of the visual field across many classes of stimuli. However, the underlying neural mechanisms remain unclear. This study aims to determine whether the visual information processing in the human brain is dependent on the location of stimuli in the visual field and the corresponding neuroarchitecture using blood-oxygenation-level-dependent functional MRI (fMRI) and diffusion kurtosis MRI, respectively, in 15 healthy individuals at 3 T. In fMRI, visual stimulation to the lower hemifield showed stronger brain responses and larger brain activation volumes than the upper hemifield, indicative of the differential sensitivity of the human brain across the visual field. In diffusion kurtosis MRI, the brain regions mapping to the lower visual field showed higher mean kurtosis, but not fractional anisotropy or mean diffusivity compared with the upper visual field. These results suggested the different distributions of microstructural organization across visual field brain representations. There was also a strong positive relationship between diffusion kurtosis and fMRI responses in the lower field brain representations. In summary, this study suggested the structural and functional brain involvements in the asymmetry of visual field responses in humans, and is important to the neurophysiological and psychological understanding of human visual information processing.

  7. Superconducting magnets for MRI

    SciTech Connect

    Williams, J.E.

    1984-08-01

    Three types of magnets are currently used to provide the background field required for magnet resonance imaging (MRI). (i) Permanent magnets produce fields of up to 0.3 T in volumes sufficient for imaging the head or up to 0.15 T for whole body imaging. Cost and simplicity of operation are advantages, but relatively low field, weight (up to 100 tonnes) and, to a small extent, instability are limitations. (ii) Water-cooled magnets provide fields of up to 0.25 T in volumes suitable for whole body imaging, but at the expense of power (up to 150 kW for 0.25 T) and water-cooling. Thermal stability of the field requires the maintenance of constant temperature through periods both of use and of quiescence. (iii) Because of the limitations imposed by permanent and resistive magnets, particularly on field strength, the superconducting magnet is now most widely used to provide background fields of up to 2 T for whole body MRI. It requires very low operating power and that only for refrigeration. Because of the constant low temperature, 4.2 K, at which its stressed structure operates, its field is stable. The following review deals principally with superconducting magnets for MRI. However, the sections on field analysis apply to all types of magnet and the description of the source terms of circular coils and of the principals of design of solenoids apply equally to resistive solenoidal magnets.

  8. Data Collection and Analysis Strategies for phMRI

    PubMed Central

    Mandeville, Joseph B.; Liu, Christina H.; Vanduffel, Wim; Marota, John J.A.; Jenkins, Bruce G.

    2014-01-01

    Although functional MRI traditionally has been applied mainly to study changes in task-induced brain function, evolving acquisition methodologies and improved knowledge of signal mechanisms have increased the utility of this method for studying responses to pharmacological stimuli, a technique often dubbed “phMRI”. The proliferation of higher magnetic field strengths and the use of exogenous contrast agent have boosted detection power, a critical factor for successful phMRI due to the restricted ability to average multiple stimuli within subjects. Receptor-based models of neurovascular coupling, including explicit pharmacological models incorporating receptor densities and affinities and data-driven models that incorporate weak biophysical constraints, have demonstrated compelling descriptions of phMRI signal induced by dopaminergic stimuli. This report describes phMRI acquisition and analysis methodologies, with an emphasis on data-driven analyses. As an example application, statistically efficient data-driven regressors were used to describe the biphasic response to the mu-opioid agonist remifentanil, and antagonism using dopaminergic and GABAergic ligands revealed modulation of the mesolimbic pathway. Results illustrate the power of phMRI as well as our incomplete understanding of mechanisms underlying the signal. Future directions are discussed for phMRI acquisitions in human studies, for evolving analysis methodologies, and for interpretative studies using the new generation of simultaneous PET/MRI scanners. PMID:24613447

  9. Thoughts turned into high-level commands: Proof-of-concept study of a vision-guided robot arm driven by functional MRI (fMRI) signals.

    PubMed

    Minati, Ludovico; Nigri, Anna; Rosazza, Cristina; Bruzzone, Maria Grazia

    2012-06-01

    Previous studies have demonstrated the possibility of using functi