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Sample records for direct mri mapping

  1. Language Mapping Using fMRI and Direct Cortical Stimulation for Brain Tumor Surgery

    PubMed Central

    Brennan, Nicole Petrovich; Peck, Kyung K.; Holodny, Andrei

    2016-01-01

    Language functional magnetic resonance imaging for neurosurgical planning is a useful but nuanced technique. Consideration of primary and secondary language anatomy, task selection, and data analysis choices all impact interpretation. In the following chapter, we consider practical considerations and nuances alike for language functional magnetic resonance imaging in the support of and comparison with the neurosurgical gold standard, direct cortical stimulation. Pitfalls and limitations are discussed. PMID:26848555

  2. MRI Technologies in Recent Human Brain Mapping

    NASA Astrophysics Data System (ADS)

    Sasaki, Yuka

    The recent magnetic resonance imaging (MRI) technology and techniques used in human brain mapping are remarkable. They are getting, faster, stronger and better. The advanced MRI technologies and techniques include, but not to limited to, the magnetic resonance imaging at higher magnetic field strengths, diffusion tensor imaging, multimodal neuroimaging, and monkey functional MRI. In this article, these advanced MRI techniques are briefly overviewed.

  3. MRI temperature map reconstruction directly from k-space with compensation for heating-induced geometric distortions

    NASA Astrophysics Data System (ADS)

    Gaur, Pooja; Grissom, William A.

    2017-03-01

    Proton resonance frequency (PRF) change is used to measure tissue heating, but also distorts the image and causes geometric distortions in temperature estimates in the same manner as other chemical shift distortions if left uncompensated. We propose an algorithm that produces PRF temperature maps free of these distortions by fitting a signal model directly to acquired k-space data that accounts for PRF-induced phase both up to and during the readout. We also introduce a faster method compatible with Cartesian data that corrects distortions from image-domain temperature maps. Gel heating experiments show the proposed CS compensation algorithms correct magnitude image artifacts and hotspot distortions. Without CS compensation, thermal dose values are overestimated in spiral data, and are spatially offset in 2DFT and EPI data. Compensating for heat-induced CS distortions improves the accuracy of temperature change and thermal dose measurements, and can have a significant positive impact on clinical and research applications of PRF-shift thermometry.

  4. Clinical applications and future directions of functional MRI.

    PubMed

    Orringer, Daniel A; Vago, David R; Golby, Alexandra J

    2012-09-01

    First described for use in mapping the human visual cortex in 1991, functional magnetic resonance imaging (fMRI) is based on blood-oxygen level dependent (BOLD) changes in cortical regions that occur during specific tasks. Typically, an overabundance of oxygenated (arterial) blood is supplied during activation of brain areas. Consequently, the venous outflow from the activated areas contains a higher concentration of oxyhemoglobin, which changes the paramagnetic properties of the tissue that can be detected during a T2-star acquisition. fMRI data can be acquired in response to specific tasks or in the resting state. fMRI has been widely applied to studying physiologic and pathophysiologic diseases of the brain. This review will discuss the most common current clinical applications of fMRI as well as emerging directions.

  5. Neuroethics and fMRI: Mapping a Fledgling Relationship

    PubMed Central

    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

  6. Neuroethics and fMRI: mapping a fledgling relationship.

    PubMed

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

    2011-04-22

    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.

  7. Phantom-based investigation of nonrigid registration constraints in mapping fMRI to anatomical MRI

    NASA Astrophysics Data System (ADS)

    Studholme, Colin; Constable, R. Todd; Duncan, James S.

    2000-06-01

    In previous work we have introduced an approach to improving the registration of EPI fMRI data with anatomical MRI by accounting for differences in magnetic field induced geometric distortion in the two types of MRI acquisition. In particular we began to explore the use of imaging physics based constraints in a non-rigid multi-modality registration algorithm. In this paper we present phantom based experimental work examining the behavior of different non-rigid registration constraints compared to a field map acquisition of the MRI distortion. This acquisition provides a pixel by pixel 'ground truth' estimate of the displacement field within the EPI data. In our registration based approach we employ a B-spline based estimate of the relative geometric distortion with a multi-grid optimization scheme. We maximize the normalized mutual information between the two types of MRI scans to estimate the B-Spline parameters. Using the field map estimates as a gold standard, registration estimates using no additional geometric constraints are compared to those using the spin echo based signal conservation. We also examine the use of logarithmic EPI values in the criteria to provide additional sensitivity in areas of low signal. Results indicate that registration of EPI to conventional MRI incorporating a spin echo distortion model can provide comparable estimates of geometric distortion to those from field mapping data without the need for significant additional acquisitions during each fMRI sequence.

  8. 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

  9. Language Mapping Using fMRI and Direct Cortical Stimulation for Brain Tumor Surgery: The Good, the Bad, and the Questionable.

    PubMed

    Brennan, Nicole Petrovich; Peck, Kyung K; Holodny, Andrei

    2016-02-01

    Language functional magnetic resonance imaging for neurosurgical planning is a useful but nuanced technique. Consideration of primary and secondary language anatomy, task selection, and data analysis choices all impact interpretation. In the following chapter, we consider practical considerations and nuances alike for language functional magnetic resonance imaging in the support of and comparison with the neurosurgical gold standard, direct cortical stimulation. Pitfalls and limitations are discussed.

  10. 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

  11. 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.

  12. Computed inverse MRI for magnetic susceptibility map reconstruction

    PubMed Central

    Chen, Zikuan; Calhoun, Vince

    2015-01-01

    Objective This paper reports on a computed inverse magnetic resonance imaging (CIMRI) model for reconstructing the magnetic susceptibility source from MRI data using a two-step computational approach. Methods The forward T2*-weighted MRI (T2*MRI) process is decomposed into two steps: 1) from magnetic susceptibility source to fieldmap establishment via magnetization in a main field, and 2) from fieldmap to MR image formation by intravoxel dephasing average. The proposed CIMRI model includes two inverse steps to reverse the T2*MRI procedure: fieldmap calculation from MR phase image and susceptibility source calculation from the fieldmap. The inverse step from fieldmap to susceptibility map is a 3D ill-posed deconvolution problem, which can be solved by three kinds of approaches: Tikhonov-regularized matrix inverse, inverse filtering with a truncated filter, and total variation (TV) iteration. By numerical simulation, we validate the CIMRI model by comparing the reconstructed susceptibility maps for a predefined susceptibility source. Results Numerical simulations of CIMRI show that the split Bregman TV iteration solver can reconstruct the susceptibility map from a MR phase image with high fidelity (spatial correlation≈0.99). The split Bregman TV iteration solver includes noise reduction, edge preservation, and image energy conservation. For applications to brain susceptibility reconstruction, it is important to calibrate the TV iteration program by selecting suitable values of the regularization parameter. Conclusions The proposed CIMRI model can reconstruct the magnetic susceptibility source of T2*MRI by two computational steps: calculating the fieldmap from the phase image and reconstructing the susceptibility map from the fieldmap. The crux of CIMRI lies in an ill-posed 3D deconvolution problem, which can be effectively solved by the split Bregman TV iteration algorithm. PMID:22446372

  13. 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.

  14. 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.

  15. Apparent exchange rate mapping with diffusion MRI.

    PubMed

    Lasič, Samo; Nilsson, Markus; Lätt, Jimmy; Ståhlberg, Freddy; Topgaard, Daniel

    2011-08-01

    Water exchange through the cell membranes is an important feature of cells and tissues. The rate of exchange is determined by factors such as membrane lipid composition and organization, as well as the type and activity of aquaporins. A method for noninvasively estimating the rate of water exchange would be useful for characterizing pathological conditions, e.g., tumors, multiple sclerosis, and ischemic stroke, expected to be associated with a change of the membrane barrier properties. This study describes the filter exchange imaging method for determining the rate of water exchange between sites having different apparent diffusion coefficients. The method is based on the filter-exchange pulsed gradient spin-echo NMR spectroscopy experiment, which is here modified to be compatible with the constraints of clinical MR scanners. The data is analyzed using a model-free approach yielding maps of the apparent exchange rate, here being introduced in analogy with the concept of the apparent diffusion coefficient. Proof-of-principle experiments are performed on microimaging and whole-body clinical scanners using yeast suspension phantoms. The limitations and appropriate experimental conditions are examined. The results demonstrate that filter exchange imaging is a fast and reliable method for characterizing exchange, and that it has the potential to become a powerful diagnostic tool.

  16. 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

  17. [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.

  18. 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

  19. Prioritizing spatial accuracy in high-resolution fMRI data using multivariate feature weight mapping

    PubMed Central

    Buschmann, Tilo; Lohmann, Gabriele; Margulies, Daniel S.; Trampel, Robert; Turner, Robert

    2014-01-01

    Although ultra-high-field fMRI at field strengths of 7T or above provides substantial gains in BOLD contrast-to-noise ratio, when very high-resolution fMRI is required such gains are inevitably reduced. The improvement in sensitivity provided by multivariate analysis techniques, as compared with univariate methods, then becomes especially welcome. Information mapping approaches are commonly used, such as the searchlight technique, which take into account the spatially distributed patterns of activation in order to predict stimulus conditions. However, the popular searchlight decoding technique, in particular, has been found to be prone to spatial inaccuracies. For instance, the spatial extent of informative areas is generally exaggerated, and their spatial configuration is distorted. We propose the combination of a non-parametric and permutation-based statistical framework with linear classifiers. We term this new combined method Feature Weight Mapping (FWM). The main goal of the proposed method is to map the specific contribution of each voxel to the classification decision while including a correction for the multiple comparisons problem. Next, we compare this new method to the searchlight approach using a simulation and ultra-high-field 7T experimental data. We found that the searchlight method led to spatial inaccuracies that are especially noticeable in high-resolution fMRI data. In contrast, FWM was more spatially precise, revealing both informative anatomical structures as well as the direction by which voxels contribute to the classification. By maximizing the spatial accuracy of ultra-high-field fMRI results, global multivariate methods provide a substantial improvement for characterizing structure-function relationships. PMID:24795548

  20. 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.

  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. 3D mapping of somatotopic reorganization with small animal functional MRI

    PubMed Central

    Yu, Xin; Wang, Shumin; Chen, Der-Yow; Dodd, Stephen; Goloshevsky, Artem; Koretsky, Alan P.

    2009-01-01

    There are few in vivo noninvasive methods to study neuroplasticity in animal brains. Functional MRI (fMRI) has been developed for animal brain mapping, but few fMRI studies have analyzed functional alteration due to plasticity in animal models. One major limitation is that fMRI maps are characterized by statistical parametric mapping making the apparent boundary dependent on the statistical threshold used. Here, we developed a method to characterize the location of center-of-mass in fMRI maps that is shown not to be sensitive to statistical threshold. Utilizing centers-of-mass as anchor points to fit the spatial distribution of the BOLD response enabled quantitative group analysis of altered boundaries of functional somatosensory maps. This approach was used to study cortical reorganization in the rat primary somatosensory cortex (S1) after sensory deprivation to the barrel cortex by follicle ablation (F.A.). FMRI demonstrated an enlarged nose S1 representation in the 3D somatotopic functional maps. This result clearly demonstrates that fMRI enables the spatial mapping of functional changes that can characterize multiple regions of S1 cortex and still be sensitive to changes due to plasticity. PMID:19770051

  4. Trabecular bone volume fraction mapping by low-resolution MRI.

    PubMed

    Fernández-Seara, M A; Song, H K; Wehrli, F W

    2001-07-01

    Trabecular bone volume fraction (TBVF) is highly associated with the mechanical competence of trabecular bone. TBVF is ordinarily measured by histomorphometry from bone biopsies or, noninvasively, by means of high-resolution microcomputed tomography and, more recently, by micro-MRI. The latter methods require spatial resolution sufficient to resolve trabeculae, along with segmentation techniques that allow unambiguous assignment of the signal to bone or bone marrow. In this article it is shown that TBVF can be measured under low-resolution conditions by exploiting the attenuation of the MR signal resulting from fractional occupancy of the imaging voxel by bone and bone marrow, provided that a reference signal is available from a marrow volume devoid of trabeculation. The method requires accurate measurement of apparent proton density, which entails correction for various sources of error. Key among these are the spatial nonuniformity in the RF field amplitude and effects of the slice profile, which are determined by B(1) field mapping and numerical integration of the Bloch equations, respectively. By contrast, errors from variations in bone marrow composition (hematopoietic vs. fatty) between trabecular and reference site are predicted to be small and usually negligible. The method was evaluated in phantoms and in vivo in the distal radius and found to be accurate to 1% in marrow volume fraction. Finally, in a group of 12 patients of varying skeletal status, TBVF in the calcaneus was found to strongly correlate with integral bone mineral density of the lumbar vertebrae (r(2) = 0.83, p < 0.0001). The method may fail in large imaging objects such as the human trunk at high magnetic field where standing wave and RF penetration effects cause intensity variations that cannot be corrected. Magn Reson Med 46:103-113, 2001.

  5. Computer-aided diagnosis of early knee osteoarthritis based on MRI T2 mapping.

    PubMed

    Wu, Yixiao; Yang, Ran; Jia, Sen; Li, Zhanjun; Zhou, Zhiyang; Lou, Ting

    2014-01-01

    This work was aimed at studying the method of computer-aided diagnosis of early knee OA (OA: osteoarthritis). Based on the technique of MRI (MRI: Magnetic Resonance Imaging) T2 Mapping, through computer image processing, feature extraction, calculation and analysis via constructing a classifier, an effective computer-aided diagnosis method for knee OA was created to assist doctors in their accurate, timely and convenient detection of potential risk of OA. In order to evaluate this method, a total of 1380 data from the MRI images of 46 samples of knee joints were collected. These data were then modeled through linear regression on an offline general platform by the use of the ImageJ software, and a map of the physical parameter T2 was reconstructed. After the image processing, the T2 values of ten regions in the WORMS (WORMS: Whole-organ Magnetic Resonance Imaging Score) areas of the articular cartilage were extracted to be used as the eigenvalues in data mining. Then,a RBF (RBF: Radical Basis Function) network classifier was built to classify and identify the collected data. The classifier exhibited a final identification accuracy of 75%, indicating a good result of assisting diagnosis. Since the knee OA classifier constituted by a weights-directly-determined RBF neural network didn't require any iteration, our results demonstrated that the optimal weights, appropriate center and variance could be yielded through simple procedures. Furthermore, the accuracy for both the training samples and the testing samples from the normal group could reach 100%. Finally, the classifier was superior both in time efficiency and classification performance to the frequently used classifiers based on iterative learning. Thus it was suitable to be used as an aid to computer-aided diagnosis of early knee OA.

  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. Vervet MRI atlas and label map for fully automated morphometric analyses.

    PubMed

    Maldjian, Joseph A; Daunais, James B; Friedman, David P; Whitlow, Christopher T

    2014-10-01

    Currently available non-human primate templates typically require input of a skull-stripped brain for structural processing. This can be a manually intensive procedure, and considerably limits their utility. The purpose of this study was to create a vervet MRI population template, associated tissue probability maps (TPM), and a label atlas to facilitate true fully automated Magnetic Resonance Imaging (MRI) structural analyses for morphometric analyses. Structural MRI scans of ten vervet monkeys (Chlorocebus aethiops) scanned at three time points were used in this study. An unbiased population average template was created using a symmetric diffeomorphic registration (SyN) procedure. Skull stripping, segmentation, and label map generation were performed using the publically available rhesus INIA19 MRI template and NeuroMap label atlas. A six-class TPM and a six-layer two-class normalization template was created from the vervet segmentation for use within the Statistical Parametric Mapping (SPM) framework. Fully automated morphologic processing of all of the vervet MRI scans was then performed using the vervet TPM and vervet normalization template including skull-stripping, segmentation and normalization. The vervet template creation procedure resulted in excellent skull stripping, segmentation, and NeuroMap atlas labeling with 720 structures successfully registered. Fully automated processing was accomplished for all vervet scans, demonstrating excellent skull-stripping, segmentation, and normalization performance. We describe creation of an unbiased vervet structural MRI population template and atlas. The template includes an associated six-class TPM and DARTEL six-layer two-class normalization template for true fully automated skull-stripping, segmentation, and normalization of vervet structural T1-weighted MRI scans. We provide the most detailed vervet label atlas currently available based on the NeuroMaps atlas with 720 labels successfully registered. We

  8. Functional circuit mapping of striatal output nuclei using simultaneous deep brain stimulation and fMRI.

    PubMed

    Van Den Berge, Nathalie; Albaugh, Daniel L; Salzwedel, Andrew; Vanhove, Christian; Van Holen, Roel; Gao, Wei; Stuber, Garret D; Ian Shih, Yen-Yu

    2017-02-01

    The substantia nigra pars reticulata (SNr) and external globus pallidus (GPe) constitute the two major output targets of the rodent striatum. Both the SNr and GPe converge upon thalamic relay nuclei (directly or indirectly, respectively), and are traditionally modeled as functionally antagonistic relay inputs. However, recent anatomical and functional studies have identified unanticipated circuit connectivity in both the SNr and GPe, demonstrating their potential as far more than relay nuclei. In the present study, we employed simultaneous deep brain stimulation and functional magnetic resonance imaging (DBS-fMRI) with cerebral blood volume (CBV) measurements to functionally and unbiasedly map the circuit- and network level connectivity of the SNr and GPe. Sprague-Dawley rats were implanted with a custom-made MR-compatible stimulating electrode in the right SNr (n=6) or GPe (n=7). SNr- and GPe-DBS, conducted across a wide range of stimulation frequencies, revealed a number of surprising evoked responses, including unexpected CBV decreases within the striatum during DBS at either target, as well as GPe-DBS-evoked positive modulation of frontal cortex. Functional connectivity MRI revealed global modulation of neural networks during DBS at either target, sensitive to stimulation frequency and readily reversed following cessation of stimulation. This work thus contributes to a growing literature demonstrating extensive and unanticipated functional connectivity among basal ganglia nuclei.

  9. A novel approach to image neural activity directly by MRI

    NASA Astrophysics Data System (ADS)

    Singh, Manbir; Sungkarat, Witaya

    2005-04-01

    Though an approach to image the electrical activity of neurons directly by detecting phase shifts in MRI was first reported in 1991, results to-date remain equivocal due to the low signal-to-noise ratio. The objective of this work was to develop a stimulus-presentation and data acquisition strategy specially geared to detect phase-dispersion effects of neuronal currents within 10-100 ms following stimulation. The key feature is to set the repeated MR data acquisition time TR and the stimulus presentation interval (TI) slightly different from each other so that the time at which images are acquired shifts gradually from one acquisition to the next with respect to stimulus onset. For example, at TR=275ms and 4 Hz stimulus presentation (TI=250ms), initial synchronization of the stimulus onset and MR acquisition would result in the first image being acquired at a latency of 0+/- (temporal width of data acquisition window), second image at a latency of 25ms, third image at a latency of 50ms and so on up to a latency of 250ms, at which time the stimulus and data acquisition times would become re-synchronized to once again acquire an image at latency=0. Human data were acquired on a 1.5T GE EXCITE scanner from two 8mm thick contiguous slices bracketing the calcarine fissure during a checkerboard flashing at 4 Hz. Preliminary results show activity in the visual cortex at latencies consistent with EEG studies, suggesting the potential of this methodology to image neural activity directly.

  10. Paradigm-free mapping with morphological component analysis: getting most out of fMRI data

    NASA Astrophysics Data System (ADS)

    Caballero Gaudes, César; Van De Ville, Dimitri; Petridou, Natalia; Lazeyras, François; Gowland, Penny

    2011-09-01

    Functional magnetic resonance imaging (fMRI) is a non-invasive imaging technique that maps the brain's response to neuronal activity based on the blood oxygenation level dependent (BOLD) effect. This work proposes a novel method for fMRI data analysis that enables the decomposition of the fMRI signal in its sources based on morphological descriptors. Beyond traditional fMRI hypothesis-based or blind data-driven exploratory approaches, this method allows the detection of BOLD responses without prior timing information. It is based on the deconvolution of the neuronal-related haemodynamic component of the fMRI signal with paradigm free mapping and also furnishes estimates of the movement-related effects, instrumental drifts and physiological fluctuations. Our algorithm is based on an overcomplete representation of the fMRI voxel time series with an additive linear model that is recovered by means of a L1-norm regularized least-squares estimators and an adapted block coordinate relaxation procedure. The performance of the technique is evaluated with simulated data and real experimental data acquired at 3T.

  11. Topographical organization of human corpus callosum: an fMRI mapping study.

    PubMed

    Fabri, Mara; Polonara, Gabriele; Mascioli, Giulia; Salvolini, Ugo; Manzoni, Tullio

    2011-01-25

    The concept of a topographical map of the corpus callosum (CC) has emerged from human lesion studies and from 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 data on the cortical representation of tactile, gustatory, and visual sensitivity and of motor activation, obtained in 36 volunteers. Activation foci were consistently detected in discrete CC regions: anterior (taste stimuli), central (motor tasks), central and posterior (tactile stimuli), and splenium (visual stimuli). These findings demonstrate that the functional topography of the CC can be explored with fMRI.

  12. Individual fMRI maps of all phalanges and digit bases of all fingers in human primary somatosensory cortex

    PubMed Central

    Schweisfurth, Meike A.; Frahm, Jens; Schweizer, Renate

    2014-01-01

    This study determined the individual maps of all fingers in Brodmann area 3b of the human primary somatosensory cortex in a single fMRI session by tactile stimulation at 19 sites across all phalanges and digit bases of the 5 right-hand digits. To quantify basic features of the digit maps within and across subjects, we applied standard descriptive measures, but also implemented a novel quantitative analysis. This so-called Direction/Order (DiOr) method tested whether subjects exhibited an ordering of peak fMRI representations along their individual direction of alignment through the set of analyzed phalanges and whether these individual directions were similar across subjects. Across-digit analysis demonstrated that for each set of homologous phalanges, the D5-to-D1 representations were successively represented along a common direction of alignment. Hence, the well-known mediolateral D5-to-D1 somatotopy was not only confirmed for the distal phalanges (p1), but could also be shown for the medial (p2) and proximal phalanges (p3). In contrast, the peak activation for the digit bases (p4) only partly elicited that digit succession. Complementary, intra-digit analysis revealed a divergent picture of map topography for the different digits. Within D5 (and in a trend: D4), an ordered p1-to-p3 succession was found across subjects, pointing to a consistent intra-digit somatotopy for D5, with p3 generally found medial-posterior to p1. In contrast, for D1, D2, and D3, most subjects did not present with ordered p1-to-p3 maps nor were directions of alignment similarly oriented between subjects. These digits therefore exhibited highly diverse representation patterns across subjects. PMID:25228867

  13. 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

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

    PubMed Central

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

    2016-01-01

    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 7 T. PMID:27181764

  15. New directions in the design of MRI gradient coils

    NASA Astrophysics Data System (ADS)

    Baig, Tanvir Noor

    In this dissertation new designs for gradient coils are presented. The principal work is on better shielding for fringe field reduction. Fringe fields from gradient coils produce eddy currents in surrounding metal structures. Such eddy currents can degrade image quality and lead to acoustic noise. The acoustic effects are magnified for high-field Magnetic Resonance Imaging (MRI) scanners because of increased Lorentz forces. Conventional actively shielded gradient assemblies consist of primary and secondary coils in the shape of cylindrical shells surrounding the imaging volume. One of the principal regions of field leakage is at the ends of the gradient structure, and these fields are responsible for substantial eddy current generation. Our new shielded gradient coil designs that feature the inclusion of an endcap have significantly reduced fringe field at the cryostat inner bore. We discuss the degree to which the suppression of peak fringe fields corresponds to a reduction in the acoustic noise generated near the end of the warm bore. Energy efficient capped actively shielded elliptical gradient coils are also designed. In comparison with traditional uncapped elliptical designs the newly proposed design substantially reduces the fringe field at the inner cryostat bore. And compared to a cylindrical design (with a diameter matched to the elliptical semi-major axis), a good reduction in magnetic energy is observed. In addition, a design for a very short, symmetrical, and winged X-gradient insertable head coil is presented. With a smaller radius, an insertable head gradient coil has the advantage of less stored magnetic energy. The corresponding smaller inductance leads to higher slew rates. Lower torque from Lorentz forces is another advantage for these coils. When designing an insertable head coil one must remember the geometry is impacted by the shoulders. In consequence, asymmetric unshielded and shielded designs have been developed. Gradient designs with a

  16. Structural and functional quantitative susceptibility mapping from standard fMRI studies.

    PubMed

    Sun, H; Seres, P; Wilman, A H

    2017-04-01

    Standard functional MRI (fMRI), which includes resting-state or paradigm-driven designs, is widely used in studies of brain function, aging, and disease. These fMRI studies typically use two-dimensional gradient echo-planar imaging, which inherently contains phase data that enables quantitative susceptibility mapping (QSM). This work focuses on the dual value of QSM within fMRI studies, by providing both a localized analysis of functional changes in activated tissue, and iron-sensitive structural maps in deep grey matter (DGM). Using a visual paradigm fMRI study on healthy volunteers at clinical (1.5 T) and high field strength (4.7 T), we perform functional analysis of magnitude and QSM time series, and at the same time harness structural QSM of iron-rich DGM, including globus pallidus, putamen, caudate head, substantia nigra, and red nucleus. The effects of fMRI spatial resolution and time series variation on structural DGM QSM are investigated. Our results indicate that structural DGM QSM is feasible within existing fMRI studies, provided that the voxel dimensions are equal to or less than 3 mm, with higher resolutions preferred. The mean DGM QSM values were about 40 to 220 ppb, while the interquartile ranges of the DGM QSM time series varied from about 3 to 9 ppb, depending on structure and resolution. In contrast, the peak voxel functional QSM (fQSM) changes in activated visual cortex ranged from about -10 to -30 ppb, and functional clusters were consistently smaller on QSM than magnitude fMRI. Mean-level DGM QSM of the time series was successfully extracted in all cases, while fQSM results were more prone to residual background fields and showed less functional change compared with standard magnitude fMRI. Under the conditions prescribed, standard fMRI studies may be used for robust mean-level DGM QSM, enabling study of DGM iron accumulation, in addition to functional analysis. Copyright © 2016 John Wiley & Sons, Ltd.

  17. Velocity Gradient Maps Directly Measured by PLF

    NASA Astrophysics Data System (ADS)

    Quintella, Cristina M.; Gonçalves, Cristiane C.; Lima, Angelo Mv; Pepe, Iuri M.

    2000-11-01

    Flows are macroscopically classified as laminar or turbulent due to their velocity distributions, nevertheless most chemical and biological phenomena are yield or enhanced by intermolecular orientation and microscopic turbulence. Here was studied a 100micra liquid sheet produced by a slit nozzle, both flowing freely into air and over a borosilicate surface (roughness bellow 5nm), ranging from 17 to 36Re (143 to 297cm/s, similar to muscles and brain blood flow). Mono ethylene glycol was used either pure, or with sodium alkyl benzene sulfated (ABS) surfactant (24.5mol/L, submicellar), or with poly(ethylene oxide) (PEO) (1409ppm, 4millions aw). Velocity gradients were directly measured by 514nm polarized laser induced fluorescence (PLF) with R6G as probe. Intermolecular alignment (IA) maps were obtained all over the flow (about 1,950 points, 0.02mm2 precision). The free jet average IA has increased 57% when flowing over borosilicate. With ABS, the IA increased, suggesting wall drag reduction. With PEO the IA decreases due to solvent intermolecular forces attenuation, generating wider turbulent areas. PLF proved to be an excellent method to evaluate IA within liquid thin flows. Chosen solute additions permits IA control over wide regions.

  18. Non-invasive temperature mapping using temperature-responsive water saturation shift referencing (T-WASSR) MRI

    PubMed Central

    Liu, Guanshu; Qin, Qin; Chan, Kannie W.Y.; Li, Yuguo; Bulte, Jeff W.M.; McMahon, Michael T.; van Zijl, Peter C.M.; Gilad, Assaf A.

    2014-01-01

    We present a non-invasive MRI approach for assessing the water proton resonance frequency (PRF) shifts associated with changes in temperature. This method is based on Water Saturation Shift Referencing (WASSR), a method first developed for assessing B0 field inhomogeneity. Temperature-induced water PRF shifts were determined by estimating the frequency of the minimum intensity of the water direct saturation spectrum at each temperature using Lorentzian line-shape fitting. The change in temperature was then calculated from the difference in water PRF shifts between temperatures. Optimal acquisition parameters were first estimated using simulations and later confirmed experimentally. Results in vitro and in vivo showed that the temperature changes measured using the temperature-responsive WASSR (T-WASSR) were in good agreement with those obtained with MR spectroscopy or phase mapping-based water PRF measurement methods,. In addition, the feasibility of temperature mapping in fat-containing tissue is demonstrated in vitro. In conclusion, the T-WASSR approach provides an alternative for non-invasive temperature mapping by MRI, especially suitable for temperature measurements in fat-containing tissues. PMID:24395616

  19. Fractional ventilation mapping using inert fluorinated gas MRI in rat models of inflammation and fibrosis.

    PubMed

    Couch, Marcus J; Fox, Matthew S; Viel, Chris; Gajawada, Gowtham; Li, Tao; Ouriadov, Alexei V; Albert, Mitchell S

    2016-05-01

    The purpose of this study was to extend established methods for fractional ventilation mapping using (19) F MRI of inert fluorinated gases to rat models of pulmonary inflammation and fibrosis. In this study, five rats were instilled with lipopolysaccharide (LPS) in the lungs two days prior to imaging, six rats were instilled with bleomycin in the lungs two weeks prior to imaging and an additional four rats were used as controls. (19) F MR lung imaging was performed at 3 T with rats continuously breathing a mixture of sulfur hexafluoride and O2 . Fractional ventilation maps were obtained using a wash-out approach, by switching the breathing mixture to pure O2 , and acquiring images following each successive wash-out breath. The mean fractional ventilation (r) was 0.29 ± 0.05 for control rats, 0.23 ± 0.10 for LPS-instilled rats and 0.19 ± 0.03 for bleomycin-instilled rats. Bleomycin-instilled rats had a significantly decreased mean r value compared with controls (P = 0.010). Although LPS-instilled rats had a slightly reduced mean r value, this trend was not statistically significant (P = 0.556). Fractional ventilation gradients were calculated in the anterior/posterior (A/P) direction, and the mean A/P gradient was -0.005 ± 0.008 cm(-1) for control rats, 0.013 ± 0.005 cm(-1) for LPS-instilled rats and 0.009 ± 0.018 cm(-1) for bleomycin-instilled rats. Fractional ventilation gradients were significantly different for control rats compared with LPS-instilled rats only (P = 0.016). The ventilation gradients calculated from control rats showed the expected gravitational relationship, while ventilation gradients calculated from LPS- and bleomycin-instilled rats showed the opposite trend. Histology confirmed that LPS-instilled rats had a significantly elevated alveolar wall thickness, while bleomycin-instilled rats showed signs of substantial fibrosis. Overall, (19)F MRI may be able to detect the effects of pulmonary

  20. 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

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

    PubMed

    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.

  2. Mapping cerebrovascular reactivity using concurrent fMRI and near infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Tong, Yunjie; Bergethon, Peter R.; Frederick, Blaise d.

    2011-02-01

    Cerebrovascular reactivity (CVR) reflects the compensatory dilatory capacity of cerebral vasculature to a dilatory stimulus and is an important indicator of brain vascular reserve. fMRI has been proven to be an effective imaging technique to obtain the CVR map when the subjects perform CO2 inhalation or the breath holding task (BH). However, the traditional data analysis inaccurately models the BOLD using a boxcar function with fixed time delay. We propose a novel way to process the fMRI data obtained during a blocked BH by using the simultaneously collected near infrared spectroscopy (NIRS) data as regressor1. In this concurrent NIRS and fMRI study, 6 healthy subjects performed a blocked BH (5 breath holds with 20s durations intermitted by 40s of regular breathing). A NIRS probe of two sources and two detectors separated by 3 cm was placed on the right side of prefrontal area of the subjects. The time course of changes in oxy-hemoglobin (Δ[HbO]) was calculated from NIRS data and shifted in time by various amounts, and resampled to the fMRI acquisition rate. Each shifted time course was used as regressor in FEAT (the analysis tool in FSL). The resulting z-statistic maps were concatenated in time and the maximal value was taken along the time for all the voxels to generate a 3-D CVR map. The new method produces more accurate and thorough CVR maps; moreover, it enables us to produce a comparable baseline cerebral vascular map if applied to resting state (RS) data.

  3. 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

  4. A Novel MRI-compatible Tactile Stimulator for Cortical Mapping of Foot Sole Pressure Stimuli with fMRI

    PubMed Central

    Hao, Ying; Manor, Brad; Liu, Jing; Zhang, Kai; Chai, Yufeng; Lipsitz, Lewis; Peng, Chung-Kang; Novak, Vera; Wang, Xiaoying; Zhang, Jue; Fang, Jing

    2013-01-01

    Foot sole somatosensory feedback is critical to motor control and declines with aging and disease. To enable study of cortical networks underlying foot sole somatosensation we developed a pneumatic tactile stimulator capable of producing 1-DOF oscillations with preset waveform, frequency (≤10 Hz), force magnitude (5-500 N), duty cycle (20%-100%) and contacted surface area over which pressures are applied to the foot sole. Image tests (anatomical/functional/field map) of a phantom demonstrated that the device is compatible with 3T MRI. GRE-EPI images of seven healthy young adults using a typical block-designed 1Hz sinusoidal stimulation protocol revealed significant activation contralaterally within the primary somatosensory cortex and paracentral gyrus, and bilaterally within the secondary somatosensory cortex. The stimulation system may therefore serve as a research tool to study functional brain networks involved in the perception and modulation of foot sole somatosensation and its relationship to motor control. PMID:22678849

  5. 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.

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

    PubMed

    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.

  7. 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).

  8. Head direction maps remain stable despite grid map fragmentation.

    PubMed

    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.

  9. 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

  10. 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.

  11. Can Visually Impaired Children Use Tactile Maps to Estimate Directions?

    ERIC Educational Resources Information Center

    Ungar, S.; And Others

    1994-01-01

    Eighty-eight children (either totally blind or with residual vision) estimated directions between landmarks in a large scale layout of objects. Children experienced the layout either directly by walking around it or indirectly by examining a tactile map. Use of tactile maps considerably facilitated the performance of the blind children. (Author/DB)

  12. 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.

  13. Does functional MRI detect activation in white matter? A review of emerging evidence, issues, and future directions

    PubMed Central

    Gawryluk, Jodie R.; Mazerolle, Erin L.; D'Arcy, Ryan C. N.

    2014-01-01

    Functional magnetic resonance imaging (fMRI) is a non-invasive technique that allows for visualization of activated brain regions. Until recently, fMRI studies have focused on gray matter. There are two main reasons white matter fMRI remains controversial: (1) the blood oxygen level dependent (BOLD) fMRI signal depends on cerebral blood flow and volume, which are lower in white matter than gray matter and (2) fMRI signal has been associated with post-synaptic potentials (mainly localized in gray matter) as opposed to action potentials (the primary type of neural activity in white matter). Despite these observations, there is no direct evidence against measuring fMRI activation in white matter and reports of fMRI activation in white matter continue to increase. The questions underlying white matter fMRI activation are important. White matter fMRI activation has the potential to greatly expand the breadth of brain connectivity research, as well as improve the assessment and diagnosis of white matter and connectivity disorders. The current review provides an overview of the motivation to investigate white matter fMRI activation, as well as the published evidence of this phenomenon. We speculate on possible neurophysiologic bases of white matter fMRI signals, and discuss potential explanations for why reports of white matter fMRI activation are relatively scarce. We end with a discussion of future basic and clinical research directions in the study of white matter fMRI. PMID:25152709

  14. Effective connectivity of the multiplication network: a functional MRI and multivariate Granger Causality Mapping study.

    PubMed

    Krueger, Frank; Landgraf, Steffen; van der Meer, Elke; Deshpande, Gopikrishna; Hu, Xiaoping

    2011-09-01

    Developmental neuropsychology and functional neuroimaging evidence indicates that simple and complex mental calculation is subserved by a fronto-parietal network. However, the effective connectivity (connection direction and strength) among regions within the fronto-parietal network is still unexplored. Combining event-related fMRI and multivariate Granger Causality Mapping (GCM), we administered a multiplication verification task to healthy participants asking them to solve single and double-digit multiplications. The goals of our study were first, to identify the effective connectivity of the multiplication network, and second, to compare the effective connectivity patterns between a low and a high arithmetical competence (AC) group. The manipulation of multiplication difficulty revealed a fronto-parietal network encompassing bilateral intraparietal sulcus (IPS), left pre-supplementary motor area (PreSMA), left precentral gyrus (PreCG), and right dorsolateral prefrontal cortex (DLPFC). The network was driven by an intraparietal IPS-IPS circuit hosting a representation of numerical quantity intertwined with a fronto-parietal DLPFC-IPS circuit engaged in temporary storage and updating of arithmetic operations. Both circuits received additional inputs from the PreCG and PreSMA playing more of a supportive role in mental calculation. The high AC group compared to the low AC group displayed a greater activation in the right IPS and based its calculation more on a feedback driven intraparietal IPS-IPS circuit, whereas the low competence group more on a feedback driven fronto-parietal DLPFC-IPS circuit. This study provides first evidence that multivariate GCM is a sensitive approach to investigate effective connectivity of mental processes involved in mental calculation and to compare group level performances for different populations.

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

    PubMed

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

    2014-12-01

    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. >20ms, the sensitivity to small axons (diameter<2μm) 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 (1-5ms). 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 of ~1.27-5.54μm). The estimated values were in good agreement with histology, including the small axon diameters (<2.5μm). This study establishes a framework for the quantification of nerve morphology using the OGSE method with high sensitivity to small axons.

  16. 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

  17. 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

  18. Imaging electric properties of biological tissues by RF field mapping in MRI.

    PubMed

    Zhang, Xiaotong; Zhu, Shanan; He, Bin

    2010-02-01

    The electric properties (EPs) of biological tissue, i.e., the electric conductivity and permittivity, can provide important information in the diagnosis of various diseases. The EPs also play an important role in specific absorption rate calculation, a major concern in high-field MRI, as well as in nonmedical areas such as wireless telecommunications. The high-field MRI system is accompanied by significant wave propagation effects, and the RF radiation is dependent on the EPs of biological tissue. On the basis of the measurement of the active transverse magnetic component of the applied RF field (known as B(1)-mapping technique), we propose a dual-excitation algorithm, which uses two sets of measured B(1) data to noninvasively reconstruct the EPs of biological tissues. The finite-element method was utilized in 3-D modeling and B(1) field calculation. A series of computer simulations were conducted to evaluate the feasibility and performance of the proposed method on a 3-D head model within a TEM coil and a birdcage coil. Using a TEM coil, when noise free, the reconstructed EP distribution of tissues in the brain has relative errors of 12%-28% and correlated coefficients of greater than 0.91. Compared with other B(1)-mapping-based reconstruction algorithms, our approach provides superior performance without the need for iterative computations. The present simulation results suggest that good reconstruction of EPs from B1 mapping can be achieved.

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

    PubMed Central

    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

  20. 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

  1. 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.

  2. A stereotaxic MRI template set for the rat brain with tissue class distribution maps and co-registered anatomical atlas: application to pharmacological MRI.

    PubMed

    Schwarz, Adam J; Danckaert, Anne; Reese, Torsten; Gozzi, Alessandro; Paxinos, George; Watson, Charles; Merlo-Pich, Emilio V; Bifone, Angelo

    2006-08-15

    We describe a stereotaxic rat brain MRI template set with a co-registered digital anatomical atlas and illustrate its application to the analysis of a pharmacological MRI (phMRI) study of apomorphine. The template set includes anatomical images and tissue class probability maps for brain parenchyma and cerebrospinal fluid (CSF). These facilitate the use of standard fMRI software for spatial normalisation and tissue segmentation of rat brain data. A volumetric reconstruction of the Paxinos and Watson rat brain atlas is also co-localised with the template, enabling the atlas structure and stereotaxic coordinates corresponding to a feature within a statistical map to be interactively reported, facilitating the localisation of functional effects. Moreover, voxels falling within selected brain structures can be combined to define anatomically based 3D volumes of interest (VOIs), free of operator bias. As many atlas structures are small relative to the typical resolution of phMRI studies, a mechanism for defining composite structures as agglomerations of individual atlas structures is also described. This provides a simple and robust means of interrogating structures that are otherwise difficult to delineate and an objective framework for comparing and classifying compounds based on an anatomical profile of their activity. These developments allow a closer alignment of pre-clinical and clinical analysis techniques.

  3. Evaluation of Field Map and Nonlinear Registration Methods for Correction of Susceptibility Artifacts in Diffusion MRI

    PubMed Central

    Wang, Sijia; Peterson, Daniel J.; Gatenby, J. C.; Li, Wenbin; Grabowski, Thomas J.; Madhyastha, Tara M.

    2017-01-01

    Correction of echo planar imaging (EPI)-induced distortions (called “unwarping”) improves anatomical fidelity for diffusion magnetic resonance imaging (MRI) and functional imaging investigations. Commonly used unwarping methods require the acquisition of supplementary images during the scanning session. Alternatively, distortions can be corrected by nonlinear registration to a non-EPI acquired structural image. In this study, we compared reliability using two methods of unwarping: (1) nonlinear registration to a structural image using symmetric normalization (SyN) implemented in Advanced Normalization Tools (ANTs); and (2) unwarping using an acquired field map. We performed this comparison in two different test-retest data sets acquired at differing sites (N = 39 and N = 32). In both data sets, nonlinear registration provided higher test-retest reliability of the output fractional anisotropy (FA) maps than field map-based unwarping, even when accounting for the effect of interpolation on the smoothness of the images. In general, field map-based unwarping was preferable if and only if the field maps were acquired optimally. PMID:28270762

  4. Temporal reliability of ultra-high field resting-state MRI for single-subject sensorimotor and language mapping.

    PubMed

    Branco, Paulo; Seixas, Daniela; Castro, São Luís

    2016-11-15

    Resting-state fMRI is a well-suited technique to map functional networks in the brain because unlike task-based approaches it requires little collaboration from subjects. This is especially relevant in clinical settings where a number of subjects cannot comply with task demands. Previous studies using conventional scanner fields have shown that resting-state fMRI is able to map functional networks in single subjects, albeit with moderate temporal reliability. Ultra-high resolution (7T) imaging provides higher signal-to-noise ratio and better spatial resolution and is thus well suited to assess the temporal reliability of mapping results, and to determine if resting-state fMRI can be applied in clinical decision making including preoperative planning. We used resting-state fMRI at ultra-high resolution to examine whether the sensorimotor and language networks are reliable over time - same session and one week after. Resting-state networks were identified for all subjects and sessions with good accuracy. Both networks were well delimited within classical regions of interest. Mapping was temporally reliable at short and medium time-scales as demonstrated by high values of overlap in the same session and one week after for both networks. Results were stable independently of data quality metrics and physiological variables. Taken together, these findings provide strong support for the suitability of ultra-high field resting-state fMRI mapping at the single-subject level.

  5. 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.

  6. Simultaneous Quantitative Imaging of Electrical Properties and Proton Density from B1 Maps Using MRI.

    PubMed

    Liu, Jiaen; Van de Moortele, Pierre-Francois; Zhang, Xiaotong; Wang, Yicun; He, Bin

    2016-03-29

    Electrical conductivity and permittivity of biological tissues are important diagnostic parameters and are useful for calculating subject-specific specific absorption rate distribution. On the other hand, water proton density also has clinical relevance for diagnosis purposes. These two kinds of tissue properties are inevitably associated in the technique of electrical properties tomography (EPT), which can be used to map in vivo electrical properties based on the measured B1 field distribution at Larmor frequency using magnetic resonance imaging (MRI). The signal magnitude in MR images is locally proportional to both the proton density of tissue and the receive B1 field; this is a source of artifact in receive B1-based EPT reconstruction because these two quantities cannot easily be disentangled. In this study, a new method was proposed for simultaneously extracting quantitative conductivity, permittivity and proton density from the measured magnitude of transmit B1 field, proton density-weighted receive B1 field, and transceiver phase, in a multi-channel radiofrequency (RF) coil using MRI, without specific assumptions to derive the proton density distribution. We evaluated the spatial resolution, sensitivity to contrast, and accuracy of the method using numerical simulations of B1 field in a phantom and in a realistic human head model. Using the proposed method, conductivity, permittivity and proton density were then experimentally obtained ex vivo in a pork tissue sample on a 7T MRI scanner equipped with a 16-channel microstrip transceiver RF coil.

  7. Simultaneous Quantitative Imaging of Electrical Properties and Proton Density From B1 Maps Using MRI.

    PubMed

    Jiaen Liu; Van de Moortele, Pierre-Francois; Xiaotong Zhang; Yicun Wang; Bin He

    2016-09-01

    Electrical conductivity and permittivity of biological tissues are important diagnostic parameters and are useful for calculating subject-specific specific absorption rate distribution. On the other hand, water proton density also has clinical relevance for diagnosis purposes. These two kinds of tissue properties are inevitably associated in the technique of electrical properties tomography (EPT), which can be used to map in vivo electrical properties based on the measured B1 field distribution at Larmor frequency using magnetic resonance imaging (MRI). The signal magnitude in MR images is locally proportional to both the proton density of tissue and the receive B1 field; this is a source of artifact in receive B1-based EPT reconstruction because these two quantities cannot easily be disentangled. In this study, a new method was proposed for simultaneously extracting quantitative conductivity, permittivity and proton density from the measured magnitude of transmit B1 field, proton density-weighted receive B1 field, and transceiver phase, in a multi-channel radiofrequency (RF) coil using MRI, without specific assumptions to derive the proton density distribution. We evaluated the spatial resolution, sensitivity to contrast, and accuracy of the method using numerical simulations of B1 field in a phantom and in a realistic human head model. Using the proposed method, conductivity, permittivity and proton density were then experimentally obtained ex vivo in a pork tissue sample on a 7T MRI scanner equipped with a 16-channel microstrip transceiver RF coil.

  8. Mapping blood flow directionality in the human brain.

    PubMed

    Park, Sung-Hong; Do, Won-Joon; Choi, Seung Hong; Zhao, Tiejun; Bae, Kyongtae Ty

    2016-07-01

    Diffusion properties of tissue are often expressed on the basis of directional variance, i.e., diffusion tensor imaging. In comparison, common perfusion-weighted imaging such as arterial spin labeling yields perfusion in a scalar quantity. The purpose of this study was to test the feasibility of mapping cerebral blood flow directionality using alternate ascending/descending directional navigation (ALADDIN), a recently-developed arterial spin labeling technique with sensitivity to blood flow directions. ALADDIN was applied along 3 orthogonal directions to assess directional blood flow in a vector form and also along 6 equally-spaced directions to extract blood flow tensor matrix (P) based on a blood flow ellipsoid model. Tensor elements (eigenvalues, eigenvectors, etc) were calculated to investigate characteristics of the blood flow tensor, in comparison with time-of-flight MR angiogram. While the directions of the main eigenvectors were heterogeneous throughout the brain, regional clusters of blood flow directionality were reproducible across subjects. The technique could show heterogeneous blood flow directionality within and around brain tumor, which was different from that of the contralateral normal side. The proposed method is deemed to provide information of blood flow directionality, which has not been demonstrated before. The results warrant further studies to assess changes in the directionality map as a function of scan parameters, to understand the signal sources, to investigate the possibility of mapping local blood perfusion directionality, and to evaluate its usefulness for clinical diagnosis.

  9. Segmentation of fat in MRI using a preparatory pair of rectangular RF pulses of opposite direction.

    PubMed

    Yee, Seonghwan

    2016-05-01

    A radiofrequency (RF) pulse-based MRI method is introduced as a novel fat (or water) segmentation method that, unlike the mostly used Dixon's method, does not depend on the echo times. A pair of rectangular RF pulses of opposite direction, when the duration of its rectangular pulse and the off-resonance of its carrier frequency are set to specific values, is proposed as a preparatory RF pulse to be used for the quantitative fat segmentation. The optimal duration of its rectangular pulse and its specific off-resonance were first determined theoretically. Then, such pair of rectangular pulses of opposite direction (PROD pulse) was applied in imaging a few phantoms and volunteers. During the imaging experiments, MRI images were dynamically acquired with the PROD pulse while its carrier frequency was varied in a predefined off-resonance range. By analyzing the dynamically acquired signal changes, the theoretical properties of the PROD pulse were confirmed and the utility of the PROD pulse for the fat segmentation was verified. All MRI scans were performed in a clinical 3T system. The PROD pulse, if the duration of each rectangular pulse was set to 1.66ms and its carrier frequency was set to a specific off-resonance (e.g. ±223.5Hz, or -670.5Hz) in 3T, was effective in optimally modulating MRI signals to be used for the fat-water segmentation. Therefore, the PROD pulse can successfully be used as a preparatory RF pulse in MRI to achieve effective fat (or water) segmentation in MRI.

  10. Combining task-evoked and spontaneous activity to improve pre-operative brain mapping with fMRI.

    PubMed

    Fox, Michael D; Qian, Tianyi; Madsen, Joseph R; Wang, Danhong; Li, Meiling; Ge, Manling; Zuo, Huan-Cong; Groppe, David M; Mehta, Ashesh D; Hong, Bo; Liu, Hesheng

    2016-01-01

    Noninvasive localization of brain function is used to understand and treat neurological disease, exemplified by pre-operative fMRI mapping prior to neurosurgical intervention. The principal approach for generating these maps relies on brain responses evoked by a task and, despite known limitations, has dominated clinical practice for over 20years. Recently, pre-operative fMRI mapping based on correlations in spontaneous brain activity has been demonstrated, however this approach has its own limitations and has not seen widespread clinical use. Here we show that spontaneous and task-based mapping can be performed together using the same pre-operative fMRI data, provide complimentary information relevant for functional localization, and can be combined to improve identification of eloquent motor cortex. Accuracy, sensitivity, and specificity of our approach are quantified through comparison with electrical cortical stimulation mapping in eight patients with intractable epilepsy. Broad applicability and reproducibility of our approach are demonstrated through prospective replication in an independent dataset of six patients from a different center. In both cohorts and every individual patient, we see a significant improvement in signal to noise and mapping accuracy independent of threshold, quantified using receiver operating characteristic curves. Collectively, our results suggest that modifying the processing of fMRI data to incorporate both task-based and spontaneous activity significantly improves functional localization in pre-operative patients. Because this method requires no additional scan time or modification to conventional pre-operative data acquisition protocols it could have widespread utility.

  11. Accuracy of the Morphology Enabled Dipole Inversion (MEDI) Algorithm for Quantitative Susceptibility Mapping in MRI

    PubMed Central

    Liu, Tian; Xu, Weiyu; Spincemaille, Pascal; Avestimehr, A. Salman

    2013-01-01

    Determining the susceptibility distribution from the magnetic field measured in a magnetic resonance (MR) scanner is an ill-posed inverse problem, because of the presence of zeroes in the convolution kernel in the forward problem. An algorithm called morphology enabled dipole inversion (MEDI), which incorporates spatial prior information, has been proposed to generate a quantitative susceptibility map (QSM). The accuracy of QSM can be validated experimentally. However, there is not yet a rigorous mathematical demonstration of accuracy for a general regularized approach or for MEDI specifically. The error in the susceptibility map reconstructed by MEDI is expressed in terms of the acquisition noise and the error in the spatial prior information. A detailed analysis demonstrates that the error in the susceptibility map reconstructed by MEDI is bounded by a linear function of these two error sources. Numerical analysis confirms that the error of the susceptibility map reconstructed by MEDI is on the same order of the noise in the original MRI data, and comprehensive edge detection will lead to reduced model error in MEDI. Additional phantom validation and human brain imaging demonstrated the practicality of the MEDI method. PMID:22231170

  12. 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/.

  13. Sodium 3D COncentration MApping (COMA 3D) Using 23Na and Proton MRI

    PubMed Central

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

    2014-01-01

    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/hour 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/ PMID:25261742

  14. Longitudinal stability of MRI for mapping brain change using tensor-based morphometry.

    PubMed

    Leow, Alex D; Klunder, Andrea D; Jack, Clifford R; Toga, Arthur W; Dale, Anders M; Bernstein, Matt A; Britson, Paula J; Gunter, Jeffrey L; Ward, Chadwick P; Whitwell, Jennifer L; Borowski, Bret J; Fleisher, Adam S; Fox, Nick C; Harvey, Danielle; Kornak, John; Schuff, Norbert; Studholme, Colin; Alexander, Gene E; Weiner, Michael W; Thompson, Paul M

    2006-06-01

    Measures of brain change can be computed from sequential MRI scans, providing valuable information on disease progression, e.g., for patient monitoring and drug trials. Tensor-based morphometry (TBM) creates maps of these brain changes, visualizing the 3D profile and rates of tissue growth or atrophy, but its sensitivity depends on the contrast and geometric stability of the images. As part of the Alzheimer's Disease Neuroimaging Initiative (ADNI), 17 normal elderly subjects were scanned twice (at a 2-week interval) with several 3D 1.5 T MRI pulse sequences: high and low flip angle SPGR/FLASH (from which Synthetic T1 images were generated), MP-RAGE, IR-SPGR (N = 10) and MEDIC (N = 7) scans. For each subject and scan type, a 3D deformation map aligned baseline and follow-up scans, computed with a nonlinear, inverse-consistent elastic registration algorithm. Voxelwise statistics, in ICBM stereotaxic space, visualized the profile of mean absolute change and its cross-subject variance; these maps were then compared using permutation testing. Image stability depended on: (1) the pulse sequence; (2) the transmit/receive coil type (birdcage versus phased array); (3) spatial distortion corrections (using MEDIC sequence information); (4) B1-field intensity inhomogeneity correction (using N3). SPGR/FLASH images acquired using a birdcage coil had least overall deviation. N3 correction reduced coil type and pulse sequence differences and improved scan reproducibility, except for Synthetic T1 images (which were intrinsically corrected for B1-inhomogeneity). No strong evidence favored B0 correction. Although SPGR/FLASH images showed least deviation here, pulse sequence selection for the ADNI project was based on multiple additional image analyses, to be reported elsewhere.

  15. Ferumoxytol enhanced resting state fMRI and relative cerebral blood volume mapping in normal human brain.

    PubMed

    D'Arceuil, Helen; Coimbra, Alexandre; Triano, Pamela; Dougherty, Margaret; Mello, Julie; Moseley, Michael; Glover, Gary; Lansberg, Maarten; Blankenberg, Francis

    2013-12-01

    The brain demonstrates spontaneous low-frequency (<0.1 Hz) cerebral blood flow (CBF) fluctuations, measurable by resting state functional MRI (rs-fMRI). Ultra small superparamagnetic iron oxide particles have been shown to enhance task-based fMRI signals (cerebral blood volume fMRI or CBV-fMRI), compared to the BOLD effect, by a factor of ≈2.5 at 3 T in primates and humans. We evaluated the use of ferumoxytol for steady state, resting state FMRI (CBV-rs-fMRI) and relative cerebral blood volume (rCBV) mapping, at 3T, in healthy volunteers. All standard resting state networks (RSNs) were identified in all subjects. On average the RSN Z statistics (MELODIC independent components) and volumes of the visual and default mode (DMN) networks were comparable. rCBV values were averaged for the visual (Vis) and DMN networks and correlated with the corresponding DMN and visual network Z statistics. There was a negative correlation between the rCBV and the Z statistics for the DMN, for both BOLD and CBV-rs-fMRI contrast (R2=0.63, 0.76). A similar correlation was not found for the visual network. Short repetition time rs-fMRI data were Fourier transformed to evaluate the effect of ferumoxytol on cardiac and respiratory fluctuations in the brain rs-BOLD, CBV signals. Cardiac and respiratory fluctuations decreased to baseline within large vessels post ferumoxytol. Robust rs-fMRI and CBV mapping is possible in normal human brain.

  16. Application of MRI phase-difference mapping to assessment of vascular concentrations of BMS agent in mice.

    PubMed

    Ribot, Emeline Julie; Thiaudière, Eric; Roulland, Richard; Brugières, Pierre; Rahmouni, Alain; Voisin, Pierre; Franconi, Jean-Michel; Miraux, Sylvain

    2008-01-01

    Direct quantitation of contrast agent concentration can be performed using dynamic susceptibility contrast MRI. This method is based on phase imaging and administration of paramagnetic agents such as gadolinium-chelates. This technique has only been applied on humans or primates. However, numerous research models have been developed on small animals like mice. For this reason, the aim of this work was the application of this MRI technique, allowing the direct quantitation of the contrast agent concentrations in vivo, in the mouse vascular system at high field. For this purpose, Dy-DOTA has been preferred to Gd-DOTA due to a lower T(2)* effect. Dy-DOTA shifts in Larmor frequency were measured by phase difference mapping, using fast gradient-echo imaging at short echo times. Such an acquisition sequence allowed the limitation of susceptibility artifacts at high magnetic fields and phase wrapping. As demonstrated in a phantom oriented parallel to the static magnetic field, it is possible to measure contrast agent concentrations between 0 and 10 mm with an uncertainty of about 100 microm. Finally, the method was applied on living mice at 4.7 T. After the bolus injection, the evolution of contrast agent concentrations was assessed in brain blood vessels parallel to B(0). Long-term disappearance of contrast agent was monitored at high spatial resolution every 15 s. Alternatively, lower resolved images at 0.72 s time-resolution allowed preliminary assessment of arterial input functions. The feasibility of quantitative bolus-tracking in small rodents opens the way for comprehensive descriptions of flow and over time-dependent biological processes, especially in pathological murine models.

  17. MRI-directed cognitive fusion-guided biopsy of the anterior prostate tumors

    PubMed Central

    Murphy, Ian G.; NiMhurchu, Elaine; Gibney, Robert G.; McMahon, Colm J.

    2017-01-01

    PURPOSE We aimed to evaluate the efficacy of magnetic resonance imaging (MRI)-directed cognitive fusion transrectal ultrasonography (TRUS)-guided anterior prostate biopsy for diagnosis of anterior prostate tumors and to illustrate this technique. METHODS A total of 39 patients with previous negative TRUS biopsy, but high clinical suspicion of occult prostate cancer, prospectively underwent prostate MRI including diffusion-weighted imaging (DWI). Patients with a suspicious anterior lesion on MRI underwent targeted anterior gland TRUS-guided biopsy with cognitive fusion technique using sagittal probe orientation. PIRADS version 1 scores (T2, DWI, and overall), lesion size, prostate-specific antigen (PSA), PSA density, and prostate gland volume were compared between positive and negative biopsy groups and between clinically significant cancer and remaining cases. Logistic regression analysis of imaging parameters and prostate cancer diagnosis was performed. RESULTS Anterior gland prostate adenocarcinoma was diagnosed in 18 patients (46.2%) on targeted anterior gland TRUS-guided biopsy. Clinically significant prostate cancer was diagnosed in 13 patients (33.3%). MRI lesion size, T2, DWI, and overall PIRADS scores were significantly higher in patients with positive targeted biopsies and those with clinically significant cancer (P < 0.05). Biopsies were positive in 90%, 33%, and 29% of patients with overall PIRADS scores of 5, 4, and 3 respectively. Overall PIRADS score was an independent predictor of all prostate cancer diagnosis and of clinically significant prostate cancer diagnosis. CONCLUSION Targeted anterior gland TRUS-guided biopsy with MRI-directed cognitive fusion enables accurate sampling and may improve tumor detection yield of anterior prostate cancer. PMID:28074780

  18. Cortical sensory map rearrangement after spinal cord injury: fMRI responses linked to Nogo signalling.

    PubMed

    Endo, Toshiki; Spenger, Christian; Tominaga, Teiji; Brené, Stefan; Olson, Lars

    2007-11-01

    Cortical sensory maps can reorganize in the adult brain in an experience-dependent manner. We monitored somatosensory cortical reorganization after sensory deafferentation using functional magnetic resonance imaging (fMRI) in rats subjected to complete transection of the mid-thoracic spinal cord. Cortical representation in response to spared forelimb stimulation was observed to enlarge and invade adjacent sensory-deprived hind limb territory in the primary somatosensory cortex as early as 3 days after injury. Functional MRI also demonstrated long-term cortical plasticity accompanied by increased thalamic activation. To support the notion that alterations of cortical neuronal circuitry after spinal cord injury may underlie the fMRI changes, we quantified transcriptional activities of several genes related to cortical plasticity including the Nogo receptor (NgR), its co-receptor LINGO-1 and brain derived neurotrophic factor (BDNF), using in situ hybridization. We demonstrate that NgR and LINGO-1 are down-regulated specifically in cortical areas deprived of sensory input and in adjacent cortex from 1 day after injury, while BDNF is up-regulated. Our results demonstrate that cortical neurons react to sensory deprivation by decreasing transcriptional activities of genes encoding the Nogo receptor components in the sensory deprived and the anatomically adjacent non-deprived area. Combined with the BDNF up-regulation, these changes presumably allow structural changes in the neuropil. Our observations therefore suggest an involvement of Nogo signalling in cortical activity-dependent plasticity in the somatosensory system. In spinal cord injury, cortical reorganization as shown here can become a disadvantage, much like the situation in amblyopia or phantom sensation. Successful strategies to repair sensory pathways at the spinal cord level may not lead to proper reestablishment of cortical connections, once deprived hind limb cortical areas have been reallocated to forelimb

  19. Sensitivity and specificity considerations for fMRI encoding, decoding, and mapping of auditory cortex at ultra-high field.

    PubMed

    Moerel, Michelle; De Martino, Federico; Kemper, Valentin G; Schmitter, Sebastian; Vu, An T; Uğurbil, Kâmil; Formisano, Elia; Yacoub, Essa

    2017-03-31

    Following rapid technological advances, ultra-high field functional MRI (fMRI) enables exploring correlates of neuronal population activity at an increasing spatial resolution. However, as the fMRI blood-oxygenation-level-dependent (BOLD) contrast is a vascular signal, the spatial specificity of fMRI data is ultimately determined by the characteristics of the underlying vasculature. At 7T, fMRI measurement parameters determine the relative contribution of the macro- and microvasculature to the acquired signal. Here we investigate how these parameters affect relevant high-end fMRI analyses such as encoding, decoding, and submillimeter mapping of voxel preferences in the human auditory cortex. Specifically, we compare a T2* weighted fMRI dataset, obtained with 2D gradient echo (GE) EPI, to a predominantly T2 weighted dataset obtained with 3D GRASE. We first investigated the decoding accuracy based on two encoding models that represented different hypotheses about auditory cortical processing. This encoding/decoding analysis profited from the large spatial coverage and sensitivity of the T2* weighted acquisitions, as evidenced by a significantly higher prediction accuracy in the GE-EPI dataset compared to the 3D GRASE dataset for both encoding models. The main disadvantage of the T2* weighted GE-EPI dataset for encoding/decoding analyses was that the prediction accuracy exhibited cortical depth dependent vascular biases. However, we propose that the comparison of prediction accuracy across the different encoding models may be used as a post processing technique to salvage the spatial interpretability of the GE-EPI cortical depth-dependent prediction accuracy. Second, we explored the mapping of voxel preferences. Large-scale maps of frequency preference (i.e., tonotopy) were similar across datasets, yet the GE-EPI dataset was preferable due to its larger spatial coverage and sensitivity. However, submillimeter tonotopy maps revealed biases in assigned frequency

  20. Mapping plasticity in the forepaw digit barrel subfield of rat brains using functional MRI

    PubMed Central

    Weng, Jun-Cheng; Chuang, Kai-Hsiang; Goloshevsky, Artem; Dodd, Stephen J.; Sharer, Kathryn

    2012-01-01

    The topographic organization of the forepaw barrel subfield in layer IV of rat primary somatosensory cortex (S1) is a good model for studying neural function and plasticity. The goal of this study was to test the feasibility of functional MRI (fMRI) to map the forepaw digit representations in the S1 of the rat and its plasticity after digit amputation. Three dimentional echo-planar imaging with 300 micron isotropic resolution at 11.7 T was used to achieve high signal-to-noise ratios and laminar layer resolution. By alternating electrical stimulation of the 2nd (D2) and 4th (D4) digits, functional activation in layer IV of the barrel subfields could be distinguished using a differential analysis. Furthermore, two and a half months after the amputation of the 3rd digit in baby rats, the overlapping area between D2 and D4 representations was increased. This indicates that the forepaw barrel subfield previously associated with the ablated digit is now associated with the representation of nearby digits, which is consistent with studies using electrophysiology and cytochrome oxidase staining. PMID:20804851

  1. 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

  2. Creating probabilistic maps of the face network in the adolescent brain: a multicentre functional MRI study.

    PubMed

    Tahmasebi, Amir M; Artiges, Eric; Banaschewski, Tobias; Barker, Gareth J; Bruehl, Ruediger; Büchel, Christian; Conrod, Patricia J; Flor, Herta; Garavan, Hugh; Gallinat, Jürgen; Heinz, Andreas; Ittermann, Bernd; Loth, Eva; Mareckova, Klara; Martinot, Jean-Luc; Poline, Jean-Baptiste; Rietschel, Marcella; Smolka, Michael N; Ströhle, Andreas; Schumann, Gunter; Paus, Tomáš

    2012-04-01

    Large-scale magnetic resonance (MR) studies of the human brain offer unique opportunities for identifying genetic and environmental factors shaping the human brain. Here, we describe a dataset collected in the context of a multi-centre study of the adolescent brain, namely the IMAGEN Study. We focus on one of the functional paradigms included in the project to probe the brain network underlying processing of ambiguous and angry faces. Using functional MR (fMRI) data collected in 1,110 adolescents, we constructed probabilistic maps of the neural network engaged consistently while viewing the ambiguous or angry faces; 21 brain regions responding to faces with high probability were identified. We were also able to address several methodological issues, including the minimal sample size yielding a stable location of a test region, namely the fusiform face area (FFA), as well as the effect of acquisition site (eight sites) and scanner (four manufacturers) on the location and magnitude of the fMRI response to faces in the FFA. Finally, we provided a comparison between male and female adolescents in terms of the effect sizes of sex differences in brain response to the ambiguous and angry faces in the 21 regions of interest. Overall, we found a stronger neural response to the ambiguous faces in several cortical regions, including the fusiform face area, in female (vs. male) adolescents, and a slightly stronger response to the angry faces in the amygdala of male (vs. female) adolescents.

  3. 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

  4. Group analysis of self-organizing maps based on functional MRI using restricted Frechet means

    PubMed Central

    Fournel, Arnaud P.; Reynaud, Emanuelle; Brammer, Michael J.; Simmons, Andrew; Ginestet, Cedric E.

    2013-01-01

    Studies of functional MRI data are increasingly concerned with the estimation of differences in spatio-temporal networks across groups of subjects or experimental conditions. Unsupervised clustering and independent component analysis (ICA) have been used to identify such spatio-temporal networks. While these approaches have been useful for estimating these networks at the subject-level, comparisons over groups or experimental conditions require further methodological development. In this paper, we tackle this problem by showing how self-organizing maps (SOMs) can be compared within a Frechean inferential framework. Here, we summarize the mean SOM in each group as a Frechet mean with respect to a metric on the space of SOMs. The advantage of this approach is twofold. Firstly, it allows the visualization of the mean SOM in each experimental condition. Secondly, this Frechean approach permits one to draw inference on group differences, using permutation of the group labels. We consider the use of different distance functions, and introduce one extension of the classical sum of minimum distance (SMD) between two SOMs, which take into account the spatial pattern of the fMRI data. The validity of these methods is illustrated on synthetic data. Through these simulations, we show that the two distance functions of interest behave as expected, in the sense that the ones capturing temporal and spatial aspects of the SOMs are more likely to reach significance under simulated scenarios characterized by temporal, spatial [and spatio-temporal] differences, respectively. In addition, a re-analysis of a classical experiment on visually-triggered emotions demonstrates the usefulness of this methodology. In this study, the multivariate functional patterns typical of the subjects exposed to pleasant and unpleasant stimuli are found to be more similar than the ones of the subjects exposed to emotionally neutral stimuli. In this re-analysis, the group-level SOM output units with the

  5. 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

  6. Noninvasive temperature mapping with MRI using chemical shift water-fat separation.

    PubMed

    Soher, Brian J; Wyatt, Cory; Reeder, Scott B; MacFall, James R

    2010-05-01

    Tissues containing both water and lipids, e.g., breast, confound standard MR proton reference frequency-shift methods for mapping temperatures due to the lack of temperature-induced frequency shift in lipid protons. Generalized Dixon chemical shift-based water-fat separation methods, such as GE's iterative decomposition of water and fat with echo asymmetry and least-squares estimation method, can result in complex water and fat images. Once separated, the phase change over time of the water signal can be used to map temperature. Phase change of the lipid signal can be used to correct for non-temperature-dependent phase changes, such as amplitude of static field drift. In this work, an image acquisition and postprocessing method, called water and fat thermal MRI, is demonstrated in phantoms containing 30:70, 50:50, and 70:30 water-to-fat by volume. Noninvasive heating was applied in an Off1-On-Off2 pattern over 50 min, using a miniannular phased radiofrequency array. Temperature changes were referenced to the first image acquisition. Four fiber optic temperature probes were placed inside the phantoms for temperature comparison. Region of interest (ROI) temperature values colocated with the probes showed excellent agreement (global mean +/- standard deviation: -0.09 +/- 0.34 degrees C) despite significant amplitude of static field drift during the experiments.

  7. 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

  8. 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.

  9. fMRI mapping of the visual system in the mouse brain with interleaved snapshot GE-EPI.

    PubMed

    Niranjan, Arun; Christie, Isabel N; Solomon, Samuel G; Wells, Jack A; Lythgoe, Mark F

    2016-06-10

    The use of functional magnetic resonance imaging (fMRI) in mice is increasingly prevalent, providing a means to non-invasively characterise functional abnormalities associated with genetic models of human diseases. The predominant stimulus used in task-based fMRI in the mouse is electrical stimulation of the paw. Task-based fMRI in mice using visual stimuli remains underexplored, despite visual stimuli being common in human fMRI studies. In this study, we map the mouse brain visual system with BOLD measurements at 9.4T using flashing light stimuli with medetomidine anaesthesia. BOLD responses were observed in the lateral geniculate nucleus, the superior colliculus and the primary visual area of the cortex, and were modulated by the flashing frequency, diffuse vs focussed light and stimulus context. Negative BOLD responses were measured in the visual cortex at 10Hz flashing frequency; but turned positive below 5Hz. In addition, the use of interleaved snapshot GE-EPI improved fMRI image quality without diminishing the temporal contrast-noise-ratio. Taken together, this work demonstrates a novel methodological protocol in which the mouse brain visual system can be non-invasively investigated using BOLD fMRI.

  10. MRI directed bilateral stimulation of the subthalamic nucleus in patients with Parkinson's disease

    PubMed Central

    Patel, N; Plaha, P; O'Sullivan, K; McCarter, R; Heywood, P; Gill, S

    2003-01-01

    Objective: Bilateral chronic high frequency deep brain stimulation (DBS) of the subthalamic nucleus (STN) has emerged as an appropriate therapy for patients with advanced Parkinson's disease refractory to medical therapy. Advances in neuroimaging and neurophysiology have led to the development of varied targeting methods for the delivery of this treatment. Intraoperative neurophysiological and clinical monitoring is regarded by many to be mandatory for accurate STN localisation. We have examined efficacy of bilateral STN stimulation using a predominantly magnetic resonance imaging (MRI)-directed technique. Methods: DBS leads were stereotactically implanted into the STN using an MRI directed method, with intraoperative macrostimulation used purely for adjustment. The effects of DBS were evaluated in 16 patients followed up to 12 months, and compared with baseline assessments. Assessments were performed in both off and on medication states, and were based on the Unified Parkinson's Disease Rating Scale (UPDRS) and timed motor tests. Functional status outcomes were examined using the PDQ-39 quality of life questionnaire. A battery of psychometric tests was used to assess cognition. Results: After 12 months, stimulation in the off medication state resulted in significant improvements in Activities of Daily Living and Motor scores (UPDRS parts II and III) by 62% and 61% respectively. Timed motor tests were significantly improved in the off medication state. Motor scores (UPDRS part III) were significantly improved by 40% in the on medication state. Dyskinesias and off duration were significantly reduced and the mean dose of L-dopa equivalents was reduced by half. Psychometric test scores were mostly unchanged or improved. Adverse events were few. Conclusions: An MRI directed targeting method for implantation of DBS leads into the STN can be used safely and effectively, and results are comparable with studies using intraoperative microelectrode neurophysiological

  11. 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.

  12. Mapping of the internal structure of human habenula with ex vivo MRI at 7T

    PubMed Central

    Strotmann, Barbara; Kögler, Carsten; Bazin, Pierre-Louis; Weiss, Marcel; Villringer, Arno; Turner, Robert

    2013-01-01

    The habenula is a small but important nucleus located next to the third ventricle in front of the pineal body. It helps to control the human reward system and is considered to play a key role in emotion, showing increased activation in major depressive disorders. Its dysfunction may underlie several neurological and psychiatric disorders. It is now possible to visualize the habenula and its anatomical subdivisions—medial habenula (MHB) and lateral habenula (LHB)—using MR techniques. The aim of this study was to further differentiate substructures within human lateral habenula (LHB) using ex vivo ultra-high field MR structural imaging, distinguishing between a medial part (m-LHB) and a lateral part (l-LHB). High resolution T1w images with 0.3-mm isotropic resolution and T2*w images with 60-micrometer isotropic resolution were acquired on a 7T MR scanner and quantitative maps of T1 and T2* were calculated. Cluster analysis of image intensity was performed using the Fuzzy and Noise Tolerant Adaptive Segmentation Method (FANTASM) tool. Ultra-high resolution structural MRI of ex vivo brain tissue at 7T provided sufficient SNR and contrast to discriminate the medial and lateral habenular nuclei. Heterogeneity was observed in the lateral habenula (LHB) nuclei, with clear distinctions between lateral and medial parts (m-LHB, l-LHB) and with the neighboring medial habenula (MHB). Clustering analysis based on the T1 and T2* maps strongly showed 4–6 clusters as subcomponents of lateral and medial habenula. PMID:24391571

  13. 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

  14. 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.

  15. A Proto-Architecture for Innate Directionally Selective Visual Maps

    PubMed Central

    Adams, Samantha V.; Harris, Chris M.

    2014-01-01

    Self-organizing artificial neural networks are a popular tool for studying visual system development, in particular the cortical feature maps present in real systems that represent properties such as ocular dominance (OD), orientation-selectivity (OR) and direction selectivity (DS). They are also potentially useful in artificial systems, for example robotics, where the ability to extract and learn features from the environment in an unsupervised way is important. In this computational study we explore a DS map that is already latent in a simple artificial network. This latent selectivity arises purely from the cortical architecture without any explicit coding for DS and prior to any self-organising process facilitated by spontaneous activity or training. We find DS maps with local patchy regions that exhibit features similar to maps derived experimentally and from previous modeling studies. We explore the consequences of changes to the afferent and lateral connectivity to establish the key features of this proto-architecture that support DS. PMID:25054209

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

    PubMed

    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 trained users

  17. 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

  18. Onsite-effects of dual-hemisphere versus conventional single-hemisphere transcranial direct current stimulation: A functional MRI study.

    PubMed

    Kwon, Yong Hyun; Jang, Sung Ho

    2012-08-25

    We performed functional MRI examinations in six right-handed healthy subjects. During functional MRI scanning, transcranial direct current stimulation was delivered with the anode over the right primary sensorimotor cortex and the cathode over the left primary sensorimotor cortex using dual-hemispheric transcranial direct current stimulation. This was compared to a cathode over the left supraorbital area using conventional single-hemispheric transcranial direct current stimulation. Voxel counts and blood oxygenation level-dependent signal intensities in the right primary sensorimotor cortex regions were estimated and compared between the two transcranial direct current stimulation conditions. Our results showed that dual-hemispheric transcranial direct current stimulation induced greater cortical activities than single-hemispheric transcranial direct current stimulation. These findings suggest that dual-hemispheric transcranial direct current stimulation may provide more effective cortical stimulation than single-hemispheric transcranial direct current stimulation.

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

    PubMed

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

    2015-02-01

    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.

  20. 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

  1. From EEG to BOLD: brain mapping and estimating transfer functions in simultaneous EEG-fMRI acquisitions.

    PubMed

    Sato, João R; Rondinoni, Carlo; Sturzbecher, Marcio; de Araujo, Draulio B; Amaro, Edson

    2010-05-01

    Simultaneous acquisition of electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) aims to disentangle the description of brain processes by exploiting the advantages of each technique. Most studies in this field focus on exploring the relationships between fMRI signals and the power spectrum at some specific frequency bands (alpha, beta, etc.). On the other hand, brain mapping of EEG signals (e.g., interictal spikes in epileptic patients) usually assumes an haemodynamic response function for a parametric analysis applying the GLM, as a rough approximation. The integration of the information provided by the high spatial resolution of MR images and the high temporal resolution of EEG may be improved by referencing them by transfer functions, which allows the identification of neural driven areas without strong assumptions about haemodynamic response shapes or brain haemodynamic's homogeneity. The difference on sampling rate is the first obstacle for a full integration of EEG and fMRI information. Moreover, a parametric specification of a function representing the commonalities of both signals is not established. In this study, we introduce a new data-driven method for estimating the transfer function from EEG signal to fMRI signal at EEG sampling rate. This approach avoids EEG subsampling to fMRI time resolution and naturally provides a test for EEG predictive power over BOLD signal fluctuations, in a well-established statistical framework. We illustrate this concept in resting state (eyes closed) and visual simultaneous fMRI-EEG experiments. The results point out that it is possible to predict the BOLD fluctuations in occipital cortex by using EEG measurements.

  2. 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.

  3. Causality Analysis of fMRI Data Based on the Directed Information Theory Framework.

    PubMed

    Wang, Zhe; Alahmadi, Ahmed; Zhu, David C; Li, Tongtong

    2016-05-01

    This paper aims to conduct fMRI-based causality analysis in brain connectivity by exploiting the directed information (DI) theory framework. Unlike the well-known Granger causality (GC) analysis, which relies on the linear prediction technique, the DI theory framework does not have any modeling constraints on the sequences to be evaluated and ensures estimation convergence. Moreover, it can be used to generate the GC graphs. In this paper, first, we introduce the core concepts in the DI framework. Second, we present how to conduct causality analysis using DI measures between two time series. We provide the detailed procedure on how to calculate the DI for two finite-time series. The two major steps involved here are optimal bin size selection for data digitization and probability estimation. Finally, we demonstrate the applicability of DI-based causality analysis using both the simulated data and experimental fMRI data, and compare the results with that of the GC analysis. Our analysis indicates that GC analysis is effective in detecting linear or nearly linear causal relationship, but may have difficulty in capturing nonlinear causal relationships. On the other hand, DI-based causality analysis is more effective in capturing both linear and nonlinear causal relationships. Moreover, it is observed that brain connectivity among different regions generally involves dynamic two-way information transmissions between them. Our results show that when bidirectional information flow is present, DI is more effective than GC to quantify the overall causal relationship.

  4. 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.

  5. Arterial spin labeling versus BOLD in direct challenge and drug-task interaction pharmacological fMRI.

    PubMed

    Stewart, Stephanie B; Koller, Jonathan M; Campbell, Meghan C; Black, Kevin J

    2014-01-01

    A carefully controlled study allowed us to compare the sensitivity of ASL (arterial spin labeling) and BOLD (blood oxygen level dependent) fMRI for detecting the effects of the adenosine A2a antagonist tozadenant in Parkinson disease. The study compared the effect of drug directly or the interaction of the drug with a cognitive task. Only ASL detected the direct effect of tozadenant. BOLD was more sensitive to the cognitive task, which (unlike most drugs) allows on-off comparisons over short periods of time. Neither ASL nor BOLD could detect a cognitive-pharmacological interaction. These results are consistent with the known relative advantages of each fMRI method, and suggest that for drug development, directly imaging pharmacodynamic effects with ASL may have advantages over cognitive-pharmacological interaction BOLD, which has hitherto been the more common approach to pharmacological fMRI.

  6. Mapping epitopes and antigenicity by site-directed masking

    PubMed Central

    Paus, Didrik; Winter, Greg

    2006-01-01

    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 (β-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 β-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 β-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. PMID:16754878

  7. Bingham-NODDI: Mapping anisotropic orientation dispersion of neurites using diffusion MRI.

    PubMed

    Tariq, Maira; Schneider, Torben; Alexander, Daniel C; Gandini Wheeler-Kingshott, Claudia A; Zhang, Hui

    2016-06-01

    This paper presents Bingham-NODDI, a clinically-feasible technique for estimating the anisotropic orientation dispersion of neurites. Direct quantification of neurite morphology on clinical scanners was recently realised by a diffusion MRI technique known as neurite orientation dispersion and density imaging (NODDI). However in its current form NODDI cannot estimate anisotropic orientation dispersion, which is widespread in the brain due to common fanning and bending of neurites. This work proposes Bingham-NODDI that extends the NODDI formalism to address this limitation. Bingham-NODDI characterises anisotropic orientation dispersion by utilising the Bingham distribution to model neurite orientation distribution. The new model estimates the extent of dispersion about the dominant orientation, separately along the primary and secondary dispersion orientations. These estimates are subsequently used to estimate the overall dispersion about the dominant orientation and the dispersion anisotropy. We systematically evaluate the ability of the new model to recover these key parameters of anisotropic orientation dispersion with standard NODDI protocol, both in silico and in vivo. The results demonstrate that the parameters of the proposed model can be estimated without additional acquisition requirements over the standard NODDI protocol. Thus anisotropic dispersion can be determined and has the potential to be used as a marker for normal brain development and ageing or in pathology. We additionally find that the original NODDI model is robust to the effects of anisotropic orientation dispersion, when the quantification of anisotropic dispersion is not of interest.

  8. Mapping, Learning, Visualization, Classification, and Understanding of fMRI Data in the NeuCube Evolving Spatiotemporal Data Machine of Spiking Neural Networks.

    PubMed

    Kasabov, Nikola K; Doborjeh, Maryam Gholami; Doborjeh, Zohreh Gholami

    2017-04-01

    This paper introduces a new methodology for dynamic learning, visualization, and classification of functional magnetic resonance imaging (fMRI) as spatiotemporal brain data. The method is based on an evolving spatiotemporal data machine of evolving spiking neural networks (SNNs) exemplified by the NeuCube architecture [1]. The method consists of several steps: mapping spatial coordinates of fMRI data into a 3-D SNN cube (SNNc) that represents a brain template; input data transformation into trains of spikes; deep, unsupervised learning in the 3-D SNNc of spatiotemporal patterns from data; supervised learning in an evolving SNN classifier; parameter optimization; and 3-D visualization and model interpretation. Two benchmark case study problems and data are used to illustrate the proposed methodology-fMRI data collected from subjects when reading affirmative or negative sentences and another one-on reading a sentence or seeing a picture. The learned connections in the SNNc represent dynamic spatiotemporal relationships derived from the fMRI data. They can reveal new information about the brain functions under different conditions. The proposed methodology allows for the first time to analyze dynamic functional and structural connectivity of a learned SNN model from fMRI data. This can be used for a better understanding of brain activities and also for online generation of appropriate neurofeedback to subjects for improved brain functions. For example, in this paper, tracing the 3-D SNN model connectivity enabled us for the first time to capture prominent brain functional pathways evoked in language comprehension. We found stronger spatiotemporal interaction between left dorsolateral prefrontal cortex and left temporal while reading a negated sentence. This observation is obviously distinguishable from the patterns generated by either reading affirmative sentences or seeing pictures. The proposed NeuCube-based methodology offers also a superior classification accuracy

  9. The spatiospectral characterization of brain networks: fusing concurrent EEG spectra and fMRI maps.

    PubMed

    Bridwell, David A; Wu, Lei; Eichele, Tom; Calhoun, Vince D

    2013-04-01

    Different imaging modalities capture different aspects of brain activity. Functional magnetic resonance imaging (fMRI) reveals intrinsic networks whose BOLD signals have periods from 100 s (0.01 Hz) to about 10s (0.1 Hz). Electroencephalographic (EEG) recordings, in contrast, commonly reflect cortical electrical fluctuations with periods up to 20 ms (50 Hz) or above. We examined the correspondence between intrinsic fMRI and EEG network activity at rest in order to characterize brain networks both spatially (with fMRI) and spectrally (with EEG). Brain networks were separately identified within the concurrently recorded fMRI and EEG at the aggregate group level with group independent component analysis and the association between spatial fMRI and frequency by spatial EEG sources was examined by deconvolving their component time courses. The two modalities are considered linked if the estimated impulse response function (IRF) is significantly non-zero at biologically plausible delays. We found that negative associations were primarily present within two of five alpha components, which highlights the importance of considering multiple alpha sources in EEG-fMRI. Positive associations were primarily present within the lower (e.g. delta and theta) and higher (e.g. upper beta and lower gamma) spectral regions, sometimes within the same fMRI components. Collectively, the results demonstrate a promising approach to characterize brain networks spatially and spectrally, and reveal that positive and negative associations appear within partially distinct regions of the EEG spectrum.

  10. 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.

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

    PubMed

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

    2004-01-21

    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 degrees sectored tubular (3.5 mm OD x 10 mm) or planar transducers (3.5 mm x 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 degrees tubular applicator (9-15 W, 12 min, 8 MHz) produced coagulated zones covering an 80 degrees 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, approximately 8 MHz) generated thermal lesions of approximately 30 degrees extending to the prostate boundary. Multiple sequential sonications (sweeping) of a planar applicator (12 W with eight rotations of 30 degrees each) demonstrated controllable coagulation of a 270 degrees 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.

  12. 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.

  13. Mapping axonal density and average diameter using non-monotonic time-dependent gradient-echo MRI

    NASA Astrophysics Data System (ADS)

    Nunes, Daniel; Cruz, Tomás L.; Jespersen, Sune N.; Shemesh, Noam

    2017-04-01

    White Matter (WM) microstructures, such as axonal density and average diameter, are crucial to the normal function of the Central Nervous System (CNS) as they are closely related with axonal conduction velocities. Conversely, disruptions of these microstructural features may result in severe neurological deficits, suggesting that their noninvasive mapping could be an important step towards diagnosing and following pathophysiology. Whereas diffusion based MRI methods have been proposed to map these features, they typically entail the application of powerful gradients, which are rarely available in the clinic, or extremely long acquisition schemes to extract information from parameter-intensive models. In this study, we suggest that simple and time-efficient multi-gradient-echo (MGE) MRI can be used to extract the axon density from susceptibility-driven non-monotonic decay in the time-dependent signal. We show, both theoretically and with simulations, that a non-monotonic signal decay will occur for multi-compartmental microstructures - such as axons and extra-axonal spaces, which were here used as a simple model for the microstructure - and that, for axons parallel to the main magnetic field, the axonal density can be extracted. We then experimentally demonstrate in ex-vivo rat spinal cords that its different tracts - characterized by different microstructures - can be clearly contrasted using the MGE-derived maps. When the quantitative results are compared against ground-truth histology, they reflect the axonal fraction (though with a bias, as evident from Bland-Altman analysis). As well, the extra-axonal fraction can be estimated. The results suggest that our model is oversimplified, yet at the same time evidencing a potential and usefulness of the approach to map underlying microstructures using a simple and time-efficient MRI sequence. We further show that a simple general-linear-model can predict the average axonal diameters from the four model parameters, and

  14. 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.

  15. 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

    2015-06-03

    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.

  16. 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

  17. 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

  18. Direct cortical mapping via solving partial differential equations on implicit surfaces.

    PubMed

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

    2007-06-01

    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.

  19. High-Resolution fMRI of Auditory Cortical Map Changes in Unilateral Hearing Loss and Tinnitus.

    PubMed

    Ghazaleh, Naghmeh; Zwaag, Wietske van der; Clarke, Stephanie; Ville, Dimitri Van De; Maire, Raphael; Saenz, Melissa

    2017-02-06

    Animal models of hearing loss and tinnitus observe pathological neural activity in the tonotopic frequency maps of the primary auditory cortex. Here, we applied ultra high-field fMRI at 7 T to test whether human patients with unilateral hearing loss and tinnitus also show altered functional activity in the primary auditory cortex. The high spatial resolution afforded by 7 T imaging allowed tonotopic mapping of primary auditory cortex on an individual subject basis. Eleven patients with unilateral hearing loss and tinnitus were compared to normal-hearing controls. Patients showed an over-representation and hyperactivity in a region of the cortical map corresponding to low frequencies sounds, irrespective of the hearing loss and tinnitus range, which in most cases affected higher frequencies. This finding of hyperactivity in low frequency map regions, irrespective of hearing loss range, is consistent with some previous studies in animal models and corroborates a previous study of human tinnitus. Thus these findings contribute to accumulating evidence that gross cortical tonotopic map reorganization is not a causal factor of tinnitus.

  20. Accelerating parallel transmit array B1 mapping in high field MRI with slice undersampling and interpolation by kriging.

    PubMed

    Ferrand, Guillaume; Luong, Michel; Cloos, Martijn A; Amadon, Alexis; Wackernagel, Hans

    2014-08-01

    Transmit arrays have been developed to mitigate the RF field inhomogeneity commonly observed in high field magnetic resonance imaging (MRI), typically above 3T. To this end, the knowledge of the RF complex-valued B1 transmit-sensitivities of each independent radiating element has become essential. This paper details a method to speed up a currently available B1-calibration method. The principle relies on slice undersampling, slice and channel interleaving and kriging, an interpolation method developed in geostatistics and applicable in many domains. It has been demonstrated that, under certain conditions, kriging gives the best estimator of a field in a region of interest. The resulting accelerated sequence allows mapping a complete set of eight volumetric field maps of the human head in about 1 min. For validation, the accuracy of kriging is first evaluated against a well-known interpolation technique based on Fourier transform as well as to a B1-maps interpolation method presented in the literature. This analysis is carried out on simulated and decimated experimental B1 maps. Finally, the accelerated sequence is compared to the standard sequence on a phantom and a volunteer. The new sequence provides B1 maps three times faster with a loss of accuracy limited potentially to about 5%.

  1. 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

  2. Haptic fMRI: using classification to quantify task-correlated noise during goal-directed reaching motions.

    PubMed

    Menon, Samir; Quigley, Paul; Yu, Michelle; Khatib, Oussama

    2014-01-01

    Neuroimaging artifacts in haptic functional magnetic resonance imaging (Haptic fMRI) experiments have the potential to induce spurious fMRI activation where there is none, or to make neural activation measurements appear correlated across brain regions when they are actually not. Here, we demonstrate that performing three-dimensional goal-directed reaching motions while operating Haptic fMRI Interface (HFI) does not create confounding motion artifacts. To test for artifacts, we simultaneously scanned a subject's brain with a customized soft phantom placed a few centimeters away from the subject's left motor cortex. The phantom captured task-related motion and haptic noise, but did not contain associated neural activation measurements. We quantified the task-related information present in fMRI measurements taken from the brain and the phantom by using a linear max-margin classifier to predict whether raw time series data could differentiate between motion planning or reaching. fMRI measurements in the phantom were uninformative (2σ, 45-73%; chance=50%), while those in primary motor, visual, and somatosensory cortex accurately classified task-conditions (2σ, 90-96%). We also localized artifacts due to the haptic interface alone by scanning a stand-alone fBIRN phantom, while an operator performed haptic tasks outside the scanner's bore with the interface at the same location. The stand-alone phantom had lower temporal noise and had similar mean classification but a tighter distribution (bootstrap Gaussian fit) than the brain phantom. Our results suggest that any fMRI measurement artifacts for Haptic fMRI reaching experiments are dominated by actual neural responses.

  3. Oxygen-enhanced MRI accurately identifies, quantifies, and maps tumor hypoxia in preclinical cancer models

    PubMed Central

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

    2015-01-01

    There is a clinical need for non-invasive 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 non-invasively and is immediately translatable to the clinic. PMID:26659574

  4. 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

  5. Enhancing the quantification of tissue sodium content by MRI: time-efficient sodium B1 mapping at clinical field strengths.

    PubMed

    Lommen, Jonathan; Konstandin, Simon; Krämer, Philipp; Schad, Lothar R

    2016-02-01

    Tissue sodium content (TSC) is a sensitive measure of pathological changes and can be detected non-invasively by MRI. For the absolute quantification of TSC, B1 inhomogeneities must be corrected, which is not well established beyond research applications. An in-depth analysis of B1 mapping methods which are suitable for application in TSC quantification is presented. On the basis of these results, a method for simultaneous B1 mapping and imaging is proposed in order to enhance accuracy and to reduce measurement time at clinical field strengths. The B1 mapping techniques used were phase-sensitive (PS), Bloch-Siegert shift (BSS), double-angle (DAM) and actual flip-angle imaging (AFI) methods. Experimental and theoretical comparisons demonstrated that the PS technique yields the most accurate field profiles and exhibits the highest signal-to-noise ratio (SNR). Simultaneous B1 mapping and imaging was performed for the PS method, employing both degrees of freedom of the MR signal: the B1 field is encoded into signal phase and the amplitude provides the concentration information. In comparison with the more established DAM, a 13% higher SNR was obtained and field effects could be corrected more accurately without the need for additional measurement time. The protocol developed was applied to measure TSC in the healthy human head at an isotropic resolution of 4 mm. TSC was determined to be 35 ± 1 mM in white matter and 134 ± 3 mM in vitreous humor. By employing the proposed simultaneous characterization of the B1 field and acquisition of the spin density-weighted sodium signal, the accuracy of the non-invasive measurement of TSC is enhanced and the measurement time is reduced. This should allow (23)Na MRI to be better incorporated into clinical studies and routine.

  6. Skeletal muscle diffusion tensor-MRI fiber tracking: rationale, data acquisition and analysis methods, applications and future directions.

    PubMed

    Damon, Bruce M; Froeling, Martijn; Buck, Amanda K W; Oudeman, Jos; Ding, Zhaohua; Nederveen, Aart J; Bush, Emily C; Strijkers, Gustav J

    2017-03-01

    The mechanical functions of muscles involve the generation of force and the actuation of movement by shortening or lengthening under load. These functions are influenced, in part, by the internal arrangement of muscle fibers with respect to the muscle's mechanical line of action. This property is known as muscle architecture. In this review, we describe the use of diffusion tensor (DT)-MRI muscle fiber tracking for the study of muscle architecture. In the first section, the importance of skeletal muscle architecture to function is discussed. In addition, traditional and complementary methods for the assessment of muscle architecture (brightness-mode ultrasound imaging and cadaver analysis) are presented. Next, DT-MRI is introduced and the structural basis for the reduced and anisotropic diffusion of water in muscle is discussed. The third section discusses issues related to the acquisition of skeletal muscle DT-MRI data and presents recommendations for optimal strategies. The fourth section discusses methods for the pre-processing of DT-MRI data, the available approaches for the calculation of the diffusion tensor and the seeding and propagating of fiber tracts, and the analysis of the tracking results to measure structural properties pertinent to muscle biomechanics. Lastly, examples are presented of how DT-MRI fiber tracking has been used to provide new insights into how muscles function, and important future research directions are highlighted. Copyright © 2016 John Wiley & Sons, Ltd.

  7. 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.

  8. Working memory capacity and the functional connectome - insights from resting-state fMRI and voxelwise centrality mapping.

    PubMed

    Markett, Sebastian; Reuter, Martin; Heeren, Behrend; Lachmann, Bernd; Weber, Bernd; Montag, Christian

    2017-02-28

    The functional connectome represents a comprehensive network map of functional connectivity throughout the human brain. To date, the relationship between the organization of functional connectivity and cognitive performance measures is still poorly understood. In the present study we use resting-state functional magnetic resonance imaging (fMRI) data to explore the link between the functional connectome and working memory capacity in an individual differences design. Working memory capacity, which refers to the maximum amount of context information that an individual can retain in the absence of external stimulation, was assessed outside the MRI scanner and estimated based on behavioral data from a change detection task. Resting-state time series were analyzed by means of voxelwise degree and eigenvector centrality mapping, which are data-driven network analytic approaches for the characterization of functional connectivity. We found working memory capacity to be inversely correlated with both centrality in the right intraparietal sulcus. Exploratory analyses revealed that this relationship was putatively driven by an increase in negative connectivity strength of the structure. This resting-state connectivity finding fits previous task based activation studies that have shown that this area responds to manipulations of working memory load.

  9. Evaluation of distance maps from fast GRE MRI as a tool to study the knee joint space

    NASA Astrophysics Data System (ADS)

    Tamez-Pena, Jose G.; Lerner, Amy L.; Yao, Jiang; Salo, Arthur D.; Totterman, Saara

    2003-05-01

    A new three-dimensional (3D) method of evaluating the joint space from fast GRE MRI has been developed that allows the reconstruction of the two dimensional (2D) distance map between the femur and the tibia bone plates. This method uses the MRI data, an automated 3D segmentation, and an unsupervised joint space extraction algorithm that identify the medial and lateral compartments of the knee joint. The extracted medial and lateral compartments of the tibia-femur joint space were analyzed by 2D distance maps, where visual as well quantitative information was extracted. This method was applied to study the dynamic behavior of the knee joint space under axial load. Three healthy volunteers' knees were imaged using fast GRE sequences in a clinical scanner under unloaded (normal) conditions and with an axial load that mimics the person's standing load. Furthermore, one volunteer's knee was imaged at four regular time intervals while the load was applied and at four regular intervals without load. The results show that changes of 50 microns in the average distance between bones can be measured and that normal axial loads reduce the joint space width significantly and can be detected by this method.

  10. Mapping Human Cortical Areas in vivo Based on Myelin Content as Revealed by T1- and T2-weighted MRI

    PubMed Central

    Glasser, Matthew F.; Van Essen, David C.

    2011-01-01

    Non-invasively mapping the layout of cortical areas in humans is a continuing challenge for neuroscience. We present a new method of mapping cortical areas based on myelin content as revealed by T1-weighted (T1w) and T2-weighted (T2w) MRI. The method is generalizable across different 3T scanners and pulse sequences. We use the ratio of T1w/T2w image intensities to eliminate the MR-related image intensity bias and enhance the contrast to noise ratio for myelin. Data from each subject was mapped to the cortical surface and aligned across individuals using surface-based registration. The spatial gradient of the group average myelin map provides an observer-independent measure of sharp transitions in myelin content across the surface—i.e. putative cortical areal borders. We found excellent agreement between the gradients of the myelin maps and the gradients of published probabilistic cytoarchitectonically defined cortical areas that were registered to the same surface-based atlas. For other cortical regions, we used published anatomical and functional information to make putative identifications of dozens of cortical areas or candidate areas. In general, primary and early unimodal association cortices are heavily myelinated and higher, multi-modal, association cortices are more lightly myelinated, but there are notable exceptions in the literature that are confirmed by our results. The overall pattern in the myelin maps also has important correlations with the developmental onset of subcortical white matter myelination, evolutionary cortical areal expansion in humans compared to macaques, postnatal cortical expansion in humans, and maps of neuronal density in non-human primates. PMID:21832190

  11. 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

  12. Early Outcome of Prostate Intensity Modulated Radiation Therapy (IMRT) Incorporating a Simultaneous Intra-Prostatic MRI Directed Boost

    PubMed Central

    Schild, Michael H; Schild, Steven E; Wong, William W; Vora, Sujay A; Silva, Alvin C; Silva, Annelise M; Daniels, Thomas B; Keole, Sameer R

    2015-01-01

    This study assessed the feasibility and outcomes of treating prostate cancer with intensity modulated radiotherapy (IMRT) incorporating a Magnetic Resonance Imaging (MRI) directed boost. Seventy-eight men received IMRT for localized prostate cancer. The entire prostate received 77.4Gy in 43 fractions and simultaneous intra-prostatic boosts (SIB) of 83Gy were administered to increase the dose to the MRI identified malignancy. In 16 (21%) patients, the MRI didn't detect a neoplasm and these patients received an SIB of 81Gy to the posterior prostate. Androgen Deprivation Therapy (ADT) was also administered to 32 (41%) patients. The 3-year rates of biochemical control, local control, distant control, and survival were 92%, 98%, 95%, and 95% respectively. While grade 1-2 toxicities were common, there were only 2 patients who suffered grade 3 toxicity. These patients developed strictures which were dilated resulting in improvement in symptoms such that both had grade 1-2 toxicity at last follow up examination. The results of this program of IMRT incorporating a MRI directed intra-prostatic boost suggest this technique is feasible and well tolerated. This technique appears to shift the therapeutic index favorably by boosting the malignancy to the highest dose without increasing the doses administered to the bladder and rectum. PMID:25717423

  13. 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.

  14. 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

  15. 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…

  16. 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…

  17. The link between diffusion MRI and tumor heterogeneity: Mapping cell eccentricity and density by diffusional variance decomposition (DIVIDE).

    PubMed

    Szczepankiewicz, Filip; van Westen, Danielle; Englund, Elisabet; Westin, Carl-Fredrik; Ståhlberg, Freddy; Lätt, Jimmy; Sundgren, Pia C; Nilsson, Markus

    2016-11-15

    only to cell density variance. The variance in meningiomas was caused primarily by microscopic anisotropy (mean±s.d.) MKA=1.11±0.33 vs MKI=0.44±0.20 (p<10(-3)), whereas in the gliomas, it was mostly caused by isotropic heterogeneity MKI=0.57±0.30 vs MKA=0.26±0.11 (p<0.05). In conclusion, DIVIDE allows non-invasive mapping of parameters that reflect variable cell eccentricity and density. These results constitute convincing evidence that a link exists between specific aspects of tissue heterogeneity and parameters from dMRI. Decomposing effects of microscopic anisotropy and isotropic heterogeneity facilitates an improved interpretation of tumor heterogeneity as well as diffusion anisotropy on both the microscopic and macroscopic scale.

  18. The Connectome Mapper: An Open-Source Processing Pipeline to Map Connectomes with MRI

    PubMed Central

    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. PMID:23272041

  19. 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.

  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. 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.

  2. Comparison of glomerular activity patterns by fMRI and wide-field calcium imaging: Implications for principles underlying odor mapping.

    PubMed

    Sanganahalli, Basavaraju G; Rebello, Michelle R; Herman, Peter; Papademetris, Xenophon; Shepherd, Gordon M; Verhagen, Justus V; Hyder, Fahmeed

    2016-02-01

    Functional imaging signals arise from distinct metabolic and hemodynamic events at the neuropil, but how these processes are influenced by pre- and post-synaptic activities need to be understood for quantitative interpretation of stimulus-evoked mapping data. The olfactory bulb (OB) glomeruli, spherical neuropil regions with well-defined neuronal circuitry, can provide insights into this issue. Optical calcium-sensitive fluorescent dye imaging (OICa(2+)) reflects dynamics of pre-synaptic input to glomeruli, whereas high-resolution functional magnetic resonance imaging (fMRI) using deoxyhemoglobin contrast reveals neuropil function within the glomerular layer where both pre- and post-synaptic activities contribute. We imaged odor-specific activity patterns of the dorsal OB in the same anesthetized rats with fMRI and OICa(2+) and then co-registered the respective maps to compare patterns in the same space. Maps by each modality were very reproducible as trial-to-trial patterns for a given odor, overlapping by ~80%. Maps evoked by ethyl butyrate and methyl valerate for a given modality overlapped by ~80%, suggesting activation of similar dorsal glomerular networks by these odors. Comparison of maps generated by both methods for a given odor showed ~70% overlap, indicating similar odor-specific maps by each method. These results suggest that odor-specific glomerular patterns by high-resolution fMRI primarily tracks pre-synaptic input to the OB. Thus combining OICa(2+) and fMRI lays the framework for studies of OB processing over a range of spatiotemporal scales, where OICa(2+) can feature the fast dynamics of dorsal glomerular clusters and fMRI can map the entire glomerular sheet in the OB.

  3. The Neural Substrates for Letter String Readings in The Normal and Reverse Directions: An fMRI Study

    NASA Astrophysics Data System (ADS)

    Ge, Sheng; Saito, Takashi; Wu, Jing-Long; Ogasawara, Jun-Ichi; Yamauchi, Shuichi; Matsunaga, Naofumi; Iramina, Keiji

    In order to investigate the difference in cortical activations between reading letter strings in the normal direction and the reverse direction, an fMRI study was conducted. In this study, the cortical activations elicited by Japanese letter string reading and Chinese letter string reading were investigated. The subjects performed the normal direction reading task (read letter strings from left to right), and the reverse direction reading task (read letter strings from right to left). According to the experimental results, the activated brain regions during the normal and the reverse direction reading tasks were compared. It was found that visuospatial transformation was involved in the reverse direction reading task, while this function was not significant during the normal direction reading task. Furthermore, we found that there was no significant difference in cortical activation between Japanese and Chinese letter string readings.

  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. An MRI receiver coil produced by inkjet printing directly on to a flexible substrate.

    PubMed

    Mager, Dario; Peter, Andreas; Tin, Laura Del; Fischer, Elmar; Smith, Patrick J; Hennig, Jürgen; Korvink, Jan G

    2010-02-01

    Inkjet printing has been used to produce resonant radio frequency coils that are comparable to those produced by conventional printed circuit board (PCB) methods. The coils, which consist of a conductive loop and in-series capacitors, form part of a receiver circuit that is used for magnetic resonance imaging (MRI). The resonant circuit is selective at the predetermined frequency of 400 MHz. The required electrical components (resistor, capacitor, and inductor) were produced by inkjet printing, with scaling experiments for resistor and capacitor performed before the complete loops with integrated capacitors were printed. Numerical simulation was used to determine the required values for the components. The inkjet printed circuit was combined with a small tuning and matching board before being connected to a network analyzer and the MRI hardware. With a matching of - 38 dB at 400 MHz the achieved results were comparable to those from standard PCB techniques. The performance of the inkjet printed component as a receiver device for nuclear magnetic resonance and MRI was verified by imaging reference phantoms and a whole kiwifruit; it compares favorably to standard MRI devices. Inkjet printing can, therefore, be considered a feasible technique for producing MRI receiver circuits on flexible substrates.

  6. Semi-automatic 10/20 Identification Method for MRI-Free Probe Placement in Transcranial Brain Mapping Techniques.

    PubMed

    Xiao, Xiang; Zhu, Hao; Liu, Wei-Jie; Yu, Xiao-Ting; Duan, Lian; Li, Zheng; Zhu, Chao-Zhe

    2017-01-01

    The International 10/20 system is an important head-surface-based positioning system for transcranial brain mapping techniques, e.g., fNIRS and TMS. As guidance for probe placement, the 10/20 system permits both proper ROI coverage and spatial consistency among multiple subjects and experiments in a MRI-free context. However, the traditional manual approach to the identification of 10/20 landmarks faces problems in reliability and time cost. In this study, we propose a semi-automatic method to address these problems. First, a novel head surface reconstruction algorithm reconstructs head geometry from a set of points uniformly and sparsely sampled on the subject's head. Second, virtual 10/20 landmarks are determined on the reconstructed head surface in computational space. Finally, a visually-guided real-time navigation system guides the experimenter to each of the identified 10/20 landmarks on the physical head of the subject. Compared with the traditional manual approach, our proposed method provides a significant improvement both in reliability and time cost and thus could contribute to improving both the effectiveness and efficiency of 10/20-guided MRI-free probe placement.

  7. 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.

  8. Semi-automatic 10/20 Identification Method for MRI-Free Probe Placement in Transcranial Brain Mapping Techniques

    PubMed Central

    Xiao, Xiang; Zhu, Hao; Liu, Wei-Jie; Yu, Xiao-Ting; Duan, Lian; Li, Zheng; Zhu, Chao-Zhe

    2017-01-01

    The International 10/20 system is an important head-surface-based positioning system for transcranial brain mapping techniques, e.g., fNIRS and TMS. As guidance for probe placement, the 10/20 system permits both proper ROI coverage and spatial consistency among multiple subjects and experiments in a MRI-free context. However, the traditional manual approach to the identification of 10/20 landmarks faces problems in reliability and time cost. In this study, we propose a semi-automatic method to address these problems. First, a novel head surface reconstruction algorithm reconstructs head geometry from a set of points uniformly and sparsely sampled on the subject's head. Second, virtual 10/20 landmarks are determined on the reconstructed head surface in computational space. Finally, a visually-guided real-time navigation system guides the experimenter to each of the identified 10/20 landmarks on the physical head of the subject. Compared with the traditional manual approach, our proposed method provides a significant improvement both in reliability and time cost and thus could contribute to improving both the effectiveness and efficiency of 10/20-guided MRI-free probe placement. PMID:28190997

  9. A Pilot Study of Quantitative MRI Parametric Response Mapping of Bone Marrow Fat for Treatment Assessment in Myelofibrosis

    PubMed Central

    Luker, Gary D.; Nguyen, Huong (Marie); Hoff, Benjamin A.; Galbán, Craig J.; Hernando, Diego; Chenevert, Thomas L.; Talpaz, Moshe; Ross, Brian D.

    2016-01-01

    Myelofibrosis (MF) is a hematologic neoplasm arising as a primary disease or secondary to other myeloproliferative neoplasms (MPNs). Both primary and secondary MF are uniquely associated with progressive bone marrow fibrosis, displacing normal hematopoietic cells from the marrow space and disrupting normal production of mature blood cells. Activation of the JAK2 signaling pathway in hematopoietic stem cells commonly causes MF, and ruxolitinib, a drug targeting this pathway, is the treatment of choice for many patients. However, current measures of disease status in MF do not necessarily predict response to treatment with ruxolitinib or other drugs in MF. Bone marrow biopsies are invasive and prone to sampling error, while measurements of spleen volume only indirectly reflect bone marrow status. Toward the goal of developing an imaging biomarker for treatment response in MF, we present preliminary results from a prospective clinical study evaluating parametric response mapping (PRM) of quantitative Dixon MRI bone marrow fat fraction maps in four MF patients treated with ruxolitinib. PRM allows for the voxel-wise identification of significant change in quantitative imaging readouts over time, in this case the bone marrow fat content. We identified heterogeneous response patterns of bone marrow fat among patients and within different bone marrow sites in the same patient. We also observed discordance between changes in bone marrow fat fraction and reductions in spleen volume, the standard imaging metric for treatment efficacy. This study provides initial support for PRM analysis of quantitative MRI of bone marrow fat to monitor response to therapy in MF, setting the stage for larger studies to further develop and validate this method as a complementary imaging biomarker for this disease. PMID:27213182

  10. Synthetic quantitative MRI through relaxometry modelling

    PubMed Central

    Mohammadi, Siawoosh; Weiskopf, Nikolaus

    2016-01-01

    Abstract Quantitative MRI (qMRI) provides standardized measures of specific physical parameters that are sensitive to the underlying tissue microstructure and are a first step towards achieving maps of biologically relevant metrics through in vivo histology using MRI. Recently proposed models have described the interdependence of qMRI parameters. Combining such models with the concept of image synthesis points towards a novel approach to synthetic qMRI, in which maps of fundamentally different physical properties are constructed through the use of biophysical models. In this study, the utility of synthetic qMRI is investigated within the context of a recently proposed linear relaxometry model. Two neuroimaging applications are considered. In the first, artefact‐free quantitative maps are synthesized from motion‐corrupted data by exploiting the over‐determined nature of the relaxometry model and the fact that the artefact is inconsistent across the data. In the second application, a map of magnetization transfer (MT) saturation is synthesized without the need to acquire an MT‐weighted volume, which directly leads to a reduction in the specific absorption rate of the acquisition. This feature would be particularly important for ultra‐high field applications. The synthetic MT map is shown to provide improved segmentation of deep grey matter structures, relative to segmentation using T 1‐weighted images or R 1 maps. The proposed approach of synthetic qMRI shows promise for maximizing the extraction of high quality information related to tissue microstructure from qMRI protocols and furthering our understanding of the interrelation of these qMRI parameters. PMID:27753154

  11. Topodiagnostic implications of hemiataxia: an MRI-based brainstem mapping analysis.

    PubMed

    Marx, Juergen J; Iannetti, Gian D; Thömke, Frank; Fitzek, Sabine; Galeotti, Francesca; Truini, Andrea; Stoeter, Peter; Dieterich, Marianne; Hopf, Hanns C; Cruccu, Giorgio

    2008-02-15

    The topodiagnostic implications of hemiataxia following lesions of the human brainstem are only incompletely understood. We performed a voxel-based statistical analysis of lesions documented on standardised MRI in 49 prospectively recruited patients with acute hemiataxia due to isolated unilateral brainstem infarction. For statistical analysis individual MRI lesions were normalised and imported in a three-dimensional voxel-based anatomical model of the human brainstem. Statistical analysis revealed hemiataxia to be associated with lesions of three distinct brainstem areas. The strongest correlation referred to ipsilateral rostral and dorsolateral medullary infarcts affecting the inferior cerebellar peduncle, and the dorsal and ventral spinocerebellar tracts. Secondly, lesions of the ventral pontine base resulted in contralateral limb ataxia, especially when ataxia was accompanied by motor hemiparesis. In patients with bilateral hemiataxia, lesions were located in a paramedian region between the upper pons and lower midbrain, involving the decussation of dentato-rubro-thalamic tracts. We conclude that ataxia following brainstem infarction may reflect three different pathophysiological mechanisms. (1) Ipsilateral hemiataxia following dorsolateral medullary infarctions results from a lesion of the dorsal spinocerebellar tract and the inferior cerebellar peduncle conveying afferent information from the ipsilateral arm and leg. (2) Pontine lesions cause contralateral and not bilateral ataxia presumably due to major damage to the descending corticopontine projections and pontine base nuclei, while already crossed pontocerebellar fibres are not completely interrupted. (3) Finally, bilateral ataxia probably reflects a lesion of cerebellar outflow on a central, rostral pontomesencephalic level.

  12. 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.

  13. 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

  14. Synergetic fMRI-EEG brain mapping in alpha-rhythm voluntary control mode.

    PubMed

    Shtark, M B; Verevkin, E G; Kozlova, L I; Mazhirina, K G; Pokrovskii, M A; Petrovskii, E D; Savelov, A A; Starostin, A S; Yarosh, S V

    2015-03-01

    For the first time in neurobiology-related issues, the synergistic spatial dynamics of EEG and fMRI (BOLD phenomenon) was studied during cognitive alpha biofeedback training in the operant conditioning mode (acoustic reinforcement of alpha-rhythm development and stability). Significant changes in alpha-rhythm intensity were found in T6 electrode area (Brodmann area 37). Brodmann areas related to solving alpha-training tasks and maximally involved in the formation of new neuronal network were middle and superior temporal gyri (areas 21, 22, and 37), fusiform gyrus, inferior frontal gyrus (areas 4, 6, and 46), anterior cingulate gyrus (areas 23 and 24), cuneus, and precuneus (area 7). Wide involvement of Brodmann areas is determined by psychological architecture of alpha-rhythm generating system control that includes complex cognitive activities: decision making, retrieval of long-term memory, evaluation of the reward and control efficiency during alpha-EEG biofeedback.

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

    NASA Astrophysics Data System (ADS)

    Seghier, Mohamed L.; Price, Cathy J.

    2016-02-01

    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.

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

    PubMed Central

    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

  17. Spiral Perfusion Imaging With Consecutive Echoes (SPICE™) for the Simultaneous Mapping of DSC- and DCE-MRI Parameters in Brain Tumor Patients: Theory and Initial Feasibility.

    PubMed

    Paulson, Eric S; Prah, Douglas E; Schmainda, Kathleen M

    2016-12-01

    Dynamic contrast-enhanced (DCE) and dynamic susceptibility contrast (DSC) magnetic resonance imaging (MRI) are the perfusion imaging techniques most frequently used to probe the angiogenic character of brain neoplasms. With these methods, T1- and T2/T2*-weighted imaging sequences are used to image the distribution of gadolinium (Gd)-based contrast agents. However, it is well known that Gd exhibits combined T1, T2, and T2* shortening effects in tissue, and therefore, the results of both DCE- and DSC-MRI can be confounded by these opposing effects. In particular, residual susceptibility effects compete with T1 shortening, which can confound DCE-MRI parameters, whereas dipolar T1 and T2 leakage and residual susceptibility effects can confound DSC-MRI parameters. We introduce here a novel perfusion imaging acquisition and postprocessing method termed Spiral Perfusion Imaging with Consecutive Echoes (SPICE) that can be used to simultaneously acquire DCE- and DSC-MRI data, which requires only a single dose of the Gd contrast agent, does not require the collection of a precontrast T1 map for DCE-MRI processing, and eliminates the confounding contrast agent effects due to contrast extravasation. A detailed mathematical description of SPICE is provided here along with a demonstration of its utility in patients with high-grade glioma.

  18. Spiral Perfusion Imaging With Consecutive Echoes (SPICE™) for the Simultaneous Mapping of DSC- and DCE-MRI Parameters in Brain Tumor Patients: Theory and Initial Feasibility

    PubMed Central

    Paulson, Eric S.; Prah, Douglas E.; Schmainda, Kathleen M.

    2017-01-01

    Dynamic contrast-enhanced (DCE) and dynamic susceptibility contrast (DSC) magnetic resonance imaging (MRI) are the perfusion imaging techniques most frequently used to probe the angiogenic character of brain neoplasms. With these methods, T1- and T2/T2*-weighted imaging sequences are used to image the distribution of gadolinium (Gd)-based contrast agents. However, it is well known that Gd exhibits combined T1, T2, and T2* shortening effects in tissue, and therefore, the results of both DCE- and DSC-MRI can be confounded by these opposing effects. In particular, residual susceptibility effects compete with T1 shortening, which can confound DCE-MRI parameters, whereas dipolar T1 and T2 leakage and residual susceptibility effects can confound DSC-MRI parameters. We introduce here a novel perfusion imaging acquisition and postprocessing method termed Spiral Perfusion Imaging with Consecutive Echoes (SPICE) that can be used to simultaneously acquire DCE- and DSC-MRI data, which requires only a single dose of the Gd contrast agent, does not require the collection of a precontrast T1 map for DCE-MRI processing, and eliminates the confounding contrast agent effects due to contrast extravasation. A detailed mathematical description of SPICE is provided here along with a demonstration of its utility in patients with high-grade glioma. PMID:28090589

  19. Spatio-Temporal Brain Mapping of Motion-Onset VEPs Combined with fMRI and Retinotopic Maps

    PubMed Central

    Pitzalis, Sabrina; Strappini, Francesca; De Gasperis, Marco; Bultrini, Alessandro; Di Russo, Francesco

    2012-01-01

    Neuroimaging studies have identified several motion-sensitive visual areas in the human brain, but the time course of their activation cannot be measured with these techniques. In the present study, we combined electrophysiological and neuroimaging methods (including retinotopic brain mapping) to determine the spatio-temporal profile of motion-onset visual evoked potentials for slow and fast motion stimuli and to localize its neural generators. We found that cortical activity initiates in the primary visual area (V1) for slow stimuli, peaking 100 ms after the onset of motion. Subsequently, activity in the mid-temporal motion-sensitive areas, MT+, peaked at 120 ms, followed by peaks in activity in the more dorsal area, V3A, at 160 ms and the lateral occipital complex at 180 ms. Approximately 250 ms after stimulus onset, activity fast motion stimuli was predominant in area V6 along the parieto-occipital sulcus. Finally, at 350 ms (100 ms after the motion offset) brain activity was visible again in area V1. For fast motion stimuli, the spatio-temporal brain pattern was similar, except that the first activity was detected at 70 ms in area MT+. Comparing functional magnetic resonance data for slow vs. fast motion, we found signs of slow-fast motion stimulus topography along the posterior brain in at least three cortical regions (MT+, V3A and LOR). PMID:22558222

  20. The Tofts model in frequency domain: fast and robust determination of pharmacokinetic maps for dynamic contrast enhancement MRI

    NASA Astrophysics Data System (ADS)

    Vajuvalli, Nithin N.; Chikkemenahally, Dharmendra Kumar K.; Nayak, Krupa N.; Bhosale, Manoj G.; Geethanath, Sairam

    2016-12-01

    Dynamic contrast enhancement magnetic resonance imaging (DCE-MRI) is a well-established method for non-invasive detection and therapeutic monitoring of pathologies through administration of intravenous contrast agent. Quantification of pharmacokinetic (PK) maps can be achieved through application of compartmental models relevant to the pathophysiology of the tissue under interrogation. The determination of PK parameters involves fitting of time-concentration data to these models. In this work, the Tofts model in frequency domain (TM-FD) is applied to a weakly vascularized tissue such as the breast. It is derived as a convolution-free model from the conventional Tofts model in the time domain (TM-TD). This reduces the dimensionality of the curve-fitting problem from two to one. The approaches of TM-FD and TM-TD were applied to two kinds of in silico phantoms and six in vivo breast DCE data sets with and without the addition of noise. The results showed that computational time taken to estimate PK maps using TM-FD was 16-25% less than with TM-TD. Normalized root mean square error (NRMSE) calculation and Pearson correlation analyses were performed to validate robustness and accuracy of the TM-FD and TM-TD approaches. These compared with ground truth values in the case of phantom studies for four different temporal resolutions. Results showed that NRMSE values for TM-FD were significantly lower than those of TM-TD as validated by a paired t-test along with reduced computational time. This approach therefore enables online evaluation of PK maps by radiologists in a clinical setting, aiding in the evaluation of 3D and/or increased coverage of the tissue of interest.

  1. 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

  2. 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

  3. Detection and characterization of single-trial fMRI bold responses: paradigm free mapping.

    PubMed

    Gaudes, César Caballero; Petridou, Natalia; Dryden, Ian L; Bai, Li; Francis, Susan T; Gowland, Penny A

    2011-09-01

    This work presents a novel method of mapping the brain's response to single stimuli in space and time without prior knowledge of the paradigm timing: paradigm free mapping (PFM). This method is based on deconvolution of the hemodynamic response from the voxel time series assuming a linear response and using a ridge-regression algorithm. Statistical inference is performed by defining a spatio-temporal t-statistic and by controlling for multiple comparisons using the false discovery rate procedure. The methodology was validated on five subjects who performed self-paced and visually cued finger tapping at 7 Tesla, with moderate (TR = 2 s) and high (TR = 0.4 s) temporal resolution. The results demonstrate that detection of single-trial BOLD events is feasible without a priori information on the stimulus paradigm. The proposed method opens up the possibility of designing temporally unconstrained paradigms to study the cortical response to unpredictable mental events.

  4. Effect of sound intensity on tonotopic fMRI maps in the unanesthetized monkey.

    PubMed

    Tanji, Kazuyo; Leopold, David A; Ye, Frank Q; Zhu, Charles; Malloy, Megan; Saunders, Richard C; Mishkin, Mortimer

    2010-01-01

    The monkey's auditory cortex includes a core region on the supratemporal plane (STP) made up of the tonotopically organized areas A1, R, and RT, together with a surrounding belt and a lateral parabelt region. The functional studies that yielded the tonotopic maps and corroborated the anatomical division into core, belt, and parabelt typically used low-amplitude pure tones that were often restricted to threshold-level intensities. Here we used functional magnetic resonance imaging in awake rhesus monkeys to determine whether, and if so how, the tonotopic maps and the pattern of activation in core, belt, and parabelt are affected by systematic changes in sound intensity. Blood oxygenation level-dependent (BOLD) responses to groups of low- and high-frequency pure tones 3-4 octaves apart were measured at multiple sound intensity levels. The results revealed tonotopic maps in the auditory core that reversed at the putative areal boundaries between A1 and R and between R and RT. Although these reversals of the tonotopic representations were present at all intensity levels, the lateral spread of activation depended on sound amplitude, with increasing recruitment of the adjacent belt areas as the intensities increased. Tonotopic organization along the STP was also evident in frequency-specific deactivation (i.e. "negative BOLD"), an effect that was intensity-specific as well. Regions of positive and negative BOLD were spatially interleaved, possibly reflecting lateral inhibition of high-frequency areas during activation of adjacent low-frequency areas, and vice versa. These results, which demonstrate the strong influence of tonal amplitude on activation levels, identify sound intensity as an important adjunct parameter for mapping the functional architecture of auditory cortex.

  5. 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.

  6. 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.

  7. 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

  8. Integrated strategy for improving functional connectivity mapping using multiecho fMRI

    PubMed Central

    Kundu, Prantik; Brenowitz, Noah D.; Voon, Valerie; Worbe, Yulia; Vértes, Petra E.; Inati, Souheil J.; Saad, Ziad S.; Bandettini, Peter A.; Bullmore, Edward T.

    2013-01-01

    Functional connectivity analysis of resting state blood oxygen level–dependent (BOLD) functional MRI is widely used for noninvasively studying brain functional networks. Recent findings have indicated, however, that even small (≤1 mm) amounts of head movement during scanning can disproportionately bias connectivity estimates, despite various preprocessing efforts. Further complications for interregional connectivity estimation from time domain signals include the unaccounted reduction in BOLD degrees of freedom related to sensitivity losses from high subject motion. To address these issues, we describe an integrated strategy for data acquisition, denoising, and connectivity estimation. This strategy builds on our previously published technique combining data acquisition with multiecho (ME) echo planar imaging and analysis with spatial independent component analysis (ICA), called ME-ICA, which distinguishes BOLD (neuronal) and non-BOLD (artifactual) components based on linear echo-time dependence of signals—a characteristic property of BOLD signal changes. Here we show for 32 control subjects that this method provides a physically principled and nearly operator-independent way of removing complex artifacts such as motion from resting state data. We then describe a robust estimator of functional connectivity based on interregional correlation of BOLD-independent component coefficients. This estimator, called independent components regression, considerably simplifies statistical inference for functional connectivity because degrees of freedom equals the number of independent coefficients. Compared with traditional connectivity estimation methods, the proposed strategy results in fourfold improvements in signal-to-noise ratio, functional connectivity analysis with improved specificity, and valid statistical inference with nominal control of type 1 error in contrasts of connectivity between groups with different levels of subject motion. PMID:24038744

  9. Validation of Sodium MRI of Intervertebral Disc

    PubMed Central

    Wang, Chenyang; McArdle, Erin; Fenty, Matthew; Witschey, Walter; Elliott, Mark; Sochor, Matthew; Reddy, Ravinder; Borthakur, Arijitt

    2009-01-01

    Study Design This study demonstrated the diagnostic potential of sodium MRI for non-invasive quantification of PG in the intervertebral discs. Objective To determine the existence of a linear correlation between intervertebral disc [Na] measured from sodium MRI and [PG] measurement from DMMB assay. Summary of Background Data Previous studies have shown the possibility of quantifying [Na] in vivo using sodium MRI, however none has shown a direct linear correlation between [Na] measured from sodium MRI and [PG]. Methods 3D sodium MRI images of bovine discs were acquired and converted into [Na] maps. Samples were systematically removed from the discs for DMMB assay. The removal locations were photographically recorded and applied to the [Na] maps to extract the [Na] measurements for comparison. In vivo sodium MRI scans were also carried out on a pair of symptomatic and asymptomatic subjects. Results The linear regression fit of [Na] versus [PG] data yielded a significant linear correlation coefficient of 0.71. The in vivo sodium MRI image of the symptomatic subject showed significant [Na] decrease when compared to that of the asymptomatic subject. Conclusion Sodium MRI's specificity for PG in the intervertebral discs makes it a promising diagnostic tool for the earlier phase of disc degeneration. PMID:20147881

  10. 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

  11. Euclidian distance-weighted smoothing for quantitative MRI: application to intervoxel anisotropy index mapping with DTI

    NASA Astrophysics Data System (ADS)

    Bonny, Jean-Marie; Renou, Jean-Pierre

    2002-12-01

    During the computation of intervoxel anisotropy features, the inclusion of both eigenvalues and eigenvectors reduces the effect of noise, but spatial averaging blurs the resulting maps. We propose a new adaptive technique that uses data-dependent weights in the averaging process so that the influence of each neighbor in the local window is proportional to the similarity of characteristics of the neighbor considered to those of the reference central voxel. This likeness criterion is based on the multidimensional Euclidian distance using the entire available multispectral information contained in the diffusion-weighted images. This solution is controlled by a single parameter β that results from a compromise between edge-preserving and noise-smoothing abilities. This Euclidian distance-weighted technique is a generic solution for filtering noise during parametric reconstruction. It was applied to map anisotropy using an intervoxel lattice index (LI) from experimental images of mouse brain in vivo and achieves noise reduction without distorting small anatomical structures. We also show how to employ in the discrimination scheme the images not used in the estimation of the considered feature.

  12. 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.

  13. 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

  14. 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

  15. Writing direction affects how people map space onto time.

    PubMed

    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.

  16. Negative cerebral blood volume fMRI response coupled with Ca²⁺-dependent brain activity in a dopaminergic road map of nociception.

    PubMed

    Hsu, Yi-Hua; Chang, Chen; Chen, Chiao-Chi V

    2014-04-15

    Decreased cerebral blood volume/flow (CBV/CBF) contributes to negative blood-oxygen-level-dependent (BOLD) functional MRI (fMRI) signals. But it is still strongly debated whether these negative BOLD or CBV/CBF signals are indicative of decreased or increased neuronal activity. The fidelity of Ca(2+) signals in reflecting neuronal excitation is well documented. However, the roles of Ca(2+) signals and Ca(2+)-dependent activity in negative fMRI signals have never been explored; an understanding of this is essential to unraveling the underlying mechanisms and correctly interpreting the hemodynamic response of interest. The present study utilized a nociception-induced negative CBV fMRI response as a model. Ca(2+) signals were investigated in vivo using Mn(2+)-enhanced MRI (MEMRI), and the downstream Ca(2+)-dependent signaling was investigated using phosphorylated cAMP response-element-binding (pCREB) immunohistology. The results showed that nociceptive stimulation led to (1) striatal CBV decreases, (2) Ca(2+) increases via the nigrostriatal pathway, and (3) substantial expression of pCREB in substantia nigra dopaminergic neurons and striatal neurons. Interestingly, the striatal negative fMRI response was abolished by blocking substantia nigra activity but was not affected by blocking the striatal activity. This suggests the importance of input activity other than output in triggering the negative CBV signals. These findings indicate that the striatal negative CBV fMRI signals are associated with Ca(2+) increases and Ca(2+)-dependent signaling along the nigrostriatal pathway. The obtained data reveal a new brain road map in response to nociceptive stimulation of hemodynamic changes in association with Ca(2+) signals within the dopaminergic system.

  17. Distinct laterality alterations distinguish mild cognitive impairment and Alzheimer's disease from healthy aging: statistical parametric mapping with high resolution MRI.

    PubMed

    Long, Xiaojing; Zhang, Lijuan; Liao, Weiqi; Jiang, Chunxiang; Qiu, Bensheng

    2013-12-01

    Laterality of human brain varies under healthy aging and diseased conditions. The alterations in hemispheric asymmetry may embed distinct biomarkers linked to the disease dynamics. Statistical parametric mapping based on high-resolution magnetic resonance imaging (MRI) and image processing techniques have allowed automated characterization of morphological features across the entire brain. In this study, 149 subjects grouped in healthy young, healthy elderly, mild cognitive impairment (MCI), and Alzheimer's disease (AD) were investigated using multivariate analysis for regional cerebral laterality indexed by surface area, curvature index, cortical thickness, and subjacent white matter volume measured on high-resolution MR images. Asymmetry alteration of MCI and AD were characterized by marked region-specific reduction, while healthy elderly featured a distinct laterality shift in the limbic system in addition to regional asymmetry loss. Lack of the laterality shift in limbic system and early loss of asymmetry in entorhinal cortex may be biomarkers to identify preclinical AD among other dementia. Multivariate analysis of hemispheric asymmetry may provide information helpful for monitoring the disease progress and improving the management of MCI and AD.

  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. 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

    2012-09-07

    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.

  20. 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

  1. An adaptive model for rapid and direct estimation of extravascular extracellular space in dynamic contrast enhanced MRI studies.

    PubMed

    Dehkordi, Azimeh N V; Kamali-Asl, Alireza; Ewing, James R; Wen, Ning; Chetty, Indrin J; Bagher-Ebadian, Hassan

    2017-02-14

    Extravascular extracellular space (ve ) is a key parameter to characterize the tissue of cerebral tumors. This study introduces an artificial neural network (ANN) as a fast, direct, and accurate estimator of ve from a time trace of the longitudinal relaxation rate, ΔR1 (R1  = 1/T1 ), in DCE-MRI studies. Using the extended Tofts equation, a set of ΔR1 profiles was simulated in the presence of eight different signal to noise ratios. A set of gain- and noise-insensitive features was generated from the simulated ΔR1 profiles and used as the ANN training set. A K-fold cross-validation method was employed for training, testing, and optimization of the ANN. The performance of the optimal ANN (12:6:1, 12 features as input vector, six neurons in hidden layer, and one output) in estimating ve at a resolution of 10% (error of ±5%) was 82%. The ANN was applied on DCE-MRI data of 26 glioblastoma patients to estimate ve in tumor regions. Its results were compared with the maximum likelihood estimation (MLE) of ve . The two techniques showed a strong agreement (r = 0.82, p < 0.0001). Results implied that the perfected ANN was less sensitive to noise and outperformed the MLE method in estimation of ve .

  2. 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.

  3. 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.

  4. FMRI and fcMRI phenotypes map the genomic effect of chromosome 13 in Brown Norway and Dahl salt-sensitive rats.

    PubMed

    Li, Zhixin; Ward, B Douglas; Dwinell, Melinda R; Lombard, Julian H; Pawela, Christopher P

    2014-04-15

    Genes have been implicated as major contributors to many biological traits and susceptibility to specific diseases. However, the mechanisms of genotype action on central nervous system function have been elusive. It has been previously observed that inbred Brown Norway (BN) rats exhibit a number of quantitative complex traits markedly different from those of inbred Dahl salt-sensitive (SS) rats. These strains have become so important to cardiovascular research that a novel chromosome substitution approach was used to create SS and BN strains that have a single chromosome replaced by the homologous chromosome of the other strain. The present study was conducted in an effort to evaluate whether fMRI neuroimaging measures could be employed as a phenotype of genetic influence on neural biology in SS, BN, and consomic SSBN13 rat strains. Electrical forepaw stimulation evoked robust differential BOLD-fMRI activation along the thalamocortical pathway among the three strains across different stimulus frequencies. Moreover, using the fMRI-guided seeds in thalamus and somatosensory cortex for the analysis of fcMRI, we were able to characterize the strain-specific difference in secondary somatosensory cortex, temporal association cortex, and the CA3 region. We were also able to define the genetic influences of Chr-13 on the projection and integration of sensory information in consomic SS-13(BN) strain. We provided objective imaging evidence supporting the hypothesis that rat strain-specific fMRI and fcMRI combined with consomic strategy can be a useful tool in identifying the complex genetic divergence that is related to neural circuits. These findings prove the concept of neuroimaging-based phenotypes as a novel approach to visualize and fine-map the genetic effects onto brain biology at a systems level.

  5. Noninvasive 4D pressure difference mapping derived from 4D flow MRI in patients with repaired aortic coarctation: comparison with young healthy volunteers.

    PubMed

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

    2015-04-01

    To assess spatial and temporal pressure characteristics in patients with repaired aortic coarctation compared to young healthy volunteers using time-resolved velocity-encoded three-dimensional phase-contrast magnetic resonance imaging (4D flow MRI) and derived 4D pressure difference maps. After in vitro validation against invasive catheterization as gold standard, 4D flow MRI of the thoracic aorta was performed at 1.5T in 13 consecutive patients after aortic coarctation repair without recoarctation and 13 healthy volunteers. Using in-house developed processing software, 4D pressure difference maps were computed based on the Navier-Stokes equation. Pressure difference amplitudes, maximum slope of pressure amplitudes and spatial pressure range at mid systole were retrospectively measured by three readers, and twice by one reader to assess inter- and intraobserver agreement. In vitro, pressure differences derived from 4D flow MRI showed excellent agreement to invasive catheter measurements. In vivo, pressure difference amplitudes, maximum slope of pressure difference amplitudes and spatial pressure range at mid systole were significantly increased in patients compared to volunteers in the aortic arch, the proximal descending and the distal descending thoracic aorta (p < 0.05). Greatest differences occurred in the proximal descending aorta with values of the three parameters for patients versus volunteers being 19.7 ± 7.5 versus 10.0 ± 2.0 (p < 0.001), 10.9 ± 10.4 versus 1.9 ± 0.4 (p = 0.002), and 8.7 ± 6.3 versus 1.6 ± 0.9 (p < 0.001). Inter- and intraobserver agreements were excellent (p < 0.001). Noninvasive 4D pressure difference mapping derived from 4D flow MRI enables detection of altered intraluminal aortic pressures and showed significant spatial and temporal changes in patients with repaired aortic coarctation.

  6. Stable Atlas-based Mapped Prior (STAMP) Machine-learning Segmentation for Multicenter Large-scale MRI Data

    PubMed Central

    Kim, Eun Young; Magnotta, Vincent A.; Liu, Dawei; Johnson, Hans J.

    2014-01-01

    Machine learning (ML)-based segmentation methods are a common technique in the medical image processing field. In spite of numerous research groups that have investigated ML-based segmentation frameworks, there remains unanswered aspects of performance variability for the choice of two key components: ML-algorithm and intensity normalization. This investigation reveals that the choice of those elements plays a major part in determining segmentation accuracy and generalizability. The approach we have used in this study aims to evaluate relative benefits of the two elements within a subcortical MRI segmentation framework. Experiments were conducted to contrast eight machine-learning algorithm configurations and 11 normalization strategies for our brain MR segmentation framework. For the intensity normalization, a stable atlas-based mapped prior (STAMP) was utilized to take better account of contrast along boundaries of structures. Comparing eight machine learning algorithms on down-sampled segmentation MR data, it was obvious that a significant improvement was obtained using ensemble-based ML algorithms (i.e., random forest) or ANN algorithms. Further investigation between these two algorithms also revealed that the random forest results provided exceptionally good agreement with manual delineations by experts. Additional experiments showed that the effect of STAMP-based intensity normalization also improved the robustness of segmentation for multicenter data sets. The constructed framework obtained good multicenter reliability and was successfully applied on a large multicenter MR data set (n > 3000). Less than 10% of automated segmentations were recommended for minimal expert intervention. These results demonstrate the feasibility of using the ML-based segmentation tools for processing large amount of multicenter MR images. We demonstrated dramatically different result profiles in segmentation accuracy according to the choice of ML algorithm and intensity

  7. Stable Atlas-based Mapped Prior (STAMP) machine-learning segmentation for multicenter large-scale MRI data.

    PubMed

    Kim, Eun Young; Magnotta, Vincent A; Liu, Dawei; Johnson, Hans J

    2014-09-01

    Machine learning (ML)-based segmentation methods are a common technique in the medical image processing field. In spite of numerous research groups that have investigated ML-based segmentation frameworks, there remains unanswered aspects of performance variability for the choice of two key components: ML algorithm and intensity normalization. This investigation reveals that the choice of those elements plays a major part in determining segmentation accuracy and generalizability. The approach we have used in this study aims to evaluate relative benefits of the two elements within a subcortical MRI segmentation framework. Experiments were conducted to contrast eight machine-learning algorithm configurations and 11 normalization strategies for our brain MR segmentation framework. For the intensity normalization, a Stable Atlas-based Mapped Prior (STAMP) was utilized to take better account of contrast along boundaries of structures. Comparing eight machine learning algorithms on down-sampled segmentation MR data, it was obvious that a significant improvement was obtained using ensemble-based ML algorithms (i.e., random forest) or ANN algorithms. Further investigation between these two algorithms also revealed that the random forest results provided exceptionally good agreement with manual delineations by experts. Additional experiments showed that the effect of STAMP-based intensity normalization also improved the robustness of segmentation for multicenter data sets. The constructed framework obtained good multicenter reliability and was successfully applied on a large multicenter MR data set (n>3000). Less than 10% of automated segmentations were recommended for minimal expert intervention. These results demonstrate the feasibility of using the ML-based segmentation tools for processing large amount of multicenter MR images. We demonstrated dramatically different result profiles in segmentation accuracy according to the choice of ML algorithm and intensity

  8. Direct estimation of patient attributes from anatomical MRI based on multi-atlas voting.

    PubMed

    Wu, Dan; Ceritoglu, Can; Miller, Michael I; Mori, Susumu

    MRI brain atlases are widely used for automated image segmentation, and in particular, recent developments in multi-atlas techniques have shown highly accurate segmentation results. In this study, we extended the role of the atlas library from mere anatomical reference to a comprehensive knowledge database with various patient attributes, such as demographic, functional, and diagnostic information. In addition to using the selected (heavily-weighted) atlases to achieve high segmentation accuracy, we tested whether the non-anatomical attributes of the selected atlases could be used to estimate patient attributes. This can be considered a context-based image retrieval (CBIR) approach, embedded in the multi-atlas framework. We first developed an image similarity measurement to weigh the atlases on a structure-by-structure basis, and then, the attributes of the multiple atlases were weighted to estimate the patient attributes. We tested this concept first by estimating age in a normal population; we then performed functional and diagnostic estimations in Alzheimer's disease patients. The accuracy of the estimated patient attributes was measured against the actual clinical data, and the performance was compared to conventional volumetric analysis. The proposed CBIR framework by multi-atlas voting would be the first step toward a knowledge-based support system for quantitative radiological image reading and diagnosis.

  9. On tests of activation map dimensionality for fMRI-based studies of learning.

    PubMed

    Yang, Juemin; Shmuelof, Lior; Xiao, Luo; Krakauer, John W; Caffo, Brian

    2015-01-01

    A methodology for investigating learning is developed using activation distributions, as opposed to standard voxel-level interaction tests. The approach uses tests of dimensionality to consider the ensemble of paired changes in voxel activation. The developed method allows for the investigation of non-focal and non-localized changes due to learning. In exchange for increased power to detect learning-based changes, this procedure sacrifices the localization information gained via voxel-level interaction testing. The test is demonstrated on an arc-pointing motor task for the study of motor learning, which served as the motivation for this methodological development. The proposed framework considers activation distribution, while the specific proposed test investigates linear tests of dimensionality. This paper includes: the development of the framework, a large scale simulation study, and the subsequent application to a study of motor learning in healthy adults. While the performance of the method was excellent when model assumptions held, complications arose in instances of massive numbers of null voxels or varying angles of principal dimension across subjects. Further analysis found that careful masking addressed the former concern, while an angle correction successfully resolved the latter. The simulation results demonstrated that the study of linear dimensionality is able to capture learning effects. The motivating data set used to illustrate the method evaluates two similar arc-pointing tasks, each over two sessions, with training on only one of the tasks in between sessions. The results suggests different activation distribution dimensionality when considering the trained and untrained tasks separately. Specifically, the untrained task evidences greater activation distribution dimensionality than the trained task. However, the direct comparison between the two tasks did not yield a significant result. The nature of the indication for greater dimensionality in

  10. Physiological noise correction using ECG-derived respiratory signals for enhanced mapping of spontaneous neuronal activity with simultaneous EEG-fMRI.

    PubMed

    Abreu, Rodolfo; Nunes, Sandro; Leal, Alberto; Figueiredo, Patrícia

    2016-08-12

    The study of spontaneous brain activity based on BOLD-fMRI may be seriously compromised by the presence of signal fluctuations of non-neuronal origin, most prominently due to cardiac and respiratory mechanisms. Methods used for modeling and correction of the so-called physiological noise usually rely on the concurrent measurement of cardiac and respiratory signals. In simultaneous EEG-fMRI recordings, which are primarily aimed at the study of spontaneous brain activity, the electrocardiogram (ECG) is typically measured as part of the EEG setup but respiratory data are not generally available. Here, we propose to use the ECG-derived respiratory (EDR) signal estimated by Empirical Mode Decomposition (EMD) as a surrogate of the respiratory signal, for retrospective physiological noise correction of typical simultaneous EEG-fMRI data. A physiological noise model based on these physiological signals (P-PNM) complemented with fMRI-derived noise regressors was generated, and evaluated, for 17 simultaneous EEG-fMRI datasets acquired from a group of seven epilepsy patients imaged at 3T. The respiratory components of P-PNM were found to explain BOLD variance significantly in addition to the cardiac components, suggesting that the EDR signal was successfully extracted from the ECG, and P-PNM outperformed an image-based model (I-PNM) in terms of total BOLD variance explained. Further, the impact of the correction using P-PNM on fMRI mapping of patient-specific epileptic networks and the resting-state default mode network (DMN) was assessed in terms of sensitivity and specificity and, when compared with an ICA-based procedure and a standard pre-processing pipeline, P-PNM achieved the best performance. Overall, our results support the feasibility and utility of extracting physiological noise models of the BOLD signal resorting to ECG data exclusively, with substantial impact on the simultaneous EEG-fMRI mapping of resting-state networks, and, most importantly, epileptic networks

  11. Regional Mapping of Gas Uptake by Blood and Tissue in the Human Lung using Hyperpolarized Xenon-129 MRI

    PubMed Central

    Qing, Kun; Ruppert, Kai; Jiang, Yun; Mata, Jaime F.; Miller, G. Wilson; Shim, Y. Michael; Wang, Chengbo; Ruset, Iulian C.; Hersman, F. William; Altes, Talissa A.; Mugler, John P.

    2013-01-01

    Purpose To develop a breath-hold acquisition for regional mapping of ventilation and the fractions of hyperpolarized xenon-129 (Xe129) dissolved in tissue (lung parenchyma and plasma) and red blood cells (RBCs), and to perform an exploratory study to characterize data obtained in human subjects. Materials and Methods A three-dimensional, multi-echo, radial-trajectory pulse sequence was developed to obtain ventilation (gaseous Xe129), tissue and RBC images in healthy subjects, smokers and asthmatics. Signal ratios (total dissolved Xe129 to gas, tissue-to-gas, RBC-to-gas and RBC-to-tissue) were calculated from the images for quantitative comparison. Results Healthy subjects demonstrated generally uniform values within coronal slices, and a gradient in values along the anterior-to-posterior direction. In contrast, images and associated ratio maps in smokers and asthmatics were generally heterogeneous and exhibited values mostly lower than those in healthy subjects. Whole-lung values of total dissolved Xe129 to gas, tissue-to-gas, and RBC-to-gas ratios in healthy subjects were significantly larger than those in diseased subjects. Conclusion Regional maps of tissue and RBC fractions of dissolved Xe129 were obtained from a short breath-hold acquisition, well tolerated by healthy volunteers and subjects with obstructive lung disease. Marked differences were observed in spatial distributions and overall amounts of Xe129 dissolved in tissue and RBCs among healthy subjects, smokers and asthmatics. PMID:23681559

  12. In-vivo MRI and in-vivo electro-anatomical voltage map characteristics of infarct heterogeneity in a swine model.

    PubMed

    Shokrollahi, E; Pop, M; Safri, M; Yang, Y; Radau, P E; Barry, J; Detsky, J; Griffin, G H; Crystal, E; Wright, G A

    2011-01-01

    The arrhythmogenic substrate in patients with prior myocardial infarct (MI) is located at the border zone, BZ. In this study we correlated the BZ identified by two methods: electro-anatomical voltage mapping (EAVM) and a novel MRI method, multi-contrast late enhancement (MCLE). A pre-clinical porcine model with chronic MI was used to characterize BZ via MRI and EAVM. Results focus on the comparison between scar percentage and BZ percentage identified by each method. The correlation coefficient for BZ percentage between the two methods was 0.74 with a p-value of less the 0.0001. Bland-Altman plots were also used to compare between the two methods (slope of 0.83 ± 0.045). For a case of subtle infarct, there was only 1.3% infarct identified on EAVM compared to 22.2% on the corresponding slice on MCLE. The percentage of infarct on MCLE in subtle infarct does not relate to percentage of infarct in EAVM. Future registration between T(1) maps and EAVM will permit a quantitative comparison of MRI and EAVM measures.

  13. Comparison of global cerebral blood flow measured by phase‐contrast mapping MRI with 15O‐H2O positron emission tomography

    PubMed Central

    Lindberg, Ulrich; Aachmann‐Andersen, Niels Jacob; Lisbjerg, Kristian; Christensen, Søren Just; Rasmussen, Peter; Olsen, Niels Vidiendal; Law, Ian; Larsson, Henrik Bo Wiberg; Henriksen, Otto Mølby

    2016-01-01

    Purpose To compare mean global cerebral blood flow (CBF) measured by phase‐contrast mapping magnetic resonance imaging (PCM MRI) and by 15O‐H2O positron emission tomography (PET) in healthy subjects. PCM MRI is increasingly being used to measure mean global CBF, but has not been validated in vivo against an accepted reference technique. Materials and Methods Same‐day measurements of CBF by 15O‐H2O PET and subsequently by PCM MRI were performed on 22 healthy young male volunteers. Global CBF by PET was determined by applying a one‐tissue compartment model with measurement of the arterial input function. Flow was measured in the internal carotid and vertebral arteries by a noncardiac triggered PCM MRI sequence at 3T. The measured flow was normalized to total brain weight determined from a volume‐segmented 3D T 1‐weighted anatomical MR‐scan. Results Mean CBF was 34.9 ± 3.4 mL/100 g/min measured by 15O‐H2O PET and 57.0 ± 6.8 mL/100 g/min measured by PCM MRI. The measurements were highly correlated (P = 0.0008, R2 = 0.44), although values obtained by PCM MRI were higher compared to 15O‐H2O PET (absolute and relative differences were 22.0 ± 5.2 mL/100 g/min and 63.4 ± 14.8%, respectively). Conclusion This study confirms the use of PCM MRI for quantification of global CBF, but also that PCM MRI systematically yields higher values relative to 15O‐H2O PET, probably related to methodological bias. Level of Evidence: 3 J. Magn. Reson. Imaging 2017;45:692–699. PMID:27619317

  14. 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 ...

  15. TROMBONE: T1-Relaxation-Oblivious Mapping of Transmit Radio-Frequency Field (B1) for MRI at High Magnetic Fields

    PubMed Central

    Fleysher, Roman; Fleysher, Lazar; Inglese, Matilde; Sodickson, Daniel

    2011-01-01

    Fast, 3D radio-frequency transmit field (B1) mapping is important for parallel transmission, spatially-selective pulse design and quantitative MRI applications. It has been shown that AFI — two interleaved spoiled gradient recalled echo (SPGR) images acquired in steady state with two very short time delays (T R1, T R2) — is an attractive method of B1 mapping. Herein, we describe the TROMBONE method which efficiently integrates AFI with EPI imaging, alleviates very short T R requirement of AFI and through their synergy yields up to 16 times higher precision in B1 estimation in the same experimental time. High precision of TROMBONE can be traded for faster scans. The map of B1 reconstructed from the ratio of intensities of two images is insensitive to longitudinal relaxation time (T1) in the physiologically relevant range. A table of the optimal acquisition protocol parameters for various target experimental conditions is provided. PMID:21394765

  16. MRI of osteoarthritis: the challenges of definition and quantification.

    PubMed

    Hayashi, Daichi; Guermazi, Ali; Roemer, Frank W

    2012-11-01

    The ability of MRI to visualize the joint as a "whole organ" and to directly and three-dimensionally assess cartilage morphology and composition has given it a crucial role in discovering the natural history of osteoarthritis (OA). Morphological analysis can be semiquantitative or quantitative. Compositional analysis such as delayed gadolinium-enhanced MRI of cartilage and T2 mapping allows quantitative evaluation of tissue ultrastructure and can detect premorphological changes of cartilage and other tissues. Contrast-enhanced MRI can accurately assess the true extent of synovial inflammation. Most MRI-based studies so far have focused on knee OA, but with the availability of new semiquantitative scoring systems for hand and hip OA, studies of these joints have begun to appear. Because of the technical complexity of MRI and ever increasing number of new and sophisticated imaging sequences and protocols, the specific MRI technique in any OA study needs to be carefully tailored to the aims of the study.

  17. 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.

  18. Mapping the pharmacological modulation of brain oxygen metabolism: the effects of caffeine on absolute CMRO2 measured using dual calibrated fMRI.

    PubMed

    Merola, Alberto; Germuska, Michael A; Warnert, Esther Ah; Richmond, Lewys; Helme, Daniel; Khot, Sharmila; Murphy, Kevin; Rogers, Peter J; Hall, Judith E; Wise, Richard G

    2017-03-17

    This study aims to map the acute effects of caffeine ingestion on grey matter oxygen metabolism and haemodynamics with a novel MRI method. Sixteen healthy caffeine consumers (8 males, age = 24.7±5.1) were recruited to this randomised, double-blind, placebo-controlled study. Each participant was scanned on two days before and after the delivery of an oral caffeine (250mg) or placebo capsule. Our measurements were obtained with a newly proposed estimation approach applied to data from a dual calibration fMRI experiment that uses hypercapnia and hyperoxia to modulate brain blood flow and oxygenation. Estimates were based on a forward model that describes analytically the contributions of cerebral blood flow (CBF) and of the measured end-tidal partial pressures of CO2 and O2 to the acquired dual-echo GRE signal. The method allows the estimation of grey matter maps of: oxygen extraction fraction (OEF), CBF, CBF-related cerebrovascular reactivity (CVR) and cerebral metabolic rate of oxygen consumption (CMRO2). Other estimates from a multi inversion time ASL acquisition (mTI-ASL), salivary samples of the caffeine concentration and behavioural measurements are also reported. We observed significant differences between caffeine and placebo on average across grey matter, with OEF showing an increase of 15.6% (SEM ±4.9%, p <0.05) with caffeine, while CBF and CMRO2 showed differences of -30.4% (SEM ±1.6%, p <0.01) and -18.6% (SEM ±2.9%, p <0.01) respectively with caffeine administration. The reduction in oxygen metabolism found is somehow unexpected, but consistent with a hypothesis of decreased energetic demand, supported by previous electrophysiological studies reporting reductions in spectral power with EEG. Moreover the maps of the physiological parameters estimated illustrate the spatial distribution of changes across grey matter enabling us to localise the effects of caffeine with voxel-wise resolution. CBF changes were widespread as reported by previous findings

  19. Morphological MRI and T2 mapping of cartilage repair tissue after mosaicplasty with tissue-engineered cartilage in a pig model.

    PubMed

    Chen, Qichun; Zuo, Qiang; Hu, Qianqian; Feng, Yang; Cui, Weiding; Fan, Weimin; Zou, Yuefen

    2014-07-01

    The aim of this study was to evaluate the efficacy of mosaicplasty with tissue-engineered cartilage for the treatment of osteochondral defects in a pig model with advanced MR technique. Eight adolescent miniature pigs were used. The right knee underwent mosaicplasty with tissue-engineered cartilage for treatment of focal osteochondral defects, while the left knee was repaired via single mosaicplasty as controls. At 6, 12, 18 and 26 weeks after surgery, repair tissue was evaluated by magnetic resonance imaging (MRI) with the cartilage repair tissue (MOCART) scoring system and T2 mapping. Then, the results of MRI for 26 weeks were compared with findings of macroscopic and histologic studies. The MOCART scores showed that the repaired tissue of the tissue-engineered cartilage group was statistically better than that of controls (P < 0.001). A significant correlation was found between macroscopic and MOCART scores (P < 0.001). Comparable mean T2 values were found between adjacent cartilage and repair tissue in the experimental group (P > 0.05). For zonal T2 value evaluation, there were no significant zonal T2 differences for repair tissue in controls (P > 0.05). For the experimental group, zonal T2 variation was found in repair tissue (P < 0.05). MRI, macroscopy and histology showed better repair results and bony incorporation in mosaicplasty with the tissue-engineered cartilage group than those of the single mosaicplasty group. Mosaicplasty with the tissue-engineered cartilage is a promising approach to repair osteochodndral defects. Morphological MRI and T2 mapping provide a non-invasive method for monitoring the maturation and integration of cartilage repair tissue in vivo.

  20. 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

  1. 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.

  2. Functional MRI and intraoperative brain mapping to evaluate brain plasticity in patients with brain tumours and hemiparesis

    PubMed Central

    Roux, F; Boulanouar, K; Ibarrola, D; Tremoulet, M; Chollet, F; Berry, I

    2000-01-01

    OBJECTIVE—To support the hypothesis about the potential compensatory role of ipsilateral corticofugal pathways when the contralateral pathways are impaired by brain tumours.
METHODS—Retrospective analysis was carried out on the results of functional MRI (fMRI) of a selected group of five paretic patients with Rolandic brain tumours who exhibited an abnormally high ipsilateral/contralateral ratio of activation—that is, movements of the paretic hand activated predominately the ipsilateral cortex. Brain activation was achieved with a flexion extension of the fingers. Statistical parametric activation was obtained using a t test and a threshold of p<0.001. These patients, candidates for tumour resection, also underwent cortical intraoperative stimulation that was correlated to the fMRI spatial data using three dimensional reconstructions of the brain. Three patients also had postoperative control fMRI.
RESULTS—The absence of fMRI activation of the primary sensorimotor cortex normally innervating the paretic hand for the threshold chosen, was correlated with completely negative cortical responses of the cortical hand area during the operation. The preoperative fMRI activation of these patients predominantly found in the ipsilateral frontal and primary sensorimotor cortices could be related to the residual ipsilateral hand function. Postoperatively, the fMRI activation returned to more classic patterns of activation, reflecting the consequences of therapy.
CONCLUSION—In paretic patients with brain tumours, ipsilateral control could be implicated in the residual hand function, when the normal primary pathways are impaired. The possibility that functional tissue still remains in the peritumorous sensorimotor cortex even when the preoperative fMRI and the cortical intraoperative stimulations are negative, should be taken into account when planning the tumour resection and during the operation.

 PMID:10990503

  3. SU-E-T-661: Quantitative MRI Assessment of a Novel Direction-Modulated Brachytherapy Tandem Applicator for Cervical Cancer

    SciTech Connect

    Soliman, A; Elzibak, A; Fatemi, A; Safigholi, H; Leung, E; Ravi, A; Song, W; Han, D

    2015-06-15

    Purpose: To quantitatively evaluate the MR image quality of a novel direction modulated brachytherapy (DMBT) tandem applicator for cervical cancer, using the clinical MRI scanning protocol for image guided brachytherapy. Methods: The tungsten alloy-based applicator was placed in a water phantom and clinical imaging protocol was performed. Axial images were acquired using 2D turbo-spin echo (TSE) T2-weighted sequence on a 1.5T GE 450w MR scanner and an 8-channel body coil. As multi-channel receiver coil was used, inhomogeneities in the B1 receive field must be considered before performing the quantification process. Therefore the applicator was removed from the phantom and the whole imaging session was performed again for the water phantom with the same parameters. Images from the two scans were then subtracted, resulting in a difference image that only shows the applicator with its surrounding magnetic susceptibility dipole artifact. Line profiles were drawn and plotted on the difference image at various angles and locations along the tandem. Full width at half maximum (FWHM) was measured at all the line profiles to quantify the extent of the artifact. Additionally, the extent of the artifact along the diameter of the tandem was measured at various angles and locations. Results: After removing the background inhomogeneities of the receiver coil, FWHM of the tandem measured 5.75 ± 0.35 mm (the physical tandem diameter is 5.4 mm). The average extent of the artifacts along the diameter of the tandem measured is 2.14 ± 0.56 mm. In contrast to CT imaging of the same applicator (not shown here), the tandem can be easily identified without additional correction algorithms. Conclusion: This work demonstrated that the novel DMBT tandem applicator has minimal susceptibility artifact in T2-weighted images employed in clinical practice for MRI-guided brachytherapy of cervical cancer.

  4. Ventral occipital lesions impair object recognition but not object-directed grasping: an fMRI study.

    PubMed

    James, Thomas W; Culham, Jody; Humphrey, G Keith; Milner, A David; Goodale, Melvyn A

    2003-11-01

    D.F., a patient with severe visual form agnosia, has been the subject of extensive research during the past decade. The fact that she could process visual input accurately for the purposes of guiding action despite being unable to perform visual discriminations on the same visual input inspired a novel interpretation of the functions of the two main cortical visual pathways or 'streams'. Within this theoretical context, the authors proposed that D.F. had suffered severe bilateral damage to her occipitotemporal visual system (the 'ventral stream'), while retaining the use of her occipitoparietal visual system (the 'dorsal stream'). The present paper reports a direct test of this idea, which was initially derived from purely behavioural data, before the advent of modern functional neuroimaging. We used functional MRI to examine activation in her ventral and dorsal streams during object recognition and object-directed grasping tasks. We found that D.F. showed no difference in activation when presented with line drawings of common objects compared with scrambled line drawings in the lateral occipital cortex (LO) of the ventral stream, an area that responded differentially to these stimuli in healthy individuals. Moreover, high-resolution anatomical MRI showed that her lesion corresponded bilaterally with the location of LO in healthy participants. The lack of activation with line drawings in D.F. mirrors her poor performance in identifying the objects depicted in the drawings. With coloured and greyscale pictures, stimuli that she can identify more often, D.F. did show some ventral-stream activation. These activations were, however, more widely distributed than those seen in control participants and did not include LO. In contrast to the absent or abnormal activation observed during these perceptual tasks, D.F. showed robust activation in the expected dorsal stream regions during object grasping, despite considerable atrophy in some regions of the parietal lobes. In

  5. 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

  6. 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.

  7. Spin-lattice distribution MRI maps nigral pathology in progressive supranuclear palsy (PSP) during life: a pilot study.

    PubMed

    Hutchinson, Michael; Raff, Ulrich; Chaná, Pedro; Huete, Isidro

    2014-01-01

    An MRI biomarker for Parkinsonism has long been sought, but almost all attempts at conventional field strengths have proved unsatisfactory, since patients and controls are not separated. The exception is Spin-Lattice Distribution MRI (SLD-MRI), a technique which detects changes in the substantia nigra (SN) due to changes in the spin-lattice relaxation time, T1. This easily separates patients with Parkinson's disease (PD) from control subjects at 1.5 Tesla, suggesting that it may be sensitive to presymptomatic disease. SLD-MRI demonstrates a topography of signal change within the SN which is the same as the known topography of pathological change, where the lateral portions of the nucleus are more affected than the medial. In a further step towards its validation, we apply SLD-MRI to a disease control, Progressive Supranuclear Palsy (PSP), the most common of the atypical forms of Parkinsonism. In PSP the topography of pathological change in the SN is reversed. We therefore hypothesized that PSP would show a topography of SLD-MRI signal change in the SN that is the reverse of PD (i.e. the medial portion is more affected than the lateral). All 7 patients showed such a topography of MR signal, and all patients were separated from control subjects. Although this is a step toward validation of SLD-MRI with respect to sensitivity and disease specificity, nevertheless we stress that this is a pilot project only. Validation will only be possible when comparing larger cohorts of PSP, PD and control subjects.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. MAP18 regulates the direction of pollen tube growth in Arabidopsis by modulating F-actin organization.

    PubMed

    Zhu, Lei; Zhang, Yan; Kang, Erfang; Xu, Qiangyi; Wang, Miaoying; Rui, Yue; Liu, Baoquan; Yuan, Ming; Fu, Ying

    2013-03-01

    For fertilization to occur in plants, the pollen tube must be guided to enter the ovule via the micropyle. Previous reports have implicated actin filaments, actin binding proteins, and the tip-focused calcium gradient as key contributors to polar growth of pollen tubes; however, the regulation of directional pollen tube growth is largely unknown. We reported previously that Arabidopsis thaliana MICROTUBULE-ASSOCIATED PROTEIN18 (MAP18) contributes to directional cell growth and cortical microtubule organization. The preferential expression of MAP18 in pollen and in pollen tubes suggests that MAP18 also may function in pollen tube growth. In this study, we demonstrate that MAP18 functions in pollen tubes by influencing actin organization, rather than microtubule assembly. In vitro biochemical results indicate that MAP18 exhibits Ca(2+)-dependent filamentous (F)-actin-severing activity. Abnormal expression of MAP18 in map18 and MAP18 OX plants was associated with disorganization of the actin cytoskeleton in the tube apex, resulting in aberrant pollen tube growth patterns and morphologies, inaccurate micropyle targeting, and fewer fertilization events. Experiments with MAP18 mutants created by site-directed mutagenesis suggest that F-actin-severing activity is essential to the effects of MAP18 on pollen tube growth direction. Our study demonstrates that in Arabidopsis, MAP18 guides the direction of pollen tube growth by modulating actin filaments.

  13. Direct mapping of Li distribution in electrochemically lithiated graphite anodes using scanning Auger electron microscopy

    NASA Astrophysics Data System (ADS)

    Ishida, Nobuyuki; Fukumitsu, Hitoshi; Kimura, Hiroshi; Fujita, Daisuke

    2014-02-01

    The spatial distribution of Li ions in electrochemically lithiated graphite anodes for Li-ion battery is characterized by scanning Auger electron microscopy. We show that direct mapping of Li KVV peak intensity reveal the spatial distribution of intercalated Li and its chemical state in a quantitative manner. Furthermore, we demonstrate that mapping using a C KVV peak also reflects the spatial distribution of Li due to the change in the electronic properties of C atoms induced by the electrode reaction (Li intercalation). Mapping measurements on three samples with different charging states (20%, 50%, and 100%) show that at the early stage of charging Li ions do not intercalate homogenously into all the graphite particles but selectively into some specific ones with higher rates. Our method provides the criteria to evaluate structure-correlated Li intercalation from nanometer- to micrometer-scale, such as conductivity network in the electrodes due to a non-uniform morphology of binder and conductive additives.

  14. 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

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

    PubMed

    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.

  16. Syntax-directed content analysis of videotext: application to a map detection recognition system

    NASA Astrophysics Data System (ADS)

    Aradhye, Hrishikesh; Herson, James A.; Myers, Gregory

    2003-01-01

    Video is an increasingly important and ever-growing source of information to the intelligence and homeland defense analyst. A capability to automatically identify the contents of video imagery would enable the analyst to index relevant foreign and domestic news videos in a convenient and meaningful way. To this end, the proposed system aims to help determine the geographic focus of a news story directly from video imagery by detecting and geographically localizing political maps from news broadcasts, using the results of videotext recognition in lieu of a computationally expensive, scale-independent shape recognizer. Our novel method for the geographic localization of a map is based on the premise that the relative placement of text superimposed on a map roughly corresponds to the geographic coordinates of the locations the text represents. Our scheme extracts and recognizes videotext, and iteratively identifies the geographic area, while allowing for OCR errors and artistic freedom. The fast and reliable recognition of such maps by our system may provide valuable context and supporting evidence for other sources, such as speech recognition transcripts. The concepts of syntax-directed content analysis of videotext presented here can be extended to other content analysis systems.

  17. 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

  18. Multispectral x-ray imaging for core temperature and density maps retrieval in direct drive implosions

    SciTech Connect

    Tommasini, Riccardo; Koch, Jeffrey A.; Izumi, Nobuhiko; Welser, Leslie A.; Mancini, Roberto C.; Delettrez, Jacques; Regan, Sean; Smalyuk, Vladimir

    2006-10-15

    We report on the experiments aimed at obtaining core temperature and density maps in direct drive implosions at the Omega laser facility using multimonochromatic x-ray imagers. These instruments use an array of pinholes and a flat multilayer mirror to provide unique multispectral images distributed over a wide spectral range. Using argon as a dopant in the direct-drive filled plastic shells produces emission images in the Ar He-{beta} and Ly-{beta} spectral regions. These images allow the retrieval of temperature and density maps of the plasma. We deployed three identical multimonochromatic x-ray imagers in a quasiorthogonal line-of-sight configuration to allow tomographic reconstruction of the structure of the imploding core.

  19. Intra- and Inter- Subject Variability of High Field fMRI Digit Maps in Somatosensory Area 3b of New World Monkeys

    PubMed Central

    Zhang, Na; Wang, Feng; Turner, Greg H.; Gore, John C.; Avison, Malcolm J.; Chen, Li M.

    2009-01-01

    This study evaluates the intra- and inter- subject variability of digit maps in area 3b of anesthetized squirrel monkeys. Maps were collected using high field Blood Oxygenation Level Dependent (BOLD) fMRI. BOLD responses to individual digit stimulations were mapped and their response properties (location, area of activation, % signal change, time to peak response) were compared within and across imaging sessions separated by up to 20 months. During single digit stimulation using a block design, the spatio-temporal response of the BOLD signal for individual runs within and across sessions and animals was well conserved, with a time to peak BOLD response of 20 ± 4 sec. The variability in the center of BOLD activation in area 3b was 0.41 ± 0.24 mm (mean ± SD) across individual 5–7 minutes runs within a scanning session and 0.55 ± 0.15 mm across sessions. The average signal change across all animals, runs and sessions was 0.62 ± 0.38 %, and varied 32% within and 40% across sessions. In a comparison of the stability and reproducibility of the area of single digit activation obtained using three approaches, use of a fixed statistical threshold (p<10−5) yielded an average area of 4.8 ± 3.5 mm2 (mean ± SD), adaptive statistical thresholding 1.32 ± 1.259 mm2 (mean ± SD), and combined fixed statistical and adaptive BOLD signal amplitude 4.4 ± 2.5 mm2 (mean ± SD) across image runs and sessions. The somatotopic organization was stable within animals across sessions, while across animals, there was some variation in overall activation pattern and inter-digit distances. These results confirm that BOLD activation maps of single digits in area 3b as characterized by activation center, signal amplitudes, and temporal profile are very stable. The activation sizes determined by various criteria are the most variable measure in this preparation, but adaptive statistical thresholding appears to yield the most stable and reproducible maps. This study serves as a baseline

  20. Retinotopic Maps, Spatial Tuning, and Locations of Human Visual Areas in Surface Coordinates Characterized with Multifocal and Blocked fMRI Designs

    PubMed Central

    Henriksson, Linda; Karvonen, Juha; Salminen-Vaparanta, Niina; Railo, Henry; Vanni, Simo

    2012-01-01

    The localization of visual areas in the human cortex is typically based on mapping the retinotopic organization with functional magnetic resonance imaging (fMRI). The most common approach is to encode the response phase for a slowly moving visual stimulus and to present the result on an individual's reconstructed cortical surface. The main aims of this study were to develop complementary general linear model (GLM)-based retinotopic mapping methods and to characterize the inter-individual variability of the visual area positions on the cortical surface. We studied 15 subjects with two methods: a 24-region multifocal checkerboard stimulus and a blocked presentation of object stimuli at different visual field locations. The retinotopic maps were based on weighted averaging of the GLM parameter estimates for the stimulus regions. In addition to localizing visual areas, both methods could be used to localize multiple retinotopic regions-of-interest. The two methods yielded consistent retinotopic maps in the visual areas V1, V2, V3, hV4, and V3AB. In the higher-level areas IPS0, VO1, LO1, LO2, TO1, and TO2, retinotopy could only be mapped with the blocked stimulus presentation. The gradual widening of spatial tuning and an increase in the responses to stimuli in the ipsilateral visual field along the hierarchy of visual areas likely reflected the increase in the average receptive field size. Finally, after registration to Freesurfer's surface-based atlas of the human cerebral cortex, we calculated the mean and variability of the visual area positions in the spherical surface-based coordinate system and generated probability maps of the visual areas on the average cortical surface. The inter-individual variability in the area locations decreased when the midpoints were calculated along the spherical cortical surface compared with volumetric coordinates. These results can facilitate both analysis of individual functional anatomy and comparisons of visual cortex topology

  1. Head position and impact direction in whiplash injuries: associations with MRI-verified lesions of ligaments and membranes in the upper cervical spine.

    PubMed

    Kaale, Bertel Rune; Krakenes, Jostein; Albrektsen, Grethe; Wester, Knut

    2005-11-01

    In the present study, we compared magnetic resonance imaging (MRI) findings of soft tissue structures in the upper cervical spine between whiplash-associated disorder (WAD) patients and population-based control persons, and examined whether MRI-verified abnormalities in WAD patients were related to accident-related factors hypothesized to be of importance for severity of injury. A total of 92 whiplash patients and 30 control persons, randomly drawn, were included. Information on the accident-related factors (i.e., head position and impact direction) was obtained by a questionnaire that was answered within 1 week after the accident. The MRI examination was performed 2-9 (mean 6) years after the accident. Focus was on MRI abnormalities of the alar and the transverse ligaments, and the tectorial and posterior atlanto-occipital membranes, graded 0-3. For all neck structures, the whiplash patients had more high-grade lesions (grade 2 or 3) than the control persons (Chi-square test, p < 0.055). An abnormal alar ligament was most common (66.3% graded 2 or 3). Whiplash patients who had been sitting with their head/neck turned to one side at the moment of collision more often had high-grade lesions of the alar and transverse ligaments (p < 0.001, p = 0.040, respectively). Severe injuries to the transverse ligament and the posterior atlanto-occipital membrane were more common in front than in rear end collisions (p < 0.001, p = 0.001, respectively). In conclusion, the difference in MRI-verified lesions between WAD patients and control persons, and in particular the association with head position and impact direction at time of accident, indicate that these lesions are caused by the whiplash trauma.

  2. Mapping stiffness perception in the brain with an fMRI-compatible particle-jamming haptic interface.

    PubMed

    Menon, Samir; Stanley, Andrew A; Zhu, Jack; Okamura, Allison M; Khatib, Oussama

    2014-01-01

    We demonstrate reliable neural responses to changes in haptic stiffness perception using a functional magnetic resonance imaging (fMRI) compatible particle-jamming haptic interface. Our haptic interface consists of a silicone tactile surface whose stiffness we can control by modulating air-pressure in a sub-surface pouch of coarsely ground particles. The particles jam together as the pressure decreases, which stiffens the surface. During fMRI acquisition, subjects performed a constant probing task, which involved continuous contact between the index fingertip and the interface and rhythmic increases and decreases in fingertip force (1.6 Hz) to probe stiffness. Without notifying subjects, we randomly switched the interface's stiffness (switch time, 300-500 ms) from soft (200 N/m) to hard (1400 N/m). Our experiment design's constant motor activity and cutaneous tactile sensation helped disassociate neural activation for both from stiffness perception, which helped localized it to a narrow region in somatosensory cortex near the supra-marginal gyrus. Testing different models of neural activation, we found that assuming indepedent stiffness-change responses at both soft-hard and hard-soft transitions provides the best explanation for observed fMRI measurements (three subjects; nine four-minute scan runs each). Furthermore, we found that neural activation related to stiffness-change and absolute stiffness can be localized to adjacent but disparate anatomical locations. We also show that classical finger-tapping experiments activate a swath of cortex and are not suitable for localizing stiffness perception. Our results demonstrate that decorrelating motor and sensory neural activation is essential for characterizing somatosensory cortex, and establish particle-jamming haptics as an attractive low-cost method for fMRI experiments.

  3. Perceptual learning of motion direction discrimination with suppressed and unsuppressed MT in humans: an fMRI study.

    PubMed

    Thompson, Benjamin; Tjan, Bosco S; Liu, Zili

    2013-01-01

    The middle temporal area of the extrastriate visual cortex (area MT) is integral to motion perception and is thought to play a key role in the perceptual learning of motion tasks. We have previously found, however, that perceptual learning of a motion discrimination task is possible even when the training stimulus contains locally balanced, motion opponent signals that putatively suppress the response of MT. Assuming at least partial suppression of MT, possible explanations for this learning are that 1) training made MT more responsive by reducing motion opponency, 2) MT remained suppressed and alternative visual areas such as V1 enabled learning and/or 3) suppression of MT increased with training, possibly to reduce noise. Here we used fMRI to test these possibilities. We first confirmed that the motion opponent stimulus did indeed suppress the BOLD response within hMT+ compared to an almost identical stimulus without locally balanced motion signals. We then trained participants on motion opponent or non-opponent stimuli. Training with the motion opponent stimulus reduced the BOLD response within hMT+ and greater reductions in BOLD response were correlated with greater amounts of learning. The opposite relationship between BOLD and behaviour was found at V1 for the group trained on the motion-opponent stimulus and at both V1 and hMT+ for the group trained on the non-opponent motion stimulus. As the average response of many cells within MT to motion opponent stimuli is the same as their response to non-directional flickering noise, the reduced activation of hMT+ after training may reflect noise reduction.

  4. 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.

  5. Large-scale, high-resolution neurophysiological maps underlying FMRI of macaque temporal lobe.

    PubMed

    Issa, Elias B; Papanastassiou, Alex M; DiCarlo, James J

    2013-09-18

    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.

  6. [Interest of EEG recording during direct electrical stimulation for brain mapping function in surgery].

    PubMed

    Trebuchon, A; Guye, M; Tcherniack, V; Tramoni, E; Bruder, N; Metellus, P

    2012-06-01

    Brain tumor surgery is at risk when lesions are located in eloquent areas. The interindividual anatomo-functional variability of the central nervous system implies that brain surgery within eloquent regions may induce neurological sequelae. Brain mapping using intraoperative direct electrical stimulation in awake patients has been for long validated as the standard for functional brain mapping. Direct electrical stimulation inducing a local transient electrical and functional disorganization is considered positive if the task performed by the patient is disturbed. The brain area stimulated is then considered as essential for the function tested. However, the exactitude of the information provided by this technique is cautious because the actual impact of cortical direct electrical stimulation is not known. Indeed, the possibility of false negative (insufficient intensity of the stimulation due to the heterogeneity of excitability threshold of different cortical areas) or false positive (current spread, interregional signal propagation responsible for remote effects, which make difficult the interpretation of positive or negative behavioural effects) constitute a limitation of this technique. To improve the sensitivity and specificity of this technique, we used an electrocorticographic recording system allowing a real time visualization of the local. We provide here evidence that direct cortical stimulation combined with electrocorticographic recording could be useful to detect remote after discharge and to adjust stimulation parameters. In addition this technique offers new perspective to better assess connectivity of cerebral networks.

  7. Estimation of the cortical functional connectivity with the multimodal integration of high-resolution EEG and fMRI data by directed transfer function.

    PubMed

    Babiloni, F; Cincotti, F; Babiloni, C; Carducci, F; Mattia, D; Astolfi, L; Basilisco, A; Rossini, P M; Ding, L; Ni, Y; Cheng, J; Christine, K; Sweeney, J; He, B

    2005-01-01

    Nowadays, several types of brain imaging device are available to provide images of the functional activity of the cerebral cortex based on hemodynamic, metabolic, or electromagnetic measurements. However, static images of brain regions activated during particular tasks do not convey the information of how these regions communicate with each other. In this study, advanced methods for the estimation of cortical connectivity from combined high-resolution electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) data are presented. These methods include a subject's multicompartment head model (scalp, skull, dura mater, cortex) constructed from individual magnetic resonance images, multidipole source model, and regularized linear inverse source estimates of cortical current density. Determination of the priors in the resolution of the linear inverse problem was performed with the use of information from the hemodynamic responses of the cortical areas as revealed by block-designed (strength of activated voxels) fMRI. We estimate functional cortical connectivity by computing the directed transfer function (DTF) on the estimated cortical current density waveforms in regions of interest (ROIs) on the modeled cortical mantle. The proposed method was able to unveil the direction of the information flow between the cortical regions of interest, as it is directional in nature. Furthermore, this method allows to detect changes in the time course of information flow between cortical regions in different frequency bands. The reliability of these techniques was further demonstrated by elaboration of high-resolution EEG and fMRI signals collected during visually triggered finger movements in four healthy subjects. Connectivity patterns estimated for this task reveal an involvement of right parietal and bilateral premotor and prefrontal cortical areas. This cortical region involvement resembles that revealed in previous studies where visually triggered finger

  8. 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.

  9. 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.

  10. Calculation of susceptibility through multiple orientation sampling (COSMOS): a method for conditioning the inverse problem from measured magnetic field map to susceptibility source image in MRI.

    PubMed

    Liu, Tian; Spincemaille, Pascal; de Rochefort, Ludovic; Kressler, Bryan; Wang, Yi

    2009-01-01

    Magnetic susceptibility differs among tissues based on their contents of iron, calcium, contrast agent, and other molecular compositions. Susceptibility modifies the magnetic field detected in the MR signal phase. The determination of an arbitrary susceptibility distribution from the induced field shifts is a challenging, ill-posed inverse problem. A method called "calculation of susceptibility through multiple orientation sampling" (COSMOS) is proposed to stabilize this inverse problem. The field created by the susceptibility distribution is sampled at multiple orientations with respect to the polarization field, B(0), and the susceptibility map is reconstructed by weighted linear least squares to account for field noise and the signal void region. Numerical simulations and phantom and in vitro imaging validations demonstrated that COSMOS is a stable and precise approach to quantify a susceptibility distribution using MRI.

  11. Multi-Parametric MRI-Directed Focal Salvage Permanent Interstitial Brachytherapy for Locally Recurrent Adenocarcinoma of the Prostate: A Novel Approach

    PubMed Central

    Wallace, T.; Avital, I.; Stojadinovic, A.; Brücher, B.L.D.M.; Cote, E.; Yu, J.

    2013-01-01

    Even with the technological advances of dose-escalated IMRT with the addition of the latest image guidance technologies, local failures still occur. The combination of MRI-based imaging techniques can yield quantitative information that reflects on the biological properties of prostatic tissues. These techniques provide unique information that can be used for tumor detection in the treated gland. With the advent of these improved imaging modalities, it has become possible to more effectively image local recurrences within the prostate gland. With better imaging, these focal recurrences can be differentially targeted with salvage brachytherapy minimizing rectal and bladder toxicity. Here we report a novel use of MRI-directed focal brachytherapy after local recurrence. This technique offers a unique opportunity to safely and successfully treat recurrent prostate cancer, previously treated with definitive radiation therapy. The use of multi-parametric MRI-directed focal salvage permanent interstitial brachytherapy for locally recurrent adenocarcinoma of the prostate is a promising strategy to avoid more aggressive and expensive treatments that are associated with increased morbidity, potentially improving survival at potentially lower costs. PMID:23412660

  12. 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.

  13. 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

  14. 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.

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

    NASA Astrophysics Data System (ADS)

    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.

  16. Simultaneous Quantitative MRI Mapping of T1, T2* and Magnetic Susceptibility with Multi-Echo MP2RAGE

    PubMed Central

    Kober, Tobias; Möller, Harald E.; Schäfer, Andreas

    2017-01-01

    The knowledge of relaxation times is essential for understanding the biophysical mechanisms underlying contrast in magnetic resonance imaging. Quantitative experiments, while offering major advantages in terms of reproducibility, may benefit from simultaneous acquisitions. In this work, we demonstrate the possibility of simultaneously recording relaxation-time and susceptibility maps with a prototype Multi-Echo (ME) Magnetization-Prepared 2 RApid Gradient Echoes (MP2RAGE) sequence. T1 maps can be obtained using the MP2RAGE sequence, which is relatively insensitive to inhomogeneities of the radio-frequency transmit field, B1+. As an extension, multiple gradient echoes can be acquired in each of the MP2RAGE readout blocks, which permits the calculation of T2* and susceptibility maps. We used computer simulations to explore the effects of the parameters on the precision and accuracy of the mapping. In vivo parameter maps up to 0.6 mm nominal resolution were acquired at 7 T in 19 healthy volunteers. Voxel-by-voxel correlations and the test-retest reproducibility were used to assess the reliability of the results. When using optimized paramenters, T1 maps obtained with ME-MP2RAGE and standard MP2RAGE showed excellent agreement for the whole range of values found in brain tissues. Simultaneously obtained T2* and susceptibility maps were of comparable quality as Fast Low-Angle SHot (FLASH) results. The acquisition times were more favorable for the ME-MP2RAGE (≈ 19 min) sequence as opposed to the sum of MP2RAGE (≈ 12 min) and FLASH (≈ 10 min) acquisitions. Without relevant sacrifice in accuracy, precision or flexibility, the multi-echo version may yield advantages in terms of reduced acquisition time and intrinsic co-registration, provided that an appropriate optimization of the acquisition parameters is performed. PMID:28081157

  17. 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 Central

    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.

    2009-01-01

    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. PMID:19041724

  18. 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.

  19. 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

  20. Power comparison of admixture mapping and direct association analysis in genome-wide association studies.

    PubMed

    Qin, Huaizhen; Zhu, Xiaofeng

    2012-04-01

    When dense markers are available, one can interrogate almost every common variant across the genome via imputation and single nucleotide polymorphism (SNP) test, which has become a routine in current genome-wide association studies (GWASs). As a complement, admixture mapping exploits the long-range linkage disequilibrium (LD) generated by admixture between genetically distinct ancestral populations. It is then questionable whether admixture mapping analysis is still necessary in detecting the disease associated variants in admixed populations. We argue that admixture mapping is able to reduce the burden of massive comparisons in GWASs; it therefore can be a powerful tool to locate the disease variants with substantial allele frequency differences between ancestral populations. In this report we studied a two-stage approach, where candidate regions are defined by conducting admixture mapping at stage 1, and single SNP association tests are followed at stage 2 within the candidate regions defined at stage 1. We first established the genome-wide significance levels corresponding to the criteria to define the candidate regions at stage 1 by simulations. We next compared the power of the two-stage approach with direct association analysis. Our simulations suggest that the two-stage approach can be more powerful than the standard genome-wide association analysis when the allele frequency difference of a causal variant in ancestral populations, is larger than 0.4. Our conclusion is consistent with a theoretical prediction by Risch and Tang ([2006] Am J Hum Genet 79:S254). Surprisingly, our study also suggests that power can be improved when we use less strict criteria to define the candidate regions at stage 1.

  1. 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.

  2. Direct Georeferencing : a New Standard in Photogrammetry for High Accuracy Mapping

    NASA Astrophysics Data System (ADS)

    Rizaldy, A.; Firdaus, W.

    2012-07-01

    Direct georeferencing is a new method in photogrammetry, especially in the digital camera era. Theoretically, this method does not require ground control points (GCP) and the Aerial Triangulation (AT), to process aerial photography into ground coordinates. Compared with the old method, this method has three main advantages: faster data processing, simple workflow and less expensive project, at the same accuracy. Direct georeferencing using two devices, GPS and IMU. GPS recording the camera coordinates (X, Y, Z), and IMU recording the camera orientation (omega, phi, kappa). Both parameters merged into Exterior Orientation (EO) parameter. This parameters required for next steps in the photogrammetric projects, such as stereocompilation, DSM generation, orthorectification and mosaic. Accuracy of this method was tested on topographic map project in Medan, Indonesia. Large-format digital camera Ultracam X from Vexcel is used, while the GPS / IMU is IGI AeroControl. 19 Independent Check Point (ICP) were used to determine the accuracy. Horizontal accuracy is 0.356 meters and vertical accuracy is 0.483 meters. Data with this accuracy can be used for 1:2.500 map scale project.

  3. 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 ...

  4. Direct mapping of local director field of nematic liquid crystals at the nano-scale

    NASA Astrophysics Data System (ADS)

    Xia, Yu; Serra, Francesca; Yang, Shu; Kamien, Randall

    2015-03-01

    The director field in liquid crystals (LCs) has been characterized mainly via polarized optical microscopy, fluorescence confocal microscopy, and Raman spectroscopy, all of which are limited by optical wavelengths - from hundreds of nanometers to several micrometers. Since LC orientation cannot be resolved directly by these methods, theory is needed to interpret the local director field of LC alignment. In this work, we introduce a new approach to directly visualize the local director field of a nematic LC (NLC) at the nano-scale using scanning electron microscopy (SEM). A new type of NLC monomer bearing crosslinkable groups was designed and synthesized. It can be well-oriented at particle surfaces and patterned polymer substrates, including micron-sized silica colloids, porous membranes, micropillar arrays, and 1D channels. After carefully crosslinking, the molecular orientation of NLCs around the particles or within the patterns could be directly visualized by SEM, showing oriented nanofibers representing LC director from the fractured samples. Here, we could precisely resolve not only the local director field by this approach, but the defect structures of NLCs, including hedgehogs and line defects. The direct mapping of LC directors at the nanoscale using this method will improve our understanding of NLC local director field, and thus their manipulation and applications. More importantly, a theoretical interpretation will no longer be a necessity to resolve a new material system in this field.

  5. 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

  6. Nanoscale direct mapping of localized and induced noise sources on conducting polymer films

    NASA Astrophysics Data System (ADS)

    Shekhar, Shashank; Cho, Duckhyung; Lee, Hyungwoo; Cho, Dong-Guk; Hong, Seunghun

    2015-12-01

    The localized noise-sources and those induced by external-stimuli were directly mapped by using a conducting-AFM integrated with a custom-designed noise measurement set-up. In this method, current and noise images of a poly(9,9-dioctylfluorene)-polymer-film on a conducting-substrate were recorded simultaneously, enabling the mapping of the resistivity and noise source density (NT). The polymer-films exhibited separate regions with high or low resistivities, which were attributed to the ordered or disordered phases, respectively. A larger number of noise-sources were observed in the disordered-phase-regions than in the ordered-phase regions, due to structural disordering. Increased bias-voltages on the disordered-phase-regions resulted in increased NT, which is explained by the structural deformation at high bias-voltages. On photo-illumination, the ordered-phase-regions exhibited a rather large increase in the conductivity and NT. Presumably, the illumination released carriers from deep-traps which should work as additional noise-sources. These results show that our methods provide valuable insights into noise-sources and, thus, can be powerful tools for basic research and practical applications of conducting polymer films.The localized noise-sources and those induced by external-stimuli were directly mapped by using a conducting-AFM integrated with a custom-designed noise measurement set-up. In this method, current and noise images of a poly(9,9-dioctylfluorene)-polymer-film on a conducting-substrate were recorded simultaneously, enabling the mapping of the resistivity and noise source density (NT). The polymer-films exhibited separate regions with high or low resistivities, which were attributed to the ordered or disordered phases, respectively. A larger number of noise-sources were observed in the disordered-phase-regions than in the ordered-phase regions, due to structural disordering. Increased bias-voltages on the disordered-phase-regions resulted in

  7. Thrombotic Thrombocytopenic Purpura with Reversible Neurological Features: Brain Diffusion MRI with ADC Map, Spect and EEG Findings. A Case Report.

    PubMed

    Yerdelen, D; Göksel, B K; Yıldırım, T; Karataş, M; Karaca, S; Reyhan, M; Ozdoğu, H

    2006-11-30

    Although nervous system involvement is common in thrombotic thrombocytopenic purpura (TTP), abnormalities on computerized tomography, magnetic resonance imaging and electroencephalography are not encountered so frequently and if present, these abnormalities are often reversible. We describe a 39-year-old woman with recurring transient focal neurological findings found to have laboratory findings consistent with TTP. In cerebral diffusion weighted images (DWI), diffuse cortical hyperintensity was noted in right frontal lobe, but the ADC (apparent diffusion coefficient) map was normal. Electroencephalography demonstrated lateralized slowing and repeated DWI showed diffuse cortical hyperintensity in the right hemisphere. SPECT showed luxury perfusion in the right hemisphere areas. The patient's condition resolved with plasmapheresis. Our patient illustrates that diffuse hemispheric involvement can be seen in DWI and EEG, and SPECT may show luxury perfusion after resolution of neurological findings in TTP cases. To our knowledge, this is the first TTP case in which the ADC map was normal.

  8. 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

  9. 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.

  10. Stepping into a map: initial heading direction influences spatial memory flexibility.

    PubMed

    Gagnon, Stephanie A; Brunyé, Tad T; Gardony, Aaron; Noordzij, Matthijs L; Mahoney, Caroline R; Taylor, Holly A

    2014-03-01

    Learning a novel environment involves integrating first-person perceptual and motoric experiences with developing knowledge about the overall structure of the surroundings. The present experiments provide insights into the parallel development of these egocentric and allocentric memories by intentionally conflicting body- and world-centered frames of reference during learning, and measuring outcomes via online and offline measures. Results of two experiments demonstrate faster learning and increased memory flexibility following route perspective reading (Experiment 1) and virtual navigation (Experiment 2) when participants begin exploring the environment on a northward (vs. any other direction) allocentric heading. We suggest that learning advantages due to aligning body-centered (left/right/forward/back) with world-centered (NSEW) reference frames are indicative of three features of spatial memory development and representation. First, memories for egocentric and allocentric information develop in parallel during novel environment learning. Second, cognitive maps have a preferred orientation relative to world-centered coordinates. Finally, this preferred orientation corresponds to traditional orientation of physical maps (i.e., north is upward), suggesting strong associations between daily perceptual and motor experiences and the manner in which we preferentially represent spatial knowledge.

  11. 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.

  12. 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

  13. 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.

  14. Classification of patients with MCI and AD from healthy controls using directed graph measures of resting-state fMRI.

    PubMed

    Khazaee, Ali; Ebrahimzadeh, Ata; Babajani-Feremi, Abbas

    2017-03-30

    Brain network alterations in patients with Alzheimer's disease (AD) has been the subject of much investigation, but the biological mechanisms underlying these alterations remain poorly understood. Here, we aim to identify the changes in brain networks in patients with AD and mild cognitive impairment (MCI), and provide an accurate algorithm for classification of these patients from healthy control subjects (HC) by using a graph theoretical approach and advanced machine learning methods. Multivariate Granger causality analysis was performed on resting-state functional magnetic resonance imaging (rs-fMRI) data of 34 AD, 89 MCI, and 45 HC to calculate various directed graph measures. The graph measures were used as the original feature set for the machine learning algorithm. Filter and wrapper feature selection methods were applied to the original feature set to select an optimal subset of features. An accuracy of 93.3% was achieved for classification of AD, MCI, and HC using the optimal features and the naïve Bayes classifier. We also performed a hub node analysis and found that the number of hubs in HC, MCI, and AD were 12, 10, and 9, respectively, suggesting that patients with AD experience disturbance of critical communication areas in their brain network as AD progresses. The findings of this study provide insight into the neurophysiological mechanisms underlying MCI and AD. The proposed classification method highlights the potential of directed graph measures of rs-fMRI data for identification of the early stage of AD.

  15. New Clinically-Feasible 3-T MRI Protocol to Discriminate Internal Brain Stem Anatomy

    PubMed Central

    Hoch, Michael J.; Chung, Sohae; Ben-Eliezer, Noam; Bruno, Mary T.; Fatterpekar, Girish M.; Shepherd, Timothy M.

    2015-01-01

    Two new 3-T MRI contrast methods, track density imaging and echo modulation curve T2 mapping were combined with simultaneous multislice acquisition to reveal exquisite anatomical detail at 7 canonical levels of the brainstem. Compared to conventional MRI contrasts, many individual brainstem tracts and nuclear groups were directly visualized for the first time at 3-T. This new approach is clinically practical and feasible (total scan time = 20 min) allowing better brainstem anatomical localization and characterization. PMID:26869471

  16. 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.

  17. 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

  18. 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

  19. Mapping the critical gestational age at birth that alters brain development in preterm-born infants using multi-modal MRI.

    PubMed

    Wu, Dan; Chang, Linda; Akazawa, Kentaro; Oishi, Kumiko; Skranes, Jon; Ernst, Thomas; Oishi, Kenichi

    2017-04-01

    Preterm birth adversely affects postnatal brain development. In order to investigate the critical gestational age at birth (GAB) that alters the developmental trajectory of gray and white matter structures in the brain, we investigated diffusion tensor and quantitative T2 mapping data in 43 term-born and 43 preterm-born infants. A novel multivariate linear model-the change point model, was applied to detect change points in fractional anisotropy, mean diffusivity, and T2 relaxation time. Change points captured the "critical" GAB value associated with a change in the linear relation between GAB and MRI measures. The analysis was performed in 126 regions across the whole brain using an atlas-based image quantification approach to investigate the spatial pattern of the critical GAB. Our results demonstrate that the critical GABs are region- and modality-specific, generally following a central-to-peripheral and bottom-to-top order of structural development. This study may offer unique insights into the postnatal neurological development associated with differential degrees of preterm birth.

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

    PubMed

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

    2016-09-06

    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.

  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. Direct motor evoked potentials and cortical mapping using the NIM® nerve monitoring system: A technical note.

    PubMed

    Bharadwaj, Suparna; Haji, Faizal; Hebb, Matthew; Chui, Jason

    2017-04-01

    Motor evoked potentials (MEPs) are commonly used to prevent neurological injury when operating in close proximity to the motor cortex or corticospinal pathway. We report a novel application of the NIM® nerve monitoring system (Medtronic@ NIM response 3.0) for intraoperative direct cortical (dc)-MEPs monitoring. A 69-year-old female patient presented with a 4month history of progressive left hemiparesis resulting from a large right sided posterior frontal meningioma that abutted and compressed the motor cortex. Motor cortical mapping and MEPs were indicated. The patient was anesthetized and maintained on total intravenous anesthetics. Compound muscle action potentials (CMAP) of the right upper limb were monitored using the NIM system. After a craniotomy was performed, we first used the Ojemann stimulator (monopolar) for dc-stimulation and then switched to use the monopolar nerve stimulator probe of the NIM system. The CMAP response was successfully elicited using the NIM stimulating probe (pulse width=250s, train frequency=7pulses/s, current=20mA). A gross total resection of the tumor was achieved with intermittent cortical mapping of MEPs. There were no intraoperative complications and the patient's motor function was preserved after the surgery. In this case, we reported the successful use of the NIM nerve monitoring system to elicit dc-MEPs under general anesthesia. The advantages of using this system include a simple set up and application, neurosurgeon familiarity, wide availability and lower cost. dc-MEPs can be achieved using the NIM system. We conclude that the NIM nerve monitoring system is a feasible alternative to standard neurophysiological monitoring systems.

  3. Evidence of a direct influence between the thalamus and hMT+ independent of V1 in the human brain as measured by fMRI.

    PubMed

    Gaglianese, Anna; Costagli, Mauro; Bernardi, Giulio; Ricciardi, Emiliano; Pietrini, Pietro

    2012-04-02

    In the present study we employed Conditional Granger Causality (CGC) and Coherence analysis to investigate whether visual motion-related information reaches the human middle temporal complex (hMT+) directly from the Lateral Geniculate Nucleus (LGN) of the thalamus, by-passing the primary visual cortex (V1). Ten healthy human volunteers underwent brain scan examinations by functional magnetic resonance imaging (fMRI) during two optic flow experiments. In addition to the classical LGN-V1-hMT+ pathway, our results showed a significant direct influence of the blood oxygenation level dependent (BOLD) signal recorded in LGN over that in hMT+, not mediated by V1 activity, which strongly supports the existence of a bilateral pathway that connects LGN directly to hMT+ and serves visual motion processing. Furthermore, we evaluated the relative latencies among areas functionally connected in the processing of visual motion. Using LGN as a reference region, hMT+ exhibited a statistically significant earlier peak of activation as compared to V1. In conclusion, our findings suggest the co-existence of an alternative route that directly links LGN to hMT+, bypassing V1. This direct pathway may play a significant functional role for the faster detection of motion and may contribute to explain persistence of unconscious motion detection in individuals with severe destruction of primary visual cortex (blindsight).

  4. 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

  5. Discretized aperture mapping with a micro-lenses array for interferometric direct imaging

    NASA Astrophysics Data System (ADS)

    Patru, Fabien; Antichi, Jacopo; Mawet, Dimitri; Jolissaint, Laurent; Carbillet, Marcel; Milli, Julien; Girard, Julien; Rabou, Patrick; Giro, Enrico; Mourard, Denis

    2014-08-01

    Discretized Aperture Mapping (DAM) appears as an original filtering technique easy to play with existing adaptive optics (AO) systems. In its essential DAM operates as an optical passive filter removing part of the phase residuals in the wavefront without introducing any difficult-to-align component in the Fourier conjugate of the entrance pupil plane. DAM reveals as a new interferometric technique combined with spatial filtering allowing direct imaging over a narrow field of view (FOV). In fact, the entrance pupil of a single telescope is divided into many sub-pupils so that the residual phase in each sub-pupil is filtered up to the DAM cut-off frequency. DAM enables to smooth the small scale wavefront defects which correspond to high spatial frequencies in the pupil plane and to low angular frequencies in the image plane. Close to the AO Nyquist frequency, such pupil plane spatial frequencies are not well measured by the wavefront sensor (WFS) due to aliasing. Once bigger than the AO Nyquist frequency, they are no more measured by the WFS due to the fitting limit responsible for the narrow AO FOV. The corresponding image plane angular frequencies are not transmitted by DAM and are useless to image small FOVs, as stated by interferometry. That is why AO and DAM are complementary assuming that the DAM cut-off frequency is equal to the AO Nyquist frequency. Here we describe the imaging capabilities when DAM is placed downstream an AO system, over a convenient pupil which precedes the scientific detector. We show firstly that the imaging properties are preserved on a narrow FOV allowing direct imaging throughout interferometry. Then we show how the residual pupil plane spatial frequencies bigger than the AO Nyquist one are filtered out, as well as the residual halo in the image is dimmed.

  6. Direct k-space mapping of the electronic structure in an oxide-oxide interface.

    PubMed

    Berner, G; Sing, M; Fujiwara, H; Yasui, A; Saitoh, Y; Yamasaki, A; Nishitani, Y; Sekiyama, A; Pavlenko, N; Kopp, T; Richter, C; Mannhart, J; Suga, S; Claessen, R

    2013-06-14

    The interface between LaAlO(3) and SrTiO(3) hosts a two-dimensional electron system of itinerant carriers, although both oxides are band insulators. Interface ferromagnetism coexisting with superconductivity has been found and attributed to local moments. Experimentally, it has been established that Ti 3d electrons are confined to the interface. Using soft x-ray angle-resolved resonant photoelectron spectroscopy we have directly mapped the interface states in k space. Our data demonstrate a charge dichotomy. A mobile fraction contributes to Fermi surface sheets, whereas a localized portion at higher binding energies is tentatively attributed to electrons trapped by O vacancies in the SrTiO(3). While photovoltage effects in the polar LaAlO(3) layers cannot be excluded, the apparent absence of surface-related Fermi surface sheets could also be fully reconciled in a recently proposed electronic reconstruction picture where the built-in potential in the LaAlO(3) is compensated by surface O vacancies serving also as a charge reservoir.

  7. A method for comprehensive glycosite-mapping and direct quantitation of plasma glycoproteins

    PubMed Central

    Hong, Qiuting; Ruhaak, L. Renee; Stroble, Carol; Parker, Evan; Huang, Jincui; Maverakis, Emanual; Lebrilla, Carlito B.

    2015-01-01

    A comprehensive glycan map was constructed for the top eight abundant plasma glycoproteins using both specific and non-specific enzyme digestions followed by nano LC–Chip/QTOF mass spectrometry (MS) analysis. Glycopeptides were identified using an in-house software tool, GPFinder. A sensitive and reproducible multiple reaction monitoring (MRM) technique on a triple quadrupole MS was developed and applied to quantify immunoglobulins G, A, M, and their site-specific glycans simultaneously and directly from human serum without protein enrichments. A total of 64 glycopeptides and 15 peptides were monitored for IgG, IgA, and IgM in a 20-min UPLC gradient. The absolute protein contents were quantified using peptide calibration curves. The glycopeptide ion abundances were normalized to the respective protein abundances to separate protein glycosylation from protein expression. This technique yields higher method reproducibility and less sample loss when compared to quantitation methods that involve protein enrichments. The absolute protein quantitation has a wide linear range (3-4 orders of magnitude) and low limit of quantitation (femtomole level). This rapid and robust quantitation technique, which provides quantitative information for both proteins and glycosylation, will further facilitate disease biomarker discoveries. PMID:26510530

  8. Capacitive ECG system with direct access to standard leads and body surface potential mapping.

    PubMed

    Oehler, Martin; Schilling, Meinhard; Esperer, Hans Dieter

    2009-12-01

    Capacitive electrodes provide the same access to the human electrocardiogram (ECG) as galvanic electrodes, but without the need of direct electrical skin contact and even through layers of clothing. Thus, potential artifacts as a result of poor electrode contact to the skin are avoided and preparation time is significantly reduced. Our system integrates such capacitive electrodes in a 15 sensor array, which is combined with a Tablet PC. This integrated lightweight ECG system (cECG) is easy to place on the chest wall and allows for simultaneous recordings of 14 ECG channels, even if the patient is slightly dressed, e.g., with a t-shirt. In this paper, we present preliminary results on the performance of the cECG regarding the capability of recording body surface potential maps (BSPMs) and obtaining reconstructed standard ECG leads including Einthoven, Goldberger and, with some limitations, Wilson leads. All signals were measured having the subject lie in a supine position and wear a cotton shirt. Signal quality and diagnostic ECG information of the extracted leads are compared with standard ECG measurements. The results show a very close correlation between both types of ECG measurements. It is concluded that the cECG lends itself to rapid screening in clinically unstable patients.

  9. A Method for Comprehensive Glycosite-Mapping and Direct Quantitation of Serum Glycoproteins.

    PubMed

    Hong, Qiuting; Ruhaak, L Renee; Stroble, Carol; Parker, Evan; Huang, Jincui; Maverakis, Emanual; Lebrilla, Carlito B

    2015-12-04

    A comprehensive glycan map was constructed for the top eight abundant glycoproteins in plasma using both specific and nonspecific enzyme digestions followed by nano liquid chromatography (LC)-chip/quadrupole time-of-flight mass spectrometry (MS) analysis. Glycopeptides were identified using an in-house software tool, GPFinder. A sensitive and reproducible multiple reaction monitoring (MRM) technique on a triple quadrupole MS was developed and applied to quantify immunoglobulins G, A, M, and their site-specific glycans simultaneously and directly from human serum/plasma without protein enrichments. A total of 64 glycopeptides and 15 peptides were monitored for IgG, IgA, and IgM in a 20 min ultra high performance (UP)LC gradient. The absolute protein contents were quantified using peptide calibration curves. The glycopeptide ion abundances were normalized to the respective protein abundances to separate protein glycosylation from protein expression. This technique yields higher method reproducibility and less sample loss when compared with the quantitation method that involves protein enrichments. The absolute protein quantitation has a wide linear range (3-4 orders of magnitude) and low limit of quantitation (femtomole level). This rapid and robust quantitation technique, which provides quantitative information for both proteins and glycosylation, will further facilitate disease biomarker discoveries.

  10. Optical mapping of site-directed cleavages on single DNA molecules by the RecA-assisted restriction endonuclease technique.

    PubMed Central

    Wang, Y K; Huff, E J; Schwartz, D C

    1995-01-01

    Fluorescence in situ hybridization (FISH) resolution has advanced because newer techniques use increasingly decondensed chromatin. FISH cannot analyze restriction enzyme cutting sites due to limitations of the hybridization and detection technologies. The RecA-assisted restriction endonuclease (RARE) technique cleaves chromosomal DNA at a single EcoRI site within a given gene or selected sequence. We recently described a mapping technique, optical mapping, which uses fluorescence microscopy to produce high-resolution restriction maps rapidly by directly imaging restriction digestion cleavage events occurring on single deproteinized DNA molecules. Ordered maps are then constructed by noting fragment order and size, using several optically based techniques. Since we also wanted to map arbitrary sequences and gene locations, we combined RARE with optical mapping to produce site-specific visible EcoRI restriction cleavage sites on single DNA molecules. Here we describe this combined method, named optical RARE, and its initial application to mapping gene locations on yeast chromosomes. Images Fig. 2 Fig. 3 PMID:7816810

  11. Strategic environmental noise mapping: methodological issues concerning the implementation of the EU Environmental Noise Directive and their policy implications.

    PubMed

    Murphy, E; King, E A

    2010-04-01

    This paper explores methodological issues and policy implications concerning the implementation of the EU Environmental Noise Directive (END) across Member States. Methodologically, the paper focuses on two key thematic issues relevant to the Directive: (1) calculation methods and (2) mapping methods. For (1), the paper focuses, in particular, on how differing calculation methods influence noise prediction results as well as the value of the EU noise indicator L(den) and its associated implications for comparability of noise data across EU states. With regard to (2), emphasis is placed on identifying the issues affecting strategic noise mapping, estimating population exposure, noise action planning and dissemination of noise mapping results to the general public. The implication of these issues for future environmental noise policy is also examined.

  12. Effect of Instructor-Provided Concept Maps and Self-Directed Learning Ability on Students' Online Hypermedia Learning Performance

    ERIC Educational Resources Information Center

    Chou, Pao-Nan

    2013-01-01

    The purpose of this experimental study was to explore the instructional effectiveness of integrating varied instructor-provided concept maps into an online hypertext learning environment, and the effect of learners' self-directed learning abilities on their learning performance. The research adopted a randomized posttest with two-control-group…

  13. 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.

  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. 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

  16. A Direct Mapping of Max k-SAT and High Order Parity Checks to a Chimera Graph.

    PubMed

    Chancellor, N; Zohren, S; Warburton, P A; Benjamin, S C; Roberts, S

    2016-11-18

    We demonstrate a direct mapping of max k-SAT problems (and weighted max k-SAT) to a Chimera graph, which is the non-planar hardware graph of the devices built by D-Wave Systems Inc. We further show that this mapping can be used to map a similar class of maximum satisfiability problems where the clauses are replaced by parity checks over potentially large numbers of bits. The latter is of specific interest for applications in decoding for communication. We discuss an example in which the decoding of a turbo code, which has been demonstrated to perform near the Shannon limit, can be mapped to a Chimera graph. The weighted max k-SAT problem is the most general class of satisfiability problems, so our result effectively demonstrates how any satisfiability problem may be directly mapped to a Chimera graph. Our methods faithfully reproduce the low energy spectrum of the target problems, so therefore may also be used for maximum entropy inference.

  17. A Direct Mapping of Max k-SAT and High Order Parity Checks to a Chimera Graph

    PubMed Central

    Chancellor, N.; Zohren, S.; Warburton, P. A.; Benjamin, S. C.; Roberts, S.

    2016-01-01

    We demonstrate a direct mapping of max k-SAT problems (and weighted max k-SAT) to a Chimera graph, which is the non-planar hardware graph of the devices built by D-Wave Systems Inc. We further show that this mapping can be used to map a similar class of maximum satisfiability problems where the clauses are replaced by parity checks over potentially large numbers of bits. The latter is of specific interest for applications in decoding for communication. We discuss an example in which the decoding of a turbo code, which has been demonstrated to perform near the Shannon limit, can be mapped to a Chimera graph. The weighted max k-SAT problem is the most general class of satisfiability problems, so our result effectively demonstrates how any satisfiability problem may be directly mapped to a Chimera graph. Our methods faithfully reproduce the low energy spectrum of the target problems, so therefore may also be used for maximum entropy inference. PMID:27857179

  18. A Direct Mapping of Max k-SAT and High Order Parity Checks to a Chimera Graph

    NASA Astrophysics Data System (ADS)

    Chancellor, N.; Zohren, S.; Warburton, P. A.; Benjamin, S. C.; Roberts, S.

    2016-11-01

    We demonstrate a direct mapping of max k-SAT problems (and weighted max k-SAT) to a Chimera graph, which is the non-planar hardware graph of the devices built by D-Wave Systems Inc. We further show that this mapping can be used to map a similar class of maximum satisfiability problems where the clauses are replaced by parity checks over potentially large numbers of bits. The latter is of specific interest for applications in decoding for communication. We discuss an example in which the decoding of a turbo code, which has been demonstrated to perform near the Shannon limit, can be mapped to a Chimera graph. The weighted max k-SAT problem is the most general class of satisfiability problems, so our result effectively demonstrates how any satisfiability problem may be directly mapped to a Chimera graph. Our methods faithfully reproduce the low energy spectrum of the target problems, so therefore may also be used for maximum entropy inference.

  19. Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics.

    PubMed

    Preto, Jordane; Clementi, Cecilia

    2014-09-28

    The reaction pathways characterizing macromolecular systems of biological interest are associated with high free energy barriers. Resorting to the standard all-atom molecular dynamics (MD) to explore such critical regions may be inappropriate as the time needed to observe the relevant transitions can be remarkably long. In this paper, we present a new method called Extended Diffusion-Map-directed Molecular Dynamics (extended DM-d-MD) used to enhance the sampling of MD trajectories in such a way as to rapidly cover all important regions of the free energy landscape including deep metastable states and critical transition paths. Moreover, extended DM-d-MD was combined with a reweighting scheme enabling to save on-the-fly information about the Boltzmann distribution. Our algorithm was successfully applied to two systems, alanine dipeptide and alanine-12. Due to the enhanced sampling, the Boltzmann distribution is recovered much faster than in plain MD simulations. For alanine dipeptide, we report a speedup of one order of magnitude with respect to plain MD simulations. For alanine-12, our algorithm allows us to highlight all important unfolded basins in several days of computation when one single misfolded event is barely observable within the same amount of computational time by plain MD simulations. Our method is reaction coordinate free, shows little dependence on the a priori knowledge of the system, and can be implemented in such a way that the biased steps are not computationally expensive with respect to MD simulations thus making our approach well adapted for larger complex systems from which little information is known.

  20. 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

  1. Optical pulse shaping based on discrete space-to-time mapping in cascaded co-directional couplers.

    PubMed

    Bazargani, Hamed Pishvai; Azaña, José

    2015-09-07

    We propose and numerically validate a new design concept for on-chip optical pulse shaping based on discrete space-to-time mapping in cascaded co-directional couplers. We show that under weak-coupling conditions, the amplitude and phase of the discrete complex apodization profile of the device can be directly mapped into its temporal impulse response. In this scheme, the amplitude and phase of the apodization profile can be controlled by tuning the coupling strength and relative time delay between the couplers, respectively. The proposed concept enables direct synthesis of the target temporal waveforms over a very broad range of time-resolution, from the femtosecond to the sub-nanosecond regime, using readily feasible integrated waveguide technologies. Moreover, the device offers compactness and the potential for reconfigurability.

  2. 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

  3. The use of concept mapping in measurement development and evaluation: Application and future directions.

    PubMed

    Rosas, Scott R; Ridings, John W

    2017-02-01

    The past decade has seen an increase of measurement development research in social and health sciences that featured the use of concept mapping as a core technique. The purpose, application, and utility of concept mapping have varied across this emerging literature. Despite the variety of uses and range of outputs, little has been done to critically review how researchers have approached the application of concept mapping in the measurement development and evaluation process. This article focuses on a review of the current state of practice regarding the use of concept mapping as methodological tool in this process. We systematically reviewed 23 scale or measure development and evaluation studies, and detail the application of concept mapping in the context of traditional measurement development and psychometric testing processes. Although several limitations surfaced, we found several strengths in the contemporary application of the method. We determined concept mapping provides (a) a solid method for establishing content validity, (b) facilitates researcher decision-making, (c) insight into target population perspectives that are integrated a priori, and (d) a foundation for analytical and interpretative choices. Based on these results, we outline how concept mapping can be situated in the measurement development and evaluation processes for new instrumentation.

  4. 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.

  5. MAP18 Regulates the Direction of Pollen Tube Growth in Arabidopsis by Modulating F-Actin Organization[C][W][OA

    PubMed Central

    Zhu, Lei; Zhang, Yan; Kang, Erfang; Xu, Qiangyi; Wang, Miaoying; Rui, Yue; Liu, Baoquan; Yuan, Ming; Fu, Ying

    2013-01-01

    For fertilization to occur in plants, the pollen tube must be guided to enter the ovule via the micropyle. Previous reports have implicated actin filaments, actin binding proteins, and the tip-focused calcium gradient as key contributors to polar growth of pollen tubes; however, the regulation of directional pollen tube growth is largely unknown. We reported previously that Arabidopsis thaliana MICROTUBULE-ASSOCIATED PROTEIN18 (MAP18) contributes to directional cell growth and cortical microtubule organization. The preferential expression of MAP18 in pollen and in pollen tubes suggests that MAP18 also may function in pollen tube growth. In this study, we demonstrate that MAP18 functions in pollen tubes by influencing actin organization, rather than microtubule assembly. In vitro biochemical results indicate that MAP18 exhibits Ca2+-dependent filamentous (F)-actin-severing activity. Abnormal expression of MAP18 in map18 and MAP18 OX plants was associated with disorganization of the actin cytoskeleton in the tube apex, resulting in aberrant pollen tube growth patterns and morphologies, inaccurate micropyle targeting, and fewer fertilization events. Experiments with MAP18 mutants created by site-directed mutagenesis suggest that F-actin-severing activity is essential to the effects of MAP18 on pollen tube growth direction. Our study demonstrates that in Arabidopsis, MAP18 guides the direction of pollen tube growth by modulating actin filaments. PMID:23463774

  6. Children's Cognitive Maps of Large-Scale Spaces: Effects of Exploration, Direction, and Repeated Experience.

    ERIC Educational Resources Information Center

    Herman, James F.

    1980-01-01

    Three experiments were conducted to examine the particular aspects of repeated experiences in a large-scale environment on the development of children's cognitive maps. Subjects were kindergartners and third graders. (MP)

  7. Quantitative Assessment of Macromolecular Concentration during Direct Infusion into an Agarose Hydrogel Phantom using Contrast-Enhanced MRI

    PubMed Central

    Chen, Xiaoming; Astary, Garrett W.; Sepulveda, Hector; Mareci, Thomas H.; Sarntinoranont, Malisa

    2011-01-01

    Convection-enhanced delivery (CED), i.e., direct tissue infusion, has emerged as a promising local drug delivery method for treating diseases of the nervous system. Determination of the spatial distribution of therapeutic agents after infusion is important in evaluating the efficacy of treatment, optimizing infusion protocols, and improving the understanding of drug pharmacokinetics. In this study, we provide a methodology to determine the concentration distribution of Gd-labeled tracers during infusion using contrast-enhanced MR imaging. To the best of our knowledge, MR studies that quantify concentration profiles for CED have not been previously reported. The methodology utilizes intrinsic material properties (T1 and R1) and reduces the effect of instrumental factors (e.g., inhomogeneity of MR detection field). As a methodology investigation, this study used an agarose hydrogel phantom as a tissue substitute for infusion. An 11.1 T magnet system was used to image infusion of Gd-DTPA labeled albumin (Gd-albumin) into the hydrogel. By using data from preliminary scans, Gd-albumin distribution was determined from the signal intensity of the MR images. As a validation test, MR-derived concentration profiles were found comparable to both results measured directly using quantitative optical imaging and results from a computational transport model in porous media. In future studies, the developed methodology will be used to quantitatively monitor the distribution of Gd-tracer following infusion directly into tissues. PMID:18583082

  8. NC-14SPEECH MAPS GENERATED BY nTMS AND CORRELATION WITH DIRECT INTRAOPERATIVE ELECTRICAL STIMULATION

    PubMed Central

    Rotta, Roger; Tummala, Sudhakar; Guillory, Sean; Prabhu, Sujit; Rao, Ganesh; Levine, Nicholas; Suki, Dima; Lang, Frederick; Weinberg, Jeffrey; Sawaya, Raymond

    2014-01-01

    INTRODUCTION: IOM of language pathways is the gold standard for the safe resection of gliomas; navigated TMS has been shown to be useful in generating speech maps prior surgery. This study test the clinical utility of nTMS for mapping language and its concordance with intraoperative stimulation. METHODS: We describe 12 patients with gliomas adjacent to language areas. All cases were performed with nTMS, DES for language mapping. We analyzed, positive and negative sites preoperatively and intraoperatively, and correlated them to the extent of resection and a 1-mo follow-up. RESULTS: Navigated TMS positive maps, was achieved in 11 (92%), and 8 (80%) of cases had language errors during DES. 3527 site were stimulated during nTMS mapping, 225 (7%) was positive, 77 (34%) speech arrest, 78 (35%) performance errors and 70 (31%) semantic errors. TP correlation was achieved in 8 (67%) of cases, TN correlation 1 (8%) and FP correlation was achieved in 1 (8%) of cases. In TP cases, GTR was achieved in 6 (75%) of cases and after 1-mo follow-up 1 (14%) case developed new deficit and improvement was seen in 1(14%) case. In the only case of TN correlation, GTR resection was achieved, without deficits after 1-mo follow-up. CONCLUSION: nTMS correlated well with DES in generated language mapping, with a rate of TP according 67% and the only case with negative response in nTMS was TN. We have shown that nTMS has a high rate of concordance with DES; nTMS has 100% sensitivity, and 50% specificity when compared with DES. PPV at 89% and NPV 100%. The majority of positive sites were achieved in Broca's area and Wernicke's area. Additionally, if the nTMS reveal speech arrest distant from surgical exposure, this may be an additional utility for nTMS in explaining apparent negative mapping results in intraoperative stimulation.

  9. Mapping of dose distribution from IMRT onto MRI-guided high dose rate brachytherapy using deformable image registration for cervical cancer treatments: preliminary study with commercially available software

    PubMed Central

    Huq, M. Saiful; Houser, Chris; Beriwal, Sushil; Michalski, Dariusz

    2014-01-01

    Purpose For patients undergoing external beam radiation therapy (EBRT) and brachytherapy, recommendations for target doses and constraints are based on calculation of the equivalent dose in 2 Gy fractions (EQD2) from each phase. At present, the EBRT dose distribution is assumed to be uniform throughout the pelvis. We performed a preliminary study to determine whether deformable dose distribution mapping from the EBRT onto magnetic resonance (MR) images for the brachytherapy would yield differences in doses for organs at risk (OARs) and high-risk clinical target volume (HR-CTV). Material and methods Nine cervical cancer patients were treated to a total dose of 45 Gy in 25 fractions using intensity-modulated radiation therapy (IMRT), followed by MRI-based 3D high dose rate (HDR) brachytherapy. Retrospectively, the IMRT planning CT images were fused with the MR image for each fraction of brachytherapy using deformable image registration. The deformed IMRT dose onto MR images were converted to EQD2 and compared to the uniform dose assumption. Results For all patients, the EQD2 from the EBRT phase was significantly higher with deformable registration than with the conventional uniform dose distribution assumption. The mean EQD2 ± SD for HR-CTV D90 was 45.7 ± 0.7 Gy vs. 44.3 Gy for deformable vs. uniform dose distribution, respectively (p < 0.001). The dose to 2 cc of the bladder, rectum, and sigmoid was 46.4 ± 1.2 Gy, 46.2 ± 1.0 Gy, and 48.0 ± 2.5 Gy, respectively with deformable dose distribution, and was significantly higher than with uniform dose distribution (43.2 Gy for all OAR, p < 0.001). Conclusions This study reveals that deformed EBRT dose distribution to HR-CTV and OARs in MR images for brachytherapy is technically feasible, and achieves differences compared to a uniform dose distribution. Therefore, the assumption that EBRT contributes the same dose value may need to be carefully investigated further based on deformable image registration. PMID:25097559

  10. Relaxation-compensated CEST-MRI at 7 T for mapping of creatine content and pH--preliminary application in human muscle tissue in vivo.

    PubMed

    Rerich, Eugenia; Zaiss, Moritz; Korzowski, Andreas; Ladd, Mark E; Bachert, Peter

    2015-11-01

    The small biomolecule creatine is involved in energy metabolism. Mapping of the total creatine (mostly PCr and Cr) in vivo has been done with chemical shift imaging. Chemical exchange saturation transfer (CEST) allows an alternative detection of creatine via water MRI. Living tissue exhibits CEST effects from different small metabolites, including creatine, with four exchanging protons of its guanidinium group resonating about 2 ppm from the water peak and hence contributing to the amine proton CEST peak. The intermediate exchange rate (≈ 1000 Hz) of the guanidinium protons requires high RF saturation amplitude B1. However, strong B1 fields also label semi-solid magnetization transfer (MT) effects originating from immobile protons with broad linewidths (~kHz) in the tissue. Recently, it was shown that endogenous CEST contrasts are strongly affected by the MT background as well as by T1 relaxation of the water protons. We show that this influence can be corrected in the acquired CEST data by an inverse metric that yields the apparent exchange-dependent relaxation (AREX). AREX has some useful linearity features that enable preparation of both concentration, and--by using the AREX-ratio of two RF irradiation amplitudes B1--purely exchange-rate-weighted CEST contrasts. These two methods could be verified in phantom experiments with different concentration and pH values, but also varying water relaxation properties. Finally, results from a preliminary application to in vivo CEST imaging data of the human calf muscle before and after exercise are presented. The creatine concentration increases during exercise as expected and as confirmed by (31)P NMR spectroscopic imaging. However, the estimated concentrations obtained by our method were higher than the literature values: cCr,rest=24.5±3.74mM to cCr,ex=38.32±13.05mM. The CEST-based pH method shows a pH decrease during exercise, whereas a slight increase was observed by (31)P NMR spectroscopy.

  11. The NIH experience in first advancing fMRI.

    PubMed

    Turner, Robert

    2012-08-15

    The introduction of functional MRI at NIH in 1992 was the outcome of research goals first formulated by Turner in 1983. Between 1988 and 1990, Turner worked at NIH on actively-shielded gradient coils and the implementation of EPI-based techniques, especially diffusion-weighted EPI. His work on hypoxia in cat brain in 1990 directly inspired Ken Kwong's demonstration of BOLD contrast in humans at MGH in May 1991. Turner collaborated actively with this MGH team, the first group to map entirely noninvasively human brain activity due to visual stimulation. He introduced BOLD fMRI at NIH in February 1992. This paper reviews the steps that led up to BOLD EPI, and Turner's initial applications of BOLD fMRI at NIH.

  12. 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.

  13. Three-dimensional optical micro-angiography maps directional blood perfusion deep within microcirculation tissue beds in vivo

    NASA Astrophysics Data System (ADS)

    Wang, Ruikang K.

    2007-12-01

    Optical micro-angiography (OMAG) is a recently developed method of imaging localized blood perfusion at capillary level resolution within microcirculatory beds. This paper reports that the OMAG is capable of directional blood perfusion mapping in vivo. This is achieved simply by translating the mirror located in the reference arm back and forth while 3D imaging is performed. The mirror which moves toward the incident beam gives the blood perfusion that flows away from the beam direction and vice versa. The approach is experimentally demonstrated by imaging of a flow phantom and then cerebro-vascular perfusion of a live mouse with cranium intact.

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

    DOE PAGES

    Barad, Benjamin A.; Echols, Nathaniel; Wang, Ray Yu-Ruei; ...

    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.

  15. Mapping nouns and finite verbs in left hemisphere tumors: a direct electrical stimulation study.

    PubMed

    Rofes, Adrià; Spena, Giannantonio; Talacchi, Andrea; Santini, Barbara; Miozzo, Antonio; Miceli, Gabriele

    2017-03-27

    Neurosurgical mapping studies with nouns and finite verbs are scarce and subcortical data are nonexistent. We used a new task that uses finite verbs in six Italian-speaking patients with gliomas in the left language-dominant hemisphere. Language-relevant positive areas were detected only with nouns in four patients, with both tasks yet in distinct cortical areas in one patient, and only with finite verbs in another patient. Positive areas and types of errors varied across participants. Finite verbs provide complementary information to nouns, and permit more accurate mapping of language production when nouns are unaffected by electrical stimulation.

  16. High-Resolution Mapping of the Drosophila Fourth Chromosome Using Site-Directed Terminal Deficiencies

    PubMed Central

    Sousa-Neves, Rui; Lukacsovich, Tamas; Mizutani, Claudia Mieko; Locke, John; Podemski, Lynn; Marsh, J. Lawrence

    2005-01-01

    For more than 80 years, the euchromatic right arm of the Drosophila fourth chromosome (101F-102F) has been one of the least genetically accessible regions of the fly genome despite the fact that many important genes reside there. To improve the mapping of genes on the fourth chromosome, we describe a strategy to generate targeted deficiencies and we describe 13 deficiencies that subdivide the 300 kb between the cytological coordinates 102A6 and 102C1 into five discrete regions plus a 200-kb region from 102C1 to 102D6. Together these deficiencies substantially improve the mapping capabilities for mutant loci on the fourth chromosome. PMID:15466427

  17. MRI-guided brachytherapy

    PubMed Central

    Tanderup, Kari; Viswanathan, Akila; Kirisits, Christian; Frank, Steven J.

    2014-01-01

    The application of MRI-guided brachytherapy has demonstrated significant growth during the last two decades. Clinical improvements in cervix cancer outcomes have been linked to the application of repeated MRI for identification of residual tumor volumes during radiotherapy. This has changed clinical practice in the direction of individualized dose administration, and mounting evidence of improved clinical outcome with regard to local control, overall survival as well as morbidity. MRI-guided prostate HDR and LDR brachytherapy has improved the accuracy of target and organs-at-risk (OAR) delineation, and the potential exists for improved dose prescription and reporting for the prostate gland and organs at risk. Furthermore, MRI-guided prostate brachytherapy has significant potential to identify prostate subvolumes and dominant lesions to allow for dose administration reflecting the differential risk of recurrence. MRI-guided brachytherapy involves advanced imaging, target concepts, and dose planning. The key issue for safe dissemination and implementation of high quality MRI-guided brachytherapy is establishment of qualified multidisciplinary teams and strategies for training and education. PMID:24931089

  18. Mapping Visual Attention with Change Blindness: New Directions for a New Method

    ERIC Educational Resources Information Center

    Tse, Peter U.

    2004-01-01

    Change blindness provides a new technique for mapping visual attention with unprecedented spatial and temporal resolution. Change blindness can occur when a brief full-field blank interferes with the detection of changes in a scene that occur during the blank. This interference can be overcome by attending to the location of a change. Because…

  19. 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

  20. Pouring or chilling a bottle of wine: an fMRI study on the prospective planning of object-directed actions.

    PubMed

    van Elk, M; Viswanathan, S; van Schie, H T; Bekkering, H; Grafton, S T

    2012-04-01

    This fMRI study investigates the neural mechanisms supporting the retrieval of action semantics. A novel motor imagery task was used in which participants were required to imagine planning actions with a familiar object (e.g. a toothbrush) or with an unfamiliar object (e.g. a pair of pliers) based on either goal-related information (i.e. where to move the object) or grip-related information (i.e. how to grasp the object). Planning actions with unfamiliar compared to familiar objects was slower and was associated with increased activation in the bilateral superior parietal lobe, the right inferior parietal lobe and the right insula. The stronger activation in parietal areas for unfamiliar objects fits well with the idea that parietal areas are involved in motor imagery and suggests that this process takes more effort in the case of novel or unfamiliar actions. In contrast, the planning of familiar actions resulted in increased activation in the anterior prefrontal cortex, suggesting that subjects maintained a stronger goal-representation when planning actions with familiar compared to unfamiliar objects. These findings provide further insight into the neural structures that support action semantic knowledge for the functional use of real-world objects and suggest that action semantic knowledge is activated most readily when actions are planned in a goal-directed manner.

  1. Multidimensional diffusion MRI

    NASA Astrophysics Data System (ADS)

    Topgaard, Daniel

    2017-02-01

    Principles from multidimensional NMR spectroscopy, and in particular solid-state NMR, have recently been transferred to the field of diffusion MRI, offering non-invasive characterization of heterogeneous anisotropic materials, such as the human brain, at an unprecedented level of detail. Here we revisit the basic physics of solid-state NMR and diffusion MRI to pinpoint the origin of the somewhat unexpected analogy between the two fields, and provide an overview of current diffusion MRI acquisition protocols and data analysis methods to quantify the composition of heterogeneous materials in terms of diffusion tensor distributions with size, shape, and orientation dimensions. While the most advanced methods allow estimation of the complete multidimensional distributions, simpler methods focus on various projections onto lower-dimensional spaces as well as determination of means and variances rather than actual distributions. Even the less advanced methods provide simple and intuitive scalar parameters that are directly related to microstructural features that can be observed in optical microscopy images, e.g. average cell eccentricity, variance of cell density, and orientational order - properties that are inextricably entangled in conventional diffusion MRI. Key to disentangling all these microstructural features is MRI signal acquisition combining isotropic and directional dimensions, just as in the field of multidimensional solid-state NMR from which most of the ideas for the new methods are derived.

  2. Direct mapping of the electric permittivity of heterogeneous non-planar thin films at gigahertz frequencies by scanning microwave microscopy.

    PubMed

    Biagi, Maria Chiara; Badino, Giorgio; Fabregas, Rene; Gramse, Georg; Fumagalli, Laura; Gomila, Gabriel

    2017-02-01

    We obtained maps of electric permittivity at ∼19 GHz frequencies on non-planar thin film heterogeneous samples by means of combined atomic force-scanning microwave microscopy (AFM-SMM). We show that the electric permittivity maps can be obtained directly from the capacitance images acquired in contact mode, after removing the topographic cross-talk effects. This result demonstrates the possibility of identifying the electric permittivity of different materials in a thin film sample irrespectively of their thickness by just direct imaging and processing. We show, in addition, that quantitative maps of the electric permittivity can be obtained with no need for any theoretical calculation or complex quantification procedures when the electric permittivity of one of the materials is known. To achieve these results the use of contact mode imaging is a key factor. For non-contact imaging modes the effects of local sample thickness and of the imaging distance make the interpretation of the capacitance images in terms of the electric permittivity properties of the materials much more complex. The present results represent a substantial contribution to the field of nanoscale microwave dielectric characterization of thin film materials with important implications for the characterization of novel 3D electronic devices and 3D nanomaterials.

  3. Soft Nanocomposite Based Multi-point, Multi-directional Strain Mapping Sensor Using Anisotropic Electrical Impedance Tomography.

    PubMed

    Lee, Hyosang; Kwon, Donguk; Cho, Haedo; Park, Inkyu; Kim, Jung

    2017-01-25

    The practical utilization of soft nanocomposites as a strain mapping sensor in tactile sensors and artificial skins requires robustness for various contact conditions as well as low-cost fabrication process for large three dimensional surfaces. In this work, we propose a multi-point and multi-directional strain mapping sensor based on multiwall carbon nanotube (MWCNT)-silicone elastomer nanocomposites and anisotropic electrical impedance tomography (aEIT). Based on the anisotropic resistivity of the sensor, aEIT technique can reconstruct anisotropic resistivity distributions using electrodes around the sensor boundary. This strain mapping sensor successfully estimated stretch displacements (error of 0.54 ± 0.53 mm), surface normal forces (error of 0.61 ± 0.62 N), and multi-point contact locations (error of 1.88 ± 0.95 mm in 30 mm × 30 mm area for a planar shaped sensor and error of 4.80 ± 3.05 mm in 40 mm × 110 mm area for a three dimensional contoured sensor). In addition, the direction of lateral stretch was also identified by reconstructing anisotropic distributions of electrical resistivity. Finally, a soft human-machine interface device was demonstrated as a practical application of the developed sensor.

  4. Soft Nanocomposite Based Multi-point, Multi-directional Strain Mapping Sensor Using Anisotropic Electrical Impedance Tomography

    PubMed Central

    Lee, Hyosang; Kwon, Donguk; Cho, Haedo; Park, Inkyu; Kim, Jung

    2017-01-01

    The practical utilization of soft nanocomposites as a strain mapping sensor in tactile sensors and artificial skins requires robustness for various contact conditions as well as low-cost fabrication process for large three dimensional surfaces. In this work, we propose a multi-point and multi-directional strain mapping sensor based on multiwall carbon nanotube (MWCNT)-silicone elastomer nanocomposites and anisotropic electrical impedance tomography (aEIT). Based on the anisotropic resistivity of the sensor, aEIT technique can reconstruct anisotropic resistivity distributions using electrodes around the sensor boundary. This strain mapping sensor successfully estimated stretch displacements (error of 0.54 ± 0.53 mm), surface normal forces (error of 0.61 ± 0.62 N), and multi-point contact locations (error of 1.88 ± 0.95 mm in 30 mm × 30 mm area for a planar shaped sensor and error of 4.80 ± 3.05 mm in 40 mm × 110 mm area for a three dimensional contoured sensor). In addition, the direction of lateral stretch was also identified by reconstructing anisotropic distributions of electrical resistivity. Finally, a soft human-machine interface device was demonstrated as a practical application of the developed sensor. PMID:28120886

  5. Soft Nanocomposite Based Multi-point, Multi-directional Strain Mapping Sensor Using Anisotropic Electrical Impedance Tomography

    NASA Astrophysics Data System (ADS)

    Lee, Hyosang; Kwon, Donguk; Cho, Haedo; Park, Inkyu; Kim, Jung

    2017-01-01

    The practical utilization of soft nanocomposites as a strain mapping sensor in tactile sensors and artificial skins requires robustness for various contact conditions as well as low-cost fabrication process for large three dimensional surfaces. In this work, we propose a multi-point and multi-directional strain mapping sensor based on multiwall carbon nanotube (MWCNT)-silicone elastomer nanocomposites and anisotropic electrical impedance tomography (aEIT). Based on the anisotropic resistivity of the sensor, aEIT technique can reconstruct anisotropic resistivity distributions using electrodes around the sensor boundary. This strain mapping sensor successfully estimated stretch displacements (error of 0.54 ± 0.53 mm), surface normal forces (error of 0.61 ± 0.62 N), and multi-point contact locations (error of 1.88 ± 0.95 mm in 30 mm × 30 mm area for a planar shaped sensor and error of 4.80 ± 3.05 mm in 40 mm × 110 mm area for a three dimensional contoured sensor). In addition, the direction of lateral stretch was also identified by reconstructing anisotropic distributions of electrical resistivity. Finally, a soft human-machine interface device was demonstrated as a practical application of the developed sensor.

  6. Direct optical imaging and flux mapping of CH4 in landscapes

    NASA Astrophysics Data System (ADS)

    Gålfalk, M.; Olofsson, G.; Crill, P. M.; Bastviken, D.

    2014-12-01

    Methane (CH4) is a very potent greenhouse gas with many and diverse natural and anthropogenic emission sources such as wetlands, animals, biogas production, waste and sewage management systems. It has increased 2.5-fold since 1750 and is expected to continue to rise, with possible large implications for future climates. Although many individual sources have unknown fluxes, and distributions could be both hotspots or continuous, measurements are mostly made on either a very small scale (chambers or flux towers) with point-like or uncertain footprints, or on the very large scale of satellites with km-sized footprints. There is thus a missing intermediate scale, a scale which would allow both pin-pointing of individual CH4 emission sources and mapping a large enough area to cover a whole landscape. A general such method would be beneficial for connecting scattered local measurements and integrated large scale estimates. Remote sensing is a tool that is often used to map surface materials and the atmosphere from space. This technique, optimized for ground-based or near-ground, sensitive CH4 detection using high spectral resolution, could be a future method for detecting and mapping CH4 sources and fluxes in the environment. We present a new camera system with the ability to both detect and quantify CH4 at low levels in landscapes using remote sensing. Detection is made through thermal infrared (IR) imaging spectroscopy, using the heat radiation of objects in a scene to provide background light (e.g. tree leaves, rocks, grass or the sky). Using spectroscopic and radiative transfer modelling for each pixel (spectrum) in an image, we can calculate a CH4 distribution map from the measured spectra. The system uses imaging at high frequency (hundreds of Hz) to build the spectra - this also enables us to make simultaneous CH4 flux movies that can be used to calculate flows. Our method has broad applications and we will present examples from different environments.

  7. Shoulder MRI

    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 ...

  8. Knee MRI

    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. Shoulder MRI

    MedlinePlus

    ... of the shoulder uses a powerful magnetic field, radio waves and a computer to produce detailed pictures of ... scans, MRI does not utilize ionizing radiation. Instead, radio waves redirect alignment of hydrogen atoms that naturally exist ...

  10. Knee MRI

    MedlinePlus

    ... of the knee uses a powerful magnetic field, radio waves and a computer to produce detailed pictures of ... scans, MRI does not utilize ionizing radiation. Instead, radio waves redirect alignment of hydrogen atoms that naturally exist ...

  11. MRI renaissance.

    PubMed

    Hensley, S

    1997-12-01

    A few years ago, magnetic resonance imaging was healthcare's version of a foreign sports car-flashy, expensive and impractical. Now, after years in the doldrums, sales of MRI systems are roaring back. An aging fleet of MRI scanners due for replacement and a hearty increase in doctors' use of the versatile imaging tools are combining to fuel the surge in demand, vendors and customers say.

  12. 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 Central

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

    2013-01-01

    Transverse relaxation time (T2) 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 T2 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 T2-induced signal attenuation, leading to non-negligible T2 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 T2 MRI technique was developed for fast and accurate T2 imaging, suitable for in vivo applications. PMID:21755552

  13. Mapping Numerical Processing, Reading, and Executive Functions in the Developing Brain: An fMRI Meta-Analysis of 52 Studies Including 842 Children

    ERIC Educational Resources Information Center

    Houde, Olivier; Rossi, Sandrine; Lubin, Amelie; Joliot, Marc

    2010-01-01

    Tracing the connections from brain functions to children's cognitive development and education is a major goal of modern neuroscience. We performed the first meta-analysis of functional magnetic resonance imaging (fMRI) data obtained over the past decade (1999-2008) on more than 800 children and adolescents in three core systems of cognitive…

  14. 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

  15. Mapping the Structure of Directed Networks: Beyond the Bow-Tie Diagram

    NASA Astrophysics Data System (ADS)

    Timár, G.; Goltsev, A. V.; Dorogovtsev, S. N.; Mendes, J. F. F.

    2017-02-01

    We reveal a hierarchical, multilayer organization of finite components—i.e., tendrils and tubes—around the giant connected components in directed networks and propose efficient algorithms allowing one to uncover the entire organization of key real-world directed networks, such as the World Wide Web, the neural network of Caenorhabditis elegans, and others. With increasing damage, the giant components decrease in size while the number and size of tendril layers increase, enhancing the susceptibility of the networks to damage.

  16. 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.

  17. Direct mapping of electrical noise sources in molecular wire-based devices

    NASA Astrophysics Data System (ADS)

    Cho, Duckhyung; Lee, Hyungwoo; Shekhar, Shashank; Yang, Myungjae; Park, Jae Yeol; Hong, Seunghun

    2017-02-01

    We report a noise mapping strategy for the reliable identification and analysis of noise sources in molecular wire junctions. Here, different molecular wires were patterned on a gold substrate, and the current-noise map on the pattern was measured and analyzed, enabling the quantitative study of noise sources in the patterned molecular wires. The frequency spectra of the noise from the molecular wire junctions exhibited characteristic 1/f2 behavior, which was used to identify the electrical signals from molecular wires. This method was applied to analyze the molecular junctions comprising various thiol molecules on a gold substrate, revealing that the noise in the junctions mainly came from the fluctuation of the thiol bonds. Furthermore, we quantitatively compared the frequencies of such bond fluctuations in different molecular wire junctions and identified molecular wires with lower electrical noise, which can provide critical information for designing low-noise molecular electronic devices. Our method provides valuable insights regarding noise phenomena in molecular wires and can be a powerful tool for the development of molecular electronic devices.

  18. Direct mapping of electrical noise sources in molecular wire-based devices

    PubMed Central

    Cho, Duckhyung; Lee, Hyungwoo; Shekhar, Shashank; Yang, Myungjae; Park, Jae Yeol; Hong, Seunghun

    2017-01-01

    We report a noise mapping strategy for the reliable identification and analysis of noise sources in molecular wire junctions. Here, different molecular wires were patterned on a gold substrate, and the current-noise map on the pattern was measured and analyzed, enabling the quantitative study of noise sources in the patterned molecular wires. The frequency spectra of the noise from the molecular wire junctions exhibited characteristic 1/f2 behavior, which was used to identify the electrical signals from molecular wires. This method was applied to analyze the molecular junctions comprising various thiol molecules on a gold substrate, revealing that the noise in the junctions mainly came from the fluctuation of the thiol bonds. Furthermore, we quantitatively compared the frequencies of such bond fluctuations in different molecular wire junctions and identified molecular wires with lower electrical noise, which can provide critical information for designing low-noise molecular electronic devices. Our method provides valuable insights regarding noise phenomena in molecular wires and can be a powerful tool for the development of molecular electronic devices. PMID:28233821

  19. Different dynamic resting state fMRI patterns are linked to different frequencies of neural activity.

    PubMed

    Thompson, Garth John; Pan, Wen-Ju; Keilholz, Shella Dawn

    2015-07-01

    Resting state functional magnetic resonance imaging (rsfMRI) results have indicated that network mapping can contribute to understanding behavior and disease, but it has been difficult to translate the maps created with rsfMRI to neuroelectrical states in the brain. Recently, dynamic analyses have revealed multiple patterns in the rsfMRI signal that are strongly associated with particular bands of neural activity. To further investigate these findings, simultaneously recorded invasive electrophysiology and rsfMRI from rats were used to examine two types of electrical activity (directly measured low-frequency/infraslow activity and band-limited power of higher frequencies) and two types of dynamic rsfMRI (quasi-periodic patterns or QPP, and sliding window correlation or SWC). The relationship between neural activity and dynamic rsfMRI was tested under three anesthetic states in rats: dexmedetomidine and high and low doses of isoflurane. Under dexmedetomidine, the lightest anesthetic, infraslow electrophysiology correlated with QPP but not SWC, whereas band-limited power in higher frequencies correlated with SWC but not QPP. Results were similar under isoflurane; however, the QPP was also correlated to band-limited power, possibly due to the burst-suppression state induced by the anesthetic agent. The results provide additional support for the hypothesis that the two types of dynamic rsfMRI are linked to different frequencies of neural activity, but isoflurane anesthesia may make this relationship more complicated. Understanding which neural frequency bands appear as particular dynamic patterns in rsfMRI may ultimately help isolate components of the rsfMRI signal that are of interest to disorders such as schizophrenia and attention deficit disorder.

  20. Different dynamic resting state fMRI patterns are linked to different frequencies of neural activity

    PubMed Central

    Thompson, Garth John; Pan, Wen-Ju

    2015-01-01

    Resting state functional magnetic resonance imaging (rsfMRI) results have indicated that network mapping can contribute to understanding behavior and disease, but it has been difficult to translate the maps created with rsfMRI to neuroelectrical states in the brain. Recently, dynamic analyses have revealed multiple patterns in the rsfMRI signal that are strongly associated with particular bands of neural activity. To further investigate these findings, simultaneously recorded invasive electrophysiology and rsfMRI from rats were used to examine two types of electrical activity (directly measured low-frequency/infraslow activity and band-limited power of higher frequencies) and two types of dynamic rsfMRI (quasi-periodic patterns or QPP, and sliding window correlation or SWC). The relationship between neural activity and dynamic rsfMRI was tested under three anesthetic states in rats: dexmedetomidine and high and low doses of isoflurane. Under dexmedetomidine, the lightest anesthetic, infraslow electrophysiology correlated with QPP but not SWC, whereas band-limited power in higher frequencies correlated with SWC but not QPP. Results were similar under isoflurane; however, the QPP was also correlated to band-limited power, possibly due to the burst-suppression state induced by the anesthetic agent. The results provide additional support for the hypothesis that the two types of dynamic rsfMRI are linked to different frequencies of neural activity, but isoflurane anesthesia may make this relationship more complicated. Understanding which neural frequency bands appear as particular dynamic patterns in rsfMRI may ultimately help isolate components of the rsfMRI signal that are of interest to disorders such as schizophrenia and attention deficit disorder. PMID:26041826

  1. Rapid and low-invasive functional brain mapping by realtime visualization of high gamma activity for awake craniotomy.

    PubMed

    Kamada, K; Ogawa, H; Kapeller, C; Prueckl, R; Guger, C

    2014-01-01

    For neurosurgery with an awake craniotomy, the critical issue is to set aside enough time to identify eloquent cortices by electrocortical stimulation (ECS). High gamma activity (HGA) ranging between 80 and 120 Hz on electrocorticogram (ECoG) is assumed to reflect localized cortical processing. In this report, we used realtime HGA mapping and functional magnetic resonance imaging (fMRI) for rapid and reliable identification of motor and language functions. Three patients with intra-axial tumors in their dominant hemisphere underwent preoperative fMRI and lesion resection with an awake craniotomy. All patients showed significant fMRI activation evoked by motor and language tasks. After the craniotomy, we recorded ECoG activity by placing subdural grids directly on the exposed brain surface. Each patient performed motor and language tasks and demonstrated realtime HGA dynamics in hand motor areas and parts of the inferior frontal gyrus. Sensitivity and specificity of HGA mapping were 100% compared to ECS mapping in the frontal lobe, which suggested HGA mapping precisely indicated eloquent cortices. The investigation times of HGA mapping was significantly shorter than that of ECS mapping. Specificities of the motor and language-fMRI, however, did not reach 85%. The results of HGA mapping was mostly consistent with those of ECS mapping, although fMRI tended to overestimate functional areas. This novel technique enables rapid and accurate functional mapping.

  2. 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

  3. 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.

  4. Discret aperture mapping with a micro-lenses array for interferometric direct imaging

    NASA Astrophysics Data System (ADS)

    Patru, Fabien; Antichi, Jacopo; Rabou, Patrick; Giro, Enrico; Mawet, Dimitri; Milli, Julien; Girard, Julien; Carbillet, Marcel; Mourard, Denis

    2013-12-01

    A challenging study for high resolution and high-contrast imaging is the detection and the characterization of planets in the habitable zone. The problem of detection in imaging is due to both the contrast ratio and the tiny separation between the hosting star and the exoplanet. Certainly, many techniques in high-contrast imaging will have to be optimized simultaneously to enhance the detection treshold and to probe the candidates for life. In this context, the objective is to demonstrate the technical faisability and to get scientific returns with a new concept called Discret Aperture Mapping or DAM (Patru et al. 2011). DAM is a new interferometric technique allowing high contrast imaging over a narrow field of view imaged by the present class of mono-pupil telescopes equipped with adaptive optics (AO). DAM consists in mapping the telescope pupil to provide a correct sampling of the spatial frequency content of the telescope. DAM can be realized by an afocal double lenslet array array (BIGRE-DAM, Antichi et al. 2011), or by a single-mode fiber combiner (Fibered-DAM, Patru et al. 2008). The spatial filtering used in interferometry allows to subdivide the entrance pupil of a large telescope into many coherent sub-pupils, so that the intra-sub-pupil residual phase is averaged out. On the other side, frequencies higher than the deformable mirror sampling one are not corected by AO impling aliasing effect and a strong impact of Fresnel propagation on the compensated wavefront up to the final focus (Antichi et al. 2010). DAM is then a high frequency optical filter able to remove part of the AO residuals and to remove most of the halo in the image. It may improve the contrast limit to explore the inner region of new stellar systems (disk, exoplanet). We show here first simulation results on the DAM concept.

  5. 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.

  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

    2015-07-07

    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. Direct mapping rather than motor prediction subserves modulation of corticospinal excitability during observation of actions in real time

    PubMed Central

    Gueugneau, Nicolas; Mc Cabe, Sofia I.; Villalta, Jorge I.; Grafton, Scott T.

    2015-01-01

    Motor facilitation refers to the specific increment in corticospinal excitability (CSE) elicited by the observation of actions performed by others. To date, the precise nature of the mechanism at the basis of this phenomenon is unknown. One possibility is that motor facilitation is driven by a predictive process reminiscent of the role of forward models in motor control. Alternatively, motor facilitation may result from a model-free mechanism by which the basic elements of the observed action are directly mapped onto their cortical representations. Our study was designed to discern these alternatives. To this aim, we recorded the time course of CSE for the first dorsal interosseous (FDI) and the abductor digiti minimi (ADM) during observation of three grasping actions in real time, two of which strongly diverged in kinematics from their natural (invariant) form. Although artificially slow movements used in most action observation studies might enhance the observer's discrimination performance, the use of videos in real time is crucial to maintain the time course of CSE within the physiological range of daily actions. CSE was measured at 4 time points within a 240-ms window that best captured the kinematic divergence from the invariant form. Our results show that CSE of the FDI, not the ADM, closely follows the functional role of the muscle despite the mismatch between the natural and the divergent kinematics. We propose that motor facilitation during observation of actions performed in real time reflects the model-free coding of perceived movement following a direct mapping mechanism. PMID:25810483

  8. Direct mapping rather than motor prediction subserves modulation of corticospinal excitability during observation of actions in real time.

    PubMed

    Gueugneau, Nicolas; Mc Cabe, Sofia I; Villalta, Jorge I; Grafton, Scott T; Della-Maggiore, Valeria

    2015-06-01

    Motor facilitation refers to the specific increment in corticospinal excitability (CSE) elicited by the observation of actions performed by others. To date, the precise nature of the mechanism at the basis of this phenomenon is unknown. One possibility is that motor facilitation is driven by a predictive process reminiscent of the role of forward models in motor control. Alternatively, motor facilitation may result from a model-free mechanism by which the basic elements of the observed action are directly mapped onto their cortical representations. Our study was designed to discern these alternatives. To this aim, we recorded the time course of CSE for the first dorsal interosseous (FDI) and the abductor digiti minimi (ADM) during observation of three grasping actions in real time, two of which strongly diverged in kinematics from their natural (invariant) form. Although artificially slow movements used in most action observation studies might enhance the observer's discrimination performance, the use of videos in real time is crucial to maintain the time course of CSE within the physiological range of daily actions. CSE was measured at 4 time points within a 240-ms window that best captured the kinematic divergence from the invariant form. Our results show that CSE of the FDI, not the ADM, closely follows the functional role of the muscle despite the mismatch between the natural and the divergent kinematics. We propose that motor facilitation during observation of actions performed in real time reflects the model-free coding of perceived movement following a direct mapping mechanism.

  9. 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.

  10. Histology-derived volumetric annotation of the human hippocampal subfields in postmortem MRI.

    PubMed

    Adler, Daniel H; Pluta, John; Kadivar, Salmon; Craige, Caryne; Gee, James C; Avants, Brian B; Yushkevich, Paul A

    2014-01-01

    Recently, there has been a growing effort to analyze the morphometry of hippocampal subfields using both in vivo and postmortem magnetic resonance imaging (MRI). However, given that boundaries between subregions of the hippocampal formation (HF) are conventionally defined on the basis of microscopic features that often lack discernible signature in MRI, subfield delineation in MRI literature has largely relied on heuristic geometric rules, the validity of which with respect to the underlying anatomy is largely unknown. The development and evaluation of such rules are challenged by the limited availability of data linking MRI appearance to microscopic hippocampal anatomy, particularly in three dimensions (3D). The present paper, for the first time, demonstrates the feasibility of labeling hippocampal subfields in a high resolution volumetric MRI dataset based directly on microscopic features extracted from histology. It uses a combination of computational techniques and manual post-processing to map subfield boundaries from a stack of histology images (obtained with 200μm spacing and 5μm slice thickness; stained using the Kluver-Barrera method) onto a postmortem 9.4Tesla MRI scan of the intact, whole hippocampal formation acquired with 160μm isotropic resolution. The histology reconstruction procedure consists of sequential application of a graph-theoretic slice stacking algorithm that mitigates the effects of distorted slices, followed by iterative affine and diffeomorphic co-registration to postmortem MRI scans of approximately 1cm-thick tissue sub-blocks acquired with 200μm isotropic resolution. These 1cm blocks are subsequently co-registered to the MRI of the whole HF. Reconstruction accuracy is evaluated as the average displacement error between boundaries manually delineated in both the histology and MRI following the sequential stages of reconstruction. The methods presented and evaluated in this single-subject study can potentially be applied to multiple

  11. Histology-derived volumetric annotation of the human hippocampal subfields in postmortem MRI

    PubMed Central

    Adler, Daniel H.; Pluta, John; Kadivar, Salmon; Craige, Caryne; Gee, James C.; Avants, Brian B.; Yushkevich, Paul A.

    2013-01-01

    Recently, there has been a growing effort to analyze the morphometry of hippocampal subfields using both in vivo and postmortem magnetic resonance imaging (MRI). However, given that boundaries between subregions of the hippocampal formation (HF) are conventionally defined on the basis of microscopic features that often lack discernible signature in MRI, subfield delineation in MRI literature has largely relied on heuristic geometric rules, the validity of which with respect to the underlying anatomy is largely unknown. The development and evaluation of such rules is challenged by the limited availability of data linking MRI appearance to microscopic hippocampal anatomy, particularly in three dimensions (3D). The present paper, for the first time, demonstrates the feasibility of labeling hippocampal subfields in a high resolution volumetric MRI dataset based directly on microscopic features extracted from histology. It uses a combination of computational techniques and manual post-processing to map subfield boundaries from a stack of histology images (obtained with 200 μm spacing and 5 μm slice thickness; stained using the Kluver-Barrera method) onto a postmortem 9.4 Tesla MRI scan of the intact, whole hippocampal formation acquired with 160 μm isotropic resolution. The histology reconstruction procedure consists of sequential application of a graph-theoretic slice stacking algorithm that mitigates the effects of distorted slices, followed by iterative affine and diffeomorphic co-registration to postmortem MRI scans of approximately 1 cm-thick tissue sub-blocks acquired with 200 μm isotropic resolution. These 1 cm blocks are subsequently co-registered to the MRI of the whole HF. Reconstruction accuracy is evaluated as the average displacement error between boundaries manually delineated in both the histology and MRI following the sequential stages of reconstruction. The methods presented and evaluated in this single-subject study can potentially be applied to

  12. Imaging methodologies and applications for nutrition research: what can functional MRI offer?

    PubMed

    Francis, Susan T; Eldeghaidy, Sally

    2015-05-01

    Food intake is influenced by a complex regulatory system involving the integration of a wide variety of sensory inputs across multiple brain areas. Over the past decade, advances in neuroimaging using functional MRI (fMRI) have provided valuable insight into these pathways in the human brain. This review provides an outline of the methodology of fMRI, introducing the widely used blood oxygenation level-dependent contrast for fMRI and direct measures of cerebral blood flow using arterial spin labelling. A review of fMRI studies of the brain's response to taste, aroma and oral somatosensation, and how fat is sensed and mapped in the brain in relation to the pleasantness of food, and appetite control is given. The influence of phenotype on individual variability in cortical responses is addressed, and an overview of fMRI studies investigating hormonal influences (e.g. peptide YY, cholecystokinin and ghrelin) on appetite-related brain processes provided. Finally, recent developments in MR technology at ultra-high field (7 T) are introduced, highlighting the advances this can provide for fMRI studies to investigate the neural underpinnings in nutrition research. In conclusion, neuroimaging methods provide valuable insight into the mechanisms of flavour perception and appetite behaviour.

  13. MRI (Magnetic Resonance Imaging)

    MedlinePlus

    ... and Procedures Medical Imaging MRI (Magnetic Resonance Imaging) MRI (Magnetic Resonance Imaging) Share Tweet Linkedin Pin it More sharing options ... usually given through an IV in the arm. MRI Research Programs at FDA Magnetic Resonance Imaging (MRI) ...

  14. MRI Safety during Pregnancy

    MedlinePlus

    ... News Physician Resources Professions Site Index A-Z MRI Safety During Pregnancy Magnetic resonance imaging (MRI) Illness ... during the exam? Contrast material MRI during pregnancy Magnetic resonance imaging (MRI) If you are pregnant and your doctor ...

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

    SciTech Connect

    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.

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

    PubMed

    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.

  17. 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.

  18. 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

  19. Magnetic Resonance Imaging (MRI) -- Head

    MedlinePlus

    ... provides detailed images of blood vessels in the brain—often without the need for contrast material. See the MRA page for more information. MRI can detect stroke at a very early stage by mapping the motion of water molecules in the tissue. ...

  20. 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.

  1. 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.

  2. 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.

  3. Implementation of the EU environmental noise directive: lessons from the first phase of strategic noise mapping and action planning in Ireland.

    PubMed

    King, E A; Murphy, E; Rice, H J

    2011-03-01

    The first phase of noise mapping and action planning in Ireland, in accordance with EU Directive 2002/49/EC, is now complete. In total this included one agglomeration, one airport and approximately 600 km of major roads outside the agglomeration. These noise maps describe the level of noise exposure of approximately 1.25 million people. The first phase of noise mapping was dealt with by five noise mapping bodies while 26 action planning authorities were involved in the development of the associated action plans. The second phase of noise mapping, due to be completed in 2012, sees a reduction in the defined thresholds describing the required agglomerations, roads and railways that have to be mapped. This will have a significant impact on the extent of mapping required. In Ireland this will result in an increased number of local authorities being required to develop strategic noise maps for their area along with the further development of associated action plans. It is appropriate at this point to review the work process and results from the first phase of noise mapping in Ireland in order to establish areas that could be improved, throughout the noise mapping project. In this paper a review of the implementation procedures focussing on (dominant) road traffic noise is presented. It is identified that more standardisation is needed and this could be achieved by the establishment of a national expert steering group.

  4. Two-Point Magnitude MRI for Rapid Mapping of Brown Adipose Tissue and Its Application to the R6/2 Mouse Model of Huntington Disease

    PubMed Central

    Müller, Hans-Peter; Bornstedt, Axel; Ludolph, Albert C.; Landwehrmeyer, G. Bernhard; Rottbauer, Wolfgang; Kassubek, Jan; Rasche, Volker

    2014-01-01

    The recent discovery of active brown fat in human adults has led to renewed interest in the role of this key metabolic tissue. This is particularly true for neurodegenerative conditions like Huntington disease (HD), an adult-onset heritable disorder with a prominent energy deficit phenotype. Current methods for imaging brown adipose tissue (BAT) are in limited use because they are equipment-wise demanding and often prohibitively expensive. This prompted us to explore how a standard MRI set-up can be modified to visualize BAT in situ by taking advantage of its characteristic fat/water content ratio to differentiate it from surrounding white fat. We present a modified MRI protocol for use on an 11.7 T small animal MRI scanner to visualize and quantify BAT in wild-type and disease model laboratory mice. In this application study using the R6/2 transgenic mouse model of HD we demonstrate a significantly reduced BAT volume in HD mice vs. matched controls (n = 5 per group). This finding provides a plausible structural explanation for the previously described temperature phenotype of HD mice and underscores the significance of peripheral tissue pathology for the HD phenotype. On a more general level, the results demonstrate the feasibility of MR-based BAT imaging in rodents and open the path towards transferring this imaging approach to human patients. Future studies are needed to determine if this method can be used to track disease progression in HD and other disease entities associated with BAT abnormalities, including metabolic conditions such as obesity, cachexia, and diabetes. PMID:25144457

  5. Detection of Brain Reorganization in Pediatric Multiple Sclerosis Using Functional MRI

    DTIC Science & Technology

    2014-10-01

    fMRI mappings of language, memory , and motor function, and performance on clinical neurocognitive examinations. Our research represents an...normative fMRI maps from the 40 healthy volunteers in order to form consensus fMRI activation maps for language, memory , and visual-motor tasks (months...volunteers for language, memory , and visual-motor processing. ii. Task 2. Acquisition and comparison of fMRI activation patterns in 30 POMS patients

  6. Direct comparison of three different methods of volcanic edifice identification from bathymetry maps

    NASA Astrophysics Data System (ADS)

    Howell, J.; White, S. M.; Bohnenstiehl, D. R.; Miller, D.

    2009-12-01

    The detection of volcanic edifices from bathymetric sonar data is often used in studies of seamount distribution near arcs, ridges and hotspots to interpret volcanic spacing and alignment. Such studies form the basis for the ongoing debate on the structural controls on volcanism and our understanding of linkages between tectonics and volcanism. Until recently, manually picking closed-contour peaks from maps was the only method of volcanic edifice identification, however this can be subjective and time consuming. In this study we have compared the results from three separate methods: manually picking closed contours, using a peakshed method based on a widely used algorithm for detecting sinkholes in topographic data, and a closed-contour picking computer algorithm. Bathymetry from the western Aleutian backarc collected in 2005, the Galapagos Spreading Centers collected in 2006 and the Mid-Atlantic Ridge collected in 1990 was used as the comparison data. To each dataset, we applied a common set of criteria: minimum peak to base heights must be greater than 25 meters and aspect ratios (long to short axis of the basal contour) must be less than 1.5. The peakshed method begins by looking for local bathymetric peaks remaining after removing regional bathymetry using a median filter. The median filtered bathymetry grid was subtracted from the original bathymetric grid to obtain the residual bathymetry representing the volcanic edifices. We use a novel application of the method used to detect and remove local sinkholes from digital terrain models to define the basal boundary of each edifice. The residual bathymetry is first inverted, so that local peaks become local sinks, and then the area of the basin that drains into each sink is calculated using a GIS algorithm and returned as a closed polygon that represents the basal area of each edifice. This method has the advantage of using the full resolution of the gridded data to determine the volume of an edifice. The closed

  7. Comparison of navigated transcranial magnetic stimulation and functional magnetic resonance imaging for preoperative mapping in rolandic tumor surgery.

    PubMed

    Coburger, Jan; Musahl, Christian; Henkes, Hans; Horvath-Rizea, Diana; Bittl, Markus; Weissbach, Claudia; Hopf, Nikolai

    2013-01-01

    Navigated transcranial magnetic stimulation (nTMS) is a novel tool for preoperative functional mapping. It detects eloquent cortical areas directly, comparable to intraoperative direct cortical stimulation (DCS). The aim of this study was to evaluate the advantage of nTMS in comparison with functional magnetic resonance imaging (fMRI) in the clinical setting. Special focus was placed on accuracy of motor cortex localization in patients with rolandic lesions. Thirty consecutive patients were enrolled in the study. All patients received an fMRI and nTMS examination preoperatively. Feasibility of the technique and spatial resolution of upper and lower extremity cortical mapping were compared with fMRI. Consistency of preoperative mapping with intraoperative DCS was assessed via the neuronavigation system. nTMS was feasible in all 30 patients. fMRI was impossible in 7 out of 30 patients with special clinical conditions, pediatric patients, central vascular lesions, or compliance issues. The mean accuracy to localize motor cortex of nTMS was higher than in fMRI. In the subgroup of intrinsic tumors, nTMS produced statistically significant higher accuracy scores of the lower extremity localization than fMRI. fMRI failed to localize hand or leg areas in 6 out of 23 cases. Using nTMS, a preoperative localization of the central sulcus was possible in all patients. Verification of nTMS motor cortex localization with DCS was achieved in all cases. The fMRI localization of the hand area proved to be postcentral in one case. nTMS has fewer restrictions for preoperative functional mapping than fMRI and requires only a limited level of compliance. nTMS scores higher on the accuracy scale than fMRI. nTMS represents a highly valuable supplement for the preoperative functional planning in the clinical routine.

  8. Whole-brain mapping of direct inputs to midbrain dopamine neurons.

    PubMed

    Watabe-Uchida, Mitsuko; Zhu, Lisa; Ogawa, Sachie K; Vamanrao, Archana; Uchida, Naoshige

    2012-06-07

    Recent studies indicate that dopamine neurons in the ventral tegmental area (VTA) and substantia nigra pars compacta (SNc) convey distinct signals. To explore this difference, we comprehensively identified each area's monosynaptic inputs using the rabies virus. We show that dopamine neurons in both areas integrate inputs from a more diverse collection of areas than previously thought, including autonomic, motor, and somatosensory areas. SNc and VTA dopamine neurons receive contrasting excitatory inputs: the former from the somatosensory/motor cortex and subthalamic nucleus, which may explain their short-latency responses to salient events; and the latter from the lateral hypothalamus, which may explain their involvement in value coding. We demonstrate that neurons in the striatum that project directly to dopamine neurons form patches in both the dorsal and ventral striatum, whereas those projecting to GABAergic neurons are distributed in the matrix compartment. Neuron-type-specific connectivity lays a foundation for studying how dopamine neurons compute outputs.

  9. Diffeomorphic Image Registration of Diffusion MRI Using Spherical Harmonics

    PubMed Central

    Geng, Xiujuan; Ross, Thomas J.; Gu, Hong; Shin, Wanyong; Zhan, Wang; Chao, Yi-Ping; Lin, Ching-Po; Schuff, Norbert; Yang, Yihong

    2013-01-01

    Non-rigid registration of diffusion MRI is crucial for group analyses and building white matter and fiber tract atlases. Most current diffusion MRI registration techniques are limited to the alignment of diffusion tensor imaging (DTI) data. We propose a novel diffeomorphic registration method for high angular resolution diffusion images by mapping their orientation distribution functions (ODFs). ODFs can be reconstructed using q-ball imaging (QBI) techniques and represented by spherical harmonics (SHs) to resolve intra-voxel fiber crossings. The registration is based on optimizing a diffeomorphic demons cost function. Unlike scalar images, deforming ODF maps requires ODF reorientation to maintain its consistency with the local fiber orientations. Our method simultaneously reorients the ODFs by computing a Wigner rotation matrix at each voxel, and applies it to the SH coefficients during registration. Rotation of the coefficients avoids the estimation of principal directions, which has no analytical solution and is time consuming. The proposed method was validated on both simulated and real data sets with various metrics, which include the distance between the estimated and simulated transformation fields, the standard deviation of the general fractional anisotropy and the directional consistency of the deformed and reference images. The registration performance using SHs with different maximum orders were compared using these metrics. Results show that the diffeomorphic registration improved the affine alignment, and registration using SHs with higher order SHs further improved the registration accuracy by reducing the shape difference and improving the directional consistency of the registered and reference ODF maps. PMID:21134814

  10. Feedback from area 21a influences orientation but not direction maps in the primary visual cortex of the cat.

    PubMed

    Tong, Lei; Zhu, Bin; Li, Zhong; Shou, Tiande; Yu, Hongbo

    2011-10-24

    In the monkey's visual cortex, there are two well-documented information processing streams: the dorsal motion and ventral form/color pathways. Similarly, two corresponding information streams were also found in the cat's visual cortices, and PMLS and area 21a are the gateways for distinct motion and form information processing. It has been shown that the feedback from PMLS solely modulates motion direction, but not orientation response, while the feedback from area 21a modulates form related features, such as spatial frequency dependency and neuronal oblique effect. Here, we postulate that feedback signals from higher cortical areas in the form or the motion information pathway may solely modulate the corresponding properties in neurons in the lower areas of the visual system. To examine the above hypothesis, the impact of feedback from higher area 21a on both orientation and direction maps was investigated in area 17 of the cat using intrinsic signal optical imaging. The results showed that the feedback from area 21a did not affect the amplitude and preference of direction, but did modulate orientation response in area 17, supporting the above hypothesis.

  11. Mapping the effect of escitalopram treatment on amplitude of low-frequency fluctuations in patients with depression: a resting-state fMRI study.

    PubMed

    Wang, Li; Li, Xueni; Li, Ke; Su, Yunai; Zeng, Yawei; Zhang, Qinge; Wang, Gang; Jin, Zhen; Kong, Qingmei; Si, Tianmei

    2017-02-01

    Antidepressant medications represent the most common treatment option for major depressive disorder (MDD), but the neuro-psychological mechanisms by which antidepressants act to improve depressive symptoms remain under-specified. We designed this study to assess the effects of escitalopram treatment on spontaneous brain activity of MDD patients using functional magnetic resonance imaging (fMRI). Twenty first-episode drug-naive MDD patients received resting-state fMRI scans before and after 8 weeks of treatment with a selective serotonin reuptake inhibitor - escitalopram. Twenty age- and gender-matched healthy controls were also scanned twice with an 8-week interval. The fractional amplitude of low-frequency fluctuation (fALFF) was used to characterize the spontaneous brain activity. The analysis of covariance (ANCOVA) was performed to determine treatment-related changes in fALFF. The symptoms were significantly improved in MDD patients after treatment. We observed significant group-by-time interaction on fALFF in the left dorsomedial prefrontal cortex, the right middle frontal gyrus, and the left putamen. Post-hoc analyses showed that the fALFF values in these regions were significantly higher in the MDD patients compared to healthy controls at baseline and were reduced after treatment. The findings suggest that abnormalities in the brain areas involved in emotional processing and regulation could be normalized by effective antidepressant treatment with escitalopram in the MDD patients and free of a task situation.

  12. A high precision method for mapping phase to amplitude in direct digital synthesis and its hardware implementation.

    PubMed

    Cao, Zhang; Song, Wei; Peng, Zhicong; Xu, Lijun

    2014-11-01

    There exist a number of algorithms to map the phase to amplitude in direct digital synthesis (DDS). For DDS with more than 14 output bits, the Coordinate Rotation Digital Computer (CORDIC) algorithm is well known for its high precision. Also, it is effective in solutions where there is the need of in-phase and quadrature components simultaneously because the algorithm calculates both. In this paper, a Taylor expansion based method was proposed to calculate both in-phase and quadrature at the same time. Numerical simulations for different data format, e.g., double and finite bits, were carried out in Matlab and Quartus, which were followed by the hardware implementation in Field Programmable Gate Array. The results demonstrated that the proposed method possessed higher precision and exhausted less logic elements than the CORDIC algorithm.

  13. 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.

  14. 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

    2016-06-08

    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.

  15. Direct mapping of Li-enabled octahedral tilt ordering and associated strain in nanostructured perovskites

    NASA Astrophysics Data System (ADS)

    Zhu, Ye; Withers, Ray L.; Bourgeois, Laure; Dwyer, Christian; Etheridge, Joanne

    2015-11-01

    Self-assembled nanostructures with periodic phase separation hold great promise for creating two- and three-dimensional superlattices with extraordinary physical properties. Understanding the mechanism(s) driving the formation of such superlattices demands an understanding of their underlying atomic structure. However, the nanoscale structural fluctuations intrinsic to these superlattices pose a new challenge for structure determination methods. Here we develop an optimized atomic-level imaging condition to measure TiO6 octahedral tilt angles, unit-cell-by-unit-cell, in perovskite-based Li0.5-3xNd0.5+xTiO3, and thereby determine the mathematical formula governing this nanoscale superstructure. We obtain a direct real-space correlation of the octahedral tilt modulation with the superstructure geometry and lattice-parameter variations. This reveals a composition-dependent, self-ordered octahedral superlattice. Amazingly, we observe a reversible annihilation/reconstruction of the octahedral superlattice correlated with the delithiation/lithiation process in this promising Li-ion conductor. This approach to quantify local octahedral tilt and correlate it with strain can be applied to characterize complex octahedral behaviours in other advanced oxide systems.

  16. Site-Directed Chemical Probing to map transient RNA/protein interactions.

    PubMed

    Duval, Mélodie; Marenna, Alessandra; Chevalier, Clément; Marzi, Stefano

    2017-03-15

    RNA-protein interactions are at the bases of many biological processes, forming either tight and stable functional ribonucleoprotein (RNP) complexes (i.e. the ribosome) or transitory ones, such as the complexes involving RNA chaperone proteins. To localize the sites where a protein interacts on an RNA molecule, a common simple and inexpensive biochemical method is the footprinting technique. The protein leaves its footprint on the RNA acting as a shield to protect the regions of interaction from chemical modification or cleavages obtained with chemical or enzymatic nucleases. This method has proven its efficiency to study in vitro the organization of stable RNA-protein complexes. Nevertheless, when the protein binds the RNA very dynamically, with high off-rates, protections are very often difficult to observe. For the analysis of these transient complexes, we describe an alternative strategy adapted from the Site Directed Chemical Probing (SDCP) approach and we compare it with classical footprinting. SDCP relies on the modification of the RNA binding protein to tether an RNA probe (usually Fe-EDTA) to specific protein positions. Local cleavages on the regions of interaction can be used to localize the protein and position its domains on the RNA molecule. This method has been used in the past to monitor stable complexes; we provide here a detailed protocol and a practical example of its application to the study of Escherichia coli RNA chaperone protein S1 and its transitory complexes with mRNAs.

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

    SciTech Connect

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

    2016-06-08

    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 offaxis 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.

  18. Three dimensional mapping of Fe dopants in ceria nanocrystals using direct spectroscopic electron tomography.

    PubMed

    Goris, Bart; Meledina, Maria; Turner, Stuart; Zhong, Zhichao; Batenburg, K Joost; Bals, Sara

    2016-12-01

    Electron tomography is a powerful technique for the 3D characterization of the morphology of nanostructures. Nevertheless, resolving the chemical composition of complex nanostructures in 3D remains challenging and the number of studies in which electron energy loss spectroscopy (EELS) is combined with tomography is limited. During the last decade, dedicated reconstruction algorithms have been developed for HAADF-STEM tomography using prior knowledge about the investigated sample. Here, we will use the prior knowledge that the experimental spectrum of each reconstructed voxel is a linear combination of a well-known set of references spectra in a so-called direct spectroscopic tomography technique. Based on a simulation experiment, it is shown that this technique provides superior results in comparison to conventional reconstruction methods for spectroscopic data, especially for spectrum images containing a relatively low signal to noise ratio. Next, this technique is used to investigate the spatial distribution of Fe dopants in Fe:Ceria nanoparticles in 3D. It is shown that the presence of the Fe(2+) dopants is correlated with a reduction of the Ce atoms from Ce(4+) towards Ce(3+). In addition, it is demonstrated that most of the Fe dopants are located near the voids inside the nanoparticle.

  19. Battlefield MRI

    DOE PAGES

    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.

  20. 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

  1. Sodium MRI.

    PubMed

    Ouwerkerk, Ronald

    2011-01-01

    Sodium ((23)Na) imaging has a place somewhere between (1)H-MRI and MR spectroscopy (MRS). Like MRS it potentially provides information on metabolic processes, but only one single resonance of ionic (23)Na is observed. Therefore pulse sequences do not need to code for a chemical shift dimension, allowing (23)Na images to be obtained at high resolutions as compared to MRS. In this chapter the biological significance of sodium in the brain will be discussed, as well as methods for observing it with (23)Na-MRI. Many vital cellular processes and interactions in excitable tissues depend on the maintenance of a low intracellular and high extracellular sodium concentration. Healthy cells maintain this concentration gradient at the cost of energy. Leaky cell membranes or an impaired energy metabolism immediately leads to an increase in cytosolic total tissue sodium. This makes sodium a biomarker for ischemia, cancer, excessive tissue activation, or tissue damage as might be caused by ablation therapy. Special techniques allow quantification of tissue sodium for the monitoring of disease or therapy in longitudinal studies or preferential observation of the intracellular component of the tissue sodium. New methods and high-field magnet technology provide new opportunities for (23)Na-MRI in clinical and biomedical research.

  2. Experimental and Numerical Assessment of MRI-Induced Temperature Change and SAR Distributions in Phantoms and In Vivo

    PubMed Central

    Oh, Sukhoon; Webb, Andrew G.; Neuberger, Thomas; Park, BuSik; Collins, Christopher M.

    2010-01-01

    It is important to accurately characterize the heating of tissues due to the radiofrequency energy applied during MRI. This has led to an increase in the use of numerical methods to predict specific energy absorption rate distributions for safety assurance in MRI. To ensure these methods are accurate for actual MRI coils, however, it is necessary to compare to experimental results. Here, we report results of some recent efforts to experimentally map temperature change and specific energy absorption rate in a phantom and in vivo where the only source of heat is the radiofrequency fields produced by the imaging coil. Results in a phantom match numerical simulation well, and preliminary results in vivo show measurable temperature increase. With further development, similar methods may be useful for verifying numerical methods for predicting specific energy absorption rate distributions and in some cases for directly measuring temperature changes and specific energy absorption rate induced by the radiofrequency fields in MRI experiments. PMID:19785018

  3. Empirical validation of directed functional connectivity.

    PubMed

    Mill, Ravi D; Bagic, Anto; Bostan, Andreea; Schneider, Walter; Cole, Michael W

    2017-02-01

    Mapping directions of influence in the human brain connectome represents the next phase in understanding its functional architecture. However, a host of methodological uncertainties have impeded the application of directed connectivity methods, which have primarily been validated via "ground truth" connectivity patterns embedded in simulated functional MRI (fMRI) and magneto-/electro-encephalography (MEG/EEG) datasets. Such simulations rely on many generative assumptions, and we hence utilized a different strategy involving empirical data in which a ground truth directed connectivity pattern could be anticipated with confidence. Specifically, we exploited the established "sensory reactivation" effect in episodic memory, in which retrieval of sensory information reactivates regions involved in perceiving that sensory modality. Subjects performed a paired associate task in separate fMRI and MEG sessions, in which a ground truth reversal in directed connectivity between auditory and visual sensory regions was instantiated across task conditions. This directed connectivity reversal was successfully recovered across different algorithms, including Granger causality and Bayes network (IMAGES) approaches, and across fMRI ("raw" and deconvolved) and source-modeled MEG. These results extend simulation studies of directed connectivity, and offer practical guidelines for the use of such methods in clarifying causal mechanisms of neural processing.

  4. Interpolation of vector fields from human cardiac DT-MRI

    NASA Astrophysics Data System (ADS)

    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.

  5. Computationally efficient particle release map determination for direct tumor-targeting in a representative hepatic artery system.

    PubMed

    Childress, E M; Kleinstreuer, C

    2014-01-01

    Implementation of a novel direct tumor-targeting technique requires a computer modeling stage to generate particle release maps (PRMs) which allow for optimal catheter positioning and selection of best injection intervals for drug-particles. This simulation task for a patient-specific PRM may require excessive computational resources and a relatively long turn-around time for a fully transient analysis. Hence, steady-state conditions were sought which generates PRMs equivalent to the pulsatile arterial flow environment. Fluid-particle transport in a representative hepatic artery system was simulated under fully transient and steady-state flow conditions and their corresponding PRMs were analyzed and compared. Comparisons of the transient PRMs from ten equal intervals of the cardiac pulse revealed that the diastolic phase produced relatively constant PRMs due to its semisteady flow conditions. Furthermore, steady-state PRMs, which best matched the transient particle release maps, were found for each interval and over the entire cardiac pulse. From these comparisons, the flow rate and outlet pressure differences proved to be important parameters for estimating the PRMs. The computational times of the fully transient and steady simulations differed greatly, i.e., about 10 days versus 0.5 to 1 h, respectively. The time-averaged scenario may provide the best steady conditions for estimating the transient particle release maps. However, given the considerable changes in the PRMs due to the accelerating and decelerating phases of the cardiac cycle, it may be better to model several steady scenarios, which encompass the wide range of flows and pressures experienced by the arterial system in order to observe how the PRMs may change throughout the pulse. While adding more computation time, this method is still significantly faster than running the full transient case. Finally, while the best steady PRMs provide a qualitative guide for best catheter placement, the final

  6. 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

  7. 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

  8. 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

  9. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads--a baiting and iterative mapping approach.

    PubMed

    Hahn, Christoph; Bachmann, Lutz; Chevreux, Bastien

    2013-07-01

    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.

  10. 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.

  11. 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.

  12. 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

  13. Voxel-based Morphometric MRI Post-processing in MRI-negative Epilepsies

    PubMed Central

    Wang, ZI; Jones, SE; Jaisani, Z; Najm, IM; Prayson, RA; Burgess, RC; Krishnan, B; Ristic, A; Wong, CH; Bingaman, W; Gonzalez-Martinez, JA; Alexopoulos, AV

    2015-01-01

    Objective In the presurgical workup of MRI-negative (MRI−, or “nonlesional”) pharmacoresistant focal epilepsy (PFE) patients, discovering a previously undetected lesion can drastically change the evaluation and likely improve surgical outcome. Our study utilizes a voxel-based MRI post-processing technique, implemented in a morphometric analysis program (MAP), to facilitate detection of subtle abnormalities in a consecutive cohort of MRI− surgical candidates. Methods Included in this retrospective study was a consecutive cohort of 150 MRI-surgical patients. MAP was performed on T1-weighted MRI, with comparison to a scanner-specific normal database. Review and analysis of MAP were performed blinded to patients’ clinical information. The pertinence of MAP+ areas was confirmed by surgical outcome and pathology. Results MAP showed a 43% positive rate, sensitivity of 0.9 and specificity of 0.67. Overall, patients with MAP+ region completely resected had the best seizure outcomes, followed by the MAP− patients, and patients who had no/partial resection of the MAP+ region had the worst outcome (p<0.001). Subgroup analysis revealed that visually identified subtle findings are more likely correct if also MAP+. False-positive rate in 52 normal controls was 2%. Surgical pathology of the resected MAP+ areas contained mainly non-balloon-cell FCD. Multiple MAP+ regions were present in 7% of patients. Conclusions MAP can be a practical and valuable tool to: (1) guide the search for subtle MRI abnormalities, and (2) confirm visually identified questionable abnormalities in patients with PFE due to suspected FCD. A MAP+ region, when concordant with the patient’s electro-clinical presentation, should provide a legitimate target for surgical exploration. PMID:25807928

  14. WE-AB-204-06: Pseudo-CT Generation Using Undersampled, Single-Acquisition UTE-MDixon and Direct-Mapping Artificial Neural Networks for MR-Based Attenuation Correction and Radiation Therapy Planning

    SciTech Connect

    Su, K; Kuo, J; Hu, L; Traughber, M; Pereira, G; Traughber, B; Herrmann, K; Muzic, R

    2015-06-15

    Purpose: Emerging technologies such as dedicated PET/MRI and MR-therapy systems require robust and clinically practical methods for determining photon attenuation. Herein, we propose using novel MR acquisition methods and processing for the generation of pseudo-CTs. Methods: A single acquisition, 190-second UTE-mDixon sequence with 25% (angular) sampling density and 3D radial readout was performed on nine volunteers. Three water-filled tubes were placed in the FOV for trajectory-delay correction. The MR data were reconstructed to generate three primitive images acquired at TEs of 0.1, 1.5 and 2.8 ms. In addition, three derived MR images were generated, i.e. two-point Dixon water/fat separation and R2* (1/T2*) map. Furthermore, two spatial features, i.e. local binary pattern (S-1) and relative spatial coordinates (S-2), were incorporated. A direct-mapping operator was generated using Artificial Neural Networks (ANNs) for transforming the MR features to a pseudo-CT. CT images served as the training data and, using a leave-one-out method, for performance evaluation using mean prediction deviation (MPD), mean absolute prediction deviation (MAPD), and correlation coefficient (R). Results: The errors between measured CT and pseudo-CT declined dramatically when the spatial features, i.e. S-1 and S-2, were included. The MPD, MAPD, and R were, respectively, 5±57 HU, 141±41 HU, and 0.815±0.066 for results generated by the ANN trained without the spatial features and were 32±26 HU, 115±18 HU, and 0.869±0.035 with the spatial features. The estimation errors of the pseudo-CT were smaller when both the S-1 and S-2 were used together than when either the S-1 or the S-2 was used. Pseudo-CT generation (256×256×256 voxels) by ANN took < 0.5 s using a computer having an Intel i7 3.4GHz CPU and 16 GB RAM. Conclusion: The proposed direct-mapping ANN approach is a technically accurate, clinically practical method for pseudo-CT generation and can potentially help improve the

  15. 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.

  16. Use of resting-state fMRI in planning epilepsy surgery.

    PubMed

    Chiang, Sharon; Haneef, Zulfi; Stern, John M; Engel, Jerome

    2017-01-01

    Epileptic seizures result from abnormal neuronal excitability and synchronization, affecting 0.5-1% of the population worldwide. Although anti-seizure drugs are often effective, a significant number of patients with epilepsy continue to experience refractory seizures and are candidates for surgical resection. Whereas standard presurgical evaluation has relied on intracranial electroencephalography (icEEG) and direct cortical stimulation to identify epileptogenic tissue and areas of cortex for which resection would produce clinical deficits, the invasive nature and limited spatial extent of icEEG has led to the investigation of less invasive imaging modalities as adjunctive tools in the presurgical workup. In the past few decades, functional connectivity MRI has emerged as a promising approach for presurgical mapping, leading to a surge in the number of proposed methods and biomarkers for identifying epileptogenic tissue. This review focuses on recent advances in the use of functional connectivity MRI toward its application for presurgical planning, including epilepsy localization and eloquent cortex mapping.

  17. Generalized total variation-based MRI Rician denoising model with spatially adaptive regularization parameters.

    PubMed

    Liu, Ryan Wen; Shi, Lin; Huang, Wenhua; Xu, Jing; Yu, Simon Chun Ho; Wang, Defeng

    2014-07-01

    Magnetic resonance imaging (MRI) is an outstanding medical imaging modality but the quality often suffers from noise pollution during image acquisition and transmission. The purpose of this study is to enhance image quality using feature-preserving denoising method. In current literature, most existing MRI denoising methods did not simultaneously take the global image prior and local image features into account. The denoising method proposed in this paper is implemented based on an assumption of spatially varying Rician noise map. A two-step wavelet-domain estimation method is developed to extract the noise map. Following a Bayesian modeling approach, a generalized total variation-based MRI denoising model is proposed based on global hyper-Laplacian prior and Rician noise assumption. The proposed model has the properties of backward diffusion in local normal directions and forward diffusion in local tangent directions. To further improve the denoising performance, a local variance estimator-based method is introduced to calculate the spatially adaptive regularization parameters related to local image features and spatially varying noise map. The main benefit of the proposed method is that it takes full advantage of the global MR image prior and local image features. Numerous experiments have been conducted on both synthetic and real MR data sets to compare our proposed model with some state-of-the-art denoising methods. The experimental results have demonstrated the superior performance of our proposed model in terms of quantitative and qualitative image quality evaluations.

  18. The Chasm Green Machine: A Rapid Data Acquisition and Mapping System For Direct Observation of Shallow Hydrological Processes.

    NASA Astrophysics Data System (ADS)

    Quinn, P.; Merrett, S.

    CHASM (Catchment Hydrology and Sustainable Management) is a major UK funded project investigating all aspects of hydrological observation from point to basin scale. The project includes a mobile instrumentation component, which is now referred to as the 'Green Machine'. This research facility includes an All Terrain Vehicle, an on board high resolution GPS mapping and navigation system, an EM31, an EM38 and a Seistronix seismic kit. The goal of the project is to observe and map unsaturated and saturated zone hydrological processes within soils and drift through repeated map- ping campaigns. The hydrogeophysics kit will be validated against a dense series of ground based observations of soil moisture deficit, suction and peizometric logging instruments. The Green Machine also includes a portable drilling and coring kit that can reach 10m in depth. Thus, the EM31 will attempt to map macroscale fluxes in the water table position, the EM38 will attempt to map the soil moisture deficit, and the seismic profile will show the depth of soil and drift. This 'go anywhere', rapid mapping facility will attempt to map hydrological processes in 4 dimensions in a non- intrusive and extensive manner. Whilst this paper will reflect only the experimental design and some early results, it is hoped that the Green Machine will play an active role in the future of hydrogeophysical research.

  19. Iopamidol as a responsive MRI-chemical exchange saturation transfer contrast agent for pH mapping of kidneys: In vivo studies in mice at 7 T.

    PubMed

    Longo, Dario Livio; Dastrù, Walter; Digilio, Giuseppe; Keupp, Jochen; Langereis, Sander; Lanzardo, Stefania; Prestigio, Simone; Steinbach, Oliver; Terreno, Enzo; Uggeri, Fulvio; Aime, Silvio

    2011-01-01

    Iopamidol (Isovue®-Bracco Diagnostic Inc.) is a clinically approved X-Ray contrast agent used in the last 30 years for a wide variety of diagnostic applications with a very good clinical acceptance. Iopamidol contains two types of amide functionalities that can be exploited for the generation of chemical exchange saturation transfer effect. The exchange rate of the two amide proton pools is markedly pH-dependent. Thus, a ratiometric method for pH assessment has been set-up based on the comparison of the saturation transfer effects induced by selective irradiation of the two resonances. This ratiometric approach allows to rule out the concentration effect of the contrast agent and provides accurate pH measurements in the 5.5-7.4 range. Upon injection of Iopamidol into healthy mice, it has been possible to acquire pH maps of kidney regions. Furthermore, it has been also shown that the proposed method is able to report about pH-changes induced in control mice fed with acidified or basified water for a period of a week before image acquisition.

  20. 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…

  1. The association between intra- and juxta-cortical pathology and cognitive impairment in multiple sclerosis by quantitative T2* mapping at 7 T MRI.

    PubMed

    Louapre, Céline; Govindarajan, Sindhuja T; Giannì, Costanza; Madigan, Nancy; Nielsen, A Scott; Sloane, Jacob A; Kinkel, Revere P; Mainero, Caterina

    2016-01-01

    Using quantitative T2* at 7 Tesla (T) magnetic resonance imaging, we investigated whether impairment in selective cognitive functions in multiple sclerosis (MS) can be explained by pathology in specific areas and/or layers of the cortex. Thirty-one MS patients underwent neuropsychological evaluation, acquisition of 7 T multi-echo T2* gradient-echo sequences, and 3 T anatomical images for cortical surfaces reconstruction. Seventeen age-matched healthy subjects served as controls. Cortical T2* maps were sampled at various depths throughout the cortex and juxtacortex. Relation between T2*, neuropsychological scores and a cognitive index (CI), calculated from a principal component analysis on the whole battery, was tested by a general linear model. Cognitive impairment correlated with T2* increase, independently from white matter lesions and cortical thickness, in cortical areas highly relevant for cognition belonging to the default-mode network (p < 0.05 corrected). Dysfunction in different cognitive functions correlated with longer T2* in selective cortical regions, most of which showed longer T2* relative to controls. For most tests, this association was strongest in deeper cortical layers. Executive dysfunction, however, was mainly related with pathology in juxtameningeal cortex. T2* explained up to 20% of the variance of the CI, independently of conventional imaging metrics (adjusted-R(2): 52-67%, p < 5.10(- 4)). Location of pathology across the cortical width and mantle showed selective correlation with impairment in differing cognitive domains. These findings may guide studies at lower field strength designed to develop surrogate markers of cognitive impairment in MS.

  2. Intracardiac Vortex Dynamics by High-Frame-Rate Doppler Vortography-In Vivo Comparison With Vector Flow Mapping and 4-D Flow MRI.

    PubMed

    Faurie, Julia; Baudet, Mathilde; Assi, Kondo Claude; Auger, Dominique; Gilbert, Guillaume; Tournoux, Francois; Garcia, Damien

    2017-02-01

    Recent studies have suggested that intracardiac vortex flow imaging could be of clinical interest to early diagnose the diastolic heart function. Doppler vortography has been introduced as a simple color Doppler method to detect and quantify intraventricular vortices. This method is able to locate a vortex core based on the recognition of an antisymmetric pattern in the Doppler velocity field. Because the heart is a fast-moving organ, high frame rates are needed to decipher the whole blood vortex dynamics during diastole. In this paper, we adapted the vortography method to high-frame-rate echocardiography using circular waves. Time-resolved Doppler vortography was first validated in vitro in an ideal forced vortex. We observed a strong correlation between the core vorticity determined by high-frame-rate vortography and the ground-truth vorticity. Vortography was also tested in vivo in ten healthy volunteers using high-frame-rate duplex ultrasonography. The main vortex that forms during left ventricular filling was tracked during two-three successive cardiac cycles, and its core vorticity was determined at a sampling rate up to 80 duplex images per heartbeat. Three echocardiographic apical views were evaluated. Vortography-derived vorticities were compared with those returned by the 2-D vector flow mapping approach. Comparison with 4-D flow magnetic resonance imaging was also performed in four of the ten volunteers. Strong intermethod agreements were observed when determining the peak vorticity during early filling. It is concluded that high-frame-rate Doppler vortography can accurately investigate the diastolic vortex dynamics.

  3. Linking MRI Postprocessing with Magnetic Source Imaging in MRI-negative Epilepsy

    PubMed Central

    Wang, Zhong I.; Alexopoulos, Andreas V.; Jones, Stephen E.; Najm, Imad M.; Ristic, Aleksandar; Wong, Chong; Prayson, Richard; Schneider, Felix; Kakisaka, Yosuke; Wang, Shuang; Bingaman, William; Gonzalez-Martinez, Jorge A.; Burgess, Richard C.

    2015-01-01

    Objective MRI-negative (MRI–) pharmacoresistant focal epilepsy (PFE) patients are most challenging for epilepsy surgical management. This study utilizes a voxel-based MRI postprocessing technique, implemented using a morphometric analysis program (MAP), aiming to facilitate detection of subtle focal cortical dysplasia (FCD) in MRI– patients. Furthermore, the study examines the concordance between MAP-identified regions and localization from magnetic source imaging (MSI). Methods Included in this retrospective study were 25 MRI– surgical patients. MAP was performed on T1-weighted MRI, with comparison to a normal database. The pertinence of MAP+ areas was confirmed by MSI, surgical outcome and pathology. Analyses of MAP and MSI were performed blindly from patients' clinical information and independently from each other. Results The detection rate of subtle changes by MAP was 48% (12/25). Once MAP+ areas were resected, patients were more likely to be seizure-free (p = 0.02). There were no false positives in the 25 age-matched normal controls. Seven patients had a concordant MSI correlate. Patients in whom a concordant area was identified by both MAP and MSI had a significantly higher chance of achieving a seizure-free outcome following complete resection of this area (p = 0.008). In the 9 resected MAP+ areas, pathology revealed FCD type IA in 7 and type IIB in 2. Interpretation MAP shows promise in identifying subtle FCD abnormalities and increasing the diagnostic yield of conventional MRI visual analysis in presurgical evaluation of PFE. Concordant MRI postprocessing and MSI analyses may lead to the noninvasive identification of a structurally and electrically abnormal subtle lesion that can be surgically targeted. PMID:24777960

  4. Mutation analysis in nephronophthisis using a combined approach of homozygosity mapping, CEL I endonuclease cleavage, and direct sequencing.

    PubMed

    Otto, Edgar A; Helou, Juliana; Allen, Susan J; O'Toole, John F; Wise, Eric L; Ashraf, Shazia; Attanasio, Massimo; Zhou, Weibin; Wolf, Matthias T F; Hildebrandt, Friedhelm

    2008-03-01

    Nephronophthisis (NPHP), an autosomal recessive kidney disease, is the most frequent genetic cause of chronic renal failure in the first three decades of life. Mutations in eight genes (NPHP1-8) have been identified. We here describe a combined approach for mutation screening of NPHP1, NPHP2, NPHP3, NPHP4, and NPHP5 in a worldwide cohort of 470 unrelated patients with NPHP. First, homozygous NPHP1 deletions were detected in 97 patients (21%) by multiplex PCR. Second, 25 patients with infantile NPHP were screened for mutations in inversin (NPHP2/INVS). We detected a novel compound heterozygous frameshift mutation (p.[Q485fs]+[R687fs]), and a homozygous nonsense mutation (p.R899X). Third, 37 patients presenting with NPHP and retinitis pigmentosa (Senior-Løken syndrome [SLS]) were screened for NPHP5/IQCB1 mutations by direct sequencing. We discovered five different (three novel) homozygous premature termination codon (PTC) mutations (p.F142fsX; p.R461X; p.R489X; p.W444X; and c.488-1G>A). The remaining 366 patients were further investigated for mutations in NPHP1, NPHP3, and NPHP4. We applied a "homozygosity only" strategy and typed three highly polymorphic microsatellite markers at the respective loci. A total of 32, eight, and 14 patients showed homozygosity, and were screened by heteroduplex crude celery extract (CEL I) endonuclease digests. The sensitivity of CEL I was established as 92%, as it detected 73 out of 79 different known mutations simply on agarose gels. A total of 10 novel PTC mutations were found in NPHP1 (p.P186fs, p.R347X, p.V492fs, p.Y509X, and c.1884+1G>A), in NPHP3 (c.3812+2T>C and p.R1259X), and in NPHP4 (p.R59X, p.T1004fs, and p.V1091fs). The combined homozygosity mapping and CEL I endonuclease mutation analysis approach allowed us to identify rare mutations in a large cohort of patients at low cost.

  5. Fusing DTI and fMRI data: a survey of methods and applications.

    PubMed

    Zhu, Dajiang; Zhang, Tuo; Jiang, Xi; Hu, Xintao; Chen, Hanbo; Yang, Ning; Lv, Jinglei; Han, Junwei; Guo, Lei; Liu, Tianming

    2014-11-15

    The relationship between brain structure and function has been one of the centers of research in neuroimaging for decades. In recent years, diffusion tensor imaging (DTI) and functional magnetic resonance imaging (fMRI) techniques have been widely available and popular in cognitive and clinical neurosciences for examining the brain's white matter (WM) micro-structures and gray matter (GM) functions, respectively. Given the intrinsic integration of WM/GM and the complementary information embedded in DTI/fMRI data, it is natural and well-justified to combine these two neuroimaging modalities together to investigate brain structure and function and their relationships simultaneously. In the past decade, there have been remarkable achievements of DTI/fMRI fusion methods and applications in neuroimaging and human brain mapping community. This survey paper aims to review recent advancements on methodologies and applications in incorporating multimodal DTI and fMRI data, and offer our perspectives on future research directions. We envision that effective fusion of DTI/fMRI techniques will play increasingly important roles in neuroimaging and brain sciences in the years to come.

  6. 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

  7. 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

  8. Image quality transfer and applications in diffusion MRI.

    PubMed

    Alexander, Daniel C; Zikic, Darko; Ghosh, Aurobrata; Tanno, Ryutaro; Wottschel, Viktor; Zhang, Jiaying; Kaden, Enrico; Dyrby, Tim B; Sotiropoulos, Stamatios N; Zhang, Hui; Criminisi, Antonio

    2017-03-03

    This paper introduces a new computational imaging technique called image quality transfer (IQT). IQT uses machine learning to transfer the rich information available from one-off experimental medical imaging devices to the abundant but lower-quality data from routine acquisitions. The procedure uses matched pairs to learn mappings from low-quality to corresponding high-quality images. Once learned, these mappings then augment unseen low quality images, for example by enhancing image resolution or information content. Here, we demonstrate IQT using a simple patch-regression implementation and the uniquely rich diffusion MRI data set from the human connectome project (HCP). Results highlight potential benefits of IQT in both brain connectivity mapping and microstructure imaging. In brain connectivity mapping, IQT reveals, from standard data sets, thin connection pathways that tractography normally requires specialised data to reconstruct. In microstructure imaging, IQT shows potential in estimating, from standard "single-shell" data (one non-zero b-value), maps of microstructural parameters that normally require specialised multi-shell data. Further experiments show strong generalisability, highlighting IQT's benefits even when the training set does not directly represent the application domain. The concept extends naturally to many other imaging modalities and reconstruction problems.

  9. Absolute Temperature Monitoring Using RF Radiometry in the MRI Scanner

    PubMed Central

    El-Sharkawy, AbdEl-Monem M.; Sotiriadis, Paul P.; Bottomley, Paul A.; Atalar, Ergin

    2007-01-01

    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

  10. Visualizing electromagnetic fields in metals by MRI

    NASA Astrophysics Data System (ADS)

    Chandrashekar, Chandrika Sefcikova; Shellikeri, Annadanesh; Chandrashekar, S.; Taylor, Erika A.; Taylor, Deanne M.

    2017-02-01

    Based upon Maxwell's equations, it has long been established that oscillating electromagnetic (EM) fields incident upon a metal surface, decay exponentially inside the conductor, leading to a virtual absence of EM fields at sufficient depths. Magnetic resonance imaging (MRI) utilizes radiofrequency (r.f.) EM fields to produce images. Here we present a visualization of a virtual EM vacuum inside a bulk metal strip by MRI, amongst several findings. At its simplest, an MRI image is an intensity map of density variations across voxels (pixels) of identical size (=Δ x Δ y Δ z ). By contrast in bulk metal MRI, we uncover that despite uniform density, intensity variations arise from differing effective elemental volumes (voxels) from different parts of the bulk metal. Further, we furnish chemical shift imaging (CSI) results that discriminate different faces (surfaces) of a metal block according to their distinct nuclear magnetic resonance (NMR) chemical shifts, which holds much promise for monitoring surface chemical reactions noninvasively. Bulk metals are ubiquitous, and MRI is a premier noninvasive diagnostic tool. Combining the two, the emerging field of bulk metal MRI can be expected to grow in importance. The findings here may impact further development of bulk metal MRI and CSI.

  11. Sinus MRI scan

    MedlinePlus

    ... sinuses. The test is noninvasive. MRI uses powerful magnets and radio waves instead of radiation. Signals from ... in the eyes. Because the MRI contains a magnet, metal-containing objects such as pens, pocketknives, and ...

  12. Arm MRI scan

    MedlinePlus

    ... arm MRI (magnetic resonance imaging) scan uses strong magnets to create pictures of the upper and lower ... in your eyes) Because the MRI contains strong magnets, metal objects are not allowed into the room ...

  13. MRI Safety during Pregnancy

    MedlinePlus

    ... 20 to 40 minutes. top of page Contrast material For some MRI exams, a contrast material called gadolinium will need to be injected into a vein in the arm. While contrast material sometimes improves the MRI images, during pregnancy the ...

  14. 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

  15. 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

  16. Cyclic generalized projection MRI.

    PubMed

    Sarty, Gordon E

    2015-04-01

    Progress in the development of portable MRI hinges on the ability to use lightweight magnets that have non-uniform magnetic fields. An image encoding method and mathematical procedure for recovering the image from the NMR signal from non-uniform magnets with closed isomagnetic contours is given. Individual frequencies in an NMR signal from an object in a non-uniform magnetic field give rise to integrals of the object along contours of constant magnetic field: generalized projections. With closed isomagnetic field contours a simple, cyclic, direct reconstruction of the image from the generalized projections is possible when the magnet and RF transmit coil are held fixed relative to the imaged object while the RF receive coil moves. Numerical simulations, using the Shepp and Logan mathematical phantom, were completed to show that the mathematical method works and to illustrate numerical limitations. The method is numerically verified and exact reconstruction demonstrated for discrete mathematical image phantoms. Correct knowledge of the RF receive field is necessary or severe image distortions will result. The cyclic mathematical reconstruction method presented here will be useful for portable MRI schemes that use non-uniform magnets with closed isomagnetic contours along with mechanically or electronically moving the RF receive coils.

  17. 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,…

  18. Modelling passive diastolic mechanics with quantitative MRI of cardiac structure and function.

    PubMed

    Wang, Vicky Y; Lam, H I; Ennis, Daniel B; Cowan, Brett R; Young, Alistair A; Nash, Martyn P

    2009-10-01

    The majority of patients with clinically diagnosed heart failure have normal systolic pump function and are commonly categorized as suffering from diastolic heart failure. The left ventricle (LV) remodels its structure and function to adapt to pathophysiological changes in geometry and loading conditions, which in turn can alter the passive ventricular mechanics. In order to better understand passive ventricular mechanics, a LV finite element (FE) model was customized to geometric data segmented from in vivo tagged magnetic resonance images (MRI) data and myofibre orientation derived from ex vivo diffusion tensor MRI (DTMRI) of a canine heart using nonlinear finite element fitting techniques. MRI tissue tagging enables quantitative evaluation of cardiac mechanical function with high spatial and temporal resolution, whilst the direction of maximum water diffusion in each voxel of a DTMRI directly corresponds to the local myocardial fibre orientation. Due to differences in myocardial geometry between in vivo and ex vivo imaging, myofibre orientations were mapped into the geometric FE model using host mesh fitting (a free form deformation technique). Pressure recordings, temporally synchronized to the tagging data, were used as the loading constraints to simulate the LV deformation during diastole. Simulation of diastolic LV mechanics allowed us to estimate the stiffness of the passive LV myocardium based on kinematic data obtained from tagged MRI. Integrated physiological modelling of this kind will allow more insight into mechanics of the LV on an individualized basis, thereby improving our understanding of the underlying structural basis of mechanical dysfunction under pathological conditions.

  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. 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.

  1. Construction of a transcription map of a 300 kb region around the human G6PD locus by direct cDNA selection.

    PubMed

    Sedlacek, Z; Korn, B; Konecki, D S; Siebenhaar, R; Coy, J F; Kioschis, P; Poustka, A

    1993-11-01

    A transcription map covering a 300 kb region around the G6PD gene in the human Xq28 region was constructed by the direct cDNA selection method and the analysis of the resulting region-specific enriched cDNA sublibrary. Seven new genes and two loci of endogenous retrovirus HERV-K were identified. The distribution of the genes across the region is strongly non-uniform and follows the non-uniform distribution of GpG islands in the area. While one of the novel genes was found to be highly homologous to bovine smg p25A GDP-dissociation inhibitor, the remaining genes did not detect any homology to known genes. The analysis of region-specific cDNA sublibraries represents a simple, rapid and efficient tool for the generation of a regional transcription map.

  2. 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

  3. 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.

  4. Current status of magnetic resonance imaging (MRI) and ultrasonography fusion software platforms for guidance of prostate biopsies.

    PubMed

    Logan, Jennifer K; Rais-Bahrami, Soroush; Turkbey, Baris; Gomella, Andrew; Amalou, Hayet; Choyke, Peter L; Wood, Bradford J; Pinto, Peter A

    2014-11-01

    Prostate MRI is currently the best diagnostic imaging method for detecting PCa. Magnetic resonance imaging (MRI)/ultrasonography (US) fusion allows the sensitivity and specificity of MRI to be combined with the real-time capabilities of transrectal ultrasonography (TRUS). Multiple approaches and techniques exist for MRI/US fusion and include direct 'in bore' MRI biopsies, cognitive fusion, and MRI/US fusion via software-based image coregistration platforms.

  5. Mapping directionality specific volume changes using tensor based morphometry: An application to the study of gyrogenesis and lateralization of the human fetal brain

    PubMed Central

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

    2013-01-01

    Tensor based morphometry (TBM) is a powerful approach to analyze local structural changes in brain anatomy. However, conventional scalar TBM methods do not completely capture all direction specific volume changes required to model complex changes such as those during brain growth. In this paper, we describe novel TBM descriptors for studying direction-specific changes in a subject population which can be used in conjunction with scalar TBM to analyze local patterns in directionality of volume change during brain development. We also extend the methodology to provide a new approach to mapping directional asymmetry in deformation tensors associated with the emergence of structural asymmetry in the developing brain. We illustrate the use of these methods by studying developmental patterns in the human fetal brain, in vivo. Results show that fetal brain development exhibits a distinct spatial pattern of anisotropic growth. The most significant changes in the directionality of growth occurs in the cortical plate at major sulci. Our analysis also detected directional growth asymmetry in the peri-sylvian region and the medial frontal lobe of the fetal brain. PMID:22503938

  6. Mapping directionality specific volume changes using tensor based morphometry: an application to the study of gyrogenesis and lateralization of the human fetal brain.

    PubMed

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

    2012-11-01

    Tensor based morphometry (TBM) is a powerful approach to analyze local structural changes in brain anatomy. However, conventional scalar TBM methods do not completely capture all direction specific volume changes required to model complex changes such as those during brain growth. In this paper, we describe novel TBM descriptors for studying direction-specific changes in a subject population which can be used in conjunction with scalar TBM to analyze local patterns in directionality of volume change during brain development. We also extend the methodology to provide a new approach to mapping directional asymmetry in deformation tensors associated with the emergence of structural asymmetry in the developing brain. We illustrate the use of these methods by studying developmental patterns in the human fetal brain, in vivo. Results show that fetal brain development exhibits a distinct spatial pattern of anisotropic growth. The most significant changes in the directionality of growth occur in the cortical plate at major sulci. Our analysis also detected directional growth asymmetry in the peri-Sylvian region and the medial frontal lobe of the fetal brain.

  7. Current Status of MRI and Ultrasound Fusion Software Platforms for Guidance of Prostate Biopsies

    PubMed Central

    Logan, Jennifer K; Rais-Bahrami, Soroush; Turkbey, Baris; Gomella, Andrew; Amalou, Hayet; Choyke, Peter L; Wood, Bradford J; Pinto, Peter A

    2015-01-01

    • Prostate MRI is currently the best diagnostic imaging method for detecting prostate cancer • Magnetic Resonance Imaging-Ultrasound (MRI/US) fusion allows the sensitivity and specificity of MRI to be combined with real time capabilities of transrectal ultrasound (TRUS). • Multiple approaches and techniques exist for MRI/US fusion and include (1) direct “in bore” MR biopsies, (2) cognitive fusion, and (3) MRI/US fusion via software-based image co-registration platforms. PMID:24298917

  8. Direct Georeferencing on Small Unmanned Aerial Platforms for Improved Reliability and Accuracy of Mapping Without the Need for Ground Control Points

    NASA Astrophysics Data System (ADS)

    Mian, O.; Lutes, J.; Lipa, G.; Hutton, J. J.; Gavelle, E.; Borghini, S.

    2015-08-01

    This paper presents results from a Direct Mapping Solution (DMS) comprised of an Applanix APX-15 UAV GNSS-Inertial system integrated with a Sony a7R camera to produce highly accurate ortho-rectified imagery without Ground Control Points on a Microdrones md4-1000 platform. A 55 millimeter Nikkor f/1.8 lens was mounted on the Sony a7R and the camera was then focused and calibrated terrestrially using the Applanix camera calibration facility, and then integrated with the APX-15 UAV GNSS-Inertial system using a custom mount specifically designed for UAV applications. In July 2015, Applanix and Avyon carried out a test flight of this system. The goal of the test flight was to assess the performance of DMS APX-15 UAV direct georeferencing system on the md4-1000. The area mapped during the test was a 250 x 300 meter block in a rural setting in Ontario, Canada. Several ground control points are distributed within the test area. The test included 8 North-South lines and 1 cross strip flown at 80 meters AGL, resulting in a ~1 centimeter Ground Sample Distance (GSD). Map products were generated from the test flight using Direct Georeferencing, and then compared for accuracy against the known positions of ground control points in the test area. The GNSS-Inertial data collected by the APX-15 UAV was post-processed in Single Base mode, using a base station located in the project area via POSPac UAV. The base-station's position was precisely determined by processing a 12-hour session using the CSRS-PPP Post Processing service. The ground control points were surveyed in using differential GNSS post-processing techniques with respect to the base-station.

  9. Detection of Brain Reorganization in Pediatric Multiple Sclerosis Using Functional MRI

    DTIC Science & Technology

    2015-10-01

    accomplish this, we apply comparative assessments of fMRI mappings of language, memory , and motor function, and performance on clinical neurocognitive...community at a target rate of 13 volunteers per quarter period; acquire fMRI data for language, memory , and visual-motor functions (months 3-12). c...consensus fMRI activation maps for language, memory , and visual-motor tasks (months 8-12). f) Subtask 1f. Prepare publication to disseminate our

  10. 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.

  11. Biochemical mapping of interactions within the intraflagellar transport (IFT) B core complex: IFT52 binds directly to four other IFT-B subunits.

    PubMed

    Taschner, Michael; Bhogaraju, Sagar; Vetter, Melanie; Morawetz, Michaela; Lorentzen, Esben

    2011-07-29

    Cilia and flagella are complex structures emanating from the surface of most eukaroytic cells and serve important functions including motility, signaling, and sensory reception. A process called intraflagellar transport (IFT) is of central importance to ciliary assembly and maintenance. The IFT complex is required for this transport and consists of two distinct multisubunit subcomplexes, IFT-A and IFT-B. Despite the importance of the IFT complex, little is known about its overall architecture. This paper presents a biochemical dissection of the molecular interactions within the IFT-B core complex. Two stable subcomplexes consisting of IFT88/70/52/46 and IFT81/74/27/25 were recombinantly co-expressed and purified. We identify a novel interaction between IFT70/52 and map the interaction domains between IFT52 and the other subunits within the IFT88/70/52/46 complex. Additionally, we show that IFT52 binds directly to the IFT81/74/27/25 complex, indicating that it could mediate the interaction between the two subcomplexes. Our data lead to an improved architectural map for the IFT-B core complex with new interactions as well as domain resolution mapping for several subunits.

  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. Dynamic three-dimensional phase-contrast technique in MRI: application to complex flow analysis around the artificial heart valve

    NASA Astrophysics Data System (ADS)

    Kim, Soo Jeong; Lee, Dong Hyuk; Song, Inchang; Kim, Nam Gook; Park, Jae-Hyeung; Kim, JongHyo; Han, Man Chung; Min, Byong Goo

    1998-07-01

    Phase-contrast (PC) method of magnetic resonance imaging (MRI) has bee used for quantitative measurements of flow velocity and volume flow rate. It is a noninvasive technique which provides an accurate two-dimensional velocity image. Moreover, Phase Contrast Cine magnetic resonance imaging combines the flow dependent contrast of PC-MRI with the ability of cardiac cine imaging to produce images throughout the cardiac cycle. However, the accuracy of the data acquired from the single through-plane velocity encoding can be reduced by the effect of flow direction, because in many practical cases flow directions are not uniform throughout the whole region of interest. In this study, we present dynamic three-dimensional velocity vector mapping method using PC-MRI which can visualize the complex flow pattern through 3D volume rendered images displayed dynamically. The direction of velocity mapping can be selected along any three orthogonal axes. By vector summation, the three maps can be combined to form a velocity vector map that determines the velocity regardless of the flow direction. At the same time, Cine method is used to observe the dynamic change of flow. We performed a phantom study to evaluate the accuracy of the suggested PC-MRI in continuous and pulsatile flow measurement. Pulsatile flow wave form is generated by the ventricular assistant device (VAD), HEMO-PULSA (Biomedlab, Seoul, Korea). We varied flow velocity, pulsatile flow wave form, and pulsing rate. The PC-MRI-derived velocities were compared with Doppler-derived results. The velocities of the two measurements showed a significant linear correlation. Dynamic three-dimensional velocity vector mapping was carried out for two cases. First, we applied to the flow analysis around the artificial heart valve in a flat phantom. We could observe the flow pattern around the valve through the 3-dimensional cine image. Next, it is applied to the complex flow inside the polymer sac that is used as ventricle in

  14. 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

  15. EEG/functional MRI in epilepsy: The Queen Square Experience.

    PubMed

    Hamandi, Khalid; Salek-Haddadi, Afraim; Fish, David R; Lemieux, Louis

    2004-01-01

    The recording of EEG during functional MRI scanning (EEG/fMRI) has opened up new dimensions in brain research. The simultaneous recording of EEG activity and its temparospatial haemodynamic correlates is a powerful tool in the non-invasive mapping of normal and pathological brain function. The technological constraints imposed by having a conductor (the EEG) within the magnetic environment of the MRI scanner have been sufficiently overcome for high quality EEG recording during MRI. The initial applications of EEG/fMRI were in the study of epileptiform discharges in epilepsy. This has been rapidly followed by studies of normal EEG rhythms and evoked response in healthy subjects. The ability to map brain areas involved in the generation of epileptiform discharges recorded on the surface EEG has been shown using EEG/fMRI in patients with epilepsy. This has potential clinical applications in providing additional localizing information in the pre-surgical workup of epilepsy patients and in gaining a greater understanding of the neurobiology of interictal epileptiform discharges and epileptic seizures. In this review we address the issues in recording EEG during fMRI and review the application of EEG/fMRI in the study of patients with epilepsy at our centre.

  16. Reconstruction of Scattered Data in Fetal Diffusion MRI

    PubMed Central

    Oubel, Estanislao; Koob, Meriam; Studholme, Colin; Dietemann, Jean-Louis; Rousseau, François

    2012-01-01

    In this paper we present a method for reconstructing D-MRI data on regular grids from sparse data without assuming specific diffusion models. This is particularly important when studying the fetal brain in utero, since registration methods applied for movement and distortion correction produce scattered data in spatial and angular (gradient) domains. We propose the use of a groupwise registration method, and a dual spatio-angular interpolation by using radial basis functions (RBF). Experiments performed on adult data showed a high accuracy of the method when estimating diffusion images in unavailable directions. The application to fetal data showed an improvement in the quality of the sequences according to criteria based on fractional anisotropy (FA) maps, and differences in the tractography results. PMID:20879277

  17. 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

  18. 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

  19. 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.

  20. Direct mapping of spin and orbital entangled wave functions under interband spin-orbit coupling of giant Rashba spin-split surface states

    NASA Astrophysics Data System (ADS)

    Noguchi, Ryo; Kuroda, Kenta; Yaji, K.; Kobayashi, K.; Sakano, M.; Harasawa, A.; Kondo, Takeshi; Komori, F.; Shin, S.

    2017-01-01

    We use spin- and angle-resolved photoemission spectroscopy (SARPES) combined with a polarization-variable laser and investigate the spin-orbit coupling effect under interband hybridization of Rashba spin-split states for the surface alloys Bi/Ag(111) and Bi/Cu(111). In addition to the conventional band mapping of photoemission for Rashba spin splitting, the different orbital and spin parts of the surface wave function are directly imaged into energy-momentum space. It is unambiguously revealed that the interband spin-orbit coupling modifies the spin and orbital character of the Rashba surface states leading to the enriched spin-orbital entanglement and the pronounced momentum dependence of the spin polarization. The hybridization thus strongly deviates the spin and orbital characters from the standard Rashba model. The complex spin texture under interband spin-orbit hybridization proposed by first-principles calculation is experimentally unraveled by SARPES with a combination of p - and s -polarized light.

  1. 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.

  2. 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

  3. Functional MRI in children: clinical and research applications.

    PubMed

    Leach, James L; Holland, Scott K

    2010-01-01

    Functional MRI has become a critical research tool for evaluating brain function and developmental trajectories in children. Its clinical use in children is becoming more common. This presentation will review the basic underlying physiologic and technical aspects of fMRI, review research applications that have direct clinical relevance, and outline the current clinical uses of this technology.

  4. 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

  5. Emerging MRI methods in rheumatoid arthritis.

    PubMed

    Borrero, Camilo G; Mountz, James M; Mountz, John D

    2011-02-01

    New MRI techniques have been developed to assess not only the static anatomy of synovial hyperplasia, bone changes and cartilage degradation in patients with rheumatoid arthritis (RA), but also the activity of the physiological events that cause these changes. This enables an estimation of the rate of change in the synovium, bone and cartilage as a result of disease activity or in response to therapy. Typical MRI signs of RA in the pre-erosive phase include synovitis, bone marrow edema and subchondral cyst formation. Synovitis can be assessed by T2-weighted imaging, dynamic contrast-enhanced MRI or diffusion tensor imaging. Bone marrow edema can be detected on fluid-sensitive sequences such as short-tau inversion recovery or T2-weighted fast-spin echo sequences. Detection of small bone erosions in the early erosive phase using T1-weighted MRI has sensitivity comparable to CT. Numerous MRI techniques have been developed for quantitative assessment of potentially pathologic changes in cartilage composition that occur before frank morphologic changes. In this Review, we summarize the advances and new directions in the field of MRI, with an emphasis on their current state of development and application in RA.

  6. 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.

  7. 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

  8. Multiresolution field map estimation using golden section search for water-fat separation.

    PubMed

    Lu, Wenmiao; Hargreaves, Brian A

    2008-07-01

    Many diagnostic MRI sequences demand reliable and uniform fat suppression. Multipoint water-fat separation methods, which are based on chemical-shift induced phase differences, have shown great success in the presence of field inhomogeneities. This work presents a computationally efficient and robust field map estimation method. The method begins with subsampling image data into a multiresolution image pyramidal structure, and then utilizes a golden section search to directly locate possible field map values at the coarsest level of the pyramidal structure. The field map estimate is refined and propagated to increasingly finer resolutions in an efficient manner until the full-resolution field map is obtained for final water-fat separation. The proposed method is validated with multiecho sequences where long echo-spacings normally impose great challenges on reliable field map estimation.

  9. 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

  10. 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

  11. 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

    2016-09-07

    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

  12. 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

  13. [MRI of the pituitary gland: indications and results in gynaecology and in obstetrics].

    PubMed

    Bonneville, J-F; Bonneville, F; Cattin, F

    2005-03-01

    MRI is the sole radiological examination to be obtained if abnormal menses, galactorrhea or anovulation evokes the diagnosis of prolactinoma. Nevertheless, iatrogenic hyperprolactinemia or presence of big prolactin has to be ruled out before MRI is asked for. MRI of the pituitary gland must be technically optimal; analysis of the images has to be directed by clinical and biological data.

  14. Pharmacological fMRI--challenges in analysing drug-induced single-event BOLD responses.

    PubMed

    Pohlmann, Andreas; Barjat, Hervé; Tilling, Lorna C; James, Michael F

    2007-01-01

    The interest in BOLD contrast based phMRI is likely to increase in the coming years, but detecting a direct modulation of regional brain activity by drugs presents a challenging problem. Based on in-vivo MRI and simulations we highlight some of the issues in detecting especially small BOLD signals in rat phMRI experiments.

  15. 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.

  16. 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

  17. Mapping brain maturation and cognitive development during adolescence.

    PubMed

    Paus, Tomás

    2005-02-01

    Non-invasive mapping of brain structure and function with magnetic resonance imaging (MRI) has opened up unprecedented opportunities for studying the neural substrates underlying cognitive development. There is an emerging consensus of a continuous increase throughout adolescence in the volume of white matter, both global and local. There is less agreement on the meaning of asynchronous age-related decreases in the volume of grey matter in different cortical regions; these might equally represent loss ("pruning") or gain (intra-cortical myelination) of tissue. Functional MRI studies have so far focused mostly on executive functions, such as working memory and behavioural inhibition, with very few addressing questions regarding the maturation of social cognition. Future directions for research in this area are discussed in the context of processing biological motion and matching perceptions and actions.

  18. 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 ...

  19. MRI of the Breast

    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 ...

  20. MRI of the Prostate

    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 ...

  1. 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 ...

  2. Magnetic Resonance Imaging (MRI)

    MedlinePlus

    ... problems (in men)Path to improved healthIf your primary care doctor determines that you should have an MRI, ... may not apply to everyone. Talk to your family doctor to find out if this information applies to ...

  3. MRI of the Breast

    MedlinePlus

    ... of the breast uses a powerful magnetic field, radio waves and a computer to produce detailed pictures of ... scans, MRI does not utilize ionizing radiation. Instead, radio waves redirect alignment of hydrogen atoms that naturally exist ...

  4. Cervical MRI scan

    MedlinePlus

    ... magnetic resonance imaging) scan uses energy from strong magnets to create pictures of the part of the ... in your eyes) Because the MRI contains strong magnets, metal objects are not allowed into the room ...

  5. 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 ...

  6. 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 ...

  7. 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.

  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.; ...

    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.