Science.gov

Sample records for direct mri mapping

  1. Visual Mapping Using BOLD fMRI

    PubMed Central

    DeYoe, Edgar A.; Raut, Ryan V.

    2014-01-01

    Synopsis Functional magnetic resonance imaging (fMRI) is used clinically to map visual cortex prior to brain surgery or other invasive treatments in order to achieve an optimal balance between therapeutic effect and the avoidance of post-operative vision deficits. Clinically optimized stimuli, behavioral task, analysis and displays permit identification of cortical subregions supporting high acuity central vision that is critical for reading and other essential visual functions. A novel data display permits instant appreciation of the functional relationship between the pattern of fMRI brain activation and the pattern of vision loss and preservation within the patient’s field of view. Neurovascular uncoupling and its detection in visual cortex are key issues for the interpretation of fMRI results in patients with existing brain pathology. Emerging techniques such as resting state fMRI may facilitate the use of fMRI-based vision mapping with a broader range of patients. PMID:25441501

  2. Mapping of cerebral oxidative metabolism with MRI

    PubMed Central

    Mellon, Eric A.; Beesam, R. Shashank; Elliott, Mark A.; Reddy, Ravinder

    2010-01-01

    Using a T1ρ MRI based indirect detection method, we demonstrate the detection of cerebral oxidative metabolism and its modulation by administration of the mitochondrial uncoupling agent 2,4-dinitrophenol (DNP) in a large animal model with minimum utilization of gas. The study was performed by inhalation in swine during imaging on clinical MRI scanners. Metabolic changes in swine were determined by two methods. First, in a series of animals, increased metabolism caused by DNP injection was measured by exhaled gas analysis. The average whole-body metabolic increase in seven swine was 11.9%+/-2.5% per mg/kg, stable over three hours. Secondly, hemispheric brain measurements of oxygen consumption stimulated by DNP injection were made in five swine using T1ρ MRI following administration of gas. Metabolism was calculated from the change in the T1ρ weighted MRI signal due to H217O generated from inhalation before and after doubling of metabolism by DNP. These results were confirmed by direct oxygen-17 MR spectroscopy, a gold standard for in vivo H217O measurement. Overall, this work underscores the ability of indirect oxygen-17 imaging to detect oxygen metabolism in an animal model with a lung capacity comparable to the human with minimal utilization of expensive gas. Given the demonstrated high efficiency in use of and the proven feasibility of performing such measurements on standard clinical MRI scanners, this work enables the adaption of this technique for human studies dealing with a broad array of metabolic derangements. PMID:20547874

  3. 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

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

    PubMed Central

    Özcan, Alpay

    2013-01-01

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

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

    PubMed

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

    2010-09-21

    In recent years, neuronal current MRI (nc-MRI) was proposed as a new imaging method to directly map the magnetic field change caused by neuronal activity. Nc-MRI could offer improved spatial and temporal resolution compared to blood hemodynamics-based functional magnetic resonance imaging (fMRI). In this paper, with a finite current dipole as the model of dendrite or dendrite branch, we investigated the spatial distribution of the magnetic field generated by synchronously activated neurons to evaluate the possibility of nc-MRI. Our simulations imply that the existence of a dendrite branch may not only increase the strength of the neuronal magnetic field (NMF), but also raise the non-uniform and unsymmetry of the NMF; therefore, it can enhance the detectability of the neuronal current magnetic field by MRI directly. The results show that the signal phase shift is enlarged, but it is unstable and is still very small, <1 radian, while the magnitude signal may be strong enough for a typical MRI voxel to be detected. We suggest making further efforts to measure the magnitude signal which may induce a large effect in an nc-MRI experiment. PMID:20808026

  6. 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.

  7. Direct probability mapping of contaminants

    SciTech Connect

    Rautman, C.A.

    1993-09-17

    Exhaustive characterization of a contaminated site is a physical and practical impossibility. Descriptions of the nature, extent, and level of contamination, as well as decisions regarding proposed remediation activities, must be made in a state of uncertainty based upon limited physical sampling. Geostatistical simulation provides powerful tools for investigating contaminant levels, and in particular, for identifying and using the spatial interrelationships among a set of isolated sample values. This additional information can be used to assess the likelihood of encountering contamination at unsampled locations and to evaluate the risk associated with decisions to remediate or not to remediate specific regions within a site. Past operation of the DOE Feed Materials Production Center has contaminated a site near Fernald, Ohio, with natural uranium. Soil geochemical data have been collected as part of the Uranium-in-Soils Integrated Demonstration Project. These data have been used to construct a number of stochastic images of potential contamination for parcels approximately the size of a selective remediation unit. Each such image accurately reflects the actual measured sample values, and reproduces the univariate statistics and spatial character of the extant data. Post-processing of a large number of these equally likely, statistically similar images produces maps directly showing the probability of exceeding specified levels of contamination. Evaluation of the geostatistical simulations can yield maps representing the expected magnitude of the contamination for various regions and other information that may be important in determining a suitable remediation process or in sizing equipment to accomplish the restoration.

  8. 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.

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

    PubMed Central

    Özcan, Alpay

    2011-01-01

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

  10. Quantitative β mapping for calibrated fMRI.

    PubMed

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

    2016-02-01

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

  11. 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

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

    PubMed Central

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

    2014-01-01

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

  13. MRI mapping of cerebrovascular reactivity via gas inhalation challenges.

    PubMed

    Lu, Hanzhang; Liu, Peiying; Yezhuvath, Uma; Cheng, Yamei; Marshall, Olga; Ge, Yulin

    2014-01-01

    The brain is a spatially heterogeneous and temporally dynamic organ, with different regions requiring different amount of blood supply at different time. Therefore, the ability of the blood vessels to dilate or constrict, known as Cerebral-Vascular-Reactivity (CVR), represents an important domain of vascular function. An imaging marker representing this dynamic property will provide new information of cerebral vessels under normal and diseased conditions such as stroke, dementia, atherosclerosis, small vessel diseases, brain tumor, traumatic brain injury, and multiple sclerosis. In order to perform this type of measurement in humans, it is necessary to deliver a vasoactive stimulus such as CO2 and/or O2 gas mixture while quantitative brain magnetic resonance images (MRI) are being collected. In this work, we presented a MR compatible gas-delivery system and the associated protocol that allow the delivery of special gas mixtures (e.g., O2, CO2, N2, and their combinations) while the subject is lying inside the MRI scanner. This system is relatively simple, economical, and easy to use, and the experimental protocol allows accurate mapping of CVR in both healthy volunteers and patients with neurological disorders. This approach has the potential to be used in broad clinical applications and in better understanding of brain vascular pathophysiology. In the video, we demonstrate how to set up the system inside an MRI suite and how to perform a complete experiment on a human participant. PMID:25549106

  14. MRI Mapping of Cerebrovascular Reactivity via Gas Inhalation Challenges

    PubMed Central

    Lu, Hanzhang; Liu, Peiying; Yezhuvath, Uma; Cheng, Yamei; Marshall, Olga; Ge, Yulin

    2014-01-01

    The brain is a spatially heterogeneous and temporally dynamic organ, with different regions requiring different amount of blood supply at different time. Therefore, the ability of the blood vessels to dilate or constrict, known as Cerebral-Vascular-Reactivity (CVR), represents an important domain of vascular function. An imaging marker representing this dynamic property will provide new information of cerebral vessels under normal and diseased conditions such as stroke, dementia, atherosclerosis, small vessel diseases, brain tumor, traumatic brain injury, and multiple sclerosis. In order to perform this type of measurement in humans, it is necessary to deliver a vasoactive stimulus such as CO2 and/or O2 gas mixture while quantitative brain magnetic resonance images (MRI) are being collected. In this work, we presented a MR compatible gas-delivery system and the associated protocol that allow the delivery of special gas mixtures (e.g., O2, CO2, N2, and their combinations) while the subject is lying inside the MRI scanner. This system is relatively simple, economical, and easy to use, and the experimental protocol allows accurate mapping of CVR in both healthy volunteers and patients with neurological disorders. This approach has the potential to be used in broad clinical applications and in better understanding of brain vascular pathophysiology. In the video, we demonstrate how to set up the system inside an MRI suite and how to perform a complete experiment on a human participant. PMID:25549106

  15. Accelerating multidimensional NMR and MRI experiments using iterated maps

    NASA Astrophysics Data System (ADS)

    Barrett, Sean; Frey, Merideth; Sethna, Zachary; Manley, Gregory; Sengupta, Suvrajit; Zilm, Kurt; Loria, J. Patrick

    2014-03-01

    Techniques that accelerate data acquisition without sacrificing the advantages of fast Fourier transform (FFT) reconstruction could benefit a wide variety of magnetic resonance experiments. Here we discuss an approach for reconstructing multidimensional nuclear magnetic resonance (NMR) spectra and MR images from sparsely-sampled time domain data, by way of iterated maps. This method exploits the computational speed of the FFT algorithm and is done in a deterministic way, by reformulating any a priori knowledge or constraints into projections, and then iterating. In this paper we explain the motivation behind this approach, the formulation of the specific projections, the benefits of using a `QUasi-Even Sampling, plus jiTter' (QUEST) sampling schedule, and various methods for handling noise. Applying the iterated maps method to real 2D NMR and 3D MRI of solids data, we show that it is flexible and robust enough to handle large data sets with significant noise and artifacts.

  16. Accelerating multidimensional NMR and MRI experiments using iterated maps

    NASA Astrophysics Data System (ADS)

    Frey, Merideth A.; Sethna, Zachary M.; Manley, Gregory A.; Sengupta, Suvrajit; Zilm, Kurt W.; Loria, J. Patrick; Barrett, Sean E.

    2013-12-01

    Techniques that accelerate data acquisition without sacrificing the advantages of fast Fourier transform (FFT) reconstruction could benefit a wide variety of magnetic resonance experiments. Here we discuss an approach for reconstructing multidimensional nuclear magnetic resonance (NMR) spectra and MR images from sparsely-sampled time domain data, by way of iterated maps. This method exploits the computational speed of the FFT algorithm and is done in a deterministic way, by reformulating any a priori knowledge or constraints into projections, and then iterating. In this paper we explain the motivation behind this approach, the formulation of the specific projections, the benefits of using a ‘QUasi-Even Sampling, plus jiTter' (QUEST) sampling schedule, and various methods for handling noise. Applying the iterated maps method to real 2D NMR and 3D MRI of solids data, we show that it is flexible and robust enough to handle large data sets with significant noise and artifacts.

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

    SciTech Connect

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

    2012-05-01

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

  18. [Cardiac MRI: technology, clinical applications, and future directions].

    PubMed

    Pesenti-Rossi, D; Peyrou, J; Baron, N; Allouch, P; Aubert, S; Boueri, Z; Livarek, B

    2013-11-01

    The field of cardiovascular MRI has evolved rapidly over the past decade, feeding new applications across a broad spectrum of clinical and research areas. Advances in magnet hardware technology, and key developments such as segmented k-space acquisitions, advanced motion encoding techniques, ultra-rapid perfusion imaging and delayed myocardial enhancement imaging have all contributed to a revolution in how patients with ischemic and non-ischemic heart disease are diagnosed and treated. Actually, cardiac MRI is a widely accepted method as the "gold standard" for detection and characterization of many forms of cardiac diseases. The aim of this review is to present an overview of cardiac MRI technology, advances in clinical applications, and future directions. PMID:24035258

  19. Directly detected (55)Mn MRI: application to phantoms for human hyperpolarized (13)C MRI development.

    PubMed

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

    2014-12-01

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

  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. Uncertainty estimations for quantitative in vivo MRI T1 mapping

    NASA Astrophysics Data System (ADS)

    Polders, Daniel L.; Leemans, Alexander; Luijten, Peter R.; Hoogduin, Hans

    2012-11-01

    Mapping the longitudinal relaxation time (T1) of brain tissue is of great interest for both clinical research and MRI sequence development. For an unambiguous interpretation of in vivo variations in T1 images, it is important to understand the degree of variability that is associated with the quantitative T1 parameter. This paper presents a general framework for estimating the uncertainty in quantitative T1 mapping by combining a slice-shifted multi-slice inversion recovery EPI technique with the statistical wild-bootstrap approach. Both simulations and experimental analyses were performed to validate this novel approach and to evaluate the estimated T1 uncertainty in several brain regions across four healthy volunteers. By estimating the T1 uncertainty, it is shown that the variation in T1 within anatomic regions for similar tissue types is larger than the uncertainty in the measurement. This indicates that heterogeneity of the inspected tissue and/or partial volume effects can be the main determinants for the observed variability in the estimated T1 values. The proposed approach to estimate T1 and its uncertainty without the need for repeated measurements may also prove to be useful for calculating effect sizes that are deemed significant when comparing group differences.

  3. Uncertainty estimations for quantitative in vivo MRI T1 mapping.

    PubMed

    Polders, Daniel L; Leemans, Alexander; Luijten, Peter R; Hoogduin, Hans

    2012-11-01

    Mapping the longitudinal relaxation time (T(1)) of brain tissue is of great interest for both clinical research and MRI sequence development. For an unambiguous interpretation of in vivo variations in T(1) images, it is important to understand the degree of variability that is associated with the quantitative T(1) parameter. This paper presents a general framework for estimating the uncertainty in quantitative T(1) mapping by combining a slice-shifted multi-slice inversion recovery EPI technique with the statistical wild-bootstrap approach. Both simulations and experimental analyses were performed to validate this novel approach and to evaluate the estimated T(1) uncertainty in several brain regions across four healthy volunteers. By estimating the T(1) uncertainty, it is shown that the variation in T(1) within anatomic regions for similar tissue types is larger than the uncertainty in the measurement. This indicates that heterogeneity of the inspected tissue and/or partial volume effects can be the main determinants for the observed variability in the estimated T(1) values. The proposed approach to estimate T(1) and its uncertainty without the need for repeated measurements may also prove to be useful for calculating effect sizes that are deemed significant when comparing group differences. PMID:23041796

  4. Current and New Directions in MRI in Multiple Sclerosis

    PubMed Central

    Klawiter, Eric C.

    2013-01-01

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

  5. 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

  6. Vervet MRI Atlas and Label Map for Fully Automated Morphometric Analyses

    PubMed Central

    Maldjian, Joseph A.; Daunais, James B.; Friedman, David P.

    2016-01-01

    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

  7. Direct mapping of the UV surface plasmons.

    PubMed

    Gan, Qiaoqiang; Zhou, Liangcheng; Dierolf, Volkmar; Bartoli, Filbert J

    2009-05-01

    Researchers employed various well-developed concepts from conventional optics in designing novel plasmonic devices, which allow us to construct a framework to describe the propagation, diffraction, and interference of surface plasmon polaritons (SPPs) on a chip. Here we present what we believe to be the first direct mapping of the UV SPPs on an Al2O3/Al surface using a UV-compatible near-field scanning optical microscope system. UV SPP modes launched by one-dimensional slits or two-dimensional groove arrays and corresponding interference phenomenon were both observed, which may enrich the studies on subwavelength optics on a chip. PMID:19412260

  8. Foundations of MRI phase imaging and processing for Quantitative Susceptibility Mapping (QSM).

    PubMed

    Schweser, Ferdinand; Deistung, Andreas; Reichenbach, Jürgen R

    2016-03-01

    Quantitative Susceptibility Mapping (QSM) is a novel MRI based technique that relies on estimates of the magnetic field distribution in the tissue under examination. Several sophisticated data processing steps are required to extract the magnetic field distribution from raw MRI phase measurements. The objective of this review article is to provide a general overview and to discuss several underlying assumptions and limitations of the pre-processing steps that need to be applied to MRI phase data before the final field-to-source inversion can be performed. Beginning with the fundamental relation between MRI signal and tissue magnetic susceptibility this review covers the reconstruction of magnetic field maps from multi-channel phase images, background field correction, and provides an overview of state of the art QSM solution strategies. PMID:26702760

  9. Distortion correction in EPI at ultra-high-field MRI using PSF mapping with optimal combination of shift detection dimension.

    PubMed

    Oh, Se-Hong; Chung, Jun-Young; In, Myung-Ho; Zaitsev, Maxim; Kim, Young-Bo; Speck, Oliver; Cho, Zang-Hee

    2012-10-01

    Despite its wide use, echo-planar imaging (EPI) suffers from geometric distortions due to off-resonance effects, i.e., strong magnetic field inhomogeneity and susceptibility. This article reports a novel method for correcting the distortions observed in EPI acquired at ultra-high-field such as 7 T. Point spread function (PSF) mapping methods have been proposed for correcting the distortions in EPI. The PSF shift map can be derived either along the nondistorted or the distorted coordinates. Along the nondistorted coordinates more information about compressed areas is present but it is prone to PSF-ghosting artifacts induced by large k-space shift in PSF encoding direction. In contrast, shift maps along the distorted coordinates contain more information in stretched areas and are more robust against PSF-ghosting. In ultra-high-field MRI, an EPI contains both compressed and stretched regions depending on the B0 field inhomogeneity and local susceptibility. In this study, we present a new geometric distortion correction scheme, which selectively applies the shift map with more information content. We propose a PSF-ghost elimination method to generate an artifact-free pixel shift map along nondistorted coordinates. The proposed method can correct the effects of the local magnetic field inhomogeneity induced by the susceptibility effects along with the PSF-ghost artifact cancellation. We have experimentally demonstrated the advantages of the proposed method in EPI data acquisitions in phantom and human brain using 7-T MRI. PMID:22213517

  10. fMRI for mapping language networks in neurosurgical cases

    PubMed Central

    Gupta, Santosh S

    2014-01-01

    Evaluating language has been a long-standing application in functional magnetic resonance imaging (fMRI) studies, both in research and clinical circumstances, and still provides challenges. Localization of eloquent areas is important in neurosurgical cases, so that there is least possible damage to these areas during surgery, maintaining their function postoperatively, therefore providing good quality of life to the patient. Preoperative fMRI study is a non-invasive tool to localize the eloquent areas, including language, with other traditional methods generally used being invasive and at times perilous. In this article, we describe methods and various paradigms to study the language areas, in clinical neurosurgical cases, along with illustrations of cases from our institute. PMID:24851003

  11. Rapid Radiofrequency Field Mapping In Vivo Using Single-Shot STEAM MRI

    PubMed Central

    Helms, Gunther; Finsterbusch, Jürgen; Weiskopf, Nikolaus; Dechent, Peter

    2008-01-01

    Higher field strengths entail less homogeneous RF fields. This may influence quantitative MRI and MRS. A method for rapidly mapping the RF field in the human head with minimal distortion was developed on the basis of a single-shot stimulated echo acquisition mode (STEAM) sequence. The flip angle of the second RF pulse in the STEAM preparation was set to 60° and 100° instead of 90°, inducing a flip angle-dependent signal change. A quadratic approximation of this trigonometric signal dependence together with a calibration accounting for slice excitation-related bias allowed for directly determining the RF field from the two measurements only. RF maps down to the level of the medulla could be obtained in less than 1 min and registered to anatomical volumes by means of the T2-weighted STEAM images. Flip angles between 75% and 125% of the nominal value were measured in line with other methods. Magn Reson Med 60:739–743, 2008. © 2008 Wiley-Liss, Inc. PMID:18727090

  12. Comparing different stimulus configurations for population receptive field mapping in human fMRI

    PubMed Central

    Alvarez, Ivan; de Haas, Benjamin; Clark, Chris A.; Rees, Geraint; Schwarzkopf, D. Samuel

    2015-01-01

    Population receptive field (pRF) mapping is a widely used approach to measuring aggregate human visual receptive field properties by recording non-invasive signals using functional MRI. Despite growing interest, no study to date has systematically investigated the effects of different stimulus configurations on pRF estimates from human visual cortex. Here we compared the effects of three different stimulus configurations on a model-based approach to pRF estimation: size-invariant bars and eccentricity-scaled bars defined in Cartesian coordinates and traveling along the cardinal axes, and a novel simultaneous “wedge and ring” stimulus defined in polar coordinates, systematically covering polar and eccentricity axes. We found that the presence or absence of eccentricity scaling had a significant effect on goodness of fit and pRF size estimates. Further, variability in pRF size estimates was directly influenced by stimulus configuration, particularly for higher visual areas including V5/MT+. Finally, we compared eccentricity estimation between phase-encoded and model-based pRF approaches. We observed a tendency for more peripheral eccentricity estimates using phase-encoded methods, independent of stimulus size. We conclude that both eccentricity scaling and polar rather than Cartesian stimulus configuration are important considerations for optimal experimental design in pRF mapping. While all stimulus configurations produce adequate estimates, simultaneous wedge and ring stimulation produced higher fit reliability, with a significant advantage in reduced acquisition time. PMID:25750620

  13. Preoperative Sensorimotor Mapping in Brain Tumor Patients using Spontaneous Fluctuations in Neuronal Activity Imaged with fMRI: Initial Experience

    PubMed Central

    Zhang, Dongyang; Johnston, James M.; Fox, Michael D.; Leuthardt, Eric C.; Grubb, Robert L.; Chicoine, Michael R.; Smyth, Matthew D.; Snyder, Abraham Z.; Raichle, Marcus E.; Shimony, Joshua S.

    2009-01-01

    Objective To describe initial experience with resting state correlation mapping as a potential aid for presurgical planning of brain tumor resections. Methods/Technique Resting state blood oxygenation dependent (BOLD) fMRI was acquired in seventeen healthy young adults and four patients with brain tumors invading sensorimotor cortex. Conventional fMRI motor mapping (finger tapping protocol) was also performed in the patients. Intraoperatively, motor hand area was mapped using cortical stimulation. Results Robust and consistent delineation of sensorimotor cortex was obtained using the resting state BOLD data. Resting state functional mapping in patients showed localization to sensorimotor areas consistent with cortical stimulation mapping (CSM) and in all cases performed as well or better than task-based fMRI. Conclusions Resting state correlation mapping is a promising tool for reliable functional localization of eloquent cortex. This method compares well with “gold standard” CSM and offers several advantages in comparison to conventional motor mapping fMRI. PMID:19934999

  14. Quantitative mapping of chemical compositions with MRI using compressed sensing

    NASA Astrophysics Data System (ADS)

    von Harbou, Erik; Fabich, Hilary T.; Benning, Martin; Tayler, Alexander B.; Sederman, Andrew J.; Gladden, Lynn F.; Holland, Daniel J.

    2015-12-01

    In this work, a magnetic resonance (MR) imaging method for accelerating the acquisition time of two dimensional concentration maps of different chemical species in mixtures by the use of compressed sensing (CS) is presented. Whilst 2D-concentration maps with a high spatial resolution are prohibitively time-consuming to acquire using full k -space sampling techniques, CS enables the reconstruction of quantitative concentration maps from sub-sampled k -space data. First, the method was tested by reconstructing simulated data. Then, the CS algorithm was used to reconstruct concentration maps of binary mixtures of 1,4-dioxane and cyclooctane in different samples with a field-of-view of 22 mm and a spatial resolution of 344 μm × 344 μm . Spiral based trajectories were used as sampling schemes. For the data acquisition, eight scans with slightly different trajectories were applied resulting in a total acquisition time of about 8 min. In contrast, a conventional chemical shift imaging experiment at the same resolution would require about 17 h. To get quantitative results, a careful weighting of the regularisation parameter (via the L-curve approach) or contrast-enhancing Bregman iterations are applied for the reconstruction of the concentration maps. Both approaches yield relative errors of the concentration map of less than 2 mol-% without any calibration prior to the measurement. The accuracy of the reconstructed concentration maps deteriorates when the reconstruction model is biased by systematic errors such as large inhomogeneities in the static magnetic field. The presented method is a powerful tool for the fast acquisition of concentration maps that can provide valuable information for the investigation of many phenomena in chemical engineering applications.

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

    PubMed

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

    2016-09-01

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

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

    PubMed

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

    2016-08-15

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

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

    PubMed

    Song, Weiguo; Truong, Dennis Q; Bikson, Marom; Martin, John H

    2015-04-01

    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

  18. 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

  19. T2 distribution mapping profiles with phase-encode MRI

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

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

  20. Assessment of myocardial fibrosis with T1 mapping MRI.

    PubMed

    Everett, R J; Stirrat, C G; Semple, S I R; Newby, D E; Dweck, M R; Mirsadraee, S

    2016-08-01

    Myocardial fibrosis can arise from a range of pathological processes and its presence correlates with adverse clinical outcomes. Cardiac magnetic resonance (CMR) can provide a non-invasive assessment of cardiac structure, function, and tissue characteristics, which includes late gadolinium enhancement (LGE) techniques to identify focal irreversible replacement fibrosis with a high degree of accuracy and reproducibility. Importantly the presence of LGE is consistently associated with adverse outcomes in a range of common cardiac conditions; however, LGE techniques are qualitative and unable to detect diffuse myocardial fibrosis, which is an earlier form of fibrosis preceding replacement fibrosis that may be reversible. Novel T1 mapping techniques allow quantitative CMR assessment of diffuse myocardial fibrosis with the two most common measures being native T1 and extracellular volume (ECV) fraction. Native T1 differentiates normal from infarcted myocardium, is abnormal in hypertrophic cardiomyopathy, and may be particularly useful in the diagnosis of Anderson-Fabry disease and amyloidosis. ECV is a surrogate measure of the extracellular space and is equivalent to the myocardial volume of distribution of the gadolinium-based contrast medium. It is reproducible and correlates well with fibrosis on histology. ECV is abnormal in patients with cardiac failure and aortic stenosis, and is associated with functional impairment in these groups. T1 mapping techniques promise to allow earlier detection of disease, monitor disease progression, and inform prognosis; however, limitations remain. In particular, reference ranges are lacking for T1 mapping values as these are influenced by specific CMR techniques and magnetic field strength. In addition, there is significant overlap between T1 mapping values in healthy controls and most disease states, particularly using native T1, limiting the clinical application of these techniques at present. PMID:27005015

  1. 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

  2. Clinical feasibility of using mean apparent propagator (MAP) MRI to characterize brain tissue microstructure.

    PubMed

    Avram, Alexandru V; Sarlls, Joelle E; Barnett, Alan S; Özarslan, Evren; Thomas, Cibu; Irfanoglu, M Okan; Hutchinson, Elizabeth; Pierpaoli, Carlo; Basser, Peter J

    2016-02-15

    Diffusion tensor imaging (DTI) is the most widely used method for characterizing noninvasively structural and architectural features of brain tissues. However, the assumption of a Gaussian spin displacement distribution intrinsic to DTI weakens its ability to describe intricate tissue microanatomy. Consequently, the biological interpretation of microstructural parameters, such as fractional anisotropy or mean diffusivity, is often equivocal. We evaluate the clinical feasibility of assessing brain tissue microstructure with mean apparent propagator (MAP) MRI, a powerful analytical framework that efficiently measures the probability density function (PDF) of spin displacements and quantifies useful metrics of this PDF indicative of diffusion in complex microstructure (e.g., restrictions, multiple compartments). Rotation invariant and scalar parameters computed from the MAP show consistent variation across neuroanatomical brain regions and increased ability to differentiate tissues with distinct structural and architectural features compared with DTI-derived parameters. The return-to-origin probability (RTOP) appears to reflect cellularity and restrictions better than MD, while the non-Gaussianity (NG) measures diffusion heterogeneity by comprehensively quantifying the deviation between the spin displacement PDF and its Gaussian approximation. Both RTOP and NG can be decomposed in the local anatomical frame for reference determined by the orientation of the diffusion tensor and reveal additional information complementary to DTI. The propagator anisotropy (PA) shows high tissue contrast even in deep brain nuclei and cortical gray matter and is more uniform in white matter than the FA, which drops significantly in regions containing crossing fibers. Orientational profiles of the propagator computed analytically from the MAP MRI series coefficients allow separation of different fiber populations in regions of crossing white matter pathways, which in turn improves our

  3. 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

  4. Women's clitoris, vagina and cervix mapped on the sensory cortex: fMRI evidence

    PubMed Central

    Komisaruk, Barry R.; Wise, Nan; Frangos, Eleni; Liu, Wen-Ching; Allen, Kachina; Brody, Stuart

    2011-01-01

    Introduction The projection of vagina, uterine cervix, and nipple to the sensory cortex in humans has not been reported. Aims To map the sensory cortical fields of the clitoris, vagina, cervix and nipple, toward an elucidation of the neural systems underlying sexual response. Methods Using functional Magnetic Resonance Imaging (fMRI) we mapped sensory cortical responses to clitoral, vaginal, cervical, and nipple self-stimulation. For points of reference on the homunculus, we also mapped responses to the thumb and great toe (hallux) stimulation. Main Outcome Measures fMRI of brain regions activated by the various sensory stimuli. Results Clitoral, vaginal, and cervical self-stimulation activate differentiable sensory cortical regions, all clustered in the medial cortex (medial paracentral lobule). Nipple self-stimulation activated the genital sensory cortex (as well as the thoracic) region of the homuncular map. Conclusion The genital sensory cortex, identified in the classical Penfield homunculus based on electrical stimulation of the brain only in men, was confirmed for the first time in the literature by the present study in women, applying clitoral, vaginal, and cervical self-stimulation, and observing their regional brain responses using fMRI. Vaginal, clitoral, and cervical regions of activation were differentiable, consistent with innervation by different afferent nerves and different behavioral correlates. Activation of the genital sensory cortex by nipple self-stimulation was unexpected, but suggests a neurological basis for women’s reports of its erotogenic quality. PMID:21797981

  5. 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.

  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. PMID:25044035

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

    PubMed Central

    Fabri, Mara; Polonara, Gabriele

    2013-01-01

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

  8. 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. PMID:26296501

  9. Resting-State Blood Oxygen Level-Dependent Functional MRI: A Paradigm Shift in Preoperative Brain Mapping.

    PubMed

    Leuthardt, Eric C; Allen, Monica; Kamran, Mudassar; Hawasli, Ammar H; Snyder, Abraham Z; Hacker, Carl D; Mitchell, Timothy J; Shimony, Joshua S

    2015-01-01

    Currently, functional magnetic resonance imaging (fMRI) facilitates a preoperative awareness of an association of an eloquent region with a tumor. This information gives the neurosurgeon helpful information that can aid in creating a surgical strategy. Typically, task-based fMRI has been employed to preoperatively localize speech and motor function. Task-based fMRI depends on the patient's ability to comply with the task paradigm, which often is impaired in the setting of a brain tumor. This problem is overcome by using resting-state fMRI (rs-fMRI) to localize function. rs-fMRI measures spontaneous fluctuations in the blood oxygen level-dependent (BOLD) signal, representing the brain's functional organization. In a neurosurgical context, it allows noninvasive simultaneous assessment of multiple large-scale distributed networks. Compared with task-related fMRI, rs-fMRI provides more comprehensive information on the functional architecture of the brain and is applicable in settings where task-related fMRI may provide inadequate information or could not be performed. Taken together, rs-fMRI substantially expands the preoperative mapping capability in efficiency, effectiveness, and scope. In this article, a brief introduction into rs-fMRI processing methods is followed by a detailed discussion on the role rs-fMRI plays in presurgical planning. PMID:26784290

  10. 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

  11. Head direction maps remain stable despite grid map fragmentation

    PubMed Central

    Whitlock, Jonathan R.; Derdikman, Dori

    2012-01-01

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

  12. Mapping resting-state functional connectivity using perfusion MRI

    PubMed Central

    Chuang, Kai-Hsiang; van Gelderen, Peter; Merkle, Hellmut; Bodurka, Jerzy; Ikonomidou, Vasiliki N.; Koretsky, Alan P.; Duyn, Jeff H.; Talagala, S. Lalith

    2008-01-01

    Resting-state, low frequency (< 0.08 Hz) fluctuations of blood oxygenation level dependent (BOLD) magnetic resonance signal have been shown to exhibit high correlation among functionally connected regions. However, correlations of cerebral blood flow (CBF) fluctuations during the resting state have not been extensively studied. The main challenges of using arterial spin labeling perfusion magnetic resonance imaging to detect CBF fluctuations are low sensitivity, low temporal resolution, and contamination from BOLD. This work demonstrates CBF-based quantitative functional connectivity mapping by combining continuous arterial spin labeling (CASL) with a neck labeling coil and a multi-channel receiver coil to achieve high perfusion sensitivity. In order to reduce BOLD contamination, the CBF signal was extracted from the CASL signal time course by high frequency filtering. This processing strategy is compatible with sinc interpolation for reducing the timing mismatch between control and label images and has the flexibility of choosing an optimal filter cutoff frequency to minimize BOLD fluctuations. Most subjects studied showed high CBF correlation in bilateral sensorimotor areas with good suppression of BOLD contamination. Root-mean-square CBF fluctuation contributing to bilateral correlation was estimated to be 29% ± 19% (N = 13) of the baseline perfusion, while BOLD fluctuation was 0.26% ± 0.14% of the mean intensity (at 3T and 12.5 ms echo time). PMID:18314354

  13. MRI

    MedlinePlus

    ... scan is an imaging test that uses powerful magnets and radio waves to create pictures of the ... in your eyes) Because the MRI contains strong magnets, metal objects are not allowed into the room ...

  14. 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).

  15. Univalent harmonic mappings convex in one direction

    NASA Astrophysics Data System (ADS)

    Ponnusamy, S.; Kaliraj, A. Sairam

    2014-09-01

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

  16. Pharmacogenomics: mapping monogenic mutations to direct therapy.

    PubMed

    Taylor, Palmer

    2012-07-01

    The molecular mapping of mutations that underlie congenital disorders of monogenic origin can result in both a broader understanding of the molecular basis of the disorder and novel therapeutic insights. Indeed, genotyping patients and then replicating the behavior of the mutant gene products in well-defined biochemical or electrophysiological systems will allow tailoring of therapy to be mutation- and protein sequence-dependent. In this issue of the JCI, Shen and colleagues describe such an approach that identified novel mutations in the α subunit of the nicotinic receptor linked to myasthenia gravis. PMID:22728931

  17. The impact of functional connectivity changes on support vector machines mapping of fMRI data.

    PubMed

    Sato, João Ricardo; Mourão-Miranda, Janaina; Morais Martin, Maria da Graça; Amaro, Edson; Morettin, Pedro Alberto; Brammer, Michael John

    2008-07-15

    Functional magnetic resonance imaging (fMRI) is currently one of the most widely used methods for studying human brain function in vivo. Although many different approaches to fMRI analysis are available, the most widely used methods employ so called "mass-univariate" modeling of responses in a voxel-by-voxel fashion to construct activation maps. However, it is well known that many brain processes involve networks of interacting regions and for this reason multivariate analyses might seem to be attractive alternatives to univariate approaches. The current paper focuses on one multivariate application of statistical learning theory: the statistical discrimination maps (SDM) based on support vector machine, and seeks to establish some possible interpretations when the results differ from univariate approaches. In fact, when there are changes not only on the activation level of two conditions but also on functional connectivity, SDM seems more informative. We addressed this question using both simulations and applications to real data. We have shown that the combined use of univariate approaches and SDM yields significant new insights into brain activations not available using univariate methods alone. In the application to a visual working memory fMRI data, we demonstrated that the interaction among brain regions play a role in SDM's power to detect discriminative voxels. PMID:18499266

  18. Temperature dependence of relaxation times and temperature mapping in ultra-low-field MRI

    NASA Astrophysics Data System (ADS)

    Vesanen, Panu T.; Zevenhoven, Koos C. J.; Nieminen, Jaakko O.; Dabek, Juhani; Parkkonen, Lauri T.; Ilmoniemi, Risto J.

    2013-10-01

    Ultra-low-field MRI is an emerging technology that allows MRI and NMR measurements in microtesla-range fields. In this work, the possibilities of relaxation-based temperature measurements with ultra-low-field MRI were investigated by measuring T1 and T2 relaxation times of agarose gel at 50 μT-52 mT and at temperatures 5-45 °C. Measurements with a 3 T scanner were made for comparison. The Bloembergen-Purcell-Pound relaxation theory was combined with a two-state model to explain the field-strength and temperature dependence of the data. The results show that the temperature dependencies of agarose gel T1 and T2 in the microtesla range differ drastically from those at 3 T; the effect of temperature on T1 is reversed at approximately 5 mT. The obtained results were used to reconstruct temperature maps from ultra-low-field scans. These time-dependent temperature maps measured from an agarose gel phantom at 50 μT reproduced the temperature gradient with good contrast.

  19. 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. PMID:26057594

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

    PubMed Central

    Amedi, Amir

    2011-01-01

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

  1. 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

  2. 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

  3. 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

  4. Mapping brain networks in awake mice using combined optical neural control and fMRI.

    PubMed

    Desai, M; Kahn, I; Knoblich, U; Bernstein, J; Atallah, H; Yang, A; Kopell, N; Buckner, R L; Graybiel, A M; Moore, C I; Boyden, E S

    2011-03-01

    Behaviors and brain disorders involve neural circuits that are widely distributed in the brain. The ability to map the functional connectivity of distributed circuits, and to assess how this connectivity evolves over time, will be facilitated by methods for characterizing the network impact of activating a specific subcircuit, cell type, or projection pathway. We describe here an approach using high-resolution blood oxygenation level-dependent (BOLD) functional MRI (fMRI) of the awake mouse brain-to measure the distributed BOLD response evoked by optical activation of a local, defined cell class expressing the light-gated ion channel channelrhodopsin-2 (ChR2). The utility of this opto-fMRI approach was explored by identifying known cortical and subcortical targets of pyramidal cells of the primary somatosensory cortex (SI) and by analyzing how the set of regions recruited by optogenetically driven SI activity differs between the awake and anesthetized states. Results showed positive BOLD responses in a distributed network that included secondary somatosensory cortex (SII), primary motor cortex (MI), caudoputamen (CP), and contralateral SI (c-SI). Measures in awake compared with anesthetized mice (0.7% isoflurane) showed significantly increased BOLD response in the local region (SI) and indirectly stimulated regions (SII, MI, CP, and c-SI), as well as increased BOLD signal temporal correlations between pairs of regions. These collective results suggest opto-fMRI can provide a controlled means for characterizing the distributed network downstream of a defined cell class in the awake brain. Opto-fMRI may find use in examining causal links between defined circuit elements in diverse behaviors and pathologies. PMID:21160013

  5. 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. PMID:26968145

  6. Direct mapping of hippocampal surfaces with intrinsic shape context.

    PubMed

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

    2007-09-01

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

  7. Direct Mapping of Hippocampal Surfaces with Intrinsic Shape Context

    PubMed Central

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

    2007-01-01

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

  8. 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

  9. A direct modulated optical link for MRI RF receive coil interconnection

    NASA Astrophysics Data System (ADS)

    Yuan, Jing; Wei, Juan; Shen, G. X.

    2007-11-01

    Optical glass fiber is a promising alternative to traditional coaxial cables for MRI RF receive coil interconnection to avoid any crosstalk and electromagnetic interference between multiple channels. A direct modulated optical link is proposed for MRI coil interconnection in this paper. The link performances of power gain, frequency response and dynamic range are measured. Phantom and in vivo human head images have been demonstrated by the connection of this direct modulated optical link to a head coil on a 0.3 T MRI scanner for the first time. Comparable image qualities to coaxial cable link verify the feasibility of using the optical link for imaging with minor modification on the existing scanners. This optical link could also be easily extended for multi-channel array interconnections at high field of 1.5 T.

  10. 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.

  11. Statistical mapping of sound-evoked activity in the mouse auditory midbrain using Mn-enhanced MRI.

    PubMed

    Yu, Xin; Zou, Jing; Babb, James S; Johnson, Glyn; Sanes, Dan H; Turnbull, Daniel H

    2008-01-01

    Manganese-enhanced MRI (MEMRI) has been developed to image brain activity in small animals, including normal and genetically modified mice. Here, we report the use of a MEMRI-based statistical parametric mapping method to analyze sound-evoked activity in the mouse auditory midbrain, the inferior colliculus (IC). Acoustic stimuli with defined frequency and amplitude components were shown to activate and enhance neuronal ensembles in the IC. These IC activity patterns were analyzed quantitatively using voxel-based statistical comparisons between groups of mice with or without sound stimulation. Repetitive 40-kHz pure tone stimulation significantly enhanced ventral IC regions, which was confirmed in the statistical maps showing active regions whose volumes increased in direct proportion to the amplitude of the sound stimuli (65 dB, 77 dB, and 89 dB peak sound pressure level). The peak values of the activity-dependent MEMRI signal enhancement also increased from 7% to 20% for the sound amplitudes employed. These results demonstrate that MEMRI statistical mapping can be used to analyze both the 3D spatial patterns and the magnitude of activity evoked by sound stimuli carrying different energy. This represents a significant advance in the development of MEMRI for quantitative and unbiased analysis of brain function in the deep brain nuclei of mice. PMID:17919926

  12. Two-dimensional T 2 distribution mapping in porous solids with phase encode MRI

    NASA Astrophysics Data System (ADS)

    Petrov, Oleg V.; Balcom, Bruce J.

    2011-09-01

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

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

    PubMed

    Petrov, Oleg V; Balcom, Bruce J

    2011-09-01

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

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

    PubMed

    Russ, Brian E; Leopold, David A

    2015-04-01

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

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

    PubMed Central

    Russ, Brian E.; Leopold, David A.

    2015-01-01

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

  16. Direct and fast detection of neuronal activation in the human brain with diffusion MRI

    PubMed Central

    Le Bihan, Denis; Urayama, Shin-ichi; Aso, Toshihiko; Hanakawa, Takashi; Fukuyama, Hidenao

    2006-01-01

    Using MRI, we found that a slowly diffusing water pool was expanding (1.7 ± 0.3%) upon activation on the human visual cortex at the detriment of a faster diffusing pool. The time course of this water phase transition preceded the activation-triggered vascular response detected by usual functional MRI by several seconds. The observed changes in water diffusion likely reflect early biophysical events that take place in the activated cells, such as cell swelling and membrane expansion. Although the exact mechanisms remain to clarify, access to such an early and direct physiological marker of cortical activation with MRI will provide opportunities for functional neuroimaging of the human brain. PMID:16702549

  17. 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. PMID:26612077

  18. 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/.

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

    PubMed

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

    2014-10-01

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

  20. 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

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

    PubMed

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

    2015-06-01

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

  2. Multiclass fMRI data decoding and visualization using supervised self-organizing maps.

    PubMed

    Hausfeld, Lars; Valente, Giancarlo; Formisano, Elia

    2014-08-01

    When multivariate pattern decoding is applied to fMRI studies entailing more than two experimental conditions, a most common approach is to transform the multiclass classification problem into a series of binary problems. Furthermore, for decoding analyses, classification accuracy is often the only outcome reported although the topology of activation patterns in the high-dimensional features space may provide additional insights into underlying brain representations. Here we propose to decode and visualize voxel patterns of fMRI datasets consisting of multiple conditions with a supervised variant of self-organizing maps (SSOMs). Using simulations and real fMRI data, we evaluated the performance of our SSOM-based approach. Specifically, the analysis of simulated fMRI data with varying signal-to-noise and contrast-to-noise ratio suggested that SSOMs perform better than a k-nearest-neighbor classifier for medium and large numbers of features (i.e. 250 to 1000 or more voxels) and similar to support vector machines (SVMs) for small and medium numbers of features (i.e. 100 to 600voxels). However, for a larger number of features (>800voxels), SSOMs performed worse than SVMs. When applied to a challenging 3-class fMRI classification problem with datasets collected to examine the neural representation of three human voices at individual speaker level, the SSOM-based algorithm was able to decode speaker identity from auditory cortical activation patterns. Classification performances were similar between SSOMs and other decoding algorithms; however, the ability to visualize decoding models and underlying data topology of SSOMs promotes a more comprehensive understanding of classification outcomes. We further illustrated this visualization ability of SSOMs with a re-analysis of a dataset examining the representation of visual categories in the ventral visual cortex (Haxby et al., 2001). This analysis showed that SSOMs could retrieve and visualize topography and neighborhood

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

    PubMed

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

    2016-08-15

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

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

    PubMed

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

    2016-01-15

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

  5. 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. PMID:21416563

  6. 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

  7. Evaluations of Tumor Acidosis Within In Vivo Tumor Models Using Parametric Maps Generated with AcidoCEST MRI

    PubMed Central

    Chen, Liu Qi; Randtke, Edward A.; Jones, Kyle M.; Moon, Brianna F.; Howison, Christine M.; Pagel, Mark D.

    2016-01-01

    Purpose We aimed to develop pixelwise maps of tumor acidosis to aid in evaluating extracellular tumor pH (pHe) in cancer biology. Procedures MCF-7 and MDA-MB-231 mouse models were imaged during a longitudinal study. AcidoCEST MRI and a series of image processing methods were used to produce parametric maps of tumor pHe, and tumor pHe was also measured with a pH microsensor. Results Sufficient contrast-to-noise for producing pHe maps was achieved by using standard image processing methods. A comparison of pHe values measured with acidoCEST MRI and a pH microsensor showed that acidoCEST MRI measured tumor pHe with an accuracy of 0.034 pH units. The MCF-7 tumor model was found to be more acidic compared to the MDA-MB-231 tumor model. The pHe was not related to tumor size during the longitudinal study. Conclusions These results show that acidoCEST MRI can create pixelwise tumor pHe maps of mouse models of cancer. PMID:25622809

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2009-01-01

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

  10. Direction of movement effects under transformed visual/motor mappings

    NASA Technical Reports Server (NTRS)

    Cunningham, H. A.; Pavel, M.

    1989-01-01

    Performance in a discrete aiming task was compared under several transformed visual/motor mappings: rotations by 45, 90, 135, and 180 deg and reflections about the horizontal and the vertical midlines. Eight aiming targets were used, corresponding to eight directions of movement: up, down, right, left, up-right, down-left, up-left, and down-right. Direction of movements were characterized in terms of separable visual and motor components, and two kinds of direction of movement effects were considered. First, a direction of movement effect paralleling that seen in rapid aiming under the usual nontransformed mapping. Second, because rotations, but not reflections, are physically realizable 2-D transformations, a visual/motor control system which is sensitive to physical constraints should perform reflections, but not rotations, in a piecemeal fashion. Results supported the hypothesis that a motor factor having to do with complexity of limb movement accounts for differences in movement accuracy between right and left oblique directions. Direction of movement effects were more evident in reflections than in rotations, and were consistent with the hypothesis that the visual/motor-control system seeks a physically realizable 2-D rotation solution to reflections. Results also suggested that reversal of two orthogonal basis dimensions is far less difficult than reversing only one and leaving the other intact.

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

    PubMed

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

    2016-01-01

    To develop effective stem cell therapies, it is important to track therapeutic cells non-invasively and monitor homing to areas of pathology. The purpose of this study was to design and evaluate the labeling efficiency of commercially available dextran-coated superparamagnetic iron oxide nanoparticles, FeraTrack Direct (FTD), in various stem and immune cells; assess the cytotoxicity and tolerability of the FTD in stem cells; and monitor stem cell homing using FTD-labeled bone-marrow-derived mesenchymal stromal cells (BMSCs) and neural stem cells (NSCs) in a tumor model by in vivo MRI. BMSCs, NSCs, hematopoietic stem cells (HSCs), T-lymphocytes, and monocytes were labeled effectively with FTD without the need for transfection agents, and Prussian blue (PB) staining and transmission electron microscopy (TEM) confirmed intracellular uptake of the agent. The viability, proliferation, and functionality of the labeled cells were minimally or not affected after labeling. When 10(6) FTD-labeled BMSCs or NSCs were injected into C6 glioma bearing nude mice, the cells homing to the tumors were detected as hypointense regions within the tumor using 3 T clinical MRI up to 10 days post injection. Histological analysis confirmed the homing of injected cells to the tumor by the presence of PB positive cells that are not macrophages. Labeling of stem cells or immune cells with FTD was non-toxic, and should facilitate the translation of this agent to clinical trials for evaluation of trafficking of cells by MRI. PMID:26234504

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

    PubMed

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

    2016-03-01

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

  13. Mapping somatosensory connectivity in adult mice using diffusion MRI tractography and super-resolution track density imaging.

    PubMed

    Richards, Kay; Calamante, Fernando; Tournier, Jacques-Donald; Kurniawan, Nyoman D; Sadeghian, Farnoosh; Retchford, Alexander R; Jones, Gabriel Davis; Reid, Christopher A; Reutens, David C; Ordidge, Roger; Connelly, Alan; Petrou, Steven

    2014-11-15

    In this study we combined ultra-high field diffusion MRI fiber tracking and super-resolution track density imaging (TDI) to map the relay locations and connectivity of the somatosensory pathway in paraformaldehyde fixed, C57Bl/6J mouse brains. Super-resolution TDI was used to achieve 20 μm isotropic resolution to inform the 3D topography of the relay locations including thalamic barreloids and brainstem barrelettes, not described previously using MRI methodology. TDI-guided mapping results for thalamo-cortical connectivity were consistent with thalamo-cortical projections labeled using virus mediated fluorescent protein expression. Trigemino-thalamic TDI connectivity maps were concordant with results obtained using anterograde dye tracing from brainstem to thalamus. Importantly, TDI mapping overcame the constraint of tissue distortion observed in mechanically sectioned tissue, enabling 3D reconstruction and long-range connectivity data. In conclusion, our results showed that diffusion micro-imaging at ultra-high field MRI revealed the stereotypical pattern of somatosensory connectivity and is a valuable tool to complement histologic methods, achieving 3D spatial preservation of whole brain networks for characterization in mouse models of human disease. PMID:25087481

  14. Mapping epitopes and antigenicity by site-directed masking

    NASA Astrophysics Data System (ADS)

    Paus, Didrik; Winter, Greg

    2006-06-01

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

  15. Mapping average axon diameters in porcine spinal cord white matter and rat corpus callosum using d-PFG MRI

    PubMed Central

    Komlosh, M.E.; Özarslan, E.; Lizak, M. J.; Horkayne-Szakaly, I.; Freidlin, R. Z.; Horkay, F.; Basser, P. J.

    2013-01-01

    Knowledge of microstructural features of nerve fascicles, such as axon diameter, is crucial for understanding normal function in the central and peripheral nervous systems as well as assessing changes due to pathologies. In this study double-pulsed field gradient (d-PFG) filtered MRI was used to map the average axon diameter (AAD) in porcine spinal cord, which was then compared to AADs measured with optical microscopy of the same specimen, as a way to further validate this MRI method. A novel 3D acquisition scheme was then used to obtain AADs in each voxel of a coronal slice of rat brain corpus callosum. AAD measurements were also acquired using optical microscopy performed on histological sections and validated using a novel MRI glass capillary array phantom. PMID:23583426

  16. Direct shear mapping - a new weak lensing tool

    NASA Astrophysics Data System (ADS)

    de Burgh-Day, C. O.; Taylor, E. N.; Webster, R. L.; Hopkins, A. M.

    2015-08-01

    We have developed a new technique called direct shear mapping (DSM) to measure gravitational lensing shear directly from observations of a single background source. The technique assumes the velocity map of an unlensed, stably rotating galaxy will be rotationally symmetric. Lensing distorts the velocity map making it asymmetric. The degree of lensing can be inferred by determining the transformation required to restore axisymmetry. This technique is in contrast to traditional weak lensing methods, which require averaging an ensemble of background galaxy ellipticity measurements, to obtain a single shear measurement. We have tested the efficacy of our fitting algorithm with a suite of systematic tests on simulated data. We demonstrate that we are in principle able to measure shears as small as 0.01. In practice, we have fitted for the shear in very low redshift (and hence unlensed) velocity maps, and have obtained null result with an error of ±0.01. This high-sensitivity results from analysing spatially resolved spectroscopic images (i.e. 3D data cubes), including not just shape information (as in traditional weak lensing measurements) but velocity information as well. Spirals and rotating ellipticals are ideal targets for this new technique. Data from any large Integral Field Unit (IFU) or radio telescope is suitable, or indeed any instrument with spatially resolved spectroscopy such as the Sydney-Australian-Astronomical Observatory Multi-Object Integral Field Spectrograph (SAMI), the Atacama Large Millimeter/submillimeter Array (ALMA), the Hobby-Eberly Telescope Dark Energy Experiment (HETDEX) and the Square Kilometer Array (SKA).

  17. fMRI brain mapping during motion capture and FES induced motor tasks: signal to noise ratio assessment.

    PubMed

    Gandolla, Marta; Ferrante, Simona; Casellato, Claudia; Ferrigno, Giancarlo; Molteni, Franco; Martegani, Alberto; Frattini, Tiziano; Pedrocchi, Alessandra

    2011-10-01

    Functional Electrical Stimulation (FES) is a well known clinical rehabilitation procedure, however the neural mechanisms that underlie this treatment at Central Nervous System (CNS) level are still not completely understood. Functional magnetic resonance imaging (fMRI) is a suitable tool to investigate effects of rehabilitative treatments on brain plasticity. Moreover, monitoring the effective executed movement is needed to correctly interpret activation maps, most of all in neurological patients where required motor tasks could be only partially accomplished. The proposed experimental set-up includes a 1.5 T fMRI scanner, a motion capture system to acquire kinematic data, and an electro-stimulation device. The introduction of metallic devices and of stimulation current in the MRI room could affect fMRI acquisitions so as to prevent a reliable activation maps analysis. What we are interested in is that the Blood Oxygenation Level Dependent (BOLD) signal, marker of neural activity, could be detected within a given experimental condition and set-up. In this paper we assess temporal Signal to Noise Ratio (SNR) as image quality index. BOLD signal change is about 1-2% as revealed by a 1.5 T scanner. This work demonstrates that, with this innovative set-up, in the main cortical sensorimotor regions 1% BOLD signal change can be detected at least in the 93% of the sub-volumes, and almost 100% of the sub-volumes are suitable for 2% signal change detection. The integrated experimental set-up will therefore allows to detect FES induced movements fMRI maps simultaneously with kinematic acquisitions so as to investigate FES-based rehabilitation treatments contribution at CNS level. PMID:21550290

  18. Implementation of a semi-automated post-processing system for parametric MRI mapping of human breast cancer.

    PubMed

    Lee, Robert E; Welch, E Brian; Cobb, Jared G; Sinha, Tuhin; Gore, John C; Yankeelov, Thomas E

    2009-08-01

    Magnetic resonance imaging (MRI) investigations of breast cancer incorporate computationally intense techniques to develop parametric maps of pathophysiological tissue characteristics. Common approaches employ, for example, quantitative measurements of T (1), the apparent diffusion coefficient, and kinetic modeling based on dynamic contrast-enhanced MRI (DCE-MRI). In this paper, an integrated medical image post-processing and archive system (MIPAS) is presented. MIPAS demonstrates how image post-processing and user interface programs, written in the interactive data language (IDL) programming language with data storage provided by a Microsoft Access database, and the file system can reduce turnaround time for creating MRI parametric maps and provide additional organization for clinical trials. The results of developing the MIPAS are discussed including potential limitations of the use of IDL for the application framework and how the MIPAS design supports extension to other programming languages and imaging modalities. We also show that network storage of images and metadata has a significant (p < 0.05) increase in data retrieval time compared to collocated storage. The system shows promise for becoming both a robust research picture archival and communications system working with the standard hospital PACS and an image post-processing environment that extends to other medical image modalities. PMID:18446412

  19. 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.

  20. Desktop MRI as a promising tool for mapping intra-aneurismal flow.

    PubMed

    Perlo, Josefina; Silletta, Emilia V; Danieli, Ernesto; Cattaneo, Giorgio; Acosta, Rodolfo H; Blümich, Bernhard; Casanova, Federico

    2015-04-01

    In this work we evaluate the performance of a 40-mm diameter bore 0.2T desktop Halbach tomograph to obtain 2D and 3D velocity maps for studying intra-aneurismal flow in the presence or absence of nitinol meshed implants with the aim of optimizing the flow diverter efficacy. Phantoms with known spatial velocity distribution were used to determine the performance of the MRI system. Maximum velocities of about 200mm/s could be measured with a precision of 1% at a spatial resolution of 0.5×0.5×1mm(3). This accuracy is suitable to evaluate in vitro intra-aneurismal flow under different conditions such as variable flow rates, different vessel-aneurysm geometry, as well as the influence of metallic flow diverters on the intra-aneurismal flow distribution. The information obtained non-invasively with desktop tomographs can be used to complement in vivo studies in order to decide the optimum flow diverter. PMID:25527392

  1. Vascular Origins of BOLD and CBV fMRI Signals: Statistical Mapping and Histological Sections Compared.

    PubMed

    Kennerley, Aneurin J; Mayhew, John E; Redgrave, Peter; Berwick, Jason

    2010-01-01

    Comparison of 3T blood oxygenation level dependent (BOLD) and cerebral blood volume (CBV) activation maps to histological sections enables the spatial discrimination of functional magnetic resonance imaging (fMRI) signal changes into different vascular compartments. We use a standard gradient echo-echo planar imaging technique to measure BOLD signal changes in the somatosensory cortex in response to whisker stimulation. Corresponding changes in CBV were estimated following the infusion of a super-paramagnetic contrast agent. We imaged in a tangential imaging plane that covered the cortical surface. Images were associated with post mortem histological sections showing both the surface vasculature and cytochrome oxidase stained whisker barrel cortex. We found a significant BOLD signal change in the large draining veins which occurred in the absence of a corresponding CBV change. Results suggest that in the venous drainage system, ~3mm distant from the area of activity, there is a robust change in blood oxygen saturation with little or no volume change. CBV changes are localised over the somatosensory barrel cortex and overlying arterial supply, supporting the theory that CBV changes are greater in the arterial than in the venous vasculature. This work investigating BOLD signal and underlying hemodynamics provides more information on the vascular origins of these important neuroimaging signals. PMID:20563253

  2. 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

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

    PubMed Central

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

    2016-01-01

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

  4. 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

  5. Multishot versus Single-Shot Pulse Sequences in Very High Field fMRI: A Comparison Using Retinotopic Mapping

    PubMed Central

    Gatenby, J. Christopher; Gore, John C.; Tong, Frank

    2012-01-01

    High-resolution functional MRI is a leading application for very high field (7 Tesla) human MR imaging. Though higher field strengths promise improvements in signal-to-noise ratios (SNR) and BOLD contrast relative to fMRI at 3 Tesla, these benefits may be partially offset by accompanying increases in geometric distortion and other off-resonance effects. Such effects may be especially pronounced with the single-shot EPI pulse sequences typically used for fMRI at standard field strengths. As an alternative, one might consider multishot pulse sequences, which may lead to somewhat lower temporal SNR than standard EPI, but which are also often substantially less susceptible to off-resonance effects. Here we consider retinotopic mapping of human visual cortex as a practical test case by which to compare examples of these sequence types for high-resolution fMRI at 7 Tesla. We performed polar angle retinotopic mapping at each of 3 isotropic resolutions (2.0, 1.7, and 1.1 mm) using both accelerated single-shot 2D EPI and accelerated multishot 3D gradient-echo pulse sequences. We found that single-shot EPI indeed led to greater temporal SNR and contrast-to-noise ratios (CNR) than the multishot sequences. However, additional distortion correction in postprocessing was required in order to fully realize these advantages, particularly at higher resolutions. The retinotopic maps produced by both sequence types were qualitatively comparable, and showed equivalent test/retest reliability. Thus, when surface-based analyses are planned, or in other circumstances where geometric distortion is of particular concern, multishot pulse sequences could provide a viable alternative to single-shot EPI. PMID:22514646

  6. 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.

  7. 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.

  8. Improved T1 mapping by motion correction and template based B1 correction in 3T MRI brain studies

    NASA Astrophysics Data System (ADS)

    Castro, Marcelo A.; Yao, Jianhua; Lee, Christabel; Pang, Yuxi; Baker, Eva; Butman, John; Thomasson, David

    2009-02-01

    Accurate estimation of relaxation time T1 from MRI images is increasingly important for some clinical applications. Low noise, high resolution, fast and accurate T1 maps from MRI images of the brain can be performed using a dual flip angle method. However, accuracy is limited by the scanners ability to deliver the prescribed flip angle due to the B1 inhomogeneity, particularly at high field strengths (e.g. 3T). One of the most accurate methods to correct that inhomogeneity is to acquire a subject-specific B1 map. However, since B1 map acquisition takes up precious scanning time and most retrospective studies do not have B1 map, it would be desirable to perform that correction from a template. For this work a dual repetition time method was used for B1 map acquisition in five normal subjects. Inaccuracies due to misregistration of acquired T1-weighted images were corrected by rigid registration, and the effects of misalignment were compared to those of B1 inhomogeneity. T1-intensity histograms were produced and three-Gaussian curves were fitted for every fully-, partially- and non-corrected histogram in order to estimate and compare the white and gray matter peaks. In addition, in order to reduce the scanning time we designed a template based correction strategy. Images from different subjects were aligned using a twelve-parameter affine registration, and B1 maps were aligned according to that transformation. Recomputed T1 maps showed a significant improvement with respect to non-corrected ones. These results are very promising and have the potential for clinical application.

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

    PubMed Central

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

    2016-01-01

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

  10. 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. PMID:26826512

  11. 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.

  12. 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. PMID:27043358

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

    PubMed Central

    Estes, Katharine Graf; Hurley, Karinna

    2012-01-01

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

  14. 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. PMID:17379568

  15. Effects of Non-Local Diffusion on Structural MRI Preprocessing and Default Network Mapping: Statistical Comparisons with Isotropic/Anisotropic Diffusion

    PubMed Central

    Zuo, Xi-Nian; Xing, Xiu-Xia

    2011-01-01

    Neuroimaging community usually employs spatial smoothing to denoise magnetic resonance imaging (MRI) data, e.g., Gaussian smoothing kernels. Such an isotropic diffusion (ISD) based smoothing is widely adopted for denoising purpose due to its easy implementation and efficient computation. Beyond these advantages, Gaussian smoothing kernels tend to blur the edges, curvature and texture of images. Researchers have proposed anisotropic diffusion (ASD) and non-local diffusion (NLD) kernels. We recently demonstrated the effect of these new filtering paradigms on preprocessing real degraded MRI images from three individual subjects. Here, to further systematically investigate the effects at a group level, we collected both structural and functional MRI data from 23 participants. We first evaluated the three smoothing strategies' impact on brain extraction, segmentation and registration. Finally, we investigated how they affect subsequent mapping of default network based on resting-state functional MRI (R-fMRI) data. Our findings suggest that NLD-based spatial smoothing maybe more effective and reliable at improving the quality of both MRI data preprocessing and default network mapping. We thus recommend NLD may become a promising method of smoothing structural MRI images of R-fMRI pipeline. PMID:22066005

  16. 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

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

    PubMed

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

    2015-06-01

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

  18. Statistical parametric mapping of LORETA using high density EEG and individual MRI: application to mismatch negativities in schizophrenia.

    PubMed

    Park, Hae-Jeong; Kwon, Jun Soo; Youn, Tak; Pae, Ji Soo; Kim, Jae-Jin; Kim, Myung-Sun; Ha, Kyoo-Seob

    2002-11-01

    We describe a method for the statistical parametric mapping of low resolution electromagnetic tomography (LORETA) using high-density electroencephalography (EEG) and individual magnetic resonance images (MRI) to investigate the characteristics of the mismatch negativity (MMN) generators in schizophrenia. LORETA, using a realistic head model of the boundary element method derived from the individual anatomy, estimated the current density maps from the scalp topography of the 128-channel EEG. From the current density maps that covered the whole cortical gray matter (up to 20,000 points), volumetric current density images were reconstructed. Intensity normalization of the smoothed current density images was used to reduce the confounding effect of subject specific global activity. After transforming each image into a standard stereotaxic space, we carried out statistical parametric mapping of the normalized current density images. We applied this method to the source localization of MMN in schizophrenia. The MMN generators, produced by a deviant tone of 1,200 Hz (5% of 1,600 trials) under the standard tone of 1,000 Hz, 80 dB binaural stimuli with 300 msec of inter-stimulus interval, were measured in 14 right-handed schizophrenic subjects and 14 age-, gender-, and handedness-matched controls. We found that the schizophrenic group exhibited significant current density reductions of MMN in the left superior temporal gyrus and the left inferior parietal gyrus (P < 0. 0005). This study is the first voxel-by-voxel statistical mapping of current density using individual MRI and high-density EEG. PMID:12391570

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

    PubMed Central

    Roe, Anna W.; Chen, Li Min

    2009-01-01

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

  20. 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

  1. 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%. PMID:24816550

  2. A similarity retrieval method for functional magnetic resonance imaging (fMRI) statistical maps

    NASA Astrophysics Data System (ADS)

    Tungaraza, R. F.; Guan, J.; Rolfe, S.; Atmosukarto, I.; Poliakov, A.; Kleinhans, N. M.; Aylward, E.; Ojemann, J.; Brinkley, J. F.; Shapiro, L. G.

    2009-02-01

    We propose a method for retrieving similar fMRI statistical images given a query fMRI statistical image. Our method thresholds the voxels within those images and extracts spatially distinct regions from the voxels that remain. Each region is defined by a feature vector that contains the region centroid, the region area, the average activation value for all the voxels within that region, the variance of those activation values, the average distance of each voxel within that region to the region's centroid, and the variance of the voxel's distance to the region's centroid. The similarity between two images is obtained by the summed minimum distance of their constituent feature vectors. Results on a dataset of fMRI statistical images from experiments involving distinct cognitive tasks are shown.

  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. 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…

  5. 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…

  6. Mapping of the prostate in endorectal coil-based MRI/MRSI and CT: A deformable registration and validation study

    SciTech Connect

    Lian, J.; Xing, L.; Hunjan, S.; Dumoulin, C.; Levin, J.; Lo, A.; Watkins, R.; Rohling, K.; Giaquinto, R.; Kim, D.; Spielman, D.; Daniel, B.

    2004-11-01

    The endorectal coil is being increasingly used in magnetic resonance imaging (MRI) and MR spectroscopic imaging (MRSI) to obtain anatomic and metabolic images of the prostate with high signal-to-noise ratio (SNR). In practice, however, the use of endorectal probe inevitably distorts the prostate and other soft tissue organs, making the analysis and the use of the acquired image data in treatment planning difficult. The purpose of this work is to develop a deformable image registration algorithm to map the MRI/MRSI information obtained using an endorectal probe onto CT images and to verify the accuracy of the registration by phantom and patient studies. A mapping procedure involved using a thin plate spline (TPS) transformation was implemented to establish voxel-to-voxel correspondence between a reference image and a floating image with deformation. An elastic phantom with a number of implanted fiducial markers was designed for the validation of the quality of the registration. Radiographic images of the phantom were obtained before and after a series of intentionally introduced distortions. After mapping the distorted phantom to the original one, the displacements of the implanted markers were measured with respect to their ideal positions and the mean error was calculated. In patient studies, CT images of three prostate patients were acquired, followed by 3 Tesla (3 T) MR images with a rigid endorectal coil. Registration quality was estimated by the centroid position displacement and image coincidence index (CI). Phantom and patient studies show that TPS-based registration has achieved significantly higher accuracy than the previously reported method based on a rigid-body transformation and scaling. The technique should be useful to map the MR spectroscopic dataset acquired with ER probe onto the treatment planning CT dataset to guide radiotherapy planning.

  7. 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.

  8. Quantitative mapping of cerebrovascular reactivity using resting-state BOLD fMRI: Validation in healthy adults.

    PubMed

    Golestani, Ali M; Wei, Luxi L; Chen, J Jean

    2016-09-01

    In conventional neuroimaging, cerebrovascular reactivity (CVR) is quantified primarily using the blood-oxygenation level-dependent (BOLD) functional MRI (fMRI) signal, specifically, as the BOLD response to intravascular carbon dioxide (CO2) modulations, in units of [%ΔBOLD/mmHg]. While this method has achieved wide appeal and clinical translation, the tolerability of CO2-related tasks amongst patients and the elderly remains a challenge in more routine and large-scale applications. In this work, we propose an improved method to quantify CVR by exploiting intrinsic fluctuations in CO2 and corresponding changes in the resting-state BOLD signal (rs-qCVR). Our rs-qCVR approach requires simultaneous monitoring of PETCO2, cardiac pulsation and respiratory volume. In 16 healthy adults, we compare our quantitative CVR estimation technique to the prospective CO2-targeting based CVR quantification approach (qCVR, the "standard"). We also compare our rs-CVR to non-quantitative alternatives including the resting-state fluctuation amplitude (RSFA), amplitude of low-frequency fluctuation (ALFF) and global-signal regression. When all subjects were pooled, only RSFA and ALFF were significantly associated with qCVR. However, for characterizing regional CVR variations within each subject, only the PETCO2-based rs-qCVR measure is strongly associated with standard qCVR in 100% of the subjects (p≤0.1). In contrast, for the more qualitative CVR measures, significant within-subject association with qCVR was only achieved in 50-70% of the subjects. Our work establishes the feasibility of extracting quantitative CVR maps using rs-fMRI, opening the possibility of mapping functional connectivity and qCVR simultaneously. PMID:27177763

  9. 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. PMID:27230379

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed

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

    2016-02-01

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

  12. 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

  13. A Hybrid Technique for Thickness-Map Visualization of the Hip Cartilages in MRI

    NASA Astrophysics Data System (ADS)

    Khanmohammadi, Mahdieh; Zoroofi, Reza Aghaiezadeh; Nishii, Takashi; Tanaka, Hisashi; Sato, Yoshinobu

    Quantification of the hip cartilages is clinically important. In this study, we propose an automatic technique for segmentation and visualization of the acetabular and femoral head cartilages based on clinically obtained multi-slice T1-weighted MR data and a hybrid approach. We follow a knowledge based approach by employing several features such as the anatomical shapes of the hip femoral and acetabular cartilages and corresponding image intensities. We estimate the center of the femoral head by a Hough transform and then automatically select the volume of interest. We then automatically segment the hip bones by a self-adaptive vector quantization technique. Next, we localize the articular central line by a modified canny edge detector based on the first and second derivative filters along the radial lines originated from the femoral head center and anatomical constraint. We then roughly segment the acetabular and femoral head cartilages using derivative images obtained in the previous step and a top-hat filter. Final masks of the acetabular and femoral head cartilages are automatically performed by employing the rough results, the estimated articular center line and the anatomical knowledge. Next, we generate a thickness map for each cartilage in the radial direction based on a Euclidian distance. Three dimensional pelvic bones, acetabular and femoral cartilages and corresponding thicknesses are overlaid and visualized. The techniques have been implemented in C++ and MATLAB environment. We have evaluated and clarified the usefulness of the proposed techniques in the presence of 40 clinical hips multi-slice MR images.

  14. Prostate Cancer Discrimination in the Peripheral Zone With a Reduced Field-of-View T2-mapping MRI Sequence

    PubMed Central

    Yamauchi, Fernando I.; Penzkofer, Tobias; Fedorov, Andriy; Fennessy, Fiona M.; Chu, Renxin; Maier, Stephan E.; Tempany, Clare M.C.; Mulkern, Robert V.; Panych, Lawrence P.

    2015-01-01

    Objectives To evaluate the performance of T2 mapping in discriminating prostate cancer from normal prostate tissue in the peripheral zone using a practical reduced field-of-view MRI sequence requiring less than 3 minutes of scan time. Materials and Methods Thirty-six patients with biopsy-proven peripheral zone prostate cancer without prior treatment underwent routine multiparametric MRI at 3.0T with an endorectal coil. An Inner-Volume Carr-Purcell-Meiboom-Gill imaging sequence that required 2.8 minutes to obtain data for quantitative T2 mapping covering the entire prostate gland was added to the routine multiparametric protocol. Suspected cancer (SC) and suspected healthy (SH) tissue in the peripheral zone were identified in consensus by three radiologists and were correlated with available biopsy results. Differences in mean T2 values in SC and SH ROIs were tested for significance using unpaired Student’s two-tailed t test. The area under the receiver operating characteristic curve was used to assess the optimal threshold T2 value for cancer discrimination. Results ROI analyses revealed significantly (p<0.0001) shorter T2 values in SC (85.4 ± 12.3 ms) compared to SH (169.6 ± 38.7 ms). An estimated T2 threshold of 99 ms yielded a sensitivity of 92% and a specificity of 97% for prostate cancer discrimination. Conclusions Quantitative values derived from this clinically practical T2-mapping sequence allow high precision discrimination between healthy and cancerous peripheral zone in the prostate. PMID:25687187

  15. 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

  16. 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.

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

    PubMed

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

    2016-08-01

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

  18. 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

  19. 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.

  20. Pulse artifact detection in simultaneous EEG-fMRI recording based on EEG map topography.

    PubMed

    Iannotti, Giannina R; Pittau, Francesca; Michel, Christoph M; Vulliemoz, Serge; Grouiller, Frédéric

    2015-01-01

    One of the major artifact corrupting electroencephalogram (EEG) acquired during functional magnetic resonance imaging (fMRI) is the pulse artifact (PA). It is mainly due to the motion of the head and attached electrodes and wires in the magnetic field occurring after each heartbeat. In this study we propose a novel method to improve PA detection by considering the strong gradient and inversed polarity between left and right EEG electrodes. We acquired high-density EEG-fMRI (256 electrodes) with simultaneous electrocardiogram (ECG) at 3 T. PA was estimated as the voltage difference between right and left signals from the electrodes showing the strongest artifact (facial and temporal). Peaks were detected on this estimated signal and compared to the peaks in the ECG recording. We analyzed data from eleven healthy subjects, two epileptic patients and four healthy subjects with an insulating layer between electrodes and scalp. The accuracy of the two methods was assessed with three criteria: (i) standard deviation, (ii) kurtosis and (iii) confinement into the physiological range of the inter-peak intervals. We also checked whether the new method has an influence on the identification of epileptic spikes. Results show that estimated PA improved artifact detection in 15/17 cases, when compared to the ECG method. Moreover, epileptic spike identification was not altered by the correction. The proposed method improves the detection of pulse-related artifacts, particularly crucial when the ECG is of poor quality or cannot be recorded. It will contribute to enhance the quality of the EEG increasing the reliability of EEG-informed fMRI analysis. PMID:25307731

  1. 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

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

    PubMed

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

    2011-02-01

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

  3. 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

  4. 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. PMID:25778652

  5. 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

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

    PubMed

    Seghier, Mohamed L; Price, Cathy J

    2016-01-01

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

  7. Mapping Alzheimer’s disease progression in 1309 MRI scans: Power estimates for different inter-scan intervals☆

    PubMed Central

    Hua, Xue; Lee, Suh; Hibar, Derrek P.; Yanovsky, Igor; Leow, Alex D.; Toga, Arthur W.; Jack, Clifford R.; Bernstein, Matt A.; Reiman, Eric M.; Harvey, Danielle J.; Kornak, John; Schuff, Norbert; Alexander, Gene E.; Weiner, Michael W.; Thompson, Paul M.

    2010-01-01

    Neuroimaging centers and pharmaceutical companies are working together to evaluate treatments that might slow the progression of Alzheimer’s disease (AD), a common but devastating late-life neuropathology. Recently, automated brain mapping methods, such as tensor-based morphometry (TBM) of structural MRI, have outperformed cognitive measures in their precision and power to track disease progression, greatly reducing sample size estimates for drug trials. In the largest TBM study to date, we studied how sample size estimates for tracking structural brain changes depend on the time interval between the scans (6–24 months). We analyzed 1309 brain scans from 91 probable AD patients (age at baseline: 75.4±7.5 years) and 189 individuals with mild cognitive impairment (MCI; 74.6±7.1 years), scanned at baseline, 6, 12, 18, and 24 months. Statistical maps revealed 3D patterns of brain atrophy at each follow-up scan relative to the baseline; numerical summaries were used to quantify temporal lobe atrophy within a statistically-defined region-of-interest. Power analyses revealed superior sample size estimates over traditional clinical measures. Only 80, 46, and 39 AD patients were required for a hypothetical clinical trial, at 6, 12, and 24 months respectively, to detect a 25% reduction in average change using a two-sided test (α=0.05, power=80%). Correspondingly, 106, 79, and 67 subjects were needed for an equivalent MCI trial aiming for earlier intervention. A 24-month trial provides most power, except when patient attrition exceeds 15–16%/year, in which case a 12-month trial is optimal. These statistics may facilitate clinical trial design using voxel-based brain mapping methods such as TBM. PMID:20139010

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

    PubMed

    Chen, A C

    2001-10-01

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

  9. 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

  10. 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.

    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.

  11. Directly labeled fluorescent DNA probes for chromosome mapping

    SciTech Connect

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

    1995-12-31

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

  12. Functional Lung MRI in Chronic Obstructive Pulmonary Disease: Comparison of T1 Mapping, Oxygen-Enhanced T1 Mapping and Dynamic Contrast Enhanced Perfusion

    PubMed Central

    Jobst, Bertram J.; Triphan, Simon M. F.; Sedlaczek, Oliver; Anjorin, Angela; Kauczor, Hans Ulrich; Biederer, Jürgen; Ley-Zaporozhan, Julia; Ley, Sebastian; Wielpütz, Mark O.

    2015-01-01

    Purpose Monitoring of regional lung function in interventional COPD trials requires alternative endpoints beyond global parameters such as FEV1. T1 relaxation times of the lung might allow to draw conclusions on tissue composition, blood volume and oxygen fraction. The aim of this study was to evaluate the potential value of lung Magnetic resonance imaging (MRI) with native and oxygen-enhanced T1 mapping for the assessment of COPD patients in comparison with contrast enhanced perfusion MRI. Materials and Methods 20 COPD patients (GOLD I-IV) underwent a coronal 2-dimensional inversion recovery snapshot flash sequence (8 slices/lung) at room air and during inhalation of pure oxygen, as well as dynamic contrast-enhanced first-pass perfusion imaging. Regional distribution of T1 at room air (T1), oxygen-induced T1 shortening (ΔT1) and peak enhancement were rated by 2 chest radiologists in consensus using a semi-quantitative 3-point scale in a zone-based approach. Results Abnormal T1 and ΔT1 were highly prevalent in the patient cohort. T1 and ΔT1 correlated positively with perfusion abnormalities (r = 0.81 and r = 0.80; p&0.001), and with each other (r = 0.80; p<0.001). In GOLD stages I and II ΔT1 was normal in 16/29 lung zones with mildly abnormal perfusion (15/16 with abnormal T1). The extent of T1 (r = 0.45; p<0.05), ΔT1 (r = 0.52; p<0.05) and perfusion abnormalities (r = 0.52; p<0.05) showed a moderate correlation with GOLD stage. Conclusion Native and oxygen-enhanced T1 mapping correlated with lung perfusion deficits and severity of COPD. Under the assumption that T1 at room air correlates with the regional pulmonary blood pool and that oxygen-enhanced T1 reflects lung ventilation, both techniques in combination are principally suitable to characterize ventilation-perfusion imbalance. This appears valuable for the assessment of regional lung characteristics in COPD trials without administration of i.v. contrast. PMID:25822195

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

    PubMed Central

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

    2009-01-01

    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. PMID:19631273

  14. 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. PMID:19631273

  15. Writing Direction Affects How People Map Space Onto Time

    PubMed Central

    Bergen, Benjamin K.; Chan Lau, Ting Ting

    2012-01-01

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

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

    PubMed

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

    2016-05-15

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

  17. Simultaneous in vivo pH and temperature mapping using a PARACEST-MRI contrast agent.

    PubMed

    McVicar, Nevin; Li, Alex X; Suchý, Mojmír; Hudson, Robert H E; Menon, Ravi S; Bartha, Robert

    2013-10-01

    Altered tissue temperature and/or pH is a common feature in pathological conditions, where metabolic demand exceeds oxygen supply such as in tumors and following stroke. Therefore, in vivo tissue temperature and pH may become valuable biomarkers for disease detection and the monitoring of disease progression or treatment response in conditions with altered metabolic demand. In this study, pH is measured using the amide protons of a thulium (Tm(3+)) complex with a DOTAM-Glycine-Lysine (ligand: Tm(3+)-DOTAM-Gly-Lys). The pH was uniquely determined from the linewidth of the asymmetry curve of the chemical exchange saturation transfer spectrum, independent of contrast agent concentration, or temperature for a given saturation pulse. pH maps with an inter-pixel standard deviation of less than 0.1 pH units were obtained in 10 mM Tm(3+)-DOTAM-Gly-Lys solutions with pH ranging from 6.0 to 8.0 pH units at 37°C. Temperature maps were simultaneously obtained using the chemical shift of the chemical exchange saturation transfer peak. Temperature and pH maps are demonstrated in the mouse leg (N = 3), where the mean and standard deviation for pH was 7.2 ± 0.2 pH unit and temperature was 37.4 ± 0.5°C. PMID:23165779

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

    PubMed

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

    2016-01-01

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

  19. 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

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2002-04-01

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

  2. 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

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

    PubMed

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

    2016-03-01

    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

  4. 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

  5. The average pathlength map: a diffusion MRI tractography-derived index for studying brain pathology.

    PubMed

    Pannek, Kerstin; Mathias, Jane L; Bigler, Erin D; Brown, Greg; Taylor, Jamie D; Rose, Stephen E

    2011-03-01

    Magnetic resonance diffusion tractography provides a powerful tool for the assessment of white matter architecture in vivo. Quantitative tractography metrics, such as streamline length, have successfully been used in the study of brain pathology. To date, these studies have relied on a priori knowledge of which tracts are affected by injury or pathology and manual delineation of regions of interest (ROIs) for use as waypoints in tractography. This limits the analyses to specific tracts under investigation and relies on the accurate and consistent placement of ROIs. We present a fully automated technique for the voxel-wise analysis of streamline length within the entire brain, the Average Pathlength Map (APM). We highlight the precision and reproducibility of voxel-wise average streamline length over time, and assess normal variability of pathlength values in a cohort of 43 healthy participants. Additionally, we demonstrate the utility of this approach by performing voxel-wise comparison between pathlength values obtained from a patient with a severe traumatic brain injury (TBI, Glasgow Coma Scale Score=7) and those from control participants. Our analysis shows that voxel-wise average pathlength values are comparable to fractional anisotropy (FA) in terms of reproducibility and variability. For the TBI patient, we observed a significant reduction in streamline pathlength in the genu of the corpus callosum and its projections into the frontal lobe. This study demonstrates that the average pathlength map can be used for voxel-based analysis of a quantitative tractography metric within the whole brain, removing both the dependence on a priori knowledge of affected pathways and time-consuming manual delineation of ROIs. PMID:21147236

  6. Microtesla MRI of the human brain combined with MEG

    PubMed Central

    Zotev, Vadim S.; Matlashov, Andrei N.; Volegov, Petr L.; Savukov, Igor M.; Espy, Michelle A.; Mosher, John C.; Gomez, John J.; Kraus, Robert H.

    2008-01-01

    One of the challenges in functional brain imaging is integration of complementary imaging modalities, such as magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI). MEG, which uses highly sensitive superconducting quantum interference devices (SQUIDs) to directly measure magnetic fields of neuronal currents, cannot be combined with conventional high-field MRI in a single instrument. Indirect matching of MEG and MRI data leads to significant co-registration errors. A recently proposed imaging method-SQUID-based microtesla MRI-can be naturally combined with MEG in the same system to directly provide structural maps for MEG-localized sources. It enables easy and accurate integration of MEG and MRI/fMRI, because microtesla MR images can be precisely matched to structural images provided by high-field MRI and other techniques. Here we report the first images of the human brain by microtesla MRI, together with auditory MEG (functional) data, recorded using the same seven-channel SQUID system during the same imaging session. The images were acquired at 46 microtesla measurement field with pre-polarization at 30 mT. We also estimated transverse relaxation times for different tissues at microtesla fields. Our results demonstrate feasibility and potential of human brain imaging by microtesla MRI. They also show that two new types of imaging equipment-low-cost systems for anatomical MRI of the human brain at microtesla fields, and more advanced instruments for combined functional (MEG) and structural (microtesla MRI) brain imaging-are practical. PMID:18619876

  7. 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.

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

    PubMed Central

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

    2007-01-01

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

  9. 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.

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

    SciTech Connect

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

    1995-12-31

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

  11. 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

  12. 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

  13. 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

  14. Asymmetric friction of nonmotor MAPs can lead to their directional motion in active microtubule networks.

    PubMed

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

    2014-04-10

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

  15. Microtesla MRI of the human brain combined with MEG

    NASA Astrophysics Data System (ADS)

    Zotev, Vadim S.; Matlashov, Andrei N.; Volegov, Petr L.; Savukov, Igor M.; Espy, Michelle A.; Mosher, John C.; Gomez, John J.; Kraus, Robert H.

    2008-09-01

    One of the challenges in functional brain imaging is integration of complementary imaging modalities, such as magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI). MEG, which uses highly sensitive superconducting quantum interference devices (SQUIDs) to directly measure magnetic fields of neuronal currents, cannot be combined with conventional high-field MRI in a single instrument. Indirect matching of MEG and MRI data leads to significant co-registration errors. A recently proposed imaging method—SQUID-based microtesla MRI—can be naturally combined with MEG in the same system to directly provide structural maps for MEG-localized sources. It enables easy and accurate integration of MEG and MRI/fMRI, because microtesla MR images can be precisely matched to structural images provided by high-field MRI and other techniques. Here we report the first images of the human brain by microtesla MRI, together with auditory MEG (functional) data, recorded using the same seven-channel SQUID system during the same imaging session. The images were acquired at 46 μT measurement field with pre-polarization at 30 mT. We also estimated transverse relaxation times for different tissues at microtesla fields. Our results demonstrate feasibility and potential of human brain imaging by microtesla MRI. They also show that two new types of imaging equipment—low-cost systems for anatomical MRI of the human brain at microtesla fields, and more advanced instruments for combined functional (MEG) and structural (microtesla MRI) brain imaging—are practical.

  16. Solar global horizontal and direct normal irradiation maps in Spain derived from geostationary satellites

    NASA Astrophysics Data System (ADS)

    Polo, J.

    2015-08-01

    Solar radiation derived from satellite imagery is a powerful and highly accurate technique for solar resource assessment due to its maturity and to the long term database of observation images available. This work presents the methodology developed at CIEMAT for mapping solar radiation from geostationary satellite information and it also shows solar irradiation maps of global horizontal and direct normal components elaborated for Spain. The maps presented here have been developed from daily solar irradiation estimated for eleven years of satellite images (2001-2011). An attempt to evaluate the uncertainty of the presented maps is made using ground measurements from 27 meteorological stations available in Spain for global horizontal irradiation obtained from the World Radiation Data Centre. In the case of direct normal irradiation the ground measurement database was scarce, having available only six ground stations with measurements for a period of 4 years. Yearly values of global horizontal irradiation are around 1800 kWh m-2 in most of the country and around 1950-2000 kWh m-2 for annual direct normal irradiation. Root mean square errors in monthly means were of 11% and of 29% for global horizontal and direct normal irradiation, respectively.

  17. Head MRI

    MedlinePlus

    ... the head; MRI - cranial; NMR - cranial; Cranial MRI; Brain MRI; MRI - brain; MRI - head ... tell your health care provider if you have: Brain aneurysm clips Certain types of artificial heart valves ...

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  19. Modulation of large-scale brain networks by transcranial direct current stimulation evidenced by resting-state functional MRI

    PubMed Central

    Peña-Gómez, Cleofé; Sala-Lonch, Roser; Junqué, Carme; Clemente, Immaculada C.; Vidal, Dídac; Bargalló, Núria; Falcón, Carles; Valls-Solé, Josep; Pascual-Leone, Álvaro; Bartrés-Faz, David

    2013-01-01

    Background Brain areas interact mutually to perform particular complex brain functions such as memory or language. Furthermore, under resting-state conditions several spatial patterns have been identified that resemble functional systems involved in cognitive functions. Among these, the default-mode network (DMN), which is consistently deactivated during task periods and is related to a variety of cognitive functions, has attracted most attention. In addition, in resting-state conditions some brain areas engaged in focused attention (such as the anticorrelated network, AN) show a strong negative correlation with DMN; as task demand increases, AN activity rises, and DMN activity falls. Objective We combined transcranial direct current stimulation (tDCS) with functional magnetic resonance imaging (fMRI) to investigate these brain network dynamics. Methods Ten healthy young volunteers underwent four blocks of resting-state fMRI (10-minutes), each of them immediately after 20 minutes of sham or active tDCS (2 mA), on two different days. On the first day the anodal electrode was placed over the left dorsolateral prefrontal cortex (DLPFC) (part of the AN) with the cathode over the contralateral supraorbital area, and on the second day, the electrode arrangement was reversed (anode right-DLPFC, cathode left-supraorbital). Results After active stimulation, functional network connectivity revealed increased synchrony within the AN components and reduced synchrony in the DMN components. Conclusions Our study reveals a reconfiguration of intrinsic brain activity networks after active tDCS. These effects may help to explain earlier reports of improvements in cognitive functions after anodal-tDCS, where increasing cortical excitability may have facilitated reconfiguration of functional brain networks to address upcoming cognitive demands. PMID:21962981

  20. 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.

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

    PubMed

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

    2013-01-01

    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

  2. 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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    Beltz, Adriene M; Molenaar, Peter C M

    2015-01-01

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

  5. Not all declarative memories are created equal: Fast Mapping as a direct route to cortical declarative representations.

    PubMed

    Merhav, Maayan; Karni, Avi; Gilboa, Asaf

    2015-08-15

    Memory formation for newly acquired associations typically depends on hippocampal-neocortical interactions. Through the process of system-consolidation, the mnemonic binding role of the hippocampus is subsequently replaced by cortical hubs, such as the ventromedial prefrontal cortex (vmPFC) or the anterior temporal lobe (ATL). Here, using BOLD-fMRI, we compared retrieval of semantic associations acquired through Fast Mapping (FM), an incidental, exclusion-based learning procedure, to retrieval of similar associations that were intentionally acquired through Explicit Encoding (EE). Despite an identical retrieval task, the encoding histories of the retrieved semantic associations (FM vs. EE) induced distinct neural substrates and disparate related neural dynamics in time. Retrieval of associations acquired through EE engaged the expected hippocampal and vmPFC related networks. Furthermore, retrieval intentionally encoded associations gave rise to a typical overnight increase in engagement of the vmPFC and increased vmPFC-hippocampal-neocortical functional connectivity. On the other hand, retrieval of associations acquired through FM immediately engaged an ATL related network that typically supports well-established semantic knowledge, a network that did not engage the hippocampus and the vmPFC. Moreover, FM learning was associated with minimal overnight changes in the BOLD responses and in the functional connectivity. Our findings indicate that FM may induce a direct, ATL-mediated acquisition and retention of novel arbitrary associations, bypassing the initial hippocampal-cortical representation phase. A direct, ATL-mediated vocabulary acquisition through FM could support the learning and retention of new associations in young children with presumably an immature hippocampal system, and possibly even in amnesic adults with hippocampal lesions. PMID:25988227

  6. The Validation of Complete Fourier Direct MR Method for Diffusion MRI via Biological and Numerical Phantoms

    PubMed Central

    Özcan, Alpay; Quirk, James D.; Wang, Yong; Wang, Qing; Sun, Peng; Spees, William M.; Song, Sheng–Kwei

    2012-01-01

    The equations of the Complete Fourier Direct (CFD) MR model are explicitly derived for diffusion weighted NMR experiments. The CFD–MR theory is validated by comparing a biological phantom constructed from nerve bundles and agar gel with its numerical implementation. The displacement integral distribution function estimated from the experimental data is in high agreement with the numerical phantom. CFD–MR’s ability to estimate accurately and fully spin diffusion properties demonstrated here, provides the experimental validation of the theoretical CFD–MR model. PMID:22255156

  7. 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

  8. Population Average T2 MRI Maps Reveal Quantitative Regional Transformations in the Degenerating Rabbit Intervertebral Disc that Vary by Lumbar Level

    PubMed Central

    Martin, John T.; Collins, Christopher M.; Mauck, Robert L.; Ikuta, Kensuke; Elliott, Dawn M.; Zhang, Yeija; Anderson, D. Greg; Vaccaro, Alexander R.; Albert, Todd J.; Arlet, Vincent; Smith, Harvey E.

    2015-01-01

    Magnetic resonance imaging (MRI) with T2-weighting is routinely performed to assess intervertebral disc degeneration. Standard clinical evaluations of MR images are qualitative, however, and do not focus on region-specific alterations in the disc. Utilizing a rabbit needle puncture model, T2 mapping was performed on injured discs to develop a quantitative description of the degenerative process following puncture. To do so, an 18G needle was inserted into four discs per rabbit (L3/L4 to L6/L7) and T2 maps were generated pre- and 4 weeks post-injury. Individual T2 maps were normalized to a disc-specific coordinate system and then averaged for pre- and post-injury population composite T2 maps. We also developed a method to automatically segment the nucleus pulposus by 2-D and 3-D curve fitting routines. Puncture injury produced alterations in MR signal intensity in a region-specific manner mirroring human degeneration. Population average T2 maps provided a quantitative representation of the injury response, and identified deviations of individual degenerate discs from the pre-injury population. We found that the response to standardized injury was modest at lower lumbar levels, likely as a result of increased disc dimensions. These tools will be valuable for the quantitative characterization of disc degeneration in future clinical and pre-clinical studies. PMID:25273831

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  10. Recent near-surface wind directions inferred from mapping sand ripples on Martian dunes

    NASA Astrophysics Data System (ADS)

    Liu, Zac Yung-Chun; Zimbelman, James R.

    2015-11-01

    The High Resolution Imaging Science Experiment (HiRISE) provides the capability to obtain orbital images of Mars that are of sufficient resolution to record wind ripple patterns on the surfaces of sand dunes. Ripple patterns provide valuable insights into aeolian erosion and deposition on Earth and Mars. In this study, we develop a systematic mapping procedure to examine sand ripple orientations and create surface process maps to evaluate the recent wind flow over the dunes, as well as the interplay of wind and dune shape. By carefully examining the morphology of the dunes and the location of grainflow and grainfall on dune slipfaces, the recent near-surface wind direction (short-term wind) can be identified. Results from the analysis of three dune fields on the floors of craters west of Hellas Basin show regional N, NW, SE, and ESE wind directions. In the three adjacent dune fields, surface process and flow maps suggest a complex wind pattern. The comparison of short-term wind with dune-constructing wind (long-term wind) shows NE and ESE winds may be persistent at least for the past thousands of years. The results also show that the orientation of inferred wind direction on linear dunes is correlated with the crestlines, which suggest that form-flow interaction may take place. The results of local wind flow documentation should improve Martian surface wind modeling and advance our understanding of sand transport, as well as the rates of sand mobility on both Mars and Earth.

  11. 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

  12. [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. PMID:22683402

  13. Regularization of diffusion-based direction maps for the tracking of brain white matter fascicles.

    PubMed

    Poupon, C; Clark, C A; Frouin, V; Régis, J; Bloch, I; Le Bihan, D; Mangin, J

    2000-08-01

    Magnetic resonance diffusion tensor imaging (DTI) provides information about fiber local directions in brain white matter. This paper addresses inference of the connectivity induced by fascicles made up of numerous fibers from such diffusion data. The usual fascicle tracking idea, which consists of following locally the direction of highest diffusion, is prone to erroneous forks because of problems induced by fiber crossing. In this paper, this difficulty is partly overcomed by the use of a priori knowledge of the low curvature of most of the fascicles. This knowledge is embedded in a model of the bending energy of a spaghetti plate representation of the white matter used to compute a regularized fascicle direction map. A new tracking algorithm is then proposed to highlight putative fascicle trajectories from this direction map. This algorithm takes into account potential fan shaped junctions between fascicles. A study of the tracking behavior according to the influence given to the a priori knowledge is proposed and concrete tracking results obtained with in vivo human brain data are illustrated. These results include putative trajectories of some pyramidal, commissural, and various association fibers. PMID:10913324

  14. 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

  15. 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.

  16. 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.

  17. Integration of quantitative DCE-MRI and ADC mapping to monitor treatment response in human breast cancer

    PubMed Central

    Yankeelov, Thomas E.; Lepage, Martin; Chakravarthy, Anuradha; Broome, Elizabeth E.; Niermann, Kenneth J.; Kelley, Mark C.; Meszoely, Ingrid; Mayer, Ingrid A.; Herman, Cheryl R.; McManus, Kevin; Price, Ronald R.; Gore, John C.

    2009-01-01

    Purpose The objective of this study was to assess changes in the water apparent diffusion coefficient (ADC) and in pharmacokinetic parameters obtained from the fast-exchange regime (FXR) modeling of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) during neoadjuvant chemotherapy in breast cancer. Materials and Methods Eleven patients with locally advanced breast cancer underwent MRI examination prior to and after chemotherapy but prior to surgery. A 1.5-T scanner was used to obtain T1, ADC and DCE-MRI data. DCE-MRI data were analyzed by the FXR model returning estimates of Ktrans (volume transfer constant), νe (extravascular extracellular volume fraction) and τsi (average intracellular water lifetime). Histogram and correlation analyses assessed parameter changes post-treatment. Results Significant ( P <.05) changes or trends towards significance ( P <.10) were seen in all parameters except τi, although there was qualitative reduction in τi values post-treatment. In particular, there was reduction ( P <.035) in voxels with Ktrans values in the range 0.2–0.5 min-1 and a decrease ( P <.05) in voxels with ADC values in the range 0.99×10-3 to 1.35×10-3 mm2/s. ADC and νe were negatively correlated (r = -.60, P <.02). Parameters sensitive to water distribution and geometry (T1, νe,τsi and ADC) correlated with a multivariable linear regression model. Conclusion The analysis presented here is sensitive to longitudinal changes in breast tumor status; Ktrans and ADC are most sensitive to these changes. Relationships between parameters provide information on water distribution and geometry in the tumor environment. PMID:17222711

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

    PubMed

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

    2013-01-15

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

  19. Perceptual Learning of Motion Direction Discrimination with Suppressed and Unsuppressed MT in Humans: An fMRI Study

    PubMed Central

    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. PMID:23326433

  20. Mapping.

    ERIC Educational Resources Information Center

    Kinney, Douglas M.; McIntosh, Willard L.

    1979-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  2. 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.

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

    PubMed

    Pavlovskaya, Galina E; Meersmann, Thomas

    2014-08-01

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

  4. 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

  5. Directed percolation criticality due to stochastic switching between attractive and repulsive coupling in coupled circle maps.

    PubMed

    Sonawane, Abhijeet R

    2010-05-01

    We study a lattice model where the coupling stochastically switches between repulsive (subtractive) and attractive (additive) at each site with probability p at every time instant. We observe that such a kind of coupling stabilizes the local fixed point of a circle map, with the resultant globally stable attractor providing a unique absorbing state. Interestingly, a continuous phase transition is observed from the absorbing state to spatiotemporal chaos via spatiotemporal intermittency for a range of values of p . It is interesting to note that the transition falls in class of directed percolation. Static and spreading exponents along with relevant scaling laws are found to be obeyed confirming the directed percolation universality class in spatiotemporal intermittency regime. PMID:20866306

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

    PubMed

    Minati, Ludovico; Cercignani, Mara; Chan, Dennis

    2013-10-01

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

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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

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

    PubMed

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

    2013-08-01

    We examined word-level reading circuits in skilled deaf readers whose primary language is American Sign Language, and hearing readers matched for reading ability (college level). During fMRI scanning, participants performed a semantic decision (concrete concept?), a phonological decision (two syllables?), and a false-font control task (string underlined?). The groups performed equally well on the semantic task, but hearing readers performed better on the phonological task. Semantic processing engaged similar left frontotemporal language circuits in deaf and hearing readers. However, phonological processing elicited increased neural activity in deaf, relative to hearing readers, in the left precentral gyrus, suggesting greater reliance on articulatory phonological codes, and in bilateral parietal cortex, suggesting increased phonological processing effort. Deaf readers also showed stronger anterior-posterior functional segregation between semantic and phonological processes in left inferior prefrontal cortex. Finally, weaker phonological decoding ability did not alter activation in the visual word form area for deaf readers. PMID:23747332

  15. Rapid Exploration of Configuration Space with Diffusion Map-directed-Molecular Dynamics

    PubMed Central

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

    2013-01-01

    The gap between the timescale of interesting behavior in macromolecular systems and that which our computational resources can afford oftentimes 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 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 300K 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. PMID:23865517

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

    NASA Astrophysics Data System (ADS)

    Gao, Hao

    2016-04-01

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

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

    PubMed

    Vankka, J

    1997-01-01

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

  18. Large scale directional anomalies in the WMAP 5yr ILC map

    SciTech Connect

    Gruppuso, Alessandro

    2010-03-01

    We study the alignments of the low multipoles of CMB anisotropies with specific directions in the sky (i.e. the dipole, the north Ecliptic pole, the north Galactic pole and the north Super Galactic pole). Performing 10{sup 5} random extractions we have found that: 1) separately quadrupole and octupole are mildly orthogonal to the dipole but when they are considered together, in analogy to Copi2006, we find an unlikely orthogonality at the level of 0.8% C.L.; 2) the multipole vectors associated to l = 4 are unlikely aligned with the dipole at 99.1% C.L.; 3) the multipole vectors associated to l = 5 are mildly orthogonal to the dipole but when we consider only maps that show exactly the same correlation among the multipoles as in the observed WMAP 5yr ILC, these multipole vectors are unlikely orthogonal to the dipole at 99.7% C.L.

  19. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  1. MAP6-F is a temperature sensor that directly binds to and protects microtubules from cold-induced depolymerization.

    PubMed

    Delphin, Christian; Bouvier, Denis; Seggio, Maxime; Couriol, Emilie; Saoudi, Yasmina; Denarier, Eric; Bosc, Christophe; Valiron, Odile; Bisbal, Mariano; Arnal, Isabelle; Andrieux, Annie

    2012-10-12

    Microtubules are dynamic structures that present the peculiar characteristic to be ice-cold labile in vitro. In vivo, microtubules are protected from ice-cold induced depolymerization by the widely expressed MAP6/STOP family of proteins. However, the mechanism by which MAP6 stabilizes microtubules at 4 °C has not been identified. Moreover, the microtubule cold sensitivity and therefore the needs for microtubule stabilization in the wide range of temperatures between 4 and 37 °C are unknown. This is of importance as body temperatures of animals can drop during hibernation or torpor covering a large range of temperatures. Here, we show that in the absence of MAP6, microtubules in cells below 20 °C rapidly depolymerize in a temperature-dependent manner whereas they are stabilized in the presence of MAP6. We further show that in cells, MAP6-F binding to and stabilization of microtubules is temperature- dependent and very dynamic, suggesting a direct effect of the temperature on the formation of microtubule/MAP6 complex. We also demonstrate using purified proteins that MAP6-F binds directly to microtubules through its Mc domain. This binding is temperature-dependent and coincides with progressive conformational changes of the Mc domain as revealed by circular dichroism. Thus, MAP6 might serve as a temperature sensor adapting its conformation according to the temperature to maintain the cellular microtubule network in organisms exposed to temperature decrease. PMID:22904321

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  3. 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.

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

    PubMed

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

    2016-09-01

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

  5. Annual Research Review: Current limitations and future directions in MRI studies of child- and adult-onset developmental psychopathologies

    PubMed Central

    Horga, Guillermo; Kaur, Tejal; Peterson, Bradley S.

    2014-01-01

    The widespread use of magnetic resonance imaging (MRI) in the study of child- and adult-onset developmental psychopathologies has generated many investigations that have measured brain structure and function in vivo throughout development, often generating great excitement over our ability to visualize the living, developing brain using the attractive, even seductive images that these studies produce. Often lost in this excitement is the recognition that brain imaging generally, and MRI in particular, is simply a technology, one that does not fundamentally differ from any other technology, be it a blood test, a genotyping assay, a biochemical assay, or behavioral test. No technology alone can generate valid scientific findings. Rather, it is only technology coupled with a strong experimental design that can generate valid and reproducible findings that lead to new insights into the mechanisms of disease and therapeutic response. In this review we discuss selected studies to illustrate the most common and important limitations of MRI study designs as most commonly implemented thus far, as well as the misunderstanding that the interpretations of findings from those studies can create for our theories of developmental psychopathologies. Those limitations are in large part responsible thus far for the generally poor reproducibility of findings across studies, poor generalizability to the larger population, failure to identify developmental trajectories, inability to distinguish causes from effects of illness, and poor ability to infer causal mechanisms in most MRI studies of developmental psychopathologies. For each of these limitations in study design and the difficulties they entail for the interpretation of findings, we discuss various approaches that numerous laboratories are now taking to address those difficulties, which have in common the yoking of brain imaging technologies to studies with inherently stronger designs that permit more valid and more powerful

  6. 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

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

    PubMed

    Jung, JeYoung; Lambon Ralph, Matthew A

    2016-08-01

    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

  8. Comparison of cardiac stroke volume measurement determined using stereological analysis of breath-hold cine MRI and phase contrast velocity mapping.

    PubMed

    Graves, M J; Dommett, D M

    2000-08-01

    Cine MRI of the heart using segmented k-space pulse sequences permits multiphase images to be acquired in a single breath-hold. Whilst image quality is improved compared with conventional (non-segmented) cine imaging, subsequent analysis can be relatively time consuming. In this study, multiple slice breath-hold cine imaging of the heart was performed in 11 normal volunteers. Left and right ventricular stroke volume (SV) was estimated from the images by application of the Cavalieri method of modern design stereology in combination with point counting. The measured SVs were compared with those obtained by cine phase contrast velocity mapping in the ascending aorta and main pulmonary artery. Excellent agreement was found between the SVs determined by the two techniques, with mean differences (+/- one SD) of 0.41 +/- 3.00 ml and 0.41 +/- 4.78 ml for left and right ventricles, respectively. Comparison of left and right ventricular SV using stereology yielded a mean difference of 0.84 +/- 5.70 ml. Breath-hold data acquisition together with stereological analysis is demonstrated to be an accurate and unbiased technique for the rapid assessment of cardiac function. PMID:11026856

  9. Quantitative Measurement of Blood-Brain Barrier Permeability in Human Using Dynamic Contrast-Enhanced MRI with Fast T1 Mapping

    PubMed Central

    Taheri, Saeid; Gasparovic, Charles; Shah, Nadim Jon; Rosenberg, Gary A.

    2016-01-01

    Breakdown of the blood-brain barrier (BBB), occurring in many neurological diseases, has been difficult to measure noninvasively in humans. Dynamic contrast-enhanced magnetic resonance imaging measures BBB permeability. However, important technical challenges remain and normative data from healthy humans is lacking. We report the implementation of a method for measuring BBB permeability, originally developed in animals, to estimate BBB permeability in both healthy subjects and patients with white matter pathology. Fast T1 mapping was used to measure the leakage of contrast agent Gadolinium diethylene triamine pentaacetic acid (Gd-DTPA) from plasma into brain. A quarter of the standard Gd-DTPA dose for dynamic contrast-enhanced magnetic resonance imaging was found to give both sufficient contrast-to-noise and high T1 sensitivity. The Patlak graphical approach was used to calculate the permeability from changes in 1/T1. Permeability constants were compared with cerebrospinal fluid albumin index. The upper limit of the 95% confidence interval for white matter BBB permeability for normal subjects was 3 × 10−4 L/g min. MRI measurements correlated strongly with levels of cerebrospinal fluid albumin in those subjects undergoing lumbar puncture. Dynamic contrast-enhanced magnetic resonance imaging with low dose Gd-DTPA and fast T1 imaging is a sensitive method to measure subtle differences in BBB permeability in humans and may have advantages over techniques based purely on the measurement of pixel contrast changes. PMID:21413067

  10. 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.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  13. High resolution (13)C MRI with hyperpolarized urea: in vivo T(2) mapping and (15)N labeling effects.

    PubMed

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

    2014-02-01

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

  14. 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

  15. The cerebral basis of mapping nonsymbolic numerical quantities onto abstract symbols: an fMRI training study.

    PubMed

    Lyons, Ian M; Ansari, Daniel

    2009-09-01

    Although significant insights into the neural basis of numerical and mathematical processing have been made, the neural processes that enable abstract symbols to become numerical remain largely unexplored in humans. In the present study, adult participants were trained to associate novel symbols with nonsymbolic numerical magnitudes (arrays of dots). Functional magnetic resonance imaging was used to examine the neural correlates of numerical comparison versus recognition of the novel symbols after each of two training stages. A left-lateralized fronto-parietal network, including the intraparietal sulcus, the precuneus, and the dorsal prefrontal cortex, was more active during numerical comparison than during perceptual recognition. In contrast, a network including bilateral temporal-occipital regions was more active during recognition than comparison. A whole-brain three-way interaction revealed that those individuals who had higher scores on a postscan numerical task (measuring their understanding of the global numerical organization of the novel symbols) exhibited increasing segregation between the two tasks in the bilateral intraparietal sulci as a function of increased training. Furthermore, whole-brain regression analysis showed that activity in the left intraparietal sulcus was systematically related to the effect of numerical distance on accuracy. These data provide converging evidence that parietal and left prefrontal cortices are involved in learning to map numerical quantities onto visual symbols. Only the parietal cortex, however, appeared systematically related to the degree to which individuals learned to associate novel symbols with their numerical referents. We conclude that the left parietal cortex, in particular, may play a central role in imbuing visual symbols with numerical meaning. PMID:18823231

  16. 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."

  17. MRI Scans

    MedlinePlus

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

  18. Heart MRI

    MedlinePlus

    ... severe kidney problems. People have been harmed in MRI machines when they did not remove metal objects from their clothes or when metal objects were left in the room by others. MRI is most often not recommended for traumatic injuries. ...

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

    USGS Publications Warehouse

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

    2007-01-01

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

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

    PubMed Central

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

    2010-01-01

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

  1. 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.

  2. Direct/Delayed Response Project: Field operations and quality-assurance report for watershed mapping in the Mid-Appalachian region of the United States

    SciTech Connect

    Kern, J.S.; Lammers, D.A.; Cassell, D.L.; Campbell, W.G.

    1990-05-01

    The report documents the mapping program of the Direct/Delayed Response Project in the Mid-Appalachian Region of the United States. The objectives of the report is to document the planning activities, field operations, and quality assurance/quality control (QA/QC) of the mapping. The protocols, QA plan, and soil legend for the watershed mapping are presented as appendices.

  3. 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

  4. EMRinger: Side-chain-directed model and map validation for 3D Electron Cryomicroscopy

    PubMed Central

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

    2015-01-01

    Advances in high resolution electron cryomicroscopy (cryo-EM) have been accompanied by the development of validation metrics to independently assess map quality and model geometry. EMRinger 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 will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM. PMID:26280328

  5. Cerebral blood flow quantification in the rat: a direct comparison of arterial spin labeling MRI with radioactive microsphere PET

    PubMed Central

    2012-01-01

    Background Arterial spin labeling magnetic resonance imaging (ASL-MRI) has been recognised as a valuable method for non-invasive assessment of cerebral blood flow but validation studies regarding quantification accuracy by comparison against an accepted gold standard are scarce, especially in small animals. We have conducted the present study with the aim of comparing ASL flow-sensitive alternating inversion recovery (FAIR)-derived unidirectional water uptake (K1) and 68Ga/64Cu microsphere (MS)-derived blood flow (f) in the rat brain. Methods In 15 animals, K1and f were determined successively in dedicated small animal positron emission tomography and MR scanners. The Renkin-Crone model modified by a scaling factor was used for the quantification of f and K1. Results Below about 1 mL/min/mL, we obtain an approximately linear relationship between f and K1. At higher flow values, the limited permeability of water at the blood brain barrier becomes apparent. Within the accessed dynamic flow range (0.2 to 1.9 mL/min/mL), the data are adequately described by the Renkin-Crone model yielding a permeability surface area product of (1.53±0.46) mL/min/mL. Conclusion The ASL-FAIR technique is suitable for absolute blood flow quantification in the rat brain when using a one-compartment model including a suitable extraction correction for data evaluation. Trial registration 24-9168.21-4/2004-1 (registered in Freistadt Sachsen, Landesdirektion Dresden) PMID:22978819

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

    NASA Astrophysics Data System (ADS)

    Rebich, S.

    2003-12-01

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

  7. Resting-state functional MRI in an intraoperative MRI setting: proof of feasibility and correlation to clinical outcome of patients.

    PubMed

    Roder, Constantin; Charyasz-Leks, Edyta; Breitkopf, Martin; Decker, Karlheinz; Ernemann, Ulrike; Klose, Uwe; Tatagiba, Marcos; Bisdas, Sotirios

    2016-08-01

    OBJECTIVE The authors' aim in this paper is to prove the feasibility of resting-state (RS) functional MRI (fMRI) in an intraoperative setting (iRS-fMRI) and to correlate findings with the clinical condition of patients pre- and postoperatively. METHODS Twelve patients underwent intraoperative MRI-guided resection of lesions in or directly adjacent to the central region and/or pyramidal tract. Intraoperative RS (iRS)-fMRI was performed pre- and intraoperatively and was correlated with patients' postoperative clinical condition, as well as with intraoperative monitoring results. Independent component analysis (ICA) was used to postprocess the RS-fMRI data concerning the sensorimotor networks, and the mean z-scores were statistically analyzed. RESULTS iRS-fMRI in anesthetized patients proved to be feasible and analysis revealed no significant differences in preoperative z-scores between the sensorimotor areas ipsi- and contralateral to the tumor. A significant decrease in z-score (p < 0.01) was seen in patients with new neurological deficits postoperatively. The intraoperative z-score in the hemisphere ipsilateral to the tumor had a significant negative correlation with the degree of paresis immediately after the operation (r = -0.67, p < 0.001) and on the day of discharge from the hospital (r = -0.65, p < 0.001). Receiver operating characteristic curve analysis demonstrated moderate prognostic value of the intraoperative z-score (area under the curve 0.84) for the paresis score at patient discharge. CONCLUSIONS The use of iRS-fMRI with ICA-based postprocessing and functional activity mapping is feasible and the results may correlate with clinical parameters, demonstrating a significant negative correlation between the intensity of the iRS-fMRI signal and the postoperative neurological changes. PMID:26722852

  8. 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.

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

    DOE PAGESBeta

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

    2015-08-17

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

  10. Direct Mapping Of Density Response in Recombinant Inbred Lines of Maize (Zea mays L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Breeding for adaptation to higher densities in maize has greatly increased maize yield potential per unit area but the genetic basis for this plant response to density is unknown as is its stability over environments. To elucidate the genetic basis of plant response to density in Maize, we mapped QT...

  11. 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. PMID:26374674

  12. 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

  13. Comparison of User-Directed and Automatic Mapping of the Planned Isocenter to Treatment Space for Prostate IGRT

    PubMed Central

    Wang, Andrew; Kress, Andrea; Qin, An; Cullip, Timothy; Tracton, Gregg; Yan, Di; Chaney, Edward

    2013-01-01

    Image-guided radiotherapy (IGRT), adaptive radiotherapy (ART), and online reoptimization rely on accurate mapping of the radiation beam isocenter(s) from planning to treatment space. This mapping involves rigid and/or nonrigid registration of planning (pCT) and intratreatment (tCT) CT images. The purpose of this study was to retrospectively compare a fully automatic approach, including a non-rigid step, against a user-directed rigid method implemented in a clinical IGRT protocol for prostate cancer. Isocenters resulting from automatic and clinical mappings were compared to reference isocenters carefully determined in each tCT. Comparison was based on displacements from the reference isocenters and prostate dose-volume histograms (DVHs). Ten patients with a total of 243 tCTs were investigated. Fully automatic registration was found to be as accurate as the clinical protocol but more precise for all patients. The average of the unsigned x, y, and z offsets and the standard deviations (σ) of the signed offsets computed over all images were (avg. ±  σ (mm)): 1.1 ± 1.4, 1.8 ± 2.3, 2.5 ± 3.5 for the clinical protocol and 0.6 ± 0.8, 1.1 ± 1.5 and 1.1 ± 1.4 for the automatic method. No failures or outliers from automatic mapping were observed, while 8 outliers occurred for the clinical protocol. PMID:24348526

  14. 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.

  15. The Opportunities Map at Cornell University: finding direction in dairy production medicine.

    PubMed

    Mitchell, Hilda M; Nydam, Daryl V; Reyher, Kristen; Gilbert, Robert O

    2004-01-01

    Discussion between faculty and interested students revealed the existence of a multitude of opportunities in dairy production medicine at the College of Veterinary Medicine at Cornell University. Many of these were not well known to students, or even to some of the faculty, and the means of accessing specific learning experiences were sometimes obscure. Together, an informal group of faculty, students, and alumni set about cataloging available educational opportunities, resulting in a 31-page publication referred to as the "Opportunities Map." Essentially a student handbook for production medicine students, the Opportunities Map at Cornell helps guide the travel of food animal-interested students through the curriculum without missing the important highlights along the way. The map was originally developed to chronicle the opportunities and resources available to students, but it has also been used to foster face-to-face communications between students and faculty, to welcome incoming students with production animal interests, and to provide a baseline description for further discussion about the curriculum. PMID:15551234

  16. 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

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

    PubMed

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

    2016-01-15

    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 7T 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

  18. 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. PMID:22349497

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  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. PMID:25571558

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

    PubMed

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

    2015-12-15

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

  3. 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

  4. 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…

  5. Musculoskeletal MRI.

    PubMed

    Sage, Jaime E; Gavin, Patrick

    2016-05-01

    MRI has the unique ability to detect abnormal fluid content, and is therefore unparalleled in its role of detection, diagnosis, prognosis, treatment planning and follow-up evaluation of musculoskeletal disease. MRI in companion animals should be considered in the following circumstances: a definitive diagnosis cannot be made on radiographs; a patient is nonresponsive to medical or surgical therapy; prognostic information is desired; assessing surgical margins and traumatic and/or infectious joint and bone disease; ruling out subtle developmental or early aggressive bone lesions. The MRI features of common disorders affecting the shoulder, elbow, stifle, carpal, and tarsal joints are included in this chapter. PMID:26928749

  6. 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.

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

    PubMed

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

    2016-01-01

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

  8. 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

  9. Scientists attack European MRI rules

    NASA Astrophysics Data System (ADS)

    Harris, Margaret

    2010-08-01

    A report by the European Science Foundation (ESF) has sharply criticized a European Union (EU) directive on electromagnetic fields, arguing that limits on workers' exposure will have "potentially disastrous" consequences for magnetic resonance imaging (MRI).

  10. Heart MRI

    MedlinePlus

    ... an imaging method that uses powerful magnets and radio waves to create pictures of the heart. It does ... radiation involved in MRI. The magnetic fields and radio waves used during the scan have not been shown ...

  11. Obstetric MRI.

    PubMed

    Levine, Deborah

    2006-07-01

    Ultrasound is the imaging modality of choice for pregnant patients. However, MRI is increasingly utilized in patients in whom the sonographic diagnosis is unclear. These include maternal conditions unique to pregnancy such as ectopic pregnancy, placenta accreta, and uterine dehiscence. MRI is also being increasingly utilized in the assessment of abdominopelvic pain in pregnancy, in particular in assessment for appendicitis. Fetal MRI is performed to assess central nervous system (CNS) abnormalities and patients who are considering fetal surgery for conditions such as neural tube defects, congenital diaphragmatic hernia, and masses that obstruct the airway. In the future, functional MRI and fetal volumetry may provide additional information that can aid in our care of complicated pregnancies. PMID:16736491

  12. Intracortical Posterior Cingulate Myelin Content Relates to Error Processing: Results from T1- and T2-Weighted MRI Myelin Mapping and Electrophysiology in Healthy Adults.

    PubMed

    Grydeland, Håkon; Westlye, Lars T; Walhovd, Kristine B; Fjell, Anders M

    2016-06-01

    Myelin content of the cerebral cortex likely impacts cognitive functioning, but this notion has scarcely been investigated in vivo in humans. Here we tested for a relationship between intracortical myelin and a direct measure of neural activity in the form of the electrophysiological response error-related negativity (ERN). Using magnetic resonance imaging, myelin mapping was performed in 81 healthy adults aged 40-60 years by means of a T1- and T2-weighted (T1w/T2w) signal intensity ratio approach. Error trials on a version of the Eriksen flanker task triggered the ERN, a negative deflection of the event-related potential reflecting performance monitoring. Compelling evidence from neuroimaging, lesion, and source localization studies indicates that the ERN stems from the cingulate cortex. Vertex-wise analyses across the cingulate demonstrated that increased amplitude of the ERN was related to higher levels of intracortical myelin in the left posterior cingulate cortex. The association was independent of general ability level and subjacent white matter myelin. The results fit the notion that degree of myelin within the posterior cingulate cortex as measured by T1w/T2w signal intensity plays a role in error processing and cognitive control through the relationship with neural activity as measured by ERN amplitude, potentially by facilitating local neural synchronization. PMID:25840423

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

    DOE PAGESBeta

    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.

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

    SciTech Connect

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

    1993-06-01

    The problems in moving from a radiance measurement made for a particular sun-target-sensor geometry to an accurate estimate of the hemispherical reflectance are considerable. A knowledge-based system called VEG was used in this study to infer hemispherical reflectance. Given directional reflectance(s) and the sun angle, VEG selects the most suitable inference technique(s) and estimates the surface hemispherical reflectance with an estimate of the error. Ideally, VEG is applied to homogeneous vegetation. However, what is typically done in GCM (global circulation model) models and related studies is to obtain an average hemispherical reflectance on a square grid cell on the order of 200 km x 200 km. All available directional data for a given cell are averaged (for each view direction), and then a particular technique for inferring hemispherical reflectance is applied to this averaged data. Any given grid cell can contain several surface types that directionally scatter radiation very differently. When averaging over a set of view angles, the resulting mean values may be atypical of the actual surface types that occur on the ground, and the resulting inferred hemispherical reflectance can be in error. These errors were explored by creating a simulated scene and applying VEG to estimate the area-averaged hemispherical reflectance using various sampling procedures. The reduction in the hemispherical reflectance errors provided by using VEG ranged from a factor of 2-4, depending on conditions. This improvement represents a shift from the calculation of a hemispherical reflectance product of relative value (errors of 20% or more), to a product that could be used quantitatively in global modeling applications, where the requirement is for errors to be limited to around 5-10 %.

  15. T₁ρ MRI of human musculoskeletal system.

    PubMed

    Wang, Ligong; Regatte, Ravinder R

    2015-03-01

    Magnetic resonance imaging (MRI) offers the direct visualization of the human musculoskeletal (MSK) system, especially all diarthrodial tissues including cartilage, bone, menisci, ligaments, tendon, hip, synovium, etc. Conventional MRI techniques based on T1 - and T2 -weighted, proton density (PD) contrast are inconclusive in quantifying early biochemically degenerative changes in MSK system in general and articular cartilage in particular. In recent years, quantitative MR parameter mapping techniques have been used to quantify the biochemical changes in articular cartilage, with a special emphasis on evaluating joint injury, cartilage degeneration, and soft tissue repair. In this article we focus on cartilage biochemical composition, basic principles of T1ρ MRI, implementation of T1ρ pulse sequences, biochemical validation, and summarize the potential applications of the T1ρ MRI technique in MSK diseases including osteoarthritis (OA), anterior cruciate ligament (ACL) injury, and knee joint repair. Finally, we also review the potential advantages, challenges, and future prospects of T1ρ MRI for widespread clinical translation. PMID:24935818

  16. Direct (13)C-detected NMR experiments for mapping and characterization of hydrogen bonds in RNA.

    PubMed

    Fürtig, Boris; Schnieders, Robbin; Richter, Christian; Zetzsche, Heidi; Keyhani, Sara; Helmling, Christina; Kovacs, Helena; Schwalbe, Harald

    2016-03-01

    In RNA secondary structure determination, it is essential to determine whether a nucleotide is base-paired and not. Base-pairing of nucleotides is mediated by hydrogen bonds. The NMR characterization of hydrogen bonds relies on experiments correlating the NMR resonances of exchangeable protons and can be best performed for structured parts of the RNA, where labile hydrogen atoms are protected from solvent exchange. Functionally important regions in RNA, however, frequently reveal increased dynamic disorder which often leads to NMR signals of exchangeable protons that are broadened beyond (1)H detection. Here, we develop (13)C direct detected experiments to observe all nucleotides in RNA irrespective of whether they are involved in hydrogen bonds or not. Exploiting the self-decoupling of scalar couplings due to the exchange process, the hydrogen bonding behavior of the hydrogen bond donor of each individual nucleotide can be determined. Furthermore, the adaption of HNN-COSY experiments for (13)C direct detection allows correlations of donor-acceptor pairs and the localization of hydrogen-bond acceptor nucleotides. The proposed (13)C direct detected experiments therefore provide information about molecular sites not amenable by conventional proton-detected methods. Such information makes the RNA secondary structure determination by NMR more accurate and helps to validate secondary structure predictions based on bioinformatics. PMID:26852414

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

    PubMed

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

    2012-10-01

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

  18. Mapping for prevention: GIS models for directing childhood lead poisoning prevention programs.

    PubMed Central

    Miranda, Marie Lynn; Dolinoy, Dana C; Overstreet, M Alicia

    2002-01-01

    Environmental threats to children's health--especially low-level lead exposure--are complex and multifaceted; consequently, mitigation of these threats has proven costly and insufficient and has produced economic and racial disparities in exposure among populations. Policy makers, public health officials, child advocates, and others currently lack the appropriate infrastructure to evaluate children's risk and exposure potential across a broad range of risks. Unable to identify where the highest risk of exposure occurs, children's environmental health programs remain mitigative instead of preventive. In this article we use geographic information system spatial analysis of data from blood lead screening, county tax assessors, and the U.S. Census to predict statistically based lead exposure risk levels mapped at the individual tax parcel unit in six counties in North Carolina. The resulting model uses weighted risk factors to spatially locate modeled exposure zones, thus highlighting critical areas for targeted intervention. The methods presented here hold promise for application and extension to the other 94 North Carolina counties and nationally, as well as to other environmental health risks. PMID:12204831

  19. 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

  20. CT and MRI evaluation of cardiac complications in patients with hematologic diseases: a pictorial review.

    PubMed

    Kim, Tae Yun; Jung, Jung Im; Kim, Yoo Jin; Kim, Hwan Wook; Lee, Hae Giu

    2015-12-01

    Cardiac complications with hematologic diseases are not uncommon but it is difficult to diagnose, due to non-specific clinical symptoms. Prompt recognition of these potentially fatal complications by cardiac computed tomography (CT) or cardiac magnetic resonance imaging (MRI) may help to direct clinicians to specific treatments according to causes. Thrombosis is often related to central venous catheter use and is usually located at the catheter tip near the atrial wall. Differentiation of thrombosis from normal structure is possible with CT and, distinction of a thrombus from a tumor is possible on a delayed enhancement MRI with a long inversion time (500-600 ms). Granulocytic sarcoma of the heart is indicated by an infiltrative nature with involvement of whole layers of myocardium on CT and MRI. MRI with T2* mapping is useful in evaluating myocardial iron content in patients with hemochromatosis. Diffuse subendocardial enhancement is typically observed on delayed MRIs in patients with cardiac amyloidosis. T1 mapping is an emerging tool to diagnose amyloidosis. Myocardial abscess can occur due to an immunocompromised status. CT and MRI show loculated lesions with fluid density and concomitant rim-like contrast enhancement. Awareness of CT and MRI findings of cardiac complications of hematologic diseases can be helpful to physicians for clinical decision making and treatment. PMID:25651878

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

    PubMed

    Wang, Yuezong; Zhao, Zhizhong; Wang, Junshuai

    2016-04-01

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

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

    PubMed

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

    2016-09-01

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

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

    PubMed Central

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

    2014-01-01

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

  4. 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.

  5. Cortical Mapping by Magnetic Resonance Imaging (MRI) and Quantitative Cytological Analysis in the Human Brain: A Feasibility Study in the Fusiform Gyrus

    PubMed Central

    Schenker-Ahmed, Natalie M.; Annese, Jacopo

    2013-01-01

    The cerebral cortex is a layered cellular structure that is tangentially organized into a mosaic of anatomically and functionally distinct fields. In spite of centuries of investigation, the precise localization and classification of many areas in the cerebral cortex remain problematic because the relationship between functional specificity and intra-cortical structure has not been firmly established. Furthermore, it is not yet clear how surface landmarks, visible through gross examination and, more recently, using non-invasive magnetic resonance imaging (MRI), relate to underlying microstructural borders and to the topography of functional activation. We have designed a multi-modal neuroimaging protocol that combines MRI and quantitative microscopic analysis in the same individual to clarify the topography of cytoarchitecture underlying gross anatomical landmarks in the cerebral cortex. We tested our approach in the region of the fusiform gyrus (FG), because in spite of its seemingly smooth appearance on the ventral aspect of both hemispheres, this structure houses many functionally defined areas whose histological borders remain unclear. In practice, we used MRI-based automated segmentation to define the region of interest from which we could then collect quantitative histological data (specifically, neuronal size and density). A modified stereological approach was used to sample the cortex within the FG without a priori assumptions on the location of architectonic boundaries. The results of these analyses illustrate architectonic variations along the FG and demonstrate that it is possible to correlate quantitative histological data to measures that are obtained in the context of large-scale, non-invasive MRI-based population studies. PMID:23628159

  6. 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. PMID:25342449

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

    SciTech Connect

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

    2012-04-01

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

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed Central

    Putnam, William C.; Daniher, Andrew T.; Trawick, Bobby N.; Bashkin, James K.

    2001-01-01

    Dramatic improvements in ribozyme mimics have been achieved by employing the principles of small molecule catalysis to the design of macromolecular, biomimetic reagents. Ribozyme mimics derived from the ligand 2,9-dimethylphenanthroline (neocuproine) show at least 30-fold improvements in efficiency at sequence-specific RNA cleavage when compared with analogous o-phenanthroline- and terpyridine-derived reagents. The suppression of hydroxide-bridged dimers and the greater activation of coordinated water by Cu(II) neocuproine (compared with the o-phananthroline and terpyridine complexes) better allow Cu(II) to reach its catalytic potential as a biomimetic RNA cleavage agent. This work demonstrates the direct mapping of molecular design principles from small-molecule cleavage to macromolecular cleavage events, generating enhanced biomimetic, sequence-specific RNA cleavage agents. PMID:11353090

  10. 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. PMID:25430130

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

    PubMed

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

    2014-10-01

    The ability to detect nanosecond backbone dynamics with site-directed spin labeling (SDSL) in soluble proteins has been well established. However, for membrane proteins, the nitroxide appears to have more interactions with the protein surface, potentially hindering the sensitivity to backbone motions. To determine whether membrane protein backbone dynamics could be mapped with SDSL, a nitroxide was introduced at 55 independent sites in a model polytopic membrane protein, TM0026. Electron paramagnetic resonance spectral parameters were compared with NMR (15)N-relaxation data. Sequential scans revealed backbone dynamics with the same trends observed for the R1 relaxation rate, suggesting that nitroxide dynamics remain coupled to the backbone on membrane proteins. PMID:25296323

  12. 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.

  13. 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.

  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

    2016-06-01

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

  15. 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.

  16. Chemiluminescence system for direct determination and mapping of ultra-trace metal impurities on a silicon wafer.

    PubMed

    Kim, Romertta; Sung, Y I; Lee, J S; Lim, H B

    2010-11-01

    A highly sensitive chemiluminescence (CL) system which consumed low sample and reagent volumes in the microlitre range was developed for direct determination and mapping of ultra-trace metal contaminants on solid surfaces, such as silicon wafers or flat display panels. The analytical result of the system was confirmed with ICP-MS. The system was composed of a scanner, sensor and a wafer moving stage. The scanner, with a scanning tip made of 0.03'' i.d. PTFE tubing, was used to collect metal impurities on the wafer surface with 5 μL of scanning solution. A coaxial sensing head of about 13 mm o.d. and 110 mm height was designed both to inject a luminescent reagent of luminol-H(2)O(2) mixture and to collect the luminescence light resulting from the reaction with metal ions of Co(2+), Fe(2+), Cu(2+), and Ni(2+). Due to the almost zero background, an extremely low limit of detection of 20.8 pg/mL for Co(2+) in 1% hydrofluoric acid (HF) was obtained from the calibration curve. In order to map the spatial distribution of the impurities, 11 cross sections of a Co-contaminated wafer were selected and scanned individually with a diluted HF solution. A contaminant level of 1.45-7.11 × 10(11) atoms cm(-2) was obtained for each section with an average of 4.21 × 10(11) atoms cm(-2), which was similar to the analytical result of 5.48 × 10(11) atoms cm(-2) obtained from vapor phase deposition-inductively coupled plasma-mass spectrometry (VPD-ICP-MS). Although this CL system does not have selectivity for each specific metal ion, its high sensitivity facilitates the monitoring and mapping of metal impurities of Co, Fe, Cu, etc. on the wafer directly and it can be used as an on-line inspection sensor for the first time in the semiconductor industry. PMID:20871885

  17. 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

  18. 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

  19. Quantitative MRI techniques of cartilage composition

    PubMed Central

    Matzat, Stephen J.; van Tiel, Jasper; Gold, Garry E.

    2013-01-01

    Due to aging populations and increasing rates of obesity in the developed world, the prevalence of osteoarthritis (OA) is continually increasing. Decreasing the societal and patient burden of this disease motivates research in prevention, early detection of OA, and novel treatment strategies against OA. One key facet of this effort is the need to track the degradation of tissues within joints, especially cartilage. Currently, conventional imaging techniques provide accurate means to detect morphological deterioration of cartilage in the later stages of OA, but these methods are not sensitive to the subtle biochemical changes during early disease stages. Novel quantitative techniques with magnetic resonance imaging (MRI) provide direct and indirect assessments of cartilage composition, and thus allow for earlier detection and tracking of OA. This review describes the most prominent quantitative MRI techniques to date—dGEMRIC, T2 mapping, T1rho mapping, and sodium imaging. Other, less-validated methods for quantifying cartilage composition are also described—Ultrashort echo time (UTE), gagCEST, and diffusion-weighted imaging (DWI). For each technique, this article discusses the proposed biochemical correlates, as well its advantages and limitations for clinical and research use. The article concludes with a detailed discussion of how the field of quantitative MRI has progressed to provide information regarding two specific patient populations through clinical research—patients with anterior cruciate ligament rupture and patients with impingement in the hip. While quantitative imaging techniques continue to rapidly evolve, specific challenges for each technique as well as challenges to clinical applications remain. PMID:23833729

  20. How to scan polymer gels with MRI?

    NASA Astrophysics Data System (ADS)

    De Deene, Y.

    2013-06-01

    The absorbed radiation dose fixated in a polymer gel dosimeter can be read out by several methods such as magnetic resonance imaging (MRI), optical CT, X-ray CT and ultrasound with MRI being the first method that was explored. Although MRI was considered as an elegant scanning technique, readily available in most hospitals, it was later found that using a non-optimized imaging protocol may result in unacceptable deviations in the obtained dose distribution. Although most medical physicists have an understanding of the basic principles of magnetic resonance imaging (MRI), the optimization of quantitative imaging sequences and protocols is often perceived as the work of MRI experts. In this paper, we aim at providing the reader with some easy guidelines in how to obtain reliable quantitative MRI maps.

  1. Robust isotropic super-resolution by maximizing a Laplace posterior for MRI volumes

    NASA Astrophysics Data System (ADS)

    Han, Xian-Hua; Iwamoto, Yutaro; Shiino, Akihiko; Chen, Yen-Wei

    2014-03-01

    Magnetic resonance imaging can only acquire volume data with finite resolution due to various factors. In particular, the resolution in one direction (such as the slice direction) is much lower than others (such as the in-plane direction), yielding un-realistic visualizations. This study explores to reconstruct MRI isotropic resolution volumes from three orthogonal scans. This proposed super- resolution reconstruction is formulated as a maximum a posterior (MAP) problem, which relies on the generation model of the acquired scans from the unknown high-resolution volumes. Generally, the deviation ensemble of the reconstructed high-resolution (HR) volume from the available LR ones in the MAP is represented as a Gaussian distribution, which usually results in some noise and artifacts in the reconstructed HR volume. Therefore, this paper investigates a robust super-resolution by formulating the deviation set as a Laplace distribution, which assumes sparsity in the deviation ensemble based on the possible insight of the appeared large values only around some unexpected regions. In addition, in order to achieve reliable HR MRI volume, we integrates the priors such as bilateral total variation (BTV) and non-local mean (NLM) into the proposed MAP framework for suppressing artifacts and enriching visual detail. We validate the proposed robust SR strategy using MRI mouse data with high-definition resolution in two direction and low-resolution in one direction, which are imaged in three orthogonal scans: axial, coronal and sagittal planes. Experiments verifies that the proposed strategy can achieve much better HR MRI volumes than the conventional MAP method even with very high-magnification factor: 10.

  2. 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

  3. The application of MRI and MRS in psychiatry and performance evaluation of magnetic field homogeneity in MRI

    NASA Astrophysics Data System (ADS)

    Chen, Hua Hsuan

    Magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) is a safe non-invasive tool to study the physiological mechanisms of the human brain. MRS has the capability to provide the information regarding neurochemicals in brains of patients with neuropsychiatric disorders. Therefore, to produce measurable and interpretable information in MRI and MRS, a quality control (QC) program is required. Magnetic field homogeneity (MFH) is an important factor for QC when the volume sizes and neurochemical levels are quantified. Poor main (B0) MFH leads to artifacts, signal losses and broadened line widths. The American College of Radiology's (ACR) MRI QC manual mandates annual checks of MFH, suggesting tests using spectral line widths (FWHM) and phase-difference (Deltaϕ) maps. A new method, dubbed the bandwidth-difference (DeltaBW) method, is proposed along with a prototype phantom for determining MFH. The DeltaBW method is compared with standard methods and has also been tested in different model MRI systems from various manufacturers. Direct comparisons of the data obtained using the DeltaBW method demonstrated good agreement with data obtained using the linewidth method and the frequency map data provided by one MRI system manufacturer. As a result, the DeltaBW method produces measurements of MFH at various Diameter Sphere Volume (DSV) values that can be obtained from a single set of phantom images. The conclusion of the study is that the accuracy of DeltaBW B0 homogeneity measurements of MFH is comparable to the other methods tested while the ease of measurement in practical clinical setting is considerably improved.

  4. Assessment of myocardial changes in athletes with native T1 mapping and cardiac functional evaluation using 3 T MRI.

    PubMed

    Görmeli, Cemile Ayşe; Görmeli, Gökay; Yağmur, Jülide; Özdemir, Zeynep Maraş; Kahraman, Ayşegül Sağır; Çolak, Cemil; Özdemir, Ramazan

    2016-06-01

    Intensive physical exercise leads to increases in left ventricular muscle mass and wall thickness. Cardiac magnetic resonance imaging allows the assessment of functional and morphological changes in an athlete's heart. In addition, a native T1 mapping technique has been suggested as a non-contrast method to detect myocardial fibrosis. The aim of this study was to show the correlation between athletes' cardiac modifications and myocardial fibrosis with a native T1 mapping technique. A total of 41 healthy non-athletic control subjects and 46 athletes underwent CMR imaging. After the functional and morphological assessments, native T1 mapping was performed in all subjects using 3.0 T magnetic resonance imaging. Most of the CMR findings were significantly higher in athletes who had ≥5 years of sports activity when compared with non-athletic controls and athletes who had <5 years of sports activity. Significantly higher results were shown in native T1 values in athletes who had <5 years of sports activity, but there were no significant differences in the left ventricular end-diastolic volume, left ventricular end-diastolic mass, or interventricular septal wall thickness between non-athletic controls and athletes who had <5 years of sports activity. The native T1 mapping technique has the potential to discriminate myocardial fibrotic changes in athletes when compared to a normal myocardium. The T1 mapping method might be a feasible technique to evaluate athletes because it does not involve contrast, is non-invasive and allows for easy evaluation of myocardial remodeling. PMID:26920720

  5. 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.

  6. Whole-brain mapping of the direct inputs and axonal projections of POMC and AgRP neurons

    PubMed Central

    Wang, Daqing; He, Xiaobing; Zhao, Zhe; Feng, Qiru; Lin, Rui; Sun, Yue; Ding, Ting; Xu, Fuqiang; Luo, Minmin; Zhan, Cheng

    2015-01-01

    Pro-opiomelanocortin (POMC) neurons in the arcuate nucleus (ARC) of the hypothalamus and nucleus tractus solitarius (NTS) of the brainstem play important roles in suppressing food intake and maintaining energy homeostasis. Previous tract-tracing studies have revealed the axonal connection patterns of these two brain areas, but the intermingling of POMC neurons with other neuron types has made it challenging to precisely identify the inputs and outputs of POMC neurons. In this study, we used the modified rabies virus to map the brain areas that provide direct inputs to the POMC neurons in the ARC and NTS as well as the inputs to the ARC AgRP neurons for comparison. ARC POMC neurons receive inputs from dozens of discrete structures throughout the forebrain and brainstem. The brain areas containing the presynaptic partners of ARC POMC neurons largely overlap with those of ARC AgRP neurons, although POMC neurons receive relatively broader, denser inputs. Furthermore, POMC neurons in the NTS receive direct inputs predominantly from the brainstem and show very different innervation patterns for POMC neurons in the ARC. By selectively expressing fluorescent markers in the ARC and NTS POMC neurons, we found that almost all of their major presynaptic partners are innervated by POMC neurons in the two areas, suggesting that there are strong reciprocal projections among the major POMC neural pathways. By comprehensively chartering the whole-brain connections of the central melanocortin system in a cell-type-specific manner, this study lays the foundation for dissecting the roles and underlying circuit mechanisms of specific neural pathways in regulating energy homeostasis. PMID:25870542

  7. Whole-brain mapping of the direct inputs and axonal projections of POMC and AgRP neurons.

    PubMed

    Wang, Daqing; He, Xiaobing; Zhao, Zhe; Feng, Qiru; Lin, Rui; Sun, Yue; Ding, Ting; Xu, Fuqiang; Luo, Minmin; Zhan, Cheng

    2015-01-01

    Pro-opiomelanocortin (POMC) neurons in the arcuate nucleus (ARC) of the hypothalamus and nucleus tractus solitarius (NTS) of the brainstem play important roles in suppressing food intake and maintaining energy homeostasis. Previous tract-tracing studies have revealed the axonal connection patterns of these two brain areas, but the intermingling of POMC neurons with other neuron types has made it challenging to precisely identify the inputs and outputs of POMC neurons. In this study, we used the modified rabies virus to map the brain areas that provide direct inputs to the POMC neurons in the ARC and NTS as well as the inputs to the ARC AgRP neurons for comparison. ARC POMC neurons receive inputs from dozens of discrete structures throughout the forebrain and brainstem. The brain areas containing the presynaptic partners of ARC POMC neurons largely overlap with those of ARC AgRP neurons, although POMC neurons receive relatively broader, denser inputs. Furthermore, POMC neurons in the NTS receive direct inputs predominantly from the brainstem and show very different innervation patterns for POMC neurons in the ARC. By selectively expressing fluorescent markers in the ARC and NTS POMC neurons, we found that almost all of their major presynaptic partners are innervated by POMC neurons in the two areas, suggesting that there are strong reciprocal projections among the major POMC neural pathways. By comprehensively chartering the whole-brain connections of the central melanocortin system in a cell-type-specific manner, this study lays the foundation for dissecting the roles and underlying circuit mechanisms of specific neural pathways in regulating energy homeostasis. PMID:25870542

  8. Battlefield MRI

    SciTech Connect

    Espy, Michelle

    2015-06-01

    Magnetic Resonance Imaging is the best method for non-invasive imaging of soft tissue anatomy, saving countless lives each year. It is regarded as the gold standard for diagnosis of mild to moderate traumatic brain injuries. Furthermore, conventional MRI relies on very high, fixed strength magnetic fields (> 1.5 T) with parts-per-million homogeneity, which requires very large and expensive magnets.

  9. Multi-directional chromosome painting maps homologies between species belonging to three genera of New World monkeys and humans.

    PubMed

    Stanyon, R; Bigoni, F; Slaby, T; Muller, S; Stone, G; Bonvicino, C R; Neusser, M; Seuánez, H N

    2004-12-01

    We mapped chromosomal homologies in two species of Chiropotes (Pitheciini, Saki Monkeys) and one species of Aotus (Aotinae, Owl Monkey) by multi-directional chromosome painting. Human chromosome probes were hybridized to Chiropotes utahicki, C. israelita and Aotus nancymae metaphases. Wooly Monkey chromosome paints were also hybridized to Owl Monkey metaphases. We established Owl Monkey chromosome paint probes by flow sorting and reciprocally hybridized them to human chromosomes. The karyotypes of the Bearded Saki Monkeys studied here are close to the hypothesized ancestral platyrrhine karytoype, while that of the Owl Monkey appears to be highly derived. The A. nancymae karyotype is highly shuffled and only three human syntenic groups were found conserved coexisting with 17 derived human homologous associations. A minimum of 14 fissions and 13 fusions would be required to derive the A. nancymae karyotype from that of the ancestral New World primate karyotype. An inversion between homologs to segments of human 10 and 16 suggests a link between Callicebus and Chiropotes, while the syntenic association of 10/11 found in Aotus and Callicebus suggests a link between these two genera. Future molecular cytogenetic work will be needed to determine whether these rearrangements represent synapomorphic chromosomal traits. PMID:15616867

  10. 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.

  11. 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

  12. 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

  13. 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

  14. Three-dimensional quantitative assessment of ablation margins based on registration of pre- and post-procedural MRI and distance map

    PubMed Central

    Tani, Soichiro; Tatli, Servet; Hata, Nobuhiko; Garcia-Rojas, Xavier; Olubiyi, Olutayo I.; Silverman, Stuart G.; Tokuda, Junichi

    2016-01-01

    Purpose Contrast-enhanced MR images are widely used to confirm the adequacy of ablation margin after liver ablation for early prediction of local recurrence. However, quantitative assessment of the ablation margin by comparing pre- and post-procedural images remains challenging. We developed and tested a novel method for three-dimensional quantitative assessment of ablation margin based on non-rigid image registration and 3D distance map. Methods Our method was tested with pre- and post-procedural MR images acquired in 21 patients who underwent image-guided percutaneous liver ablation. The two images were co-registered using non-rigid intensity-based registration. After the tumor and ablation volumes were segmented, target volume coverage, percent of tumor coverage, and Dice Similarity Coefficient were calculated as metrics representing overall adequacy of ablation. In addition, 3D distance map around the tumor was computed and superimposed on the ablation volume to identify the area with insufficient margins. For patients with local recurrences, the follow-up images were registered to the post-procedural image. Three-D minimum distance between the recurrence and the areas with insufficient margins were quantified. Results The percent tumor coverage for all non-recurrent cases was 100%. Five cases had tumor recurrences, and the 3D distance map revealed insufficient tumor coverage or a 0-millimeter margin. It also showed that two recurrences were remote to the insufficient margin. Conclusions Non-rigid registration and 3D distance map allows us to quantitatively evaluate the adequacy of the ablation margin after percutaneous liver ablation. The method may be useful to predict local recurrences immediately following ablation procedure. PMID:27038962

  15. 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…

  16. A method for quantitative analysis of regional lung ventilation using deformable image registration of CT and hybrid hyperpolarized gas/1H MRI.

    PubMed

    Tahir, Bilal A; Swift, Andrew J; Marshall, Helen; Parra-Robles, Juan; Hatton, Matthew Q; Hartley, Ruth; Kay, Richard; Brightling, Christopher E; Vos, Wim; Wild, Jim M; Ireland, Rob H

    2014-12-01

    Hyperpolarized gas magnetic resonance imaging (MRI) generates highly detailed maps of lung ventilation and physiological function while CT provides corresponding anatomical and structural information. Fusion of such complementary images enables quantitative analysis of pulmonary structure-function. However, direct image registration of hyperpolarized gas MRI to CT is problematic, particularly in lungs whose boundaries are difficult to delineate due to ventilation heterogeneity. This study presents a novel indirect method of registering hyperpolarized gas MRI to CT utilizing (1)H-structural MR images that are acquired in the same breath-hold as the gas MRI. The feasibility of using this technique for regional quantification of ventilation of specific pulmonary structures is demonstrated for the lobes.The direct and indirect methods of hyperpolarized gas MRI to CT image registration were compared using lung images from 15 asthma patients. Both affine and diffeomorphic image transformations were implemented. Registration accuracy was evaluated using the target registration error (TRE) of anatomical landmarks identified on (1)H MRI and CT. The Wilcoxon signed-rank test was used to test statistical significance.For the affine transformation, the indirect method of image registration was significantly more accurate than the direct method (TRE = 14.7 ± 3.2 versus 19.6 ± 12.7 mm, p = 0.036). Using a deformable transformation, the indirect method was also more accurate than the direct method (TRE = 13.5 ± 3.3 versus 20.4 ± 12.8 mm, p = 0.006).Accurate image registration is critical for quantification of regional lung ventilation with hyperpolarized gas MRI within the anatomy delineated by CT. Automatic deformable image registration of hyperpolarized gas MRI to CT via same breath-hold (1)H MRI is more accurate than direct registration. Potential applications include improved multi-modality image fusion, functionally weighted radiotherapy planning, and quantification of

  17. Occupational exposure in MRI.

    PubMed

    McRobbie, D W

    2012-04-01

    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 B(0), 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 B(0) 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 B(0), 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 B(0) 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

  18. Dissociating visual and motor directional selectivity using visuomotor adaptation.

    PubMed

    Haar, Shlomi; Donchin, Opher; Dinstein, Ilan

    2015-04-29

    Directional selectivity during visually guided hand movements is a fundamental characteristic of neural populations in multiple motor areas of the primate brain. In the current study, we assessed how directional selectivity changes when reaching movements are dissociated from their visual feedback by rotating the visual field. We recorded simultaneous movement kinematics and fMRI activity while human subjects performed out-and-back movements to four peripheral targets before and after adaptation to a 45° visuomotor rotation. A classification algorithm was trained to identify movement direction according to voxel-by-voxel fMRI patterns in each of several brain areas. The direction of movements was successfully decoded with above-chance accuracy in multiple motor and visual areas when training and testing the classifier on trials within each condition, thereby demonstrating the existence of directionally selective fMRI patterns within each stage of the experiment. Most importantly, when training the classifier on baseline trials and decoding rotated trials, motor brain areas exhibited above-chance decoding according to the original movement direction and visual brain areas exhibited above-chance decoding according to the rotated visual target location, while posterior parietal cortex (PPC) exhibited chance-level decoding according to both. These results reveal that directionally selective fMRI patterns in motor system areas faithfully represent movement direction regardless of visual feedback, while fMRI patterns in visual system areas faithfully represent target location regardless of movement direction. Directionally selective fMRI patterns in PPC, however, were altered following adaptation learning, thereby suggesting that the novel visuomotor mapping, which was learned during visuomotor adaptation, is stored in PPC. PMID:25926457

  19. Leg MRI scan

    MedlinePlus

    ... imaging - leg; Magnetic resonance imaging - lower extremity; MRI - ankle; Magnetic resonance imaging - ankle; MRI - femur; MRI - leg ... or bone scan Birth defects of the leg, ankle, or foot Bone pain and fever Broken bone ...

  20. MRI Safety during Pregnancy

    MedlinePlus

    ... during the exam? Contrast material MRI during pregnancy Magnetic resonance imaging (MRI) If you are pregnant and your doctor wants to perform a magnetic resonance imaging (MRI) exam, there is a possibility that your ...

  1. Evidence for an anterior-posterior differentiation in the human hippocampal formation revealed by meta-analytic parcellation of fMRI coordinate maps: Focus on the subiculum

    PubMed Central

    Chase, Henry W.; Clos, Mareike; Dibble, Sofia; Fox, Peter; Grace, Anthony A.; Phillips, Mary L.; Eickhoff, Simon B.

    2015-01-01

    Previous studies, predominantly in experimental animals, have suggested the presence of a differentiation of function across the hippocampal formation. In rodents, ventral regions are thought to be involved in emotional behavior while dorsal regions mediate cognitive or spatial processes. Using a combination of modeling the co-occurrence of significant activations across thousands of neuroimaging experiments and subsequent data-driven clustering of these data we were able to provide evidence of distinct subregions within a region corresponding to the human subiculum, a critical hub within the hippocampal formation. This connectivity-based model consists of a bilateral anterior region, as well as separate posterior and intermediate regions on each hemisphere. Functional connectivity assessed both by meta-analytic and resting fMRI approaches revealed that more anterior regions were more strongly connected to the default mode network, and more posterior regions were more strongly connected to ‘task positive’ regions. In addition, our analysis revealed that the anterior subregion was functionally connected to the ventral striatum, midbrain and amygdala, a circuit that is central to models of stress and motivated behavior. Analysis of a behavioral taxonomy provided evidence for a role for each subregion in mnemonic processing, as well as implication of the anterior subregion in emotional and visual processing and the right posterior subregion in reward processing. These findings lend support to models which posit anterior-posterior differentiation of function within the human hippocampal formation and complement other early steps toward a comparative (cross-species) model of the region. PMID:25776219

  2. Impact of the MLC on the MRI field distortion of a prototype MRI-linac

    SciTech Connect

    Kolling, Stefan; Keall, Paul; Oborn, Brad

    2013-12-15

    Purpose: To cope with intrafraction tumor motion, integrated MRI-linac systems for real-time image guidance are currently under development. The multileaf collimator (MLC) is a key component in every state-of-the-art radiotherapy treatment system, allowing for accurate field shaping and tumor tracking. This work quantifies the magnetic impact of a widely used MLC on the MRI field homogeneity for such a modality.Methods: The finite element method was employed to model a MRI-linac assembly comprised of a 1.0 T split-bore MRI magnet and the key ferromagnetic components of a Varian Millennium 120 MLC, namely, the leaves and motors. Full 3D magnetic field maps of the system were generated. From these field maps, the peak-to-peak distortion within the MRI imaging volume was evaluated over a 30 cm diameter sphere volume (DSV) around the isocenter and compared to a maximum preshim inhomogeneity of 300 μT. Five parametric studies were performed: (1) The source-to-isocenter distance (SID) was varied from 100 to 200 cm, to span the range of a compact system to that with lower magnetic coupling. (2) The MLC model was changed from leaves only to leaves with motors, to determine the contribution to the total distortion caused by MLC leaves and motors separately. (3) The system was configured in the inline or perpendicular orientation, i.e., the linac treatment beam was oriented parallel or perpendicular to the magnetic field direction. (4) The treatment field size was varied from 0 × 0 to 20×20 cm{sup 2}, to span the range of clinical treatment fields. (5) The coil currents were scaled linearly to produce magnetic field strengths B{sub 0} of 0.5, 1.0, and 1.5 T, to estimate how the MLC impact changes with B{sub 0}.Results: (1) The MLC-induced MRI field distortion fell continuously with increasing SID. (2) MLC leaves and motors were found to contribute to the distortion in approximately equal measure. (3) Due to faster falloff of the fringe field, the field

  3. 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

  4. 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…

  5. Magnetic Resonance Imaging (MRI)

    MedlinePlus

    ... How Can I Help a Friend Who Cuts? Magnetic Resonance Imaging (MRI) KidsHealth > For Teens > Magnetic Resonance Imaging (MRI) Print A A A Text Size What's ... Exam Safety Getting Your Results What Is MRI? Magnetic resonance imaging (MRI) is a type of safe, painless testing ...

  6. Sensory and optogenetically driven single-vessel fMRI.

    PubMed

    Yu, Xin; He, Yi; Wang, Maosen; Merkle, Hellmut; Dodd, Stephen J; Silva, Afonso C; Koretsky, Alan P

    2016-04-01

    Magnetic resonance imaging (MRI) sensitivity approaches vessel specificity. We developed a single-vessel functional MRI (fMRI) method to image the contribution of vascular components to blood oxygenation level-dependent (BOLD) and cerebral blood volume (CBV) fMRI signal. We mapped individual vessels penetrating the rat somatosensory cortex with 100-ms temporal resolution by MRI with sensory or optogenetic stimulation. The BOLD signal originated primarily from venules, and the CBV signal from arterioles. The single-vessel fMRI method and its combination with optogenetics provide a platform for mapping the hemodynamic signal through the neurovascular network with specificity at the level of individual arterioles and venules. PMID:26855362

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

    PubMed

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

    2006-11-01

    Temperature detection using microwave radiometry has proven value for noninvasively measuring the absolute temperature of tissues inside the body. However, current clinical radiometers operate in the gigahertz range, which limits their depth of penetration. We have designed and built a noninvasive radiometer which operates at radio frequencies (64 MHz) with ∼100-kHz bandwidth, using an external RF loop coil as a thermal detector. The core of the radiometer is an accurate impedance measurement and automatic matching circuit of 0.05 Ω accuracy to compensate for any load variations. The radiometer permits temperature measurements with accuracy of ±0.1°K, over a tested physiological range of 28° C-40° C in saline phantoms whose electric properties match those of tissue. Because 1.5 T magnetic resonance imaging (MRI) scanners also operate at 64 MHz, we demonstrate the feasibility of integrating our radiometer with an MRI scanner to monitor RF power deposition and temperature dosimetry, obtaining coarse, spatially resolved, absolute thermal maps in the physiological range. We conclude that RF radiometry offers promise as a direct, noninvasive method of monitoring tissue heating during MRI studies and thereby providing an independent means of verifying patient-safe operation. Other potential applications include titration of hyper- and hypo-therapies. PMID:18026562

  8. The Simpson's paradox and fMRI: Similarities and differences between functional connectivity measures derived from within-subject and across-subject correlations.

    PubMed

    Roberts, Reece P; Hach, Sylvia; Tippett, Lynette J; Addis, Donna Rose

    2016-07-15

    Task-related functional connectivity (fc-MRI) indexes the interaction of brain regions during cognitive tasks. Two general classes of methods exist to investigate fc-MRI: the most widely-used method calculates temporal correlations between voxels/regions within subjects, and then determines if within-subject correlations are reliable across subjects (ws-fcMRI); the other calculates the average (BOLD) signal within voxels/regions and then performs correlations across subjects (as-fcMRI). That is, while both methods rely on correlational techniques, the level at which correlations are calculated is fundamentally different. While conceptually distinct, it is not known how well these two methods of fc-MRI analyses converge on the same findings. The current study addresses this question across a number of analyses. First, using default-mode network regions as seeds, we show that as-fcMRI does not strongly predict ws-fcMRI during episodic simulation tasks. Next, we show that the relationship between as-fcMRI and ws-fcMRI is contingent on whether correlations are calculated between regions from the same functional network (default mode or dorsal attention networks) or between regions from different functional networks. Lastly, we compare seed partial least squares (PLS) - a well-established as-fcMRI method - with a novel version of seed PLS that combines the multivariate approach of PLS analyses and within-subject correlations. The results showed that while many regions exhibited congruent as-fcMRI and ws-fcMRI effects, in some regions the two analyses produced effects in opposite directions. Results are discussed in relation to the Simpson's Paradox, a phenomenon in which across-subject correlations are reversed within individuals present in a sample. Overall, our results suggest that the findings of as-fcMRI do not always map onto those from ws-fcMRI. We end by discussing the advantages associated with using ws-fcMRI to assess the task-related interactions between brain

  9. 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

  10. Effect of direct eye contact in PTSD related to interpersonal trauma: an fMRI study of activation of an innate alarm system

    PubMed Central

    Steuwe, Carolin; Daniels, Judith K.; Frewen, Paul A.; Densmore, Maria; Pannasch, Sebastian; Beblo, Thomas; Reiss, Jeffrey; Lanius, Ruth A.

    2014-01-01

    In healthy individuals, direct eye contact initially leads to activation of a fast subcortical pathway, which then modulates a cortical route eliciting social cognitive processes. The aim of this study was to gain insight into the neurobiological effects of direct eye-to-eye contact using a virtual reality paradigm in individuals with posttraumatic stress disorder (PTSD) related to prolonged childhood abuse. We examined 16 healthy comparison subjects and 16 patients with a primary diagnosis of PTSD using a virtual reality functional magnetic resonance imaging paradigm involving direct vs averted gaze (happy, sad, neutral) as developed by Schrammel et al. in 2009. Irrespective of the displayed emotion, controls exhibited an increased blood oxygenation level-dependent response during direct vs averted gaze within the dorsomedial prefrontal cortex, left temporoparietal junction and right temporal pole. Under the same conditions, individuals with PTSD showed increased activation within the superior colliculus (SC)/periaqueductal gray (PAG) and locus coeruleus. Our findings suggest that healthy controls react to the exposure of direct gaze with an activation of a cortical route that enhances evaluative ‘top–down’ processes underlying social interactions. In individuals with PTSD, however, direct gaze leads to sustained activation of a subcortical route of eye-contact processing, an innate alarm system involving the SC and the underlying circuits of the PAG. PMID:22977200

  11. Effect of direct eye contact in PTSD related to interpersonal trauma: an fMRI study of activation of an innate alarm system.

    PubMed

    Steuwe, Carolin; Daniels, Judith K; Frewen, Paul A; Densmore, Maria; Pannasch, Sebastian; Beblo, Thomas; Reiss, Jeffrey; Lanius, Ruth A

    2014-01-01

    In healthy individuals, direct eye contact initially leads to activation of a fast subcortical pathway, which then modulates a cortical route eliciting social cognitive processes. The aim of this study was to gain insight into the neurobiological effects of direct eye-to-eye contact using a virtual reality paradigm in individuals with posttraumatic stress disorder (PTSD) related to prolonged childhood abuse. We examined 16 healthy comparison subjects and 16 patients with a primary diagnosis of PTSD using a virtual reality functional magnetic resonance imaging paradigm involving direct vs averted gaze (happy, sad, neutral) as developed by Schrammel et al. in 2009. Irrespective of the displayed emotion, controls exhibited an increased blood oxygenation level-dependent response during direct vs averted gaze within the dorsomedial prefrontal cortex, left temporoparietal junction and right temporal pole. Under the same conditions, individuals with PTSD showed increased activation within the superior colliculus (SC)/periaqueductal gray (PAG) and locus coeruleus. Our findings suggest that healthy controls react to the exposure of direct gaze with an activation of a cortical route that enhances evaluative 'top-down' processes underlying social interactions. In individuals with PTSD, however, direct gaze leads to sustained activation of a subcortical route of eye-contact processing, an innate alarm system involving the SC and the underlying circuits of the PAG. PMID:22977200

  12. 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

  13. [Incidence and causes of early end in awake surgery for language mapping not directly related to eloquence].

    PubMed

    Villalba, Gloria; Pacreu, Susana; Fernández-Candil, Juan Luis; León, Alba; Serrano, Laura; Conesa, Gerardo

    2016-01-01

    The incidence and causes that may lead to an early end (unfinished cortical/subcortical mapping) of awake surgery for language mapping are little known. A study was conducted on 41 patients with brain glioma located in the language area that had awake surgery under conscious sedation. Surgery was ended early in 6 patients. The causes were: tonic-clonic seizure (1), lack of cooperation due to fatigue/sleep (4), whether or not word articulation was involved, a decreased level of consciousness for ammonia encephalopathy that required endotracheal intubation (1). There are causes that could be expected and in some cases avoided. Tumour size, preoperative aphasia, valproate treatment, and type of anaesthesia used are variables to consider to avoid failure in awake surgery for language mapping. With these results, the following measures are proposed: l) If the tumour is large, perform surgery in two times to avoid fatigue, 2) if patient has a preoperative aphasia, do not use sedation during surgery to ensure that sleepiness does not cause worse word articulation, 3) if the patient is on valproate treatment, it is necessary to rule out the pre-operative symptoms that are not due to ammonia encephalopathy. PMID:26260205

  14. 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,…

  15. 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.

  16. 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.

  17. What Is Chest MRI?

    MedlinePlus

    ... page from the NHLBI on Twitter. What Is Chest MRI? Chest MRI (magnetic resonance imaging) is a safe, noninvasive ... creates detailed pictures of the structures in your chest, such as your chest wall, heart, and blood ...

  18. 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 ...

  19. Breast MRI scan

    MedlinePlus

    ... breast MRI may be done in combination with mammography or ultrasound . It is not a replacement for mammography. ... breast screening with MRI as an adjunct to mammography. CA Cancer J Clin . 2007;57:75-89. ...

  20. Pelvis MRI scan

    MedlinePlus

    ... The table slides into the middle of the MRI machine. Small devices, called coils, may be placed around ... anxious. Or your provider may suggest an open MRI in which the machine is not as close to the body. Before ...

  1. Lumbar MRI scan

    MedlinePlus

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

  2. Multi-view areal-density maps of compressed shells in OMEGA direct-drive implosions extracted from MMI data

    NASA Astrophysics Data System (ADS)

    Johns, Heather; Joshi, Tirtha; Mayes, Daniel; Durmaz, Tunay; Mancini, Roberto; Tommasini, Riccardo; Delettrez, Jacques; Regan, Sean; Nagayama, Taisuke

    2012-10-01

    In a series of implosion experiments performed at the OMEGA laser facility, spherical plastic shells doped with an embedded titanium tracer-layer and filled with deuterium gas were driven with high- and low-adiabat laser pulse shapes. The titanium emergent intensity distribution was recorded with a streaked spectrometer and three identical gated, multi-monochromatic x-ray imaging instruments (MMI) that observed the implosion along three quasi-orthogonal lines-of-sight. The data shows spectral signatures due to absorption K-shell line transitions in titanium L-shell ions that are backlit by the continuum radiation from the hot core. To interpret these observations, the MMI spectrally-resolved image data were processed to obtain narrow-band images and spatially-resolved spectra based on the titanium spectral features.footnotetextT. Nagayama, R.C. Mancini, R. Florido, et al, J. App. Phys. 109, 093303 (2011) Areal-density maps were extracted using two independent methods based on narrow-band images and spatially-resolved spectra. The areal-density maps reveal the 3D structure and state of the compressed shell through the collapse of the implosion and the performance differences between high- and low-adiabat implosions.

  3. Phage display revisited: Epitope mapping of a monoclonal antibody directed against Neisseria meningitidis adhesin A using the PROFILER technology.

    PubMed

    Cariccio, Veronica Lanza; Domina, Maria; Benfatto, Salvatore; Venza, Mario; Venza, Isabella; Faleri, Agnese; Bruttini, Marco; Bartolini, Erika; Giuliani, Marzia Monica; Santini, Laura; Brunelli, Brunella; Norais, Nathalie; Borgogni, Erica; Midiri, Angelina; Galbo, Roberta; Romeo, Letizia; Biondo, Carmelo; Masignani, Vega; Teti, Giuseppe; Felici, Franco; Beninati, Concetta

    2016-01-01

    There is a strong need for rapid and reliable epitope mapping methods that can keep pace with the isolation of increasingly larger numbers of mAbs. We describe here the identification of a conformational epitope using Phage-based Representation OF ImmunoLigand Epitope Repertoire (PROFILER), a recently developed high-throughput method based on deep sequencing of antigen-specific lambda phage-displayed libraries. A novel bactericidal monoclonal antibody (mAb 9F11) raised against Neisseria meningitidis adhesin A (NadA), an important component of the Bexsero(®) anti-meningococcal vaccine, was used to evaluate the technique in comparison with other epitope mapping methods. The PROFILER technology readily identified NadA fragments that were capable of fully recapitulating the reactivity of the entire antigen against mAb 9F11. Further analysis of these fragments using mutagenesis and hydrogen-deuterium exchange mass-spectrometry allowed us to identify the binding site of mAb 9F11 (A250-D274) and an adjoining sequence (V275-H312) that was also required for the full functional reconstitution of the epitope. These data suggest that, by virtue of its ability to detect a great variety of immunoreactive antigen fragments in phage-displayed libraries, the PROFILER technology can rapidly and reliably identify epitope-containing regions and provide, in addition, useful clues for the functional characterization of conformational mAb epitopes. PMID:26963435

  4. MRI in cranial tuberculosis.

    PubMed

    Just, M; Higer, H P; Betting, O; Bockenheimer, S; Pfannenstiel, P

    1987-11-01

    A case of multiple intracranial tuberculomas is presented. CT and MRI findings are discussed and compared. MRI showed multiple tuberculomas characterised by the same signal intensity as the surrounding brain parenchyma. Differentiation could be achieved only by the perifocal oedema of high signal intensity. Changes of the lesions during chemotherapy were monitored by CT and MRI and the results are presented. PMID:3691545

  5. 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.

  6. 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. PMID:26298503

  7. 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

  8. In-situ phase mapping and direct observations of phase transformations during arc welding of 1045 steel

    NASA Astrophysics Data System (ADS)

    Elmer, J. W.; Palmer, T. A.

    2006-07-01

    In-situ spatially resolved X-ray diffraction (SRXRD) experiments were performed during gas tung-sten arc (GTA) welding of AISI 1045 C-Mn steel. Ferrite (α) and austenite (γ) phases were identified and quantified in the weld heat-affected zone (HAZ) from the real time SRXRD data. The results were compiled with weld temperatures calculated using a coupled thermal fluids model to create a phase map of the HAZ. Kinetics of the α → γ transformation during weld heating and the reverse γ → α transformation during weld cooling were extracted from the map. Superheating as high as 250 °C above the A3 temperature was observed for the α → γ phase transformation to reach completion at locations near the fusion zone (FZ) boundary. The SRXRD experiments revealed that the newly created γ phase exists with two distinct lattice parameters, resulting from the inhomogeneous distribution of carbon and manganese in the starting pearlitic/ferritic microstructure. During cooling, the reverse γ → α phase transformation was shown to depend on the HAZ location. In the fine-grained region of the HAZ, the γ → α transformation begins near the A3 temperature and ends near the A1 temperature. In this region, where the cooling rates are below 40 °C/s, the transformation occurs by nucleation and growth of pearlite. In the coarse-grained region of the HAZ, the γ → α transformation requires 200 °C of undercooling for completion. This high degree of undercooling is caused by the large grains coupled with cooling rates in excess of 50 °C/s that result in a bainitic transformation mechanism.

  9. 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.

  10. 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

  11. Genetic Identification of an On-Off Direction-Selective Retinal Ganglion Cell Subtype Reveals a Layer-Specific Subcortical Map of Posterior Motion

    PubMed Central

    Huberman, Andrew D.; Wei, Wei; Elstrott, Justin; Stafford, Ben K.; Feller, Marla B.; Barres, Ben A.

    2011-01-01

    SUMMARY Motion detection is an essential component of visual processing. On-Off direction-selective retinal ganglion cells (On-Off DSGCs) detect objects moving along specific axes of the visual field due to their precise retinal circuitry. The brain circuitry of On-Off DSGCs, however, is largely unknown. We report a mouse with GFP expressed selectively by the On-Off DSGCs that detect posterior motion (On-Off pDSGCs), allowing two-photon targeted recordings of their light responses and delineation of their complete map of central connections. On-Off pDSGCs project exclusively to the dorsal lateral geniculate nucleus and superior colliculus and in both targets form synaptic lamina that are separate from a lamina corresponding to non-DSGCs. Thus, individual On-Off DSGC subtypes are molecularly distinct and establish circuits that map specific qualities of directional motion to dedicated subcortical areas. This suggests that each RGC subtype represents a unique parallel pathway whose synaptic specificity in the retina is recapitulated in central targets. PMID:19447089

  12. A multi-zone chemistry mapping approach for direct numerical simulation of auto-ignition and flame propagation in a constant volume enclosure

    NASA Astrophysics Data System (ADS)

    Jangi, M.; Yu, R.; Bai, X. S.

    2012-04-01

    A direct numerical simulation (DNS) coupling with multi-zone chemistry mapping (MZCM) is presented to simulate flame propagation and auto-ignition in premixed fuel/air mixtures. In the MZCM approach, the physical domain is mapped into a low-dimensional phase domain with a few thermodynamic variables as the independent variables. The approach is based on the fractional step method, in which the flow and transport are solved in the flow time steps whereas the integration of the chemical reaction rates and heat release rate is performed in much finer time steps to accommodate the small time scales in the chemical reactions. It is shown that for premixed mixtures, two independent variables can be sufficient to construct the phase space to achieve a satisfactory mapping. The two variables can be the temperature of the mixture and the specific element mass ratio of H atom for fuels containing hydrogen atoms. An aliasing error in the MZCM is investigated. It is shown that if the element mass ratio is based on the element involved in the most diffusive molecules, the aliasing error of the model can approach zero when the grid in the phase space is refined. The results of DNS coupled with MZCM (DNS-MZCM) are compared with full DNS that integrates the chemical reaction rates and heat release rate directly in physical space. Application of the MZCM to different mixtures of fuel and air is presented to demonstrate the performance of the method for combustion processes with different complexity in the chemical kinetics, transport and flame-turbulence interaction. Good agreement between the results from DNS and DNS-MZCM is obtained for different fuel/air mixtures, including H2/air, CO/H2/air and methane/air, while the computational time is reduced by nearly 70%. It is shown that the MZCM model can properly address important phenomena such as differential diffusion, local extinction and re-ignition in premixed combustion.

  13. Identifying Neural Drivers with Functional MRI: An Electrophysiological Validation

    PubMed Central

    David, Olivier; Guillemain, Isabelle; Saillet, Sandrine; Reyt, Sebastien; Deransart, Colin; Segebarth, Christoph; Depaulis, Antoine

    2008-01-01

    Whether functional magnetic resonance imaging (fMRI) allows the identification of neural drivers remains an open question of particular importance to refine physiological and neuropsychological models of the brain, and/or to understand neurophysiopathology. Here, in a rat model of absence epilepsy showing spontaneous spike-and-wave discharges originating from the first somatosensory cortex (S1BF), we performed simultaneous electroencephalographic (EEG) and fMRI measurements, and subsequent intracerebral EEG (iEEG) recordings in regions strongly activated in fMRI (S1BF, thalamus, and striatum). fMRI connectivity was determined from fMRI time series directly and from hidden state variables using a measure of Granger causality and Dynamic Causal Modelling that relates synaptic activity to fMRI. fMRI connectivity was compared to directed functional coupling estimated from iEEG using asymmetry in generalised synchronisation metrics. The neural driver of spike-and-wave discharges was estimated in S1BF from iEEG, and from fMRI only when hemodynamic effects were explicitly removed. Functional connectivity analysis applied directly on fMRI signals failed because hemodynamics varied between regions, rendering temporal precedence irrelevant. This paper provides the first experimental substantiation of the theoretical possibility to improve interregional coupling estimation from hidden neural states of fMRI. As such, it has important implications for future studies on brain connectivity using functional neuroimaging. PMID:19108604

  14. Direct mapping of recoil in the ion-pair dissociation of molecular oxygen by a femtosecond depletion method.

    PubMed

    Baklanov, Alexey V; Janssen, Liesbeth M C; Parker, David H; Poisson, Lionel; Soep, Benoit; Mestdagh, Jean-Michel; Gobert, Olivier

    2008-12-01

    Time-resolved dynamics of the photodissociation of molecular oxygen, O(2), via the (3)Sigma(u) (-) ion-pair state have been studied with femtosecond time resolution using a pump-probe scheme in combination with velocity map imaging of the resulting O(+) and O(-) ions. The fourth harmonic of a femtosecond titanium-sapphire (Ti:sapphire) laser (lambda approximately 205 nm) was found to cause three-photon pumping of O(2) to a level at 18.1 eV. The parallel character of the observed O(+) and O(-) images allowed us to conclude that dissociation takes place on the (3)Sigma(u) (-) ion-pair state. The 815 nm fundamental of the Ti:sapphire laser used as probe was found to cause two-photon electron photodetachment starting from the O(2) ion-pair state, giving rise to (O((3)P)+O(+)((4)S)) products. This was revealed by the observed depletion of the yield of the O(-) anion and the appearance of a new O(+) cation signal with a kinetic energy E(transl)(O(+)) dependent on the time delay between the pump and probe lasers. This time-delay dependence of the dissociation dynamics on the ion-pair state has also been simulated, and the experimental and simulated results coincide very well over the experimental delay-time interval from about 130 fs to 20 ps where two- or one-photon photodetachment takes place, corresponding to a change in the R(O(+),O(-)) interatomic distance from 12 to about 900 A. This is one of the first implementations of a depletion scheme in femtosecond pump-probe experiments which could prove to be quite versatile and applicable to many femtosecond time-scale experiments. PMID:19063560

  15. Developing high-resolution carbon-13 and silicon-29 MRI of solids in sedimentary rocks

    NASA Astrophysics Data System (ADS)

    Blum, Robert; Barrett, Sean; Viswanathan, Ravinath; Song, Yi-Qiao

    2014-03-01

    Mapping pore structure and flow properties of sedimentary rock is directly relevant to current challenges in geophysics like carbon sequestration and oil/gas exploration. Such applications require detailed information about both structure and composition of porous rocks. However, existing scanning methods tend to be limited to gathering one or the other type of information. MRI could be used to measure both composition and structure simultaneously, but conventional MRI in such systems, which targets the proton signal of interstitial fluid, is severely limited by signal losses due to magnetic susceptibility inhomogeneity. Our lab has recently made advances in obtaining high spatial resolution (sub-400 μm)3 three-dimensional 31P MRI of bone through use of the quadratic echo line-narrowing sequence (1). In this talk, we describe our current work applying these methods to sedimentary rock, targeting the isotopes 13C and 29Si. We describe the results of characterization of limestone and shale samples, and we discuss our progress with producing MRI of these systems. (1) M. Frey, et al. PNAS 109: 5190 (2012)

  16. An MRI-based attenuation correction method for combined PET/MRI applications

    NASA Astrophysics Data System (ADS)

    Fei, Baowei; Yang, Xiaofeng; Wang, Hesheng

    2009-02-01

    We are developing MRI-based attenuation correction methods for PET images. PET has high sensitivity but relatively low resolution and little anatomic details. MRI can provide excellent anatomical structures with high resolution and high soft tissue contrast. MRI can be used to delineate tumor boundaries and to provide an anatomic reference for PET, thereby improving quantitation of PET data. Combined PET/MRI can offer metabolic, functional and anatomic information and thus can provide a powerful tool to study the mechanism of a variety of diseases. Accurate attenuation correction represents an essential component for the reconstruction of artifact-free, quantitative PET images. Unfortunately, the present design of hybrid PET/MRI does not offer measured attenuation correction using a transmission scan. This problem may be solved by deriving attenuation maps from corresponding anatomic MR images. Our approach combines image registration, classification, and attenuation correction in a single scheme. MR images and the preliminary reconstruction of PET data are first registered using our automatic registration method. MRI images are then classified into different tissue types using our multiscale fuzzy C-mean classification method. The voxels of classified tissue types are assigned theoretical tissue-dependent attenuation coefficients to generate attenuation correction factors. Corrected PET emission data are then reconstructed using a threedimensional filtered back projection method and an order subset expectation maximization method. Results from simulated images and phantom data demonstrated that our attenuation correction method can improve PET data quantitation and it can be particularly useful for combined PET/MRI applications.

  17. MRI and MRS of human brain tumors.

    PubMed

    Hou, Bob L; Hu, Jiani

    2009-01-01

    The purpose of this chapter is to provide an introduction to magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) of human brain tumors, including the primary applications and basic terminology involved. Readers who wish to know more about this broad subject should seek out the referenced books (1. Tofts (2003) Quantitative MRI of the brain. Measuring changes caused by disease. Wiley; Bradley and Stark (1999) 2. Magnetic resonance imaging, 3rd Edition. Mosby Inc; Brown and Semelka (2003) 3. MRI basic principles and applications, 3rd Edition. Wiley-Liss) or reviews (4. Top Magn Reson Imaging 17:127-36, 2006; 5. JMRI 24:709-724, 2006; 6. Am J Neuroradiol 27:1404-1411, 2006).MRI is the most popular means of diagnosing human brain tumors. The inherent difference in the magnetic resonance (MR) properties of water between normal tissues and tumors results in contrast differences on the image that provide the basis for distinguishing tumors from normal tissues. In contrast to MRI, which provides spatial maps or images using water signals of the tissues, proton MRS detects signals of tissue metabolites. MRS can complement MRI because the observed MRS peaks can be linked to inherent differences in biochemical profiles between normal tissues and tumors.The goal of MRI and MRS is to characterize brain tumors, including tumor core, edge, edema, volume, types, and grade. The commonly used brain tumor MRI protocol includes T2-weighted images and T1-weighted images taken both before and after the injection of a contrast agent (typically gadolinium: Gd). The commonly used MRS technique is either point-resolved spectroscopy (PRESS) or stimulated echo acquisition mode (STEAM). PMID:19381963

  18. Fast interactive exploration of 4D MRI flow data

    NASA Astrophysics Data System (ADS)

    Hennemuth, A.; Friman, O.; Schumann, C.; Bock, J.; Drexl, J.; Huellebrand, M.; Markl, M.; Peitgen, H.-O.

    2011-03-01

    1- or 2-directional MRI blood flow mapping sequences are an integral part of standard MR protocols for diagnosis and therapy control in heart diseases. Recent progress in rapid MRI has made it possible to acquire volumetric, 3-directional cine images in reasonable scan time. In addition to flow and velocity measurements relative to arbitrarily oriented image planes, the analysis of 3-dimensional trajectories enables the visualization of flow patterns, local features of flow trajectories or possible paths into specific regions. The anatomical and functional information allows for advanced hemodynamic analysis in different application areas like stroke risk assessment, congenital and acquired heart disease, aneurysms or abdominal collaterals and cranial blood flow. The complexity of the 4D MRI flow datasets and the flow related image analysis tasks makes the development of fast comprehensive data exploration software for advanced flow analysis a challenging task. Most existing tools address only individual aspects of the analysis pipeline such as pre-processing, quantification or visualization, or are difficult to use for clinicians. The goal of the presented work is to provide a software solution that supports the whole image analysis pipeline and enables data exploration with fast intuitive interaction and visualization methods. The implemented methods facilitate the segmentation and inspection of different vascular systems. Arbitrary 2- or 3-dimensional regions for quantitative analysis and particle tracing can be defined interactively. Synchronized views of animated 3D path lines, 2D velocity or flow overlays and flow curves offer a detailed insight into local hemodynamics. The application of the analysis pipeline is shown for 6 cases from clinical practice, illustrating the usefulness for different clinical questions. Initial user tests show that the software is intuitive to learn and even inexperienced users achieve good results within reasonable processing

  19. Mapping protein conformational heterogeneity under pressure with site-directed spin labeling and double electron-electron resonance.

    PubMed

    Lerch, Michael T; Yang, Zhongyu; Brooks, Evan K; Hubbell, Wayne L

    2014-04-01

    The dominance of a single native state for most proteins under ambient conditions belies the functional importance of higher-energy conformational states (excited states), which often are too sparsely populated to allow spectroscopic investigation. Application of high hydrostatic pressure increases the population of excited states for study, but structural characterization is not trivial because of the multiplicity of states in the ensemble and rapid (microsecond to millisecond) exchange between them. Site-directed spin labeling in combination with double electron-electron resonance (DEER) provides long-range (20-80 Å) distance distributions with angstrom-level resolution and thus is ideally suited to resolve conformational heterogeneity in an excited state populated under high pressure. DEER currently is performed at cryogenic temperatures. Therefore, a method was developed for rapidly freezing spin-labeled proteins under pressure to kinetically trap the high-pressure conformational ensemble for subsequent DEER data collection at atmospheric pressure. The methodology was evaluated using seven doubly-labeled mutants of myoglobin designed to monitor selected interhelical distances. For holomyoglobin, the distance distributions are narrow and relatively insensitive to pressure. In apomyoglobin, on the other hand, the distributions reveal a striking conformational heterogeneity involving specific helices in the pressure range of 0-3 kbar, where a molten globule state is formed. The data directly reveal the amplitude of helical fluctuations, information unique to the DEER method that complements previous rate determinations. Comparison of the distance distributions for pressure- and pH-populated molten globules shows them to be remarkably similar despite a lower helical content in the latter. PMID:24707053

  20. Mapping protein conformational heterogeneity under pressure with site-directed spin labeling and double electron–electron resonance

    PubMed Central

    Lerch, Michael T.; Yang, Zhongyu; Brooks, Evan K.; Hubbell, Wayne L.

    2014-01-01

    The dominance of a single native state for most proteins under ambient conditions belies the functional importance of higher-energy conformational states (excited states), which often are too sparsely populated to allow spectroscopic investigation. Application of high hydrostatic pressure increases the population of excited states for study, but structural characterization is not trivial because of the multiplicity of states in the ensemble and rapid (microsecond to millisecond) exchange between them. Site-directed spin labeling in combination with double electron–electron resonance (DEER) provides long-range (20–80 Å) distance distributions with angstrom-level resolution and thus is ideally suited to resolve conformational heterogeneity in an excited state populated under high pressure. DEER currently is performed at cryogenic temperatures. Therefore, a method was developed for rapidly freezing spin-labeled proteins under pressure to kinetically trap the high-pressure conformational ensemble for subsequent DEER data collection at atmospheric pressure. The methodology was evaluated using seven doubly-labeled mutants of myoglobin designed to monitor selected interhelical distances. For holomyoglobin, the distance distributions are narrow and relatively insensitive to pressure. In apomyoglobin, on the other hand, the distributions reveal a striking conformational heterogeneity involving specific helices in the pressure range of 0–3 kbar, where a molten globule state is formed. The data directly reveal the amplitude of helical fluctuations, information unique to the DEER method that complements previous rate determinations. Comparison of the distance distributions for pressure- and pH-populated molten globules shows them to be remarkably similar despite a lower helical content in the latter. PMID:24707053

  1. Development, Calibration and Evaluation of a Portable and Direct Georeferenced Laser Scanning System for Kinematic 3D Mapping

    NASA Astrophysics Data System (ADS)

    Heinz, Erik; Eling, Christian; Wieland, Markus; Klingbeil, Lasse; Kuhlmann, Heiner

    2015-12-01

    In recent years, kinematic laser scanning has become increasingly popular because it offers many benefits compared to static laser scanning. The advantages include both saving of time in the georeferencing and a more favorable scanning geometry. Often mobile laser scanning systems are installed on wheeled platforms, which may not reach all parts of the object. Hence, there is an interest in the development of portable systems, which remain operational even in inaccessible areas. The development of such a portable laser scanning system is presented in this paper. It consists of a lightweight direct georeferencing unit for the position and attitude determination and a small low-cost 2D laser scanner. This setup provides advantages over existing portable systems that employ heavy and expensive 3D laser scanners in a profiling mode. A special emphasis is placed on the system calibration, i. e. the determination of the transformation between the coordinate frames of the direct georeferencing unit and the 2D laser scanner. To this end, a calibration field is used, which consists of differently orientated georeferenced planar surfaces, leading to estimates for the lever arms and boresight angles with an accuracy of mm and one-tenth of a degree. Finally, point clouds of the mobile laser scanning system are compared with georeferenced point clouds of a high-precision 3D laser scanner. Accordingly, the accuracy of the system is in the order of cm to dm. This is in good agreement with the expected accuracy, which has been derived from the error propagation of previously estimated variance components.

  2. Cortical Hemisphere Registration Via Large Deformation Diffeomorphic Metric Curve Mapping

    PubMed Central

    Qiu, Anqi; Miller, Michael I.

    2010-01-01

    We present large deformation diffeomorphic metric curve mapping (LDDMM-Curve) for registering cortical hemispheres. We showed global cortical hemisphere matching and evaluated the mapping accuracy in five subregions of the cortex in fourteen MRI scans. PMID:18051058

  3. Epitope Mapping of a Monoclonal Antibody Directed against Neisserial Heparin Binding Antigen Using Next Generation Sequencing of Antigen-Specific Libraries.

    PubMed

    Domina, Maria; Lanza Cariccio, Veronica; Benfatto, Salvatore; Venza, Mario; Venza, Isabella; Donnarumma, Danilo; Bartolini, Erika; Borgogni, Erica; Bruttini, Marco; Santini, Laura; Midiri, Angelina; Galbo, Roberta; Romeo, Letizia; Patanè, Francesco; Biondo, Carmelo; Norais, Nathalie; Masignani, Vega; Teti, Giuseppe; Felici, Franco; Beninati, Concetta

    2016-01-01

    We explore here the potential of a newly described technology, which is named PROFILER and is based on next generation sequencing of gene-specific lambda phage-displayed libraries, to rapidly and accurately map monoclonal antibody (mAb) epitopes. For this purpose, we used a novel mAb (designated 31E10/E7) directed against Neisserial Heparin-Binding Antigen (NHBA), a component of the anti-group B meningococcus Bexsero® vaccine. An NHBA phage-displayed library was affinity-selected with mAb 31E10/E7, followed by massive sequencing of the inserts present in antibody-selected phage pools. Insert analysis identified an amino acid stretch (D91-A128) in the N-terminal domain, which was shared by all of the mAb-enriched fragments. Moreover, a recombinant fragment encompassing this sequence could recapitulate the immunoreactivity of the entire NHBA molecule against mAb 31E10/E7. These results were confirmed using a panel of overlapping recombinant fragments derived from the NHBA vaccine variant and a set of chemically synthetized peptides covering the 10 most frequent antigenic variants. Furthermore, hydrogen-deuterium exchange mass-spectrometry analysis of the NHBA-mAb 31E10/E7 complex was also compatible with mapping of the epitope to the D91-A128 region. Collectively, these results indicate that the PROFILER technology can reliably identify epitope-containing antigenic fragments and requires considerably less work, time and reagents than other epitope mapping methods. PMID:27508302

  4. Epitope Mapping of a Monoclonal Antibody Directed against Neisserial Heparin Binding Antigen Using Next Generation Sequencing of Antigen-Specific Libraries

    PubMed Central

    Domina, Maria; Lanza Cariccio, Veronica; Benfatto, Salvatore; Venza, Mario; Venza, Isabella; Donnarumma, Danilo; Bartolini, Erika; Borgogni, Erica; Bruttini, Marco; Santini, Laura; Midiri, Angelina; Galbo, Roberta; Romeo, Letizia; Patanè, Francesco; Biondo, Carmelo; Norais, Nathalie; Masignani, Vega; Teti, Giuseppe; Felici, Franco; Beninati, Concetta

    2016-01-01

    We explore here the potential of a newly described technology, which is named PROFILER and is based on next generation sequencing of gene-specific lambda phage-displayed libraries, to rapidly and accurately map monoclonal antibody (mAb) epitopes. For this purpose, we used a novel mAb (designated 31E10/E7) directed against Neisserial Heparin-Binding Antigen (NHBA), a component of the anti-group B meningococcus Bexsero® vaccine. An NHBA phage-displayed library was affinity-selected with mAb 31E10/E7, followed by massive sequencing of the inserts present in antibody-selected phage pools. Insert analysis identified an amino acid stretch (D91-A128) in the N-terminal domain, which was shared by all of the mAb-enriched fragments. Moreover, a recombinant fragment encompassing this sequence could recapitulate the immunoreactivity of the entire NHBA molecule against mAb 31E10/E7. These results were confirmed using a panel of overlapping recombinant fragments derived from the NHBA vaccine variant and a set of chemically synthetized peptides covering the 10 most frequent antigenic variants. Furthermore, hydrogen-deuterium exchange mass-spectrometry analysis of the NHBA-mAb 31E10/E7 complex was also compatible with mapping of the epitope to the D91-A128 region. Collectively, these results indicate that the PROFILER technology can reliably identify epitope-containing antigenic fragments and requires considerably less work, time and reagents than other epitope mapping methods. PMID:27508302

  5. Current Role of fMRI in diagnosis of movement disorders

    PubMed Central

    Hallett, Mark

    2016-01-01

    The emergence of functional magnetic resonance techniques for the purpose of brain mapping serves as a valuable tool for understanding both normal physiology and the dysfunction taking place in disorders of the brain. This article provides an overview of fMRI methods and their applications in the study of neurological movement disorders. We then review the current neuroimaging literature regarding Parkinsonisms, Dystonia, Essential Tremor, and Huntington’s disease, including discussion of current methodological limitations and future directions for this exciting field. PMID:19959022

  6. A Lagrangian-Eulerian Mapping Solver for Direct Numerical Simulation of Bubble-Laden Turbulent Shear Flows Using the Two-Fluid Formulation

    NASA Astrophysics Data System (ADS)

    Druzhinin, O. A.; Elghobashi, S. E.

    1999-09-01

    In a recent study we showed that the two-fluid (TF) formulation can be used in the direct numerical simulation (DNS) of bubble- (or particle-) laden decaying isotropic turbulence with considerable saving in CPU-time and memory as compared to the trajectory approach employed by many researchers. In the present paper, we develop a Lagrangian-Eulerian mapping (LEM) solver for DNS of bubble-laden turbulent shear flows using TF. The purpose of LEM is to resolve the large gradients of bubble velocity and concentration which result from the absence of the diffusion terms in the equations of bubble-phase motion and the preferential accumulation of bubbles. A standard finite-difference scheme (FDS) fails to resolve these gradients. We examine the performance of the new method in DNS of a bubble-laden Taylor-Green vortex, spatially developing plane mixing layer, and homogeneous shear turbulent flow.

  7. 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

  8. Bakuchiol suppresses proliferation of skin cancer cells by directly targeting Hck, Blk, and p38 MAP kinase.

    PubMed

    Kim, Jong-Eun; Kim, Jae Hwan; Lee, Younghyun; Yang, Hee; Heo, Yong-Seok; Bode, Ann M; Lee, Ki Won; Dong, Zigang

    2016-03-22

    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

  9. Directional mapping of DNA nicking in ejaculated and cauda epididymidal spermatozoa of the short-beaked echidna (Tachyglossus aculeatus: Monotremata).

    PubMed

    Johnston, S D; López-Fernández, C; Gosálbez, A; Holt, W V; Gosálvez, J

    2009-01-01

    Prototherian spermatozoa are unique amongst the Mammalia in terms of their filiform morphology, tandem arrangement of chromosomes and formation of sperm bundles. In the present study, we provide observations of echidna spermatozoa and note that the superstructure of the bundle is engineered around the shape of the individual sperm head and that this in turn may be a consequence of the unusual circumferential and helicoidal condensation of the DNA during spermiogenesis. Frozen-thawed ejaculated echidna spermatozoa were incubated and examined for the presence of non-typical DNA conformation by means of in situ labelling of DNA breaks using Klenow polymerase and via alkaline single-cell comet assays for detection of fragmented DNA. Both techniques successfully revealed the presence of what appeared to be directional DNA nicking, co-localised with the presence of highly sensitive alkali sites along the length of the sperm nucleus. It was not possible to define whether these alternative DNA configurations were associated with a failure of the sperm nucleus to condense appropriately during spermiogenesis or were evidence of DNA fragmentation following post-thaw incubation or a sequential structural chromatin rearrangement necessary for fertilisation. PMID:19874725

  10. MRI of the shoulder

    SciTech Connect

    Zlatkin, M.B.; Iannotti, J.P.; Schnall, M.D.

    1991-01-01

    This book reports on the use of magnetic resonance imaging (MRI) in evaluating shoulder disorders. The book gives detailed information on MRI techniques and shoulder anatomy, describes and illustrates MRI findings for a wide range of shoulder disorders, and explains how abnormalities seen on MIR images relate to pathophysiology and clinical signs. Special attention is given to imaging of rotator cuff disease and shoulder instability conditions for which MRI is the imaging procedure of choice. Complementing the text are 365 high-quality scans depicting normal shoulder anatomy and showing the wide variety of pathologic findings encountered in practice.

  11. High-resolution mapping of the HyHEL-10 epitope of chicken lysozyme by site-directed mutagenesis

    SciTech Connect

    Kam-Morgan, L.N.; Taylor, M.G.; Kirsch, J.F. ); Smith-Gill, S.J. ); Wilson, A.C.

    1993-05-01

    The complex formed between hen egg white lysozyme (HEL) and the monoclonal antibody HyHEL-10 Fab fragment has an interface composed of van der Waals interactions, hydrogen bonds, and a single ion pair. The antibody overlaps part of the active site cleft. Putative critical residues within the epitope region of HEL, identified from the x-ray crystallographic structure of the complex, were replaced by site-directed mutagenesis to probe their relative importance in determining affinity of the antibody for HEL. Twenty single mutations of HEL at three contact residues (Arg-21[sub HEL], Asp-101[sub HEL], and Gly-102[sub HEL]) and at a partially buried residue (Asn-19[sub HEL]) in the epitope were made, and the effects on the free energies of dissociation were measured. A correlation between increased amino acid side-chain volume and reduced affinity for HELs with mutations at position 101 was observed. The D101G[sub HEL] mutant is bound to HyHEL-10 as tightly as wild-type enzyme, but the [delta][delta]G[sub dissoc] is increased by about 2.2 kcal (9.2 kJ)/mol for the larger residues in this position. HEL variants with lysine or histidine replacements for arginine at position 21 are bound 1.4-2.7 times more tightly than those with neutral or negatively charged amino acids in this position. These exhibit 1/40 the affinity for HyHEL-10 Fab compared with wild type. There is no side-chain volume correlation with [delta][delta]G[sub dissoc] at position 21. Although Gly-102[sub HEL] and Asn-19[sub HEL] are in the epitope, replacements at these positions have no effect on the affinity of HEL for the antibody. 34 refs., 2 figs., 3 tabs.

  12. 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

  13. 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

  14. 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

  15. 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.

  16. Anemia rather than hypertension contributes to cerebral hyperperfusion in young adults undergoing hemodialysis: A phase contrast MRI study

    PubMed Central

    Zheng, Gang; Wen, Jiqiu; Yu, Wenkui; Li, Xue; Zhang, Zhe; Chen, Huijuan; Kong, Xiang; Luo, Song; Jiang, Xiaolu; Liu, Ya; Zhang, Zongjun; Zhang, Long Jiang; Lu, Guang Ming

    2016-01-01

    Cerebral hyperperfusion, anemia and hypertension are common in patients with end-stage renal disease (ESRD). Young ESRD adults might afford a better hemodynamic tolerance; however, their cerebral vascular disorders are often overlooked. This phase-contrast MRI study investigated relationships between cerebral blood flow (CBF), anemia and hypertension in young adults undergoing hemodialysis (HD). Blood flows, velocities, and cross-sectional areas of bilateral internal carotid arteries and vertebral arteries were quantified on phase maps in 33 patients and 27 healthy controls. Cerebral oxygen delivery (COD) and vascular resistance were (CVR) were computed based on CBF, hemoglobin and mean arterial pressure (MAP). We found strong correlations among hemoglobin, MAP and CBF. Hemoglobin rather than MAP was directly related to CBF. COD was negatively related to MAP, while CVR was positively related to hemoglobin. The cross-sectional areas of arteries were increased which were directly associated with hemoglobin rather than MAP. HD patients were of elevated CBF, decreased COD and unchanged CVR. Although elevated CBF compensated anemia-induced hypoxia, COD of these patients was still lower. Anemia directly contributed to elevated CBF and hypertension affected CBF through anemia. Unaffected CVR of young patients probably indicated that they could maintain basic functions of cerebral circulation under multiple risk factors. PMID:26923866

  17. Anemia rather than hypertension contributes to cerebral hyperperfusion in young adults undergoing hemodialysis: A phase contrast MRI study.

    PubMed

    Zheng, Gang; Wen, Jiqiu; Yu, Wenkui; Li, Xue; Zhang, Zhe; Chen, Huijuan; Kong, Xiang; Luo, Song; Jiang, Xiaolu; Liu, Ya; Zhang, Zongjun; Zhang, Long Jiang; Lu, Guang Ming

    2016-01-01

    Cerebral hyperperfusion, anemia and hypertension are common in patients with end-stage renal disease (ESRD). Young ESRD adults might afford a better hemodynamic tolerance; however, their cerebral vascular disorders are often overlooked. This phase-contrast MRI study investigated relationships between cerebral blood flow (CBF), anemia and hypertension in young adults undergoing hemodialysis (HD). Blood flows, velocities, and cross-sectional areas of bilateral internal carotid arteries and vertebral arteries were quantified on phase maps in 33 patients and 27 healthy controls. Cerebral oxygen delivery (COD) and vascular resistance were (CVR) were computed based on CBF, hemoglobin and mean arterial pressure (MAP). We found strong correlations among hemoglobin, MAP and CBF. Hemoglobin rather than MAP was directly related to CBF. COD was negatively related to MAP, while CVR was positively related to hemoglobin. The cross-sectional areas of arteries were increased which were directly associated with hemoglobin rather than MAP. HD patients were of elevated CBF, decreased COD and unchanged CVR. Although elevated CBF compensated anemia-induced hypoxia, COD of these patients was still lower. Anemia directly contributed to elevated CBF and hypertension affected CBF through anemia. Unaffected CVR of young patients probably indicated that they could maintain basic functions of cerebral circulation under multiple risk factors. PMID:26923866

  18. MRI of perianal fistulae: a pictorial kaleidoscope.

    PubMed

    Kumar, N; Agarwal, Y; Chawla, A Singh; Jain, R; Thukral, B Bhushan

    2015-12-01

    Perianal fistulae are an abnormal communication between the anorectum and the perianal skin. A seemingly benign condition, it can be a cause of considerable distress to the patient if it is not mapped out adequately before embarking upon surgical correction. The persistence of residual disease complicates and up-stages the grade of the remnant fistula with increased risk of anal incontinence following surgery secondary to damage to the anal sphincter complex. Magnetic resonance imaging (MRI) can play a critical role in mapping the fistulae tract in relation to the anal sphincter complex and hence, act as a reliable guide for the surgeon to chart the optimised management of perianal fistulae. This review illustrates the role of MRI in the imaging evaluation of perianal fistulae, to facilitate a well-planned surgical course. PMID:26455651

  19. 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

  20. MRI-Safe Robot for Endorectal Prostate Biopsy.

    PubMed

    Stoianovici, Dan; Kim, Chunwoo; Srimathveeravalli, Govindarajan; Sebrecht, Peter; Petrisor, Doru; Coleman, Jonathan; Solomon, Stephen B; Hricak, Hedvig

    2013-09-16

    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

  1. MRI-Safe Robot for Endorectal Prostate Biopsy

    PubMed Central

    Stoianovici, Dan; Kim, Chunwoo; Srimathveeravalli, Govindarajan; Sebrecht, Peter; Petrisor, Doru; Coleman, Jonathan; Solomon, Stephen B.; Hricak, Hedvig

    2014-01-01

    This paper reports the development of an MRI-Safe robot for direct (interventional) MRI-guided endorectal prostate biopsy. The robot is constructed of nonmagnetic and electrically nonconductive materials, and is electricity free, using pneumatic actuation and optical sensors. Targeting biopsy lesions of MRI abnormality presents substantial clinical potential for the management of prostate cancer. The paper describes MRI-Safe requirements, presents the kinematic architecture, design and construction of the robot, and a comprehensive set of preclinical tests for MRI compatibility and needle targeting accuracy. The robot has a compact and simple 3 degree-of-freedom (DoF) structure, two for orienting a needle-guide and one to preset the depth of needle insertion. The actual insertion is performed manually through the guide and up to the preset depth. To reduce the complexity and size of the robot next to the patient, the depth setting DoF is remote. Experimental results show that the robot is safe to use in any MRI environment (MRI-Safe). Comprehensive MRI tests show that the presence and motion of the robot in the MRI scanner cause virtually no image deterioration or signal to noise ratio (SNR) change. Robot’s accuracy in bench test, CT-guided in-vitro, MRI-guided in-vitro and animal tests are 0.37mm, 1.10mm, 2.09mm, and 2.58mm respectively. These values are acceptable for clinical use. PMID:25378897

  2. Advanced flow MRI: emerging techniques and applications.

    PubMed

    Markl, M; Schnell, S; Wu, C; Bollache, E; Jarvis, K; Barker, A J; Robinson, J D; Rigsby, C K

    2016-08-01

    Magnetic resonance imaging (MRI) techniques provide non-invasive and non-ionising methods for the highly accurate anatomical depiction of the heart and vessels throughout the cardiac cycle. In addition, the intrinsic sensitivity of MRI to motion offers the unique ability to acquire spatially registered blood flow simultaneously with the morphological data, within a single measurement. In clinical routine, flow MRI is typically accomplished using methods that resolve two spatial dimensions in individual planes and encode the time-resolved velocity in one principal direction, typically oriented perpendicular to the two-dimensional (2D) section. This review describes recently developed advanced MRI flow techniques, which allow for more comprehensive evaluation of blood flow characteristics, such as real-time flow imaging, 2D multiple-venc phase contrast MRI, four-dimensional (4D) flow MRI, quantification of complex haemodynamic properties, and highly accelerated flow imaging. Emerging techniques and novel applications are explored. In addition, applications of these new techniques for the improved evaluation of cardiovascular (aorta, pulmonary arteries, congenital heart disease, atrial fibrillation, coronary arteries) as well as cerebrovascular disease (intra-cranial arteries and veins) are presented. PMID:26944696

  3. 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. PMID:26573018

  4. 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 PAGESBeta

    Johns, H. M.; Mancini, R. C.; Nagayama, T.; Mayes, D. C.; Tommasini, R.; Smalyuk, V. A.; Regan, S. P.; Delettrez, J. A.

    2016-01-25

    In warm target direct-drive ICF implosion experiments performed at the OMEGA laser facility, plastic microballoons doped with a titanium tracer layer in the shell and filled with deuterium gas were imploded using a low-adiabat shaped laser pulse. Continuum radiation emitted in the core is transmitted through the tracer layer and the resulting spectrum recorded with a gated multi-monochromatic x-ray imager (MMI). Titanium K-shell line absorption spectra observed in the data are due to transitions in L-shell titanium ions driven by the backlighting continuum. The MMI data consist of an array of spectrally resolved images of the implosion. These 2-D space-resolvedmore » titanium spectral features constrain the plasma conditions and areal density of the titanium doped region of the shell. The MMI data were processed to obtain narrow-band images and space resolved spectra of titanium spectral features. Shell areal density maps, ρL(x,y), extracted using a new method using both narrow-band images and space resolved spectra are confirmed to be consistent within uncertainties. We report plasma conditions in the titanium-doped region of electron temperature (Te) = 400±28eV, electron number density (Ne) = 8.5x1024±2.5x1024 cm-3, and average areal density <ρR> = 86±7mg/cm2. Fourier analysis of areal density maps reveals shell modulations caused by hydrodynamic instability growth near the fuel-shell interface in the deceleration phase. We observe significant structure in modes l = 2-9, dominated by l = 2. We extract a target breakup fraction of 7.1±1.5% from our Fourier analysis. A new method for estimating mix width is evaluated against existing literature and our target breakup fraction. We estimate a mix width of 10.5±1μm.« less

  5. 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.

  6. Shell stability and conditions analyzed using a new method of extracting shell areal density maps from spectrally resolved images of direct-drive inertial confinement fusion implosions

    NASA Astrophysics Data System (ADS)

    Johns, H. M.; Mancini, R. C.; Nagayama, T.; Mayes, D. C.; Tommasini, R.; Smalyuk, V. A.; Regan, S. P.; Delettrez, J. A.

    2016-01-01

    In warm target direct-drive inertial confinement fusion implosion experiments performed at the OMEGA laser facility, plastic micro-balloons doped with a titanium tracer layer in the shell and filled with deuterium gas were imploded using a low-adiabat shaped laser pulse. Continuum radiation emitted in the core is transmitted through the tracer layer and the resulting spectrum recorded with a gated multi-monochromatic x-ray imager (MMI). Titanium K-shell line absorption spectra observed in the data are due to transitions in L-shell titanium ions driven by the backlighting continuum. The MMI data consist of an array of spectrally resolved images of the implosion. These 2-D space-resolved titanium spectral features constrain the plasma conditions and areal density of the titanium doped region of the shell. The MMI data were processed to obtain narrow-band images and space resolved spectra of titanium spectral features. Shell areal density maps, ρL(x,y), extracted using a new method using both narrow-band images and space resolved spectra are confirmed to be consistent within uncertainties. We report plasma conditions in the titanium-doped region of electron temperature (Te) = 400 ± 28 eV, electron number density (Ne) = 8.5 × 1024 ± 2.5 × 1024 cm-3, and average areal density <ρR> = 86 ± 7 mg/cm2. Fourier analysis of areal density maps reveals shell modulations caused by hydrodynamic instability growth near the fuel-shell interface in the deceleration phase. We observe significant structure in modes l = 2-9, dominated by l = 2. We extract a target breakup fraction of 7.1 ± 1.5% from our Fourier analysis. A new method for estimating mix width is evaluated against existing literature and our target breakup fraction. We estimate a mix width of 10.5 ± 1 μm.

  7. 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

  8. Towards motion insensitive EEG-fMRI: Correcting motion-induced voltages and gradient artefact instability in EEG using an fMRI prospective motion correction (PMC) system.

    PubMed

    Maziero, Danilo; Velasco, Tonicarlo R; Hunt, Nigel; Payne, Edwin; Lemieux, Louis; Salmon, Carlos E G; Carmichael, David W

    2016-09-01

    The simultaneous acquisition of electroencephalography and functional magnetic resonance imaging (EEG-fMRI) is a multimodal technique extensively applied for mapping the human brain. However, the quality of EEG data obtained within the MRI environment is strongly affected by subject motion due to the induction of voltages in addition to artefacts caused by the scanning gradients and the heartbeat. This has limited its application in populations such as paediatric patients or to study epileptic seizure onset. Recent work has used a Moiré-phase grating and a MR-compatible camera to prospectively update image acquisition and improve fMRI quality (prospective motion correction: PMC). In this study, we use this technology to retrospectively reduce the spurious voltages induced by motion in the EEG data acquired inside the MRI scanner, with and without fMRI acquisitions. This was achieved by modelling induced voltages from the tracking system motion parameters; position and angles, their first derivative (velocities) and the velocity squared. This model was used to remove the voltages related to the detected motion via a linear regression. Since EEG quality during fMRI relies on a temporally stable gradient artefact (GA) template (calculated from averaging EEG epochs matched to scan volume or slice acquisition), this was evaluated in sessions both with and without motion contamination, and with and without PMC. We demonstrate that our approach is capable of significantly reducing motion-related artefact with a magnitude of up to 10mm of translation, 6° of rotation and velocities of 50mm/s, while preserving physiological information. We also demonstrate that the EEG-GA variance is not increased by the gradient direction changes associated with PMC. Provided a scan slice-based GA template is used (rather than a scan volume GA template) we demonstrate that EEG variance during motion can be supressed towards levels found when subjects are still. In summary, we show that

  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. Electrical tissue property imaging using MRI at dc and Larmor frequency

    NASA Astrophysics Data System (ADS)

    Seo, Jin Keun; Kim, Dong-Hyun; Lee, Joonsung; In Kwon, Oh; Sajib, Saurav Z. K.; Woo, Eung Je

    2012-08-01

    Cross-sectional imaging of conductivity and permittivity distributions inside the human body has been actively investigated in impedance imaging areas such as electrical impedance tomography (EIT) and magnetic induction tomography (MIT). Since the conductivity and permittivity values exhibit frequency-dependent changes, it is worthwhile to perform spectroscopic imaging from almost dc to hundreds of MHz. To probe the human body, we may inject current using surface electrodes or induce current using external coils. In EIT and MIT, measured data are only available on the boundary or exterior of the body unless we invasively place sensors inside the body. Their image reconstruction problems are nonlinear and ill-posed to result in images with a relatively low spatial resolution. Noting that an MRI scanner can noninvasively measure magnetic fields inside the human body, electrical tissue property imaging methods using MRI have lately been proposed. Magnetic resonance EIT (MREIT) performs conductivity imaging at dc or below 1 kHz by externally injecting current into the human body and measuring induced internal magnetic flux density data using an MRI scanner. Magnetic resonance electrical property tomography (MREPT) produces both conductivity and permittivity images at the Larmor frequency of an MRI scanner based on B1-mapping techniques. Since internal data are only available in MREIT and MREPT, we may formulate well-posed inverse problems for image reconstructions. To develop related imaging techniques, we should clearly understand the basic principles of MREIT and MREPT, which are based on coupled physics of bioelectromagnetism and MRI as well as associated mathematical methods. In this paper, we describe the physical principles of MREIT and MREPT in a unified way and associate measurable quantities with the conductivity and permittivity. Clarifying the key relations among them, we examine existing image reconstruction algorithms to reveal their capabilities and

  11. Implications of inconsistencies between fMRI and dMRI on multimodal connectivity estimation.

    PubMed

    Ng, Bernard; Varoquaux, Gael; Poline, Jean Baptiste; Thirion, Bertrand

    2013-01-01

    There is a recent trend towards integrating resting state functional magnetic resonance imaging (RS-fMRI) and diffusion MRI (dMRI) for brain connectivity estimation, as motivated by how estimates from these modalities are presumably two views reflecting the same underlying brain circuitry. In this paper, we show on a cohort of 60 subjects that conventional functional connectivity (FC) estimates based on Pearson's correlation and anatomical connectivity (AC) estimates based on fiber counts are actually not that highly correlated for typical RS-fMRI (approximately 7 min) and dMRI (approximately 32 gradient directions) data. The FC-AC correlation can be significantly increased by considering sparse partial correlation and modeling fiber endpoint uncertainty, but the resulting FC-AC correlation is still rather low in absolute terms. We further exemplify the inconsistencies between FC and AC estimates by integrating them as priors into activation detection and demonstrating significant differences in their detection sensitivity. Importantly, we illustrate that these inconsistencies can be useful in fMRI-dMRI integration for improving brain connectivity estimation. PMID:24505817

  12. Atlas-guided generation of pseudo-CT images for MRI-only and hybrid PET-MRI-guided radiotherapy treatment planning.

    PubMed

    Arabi, Hossein; Koutsouvelis, Nikolaos; Rouzaud, Michel; Miralbell, Raymond; Zaidi, Habib

    2016-09-01

    Magnetic resonance imaging (MRI)-guided attenuation correction (AC) of positron emission tomography (PET) data and/or radiation therapy (RT) treatment planning is challenged by the lack of a direct link between MRI voxel intensities and electron density. Therefore, even if this is not a trivial task, a pseudo-computed tomography (CT) image must be predicted from MRI alone. In this work, we propose a two-step (segmentation and fusion) atlas-based algorithm focusing on bone tissue identification to create a pseudo-CT image from conventional MRI sequences and evaluate its performance against the conventional MRI segmentation technique and a recently proposed multi-atlas approach. The clinical studies consisted of pelvic CT, PET and MRI scans of 12 patients with loco-regionally advanced rectal disease. In the first step, bone segmentation of the target image is optimized through local weighted atlas voting. The obtained bone map is then used to assess the quality of deformed atlases to perform voxel-wise weighted atlas fusion. To evaluate the performance of the method, a leave-one-out cross-validation (LOOCV) scheme was devised to find optimal parameters for the model. Geometric evaluation of the produced pseudo-CT images and quantitative analysis of the accuracy of PET AC were performed. Moreover, a dosimetric evaluation of volumetric modulated arc therapy photon treatment plans calculated using the different pseudo-CT images was carried out and compared to those produced using CT images serving as references. The pseudo-CT images produced using the proposed method exhibit bone identification accuracy of 0.89 based on the Dice similarity metric compared to 0.75 achieved by the other atlas-based method. The superior bone extraction resulted in a mean standard uptake value bias of  -1.5  ±  5.0% (mean  ±  SD) in bony structures compared to  -19.9  ±  11.8% and  -8.1  ±  8.2% achieved by MRI segmentation-based (water

  13. Myelin and iron concentration in the human brain: a quantitative study of MRI contrast.

    PubMed

    Stüber, Carsten; Morawski, Markus; Schäfer, Andreas; Labadie, Christian; Wähnert, Miriam; Leuze, Christoph; Streicher, Markus; Barapatre, Nirav; Reimann, Katja; Geyer, Stefan; Spemann, Daniel; Turner, Robert

    2014-06-01

    During the last five years ultra-high-field magnetic resonance imaging (MRI) has enabled an unprecedented view of living human brain. Brain tissue contrast in most MRI sequences is known to reflect mainly the spatial distributions of myelin and iron. These distributions have been shown to overlap significantly in many brain regions, especially in the cortex. It is of increasing interest to distinguish and identify cortical areas by their appearance in MRI, which has been shown to be feasible in vivo. Parcellation can benefit greatly from quantification of the independent contributions of iron and myelin to MRI contrast. Recent studies using susceptibility mapping claim to allow such a separation of the effects of myelin and iron in MRI. We show, using post-mortem human brain tissue, that this goal can be achieved. After MRI scanning of the block with appropriate T1 mapping and T2* weighted sequences, we section the block and apply a novel technique, proton induced X-ray emission (PIXE), to spatially map iron, phosphorus and sulfur elemental concentrations, simultaneously with 1μm spatial resolution. Because most brain phosphorus is located in myelin phospholipids, a calibration step utilizing element maps of sulfur enables semi-quantitative ex vivo mapping of myelin concentration. Combining results for iron and myelin concentration in a linear model, we have accurately modeled MRI tissue contrasts. Conversely, iron and myelin concentrations can now be estimated from appropriate MRI measurements in post-mortem brain samples. PMID:24607447

  14. 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.

  15. Probabilistic Seismic Hazard Maps of Seattle, Washington, Including 3D Sedimentary Basin Effects and Rupture Directivity: Implications of 3D Random Velocity Variations (Invited)

    NASA Astrophysics Data System (ADS)

    Frankel, A. D.; Stephenson, W. J.; Carver, D.; Odum, J.; Williams, R. A.; Rhea, S.

    2010-12-01

    We have produced probabilistic seismic hazard maps of Seattle for 1 Hz spectral acceleration, using over five hundred 3D finite-difference simulations of earthquakes on the Seattle fault, Southern Whidbey Island fault, and Cascadia subduction zone, as well as for random deep and shallow earthquakes at various locations. The 3D velocity model was validated by modeling the observed waveforms for the 2001 M6.8 Nisqually earthquake and several smaller events in the region. At these longer periods (≥ 1 sec) that are especially important to the response of buildings of ten stories or higher, seismic waves are strongly influenced by sedimentary basins and rupture directivity. We are investigating how random spatial variations in the 3D velocity model affect the simulated ground motions for M6.7 earthquakes on the Seattle fault. A fractal random variation of shear-wave velocity with a Von Karman correlation function produces spatial variations of peak ground velocity with multiple scale lengths. We find that a 3D velocity model with a 10% standard deviation in shear-wave velocity in the top 1.5 km and 5% standard deviation from 1.5-10 km depth produces variations in peak ground velocities of as much as a factor of two, relative to the case with no random variations. The model with random variations generally reduces the peak ground velocity of the forward rupture directivity pulse for sites near the fault where basin-edge focusing of S-waves occurs. It also tends to reduce the peak velocity of localized areas where basin surface waves are focused. However, the medium with random variations also causes small-scale amplification of ground motions over distances of a few kilometers. We are also evaluating alternative methods of characterizing the aleatory uncertainty in the probabilistic hazard calculations.

  16. Discriminating the indistinguishable sapwood from heartwood in discolored ancient wood by direct molecular mapping of specific extractives using time-of-flight secondary ion mass spectrometry.

    PubMed

    Saito, Kaori; Mitsutani, Takumi; Imai, Takanori; Matsushita, Yasuyuki; Fukushima, Kazuhiko

    2008-03-01

    A new method that can chemically discriminate the visually indistinguishable sapwood from heartwood in discolored woods is presented in this paper. Discriminating between sapwood and heartwood, which are normally recognized by color in cross sections of stems of tress, is important in dendrochronological dating, as well as in evaluating qualities of woods such as durability. In tree-ring chronology, the felling date, which affects the construction date of architectures, can be estimated only in woods that have a recognizable sapwood/heartwood boundary. However, the felling date cannot be estimated in discolored woods because it has indistinguishable sapwood. Time-of-flight secondary ion mass spectrometry (TOF-SIMS) analysis of specific chemical substances retained for approximately 1300 years after felling demonstrated the presence of sapwood in a discolored ancient architectural wood of Hinoki cypress (Chamaecyparis obtusa). Direct molecular mapping by TOF-SIMS clearly indicated that the specific substances, hinokinin, hinokiresinol, hinokione, and hinokiol, started to accumulate at the sapwood/heartwood boundary where only hinokinin was localized and retained predominantly in ray parenchyma cells. The result allowed the determination of the felling date of the discolored wood. TOF-SIMS has shown to be useful for investigating the distribution of minute amounts of chemical components in woods. PMID:18232669

  17. MRI Zooms in on Microscopic Flow

    SciTech Connect

    2010-01-01

    MRI images of water flow through a constricted microfluidic channel with the XZ axis on the left and the YZ axis on the right. Note that fast moving components directly aligned with the constricted region emerge at the detector first, followed by components that are not aligned with the constriction.

  18. Implantable medical devices MRI safe.

    PubMed

    Dal Molin, Renzo; Hecker, Bertrand

    2013-01-01

    Pacemakers, ICDs, neurostimulators like deep brain stimulator electrodes, spiral cord stimulators, insulin pumps, cochlear implants, retinal implants, hearing aids, electro cardio gram (ECG) leads, or devices in interventional MRI such as vascular guide wires or catheters are affected by MRI magnetic and electromagnetic fields. Design of MRI Safe medical devices requires computer modeling, bench testing, phantom testing, and animal studies. Implanted medical devices can be MRI unsafe, MRI conditional or MRI safe (see glossary). In the following paragraphs we will investigate how to design implanted medical devices MRI safe. PMID:23739365

  19. Quantitative DNA fiber mapping

    DOEpatents

    Gray, Joe W.; Weier, Heinz-Ulrich G.

    1998-01-01

    The present invention relates generally to the DNA mapping and sequencing technologies. In particular, the present invention provides enhanced methods and compositions for the physical mapping and positional cloning of genomic DNA. The present invention also provides a useful analytical technique to directly map cloned DNA sequences onto individual stretched DNA molecules.

  20. Anisotropic conductivity tensor imaging in MREIT using directional diffusion rate of water molecules

    NASA Astrophysics Data System (ADS)

    In Kwon, Oh; Jeong, Woo Chul; Sajib, Saurav Z. K.; Kim, Hyung Joong; Woo, Eung Je

    2014-06-01

    Magnetic resonance electrical impedance tomography (MREIT) is an emerging method to visualize electrical conductivity and/or current density images at low frequencies (below 1 KHz). Injecting currents into an imaging object, one component of the induced magnetic flux density is acquired using an MRI scanner for isotropic conductivity image reconstructions. Diffusion tensor MRI (DT-MRI) measures the intrinsic three-dimensional diffusion property of water molecules within a tissue. It characterizes the anisotropic water transport by the effective diffusion tensor. Combining the DT-MRI and MREIT techniques, we propose a novel direct method for absolute conductivity tensor image reconstructions based on a linear relationship between the water diffusion tensor and the electrical conductivity tensor. We first recover the projected current density, which is the best approximation of the internal current density one can obtain from the measured single component of the induced magnetic flux density. This enables us to estimate a scale factor between the diffusion tensor and the conductivity tensor. Combining these values at all pixels with the acquired diffusion tensor map, we can quantitatively recover the anisotropic conductivity tensor map. From numerical simulations and experimental verifications using a biological tissue phantom, we found that the new method overcomes the limitations of each method and successfully reconstructs both the direction and magnitude of the conductivity tensor for both the anisotropic and isotropic regions.

  1. Future perspectives for intraoperative MRI.

    PubMed

    Jolesz, Ferenc A

    2005-01-01

    MRI-guided neurosurgery not only represents a technical challenge but a transformation from conventional hand-eye coordination to interactive navigational operations. In the future, multimodality-based images will be merged into a single model, in which anatomy and pathologic changes are at once distinguished and integrated into the same intuitive framework. The long-term goals of improving surgical procedures and attendant outcomes, reducing costs, and achieving broad use can be achieved with a three-pronged approach: 1. Improving the presentation of preoperative and real-time intraoperative image information 2. Integrating imaging and treatment-related technology into therapy delivery systems 3. Testing the clinical utility of image guidance in surgery The recent focus in technology development is on improving our ability to understand and apply medical images and imaging systems. Areas of active research include image processing, model-based image analysis, model deformation, real-time registration, real-time 3D (so-called "four-dimensional") imaging, and the integration and presentation of image and sensing information in the operating room. Key elements of the technical matrix also include visualization and display platforms and related software for information and display, model-based image understanding, the use of computing clusters to speed computation (ie, algorithms with partitioned computation to optimize performance), and advanced devices and systems for 3D device tracking (navigation). Current clinical applications are successfully incorporating real-time and/or continuously up-dated image-based information for direct intra-operative visualization. In addition to using traditional imaging systems during surgery, we foresee optimized use of molecular marker technology, direct measures of tissue characterization (ie, optical measurements and/or imaging), and integration of the next generation of surgical and therapy devices (including image

  2. Sodium and T1ρ MRI for molecular and diagnostic imaging of articular cartilage†

    PubMed Central

    Borthakur, Arijitt; Mellon, Eric; Niyogi, Sampreet; Witschey, Walter; Kneeland, J. Bruce; Reddy, Ravinder

    2010-01-01

    In this article, both sodium magnetic resonance (MR) and T1ρ relaxation mapping aimed at measuring molecular changes in cartilage for the diagnostic imaging of osteoarthritis are reviewed. First, an introduction to structure of cartilage, its degeneration in osteoarthritis (OA) and an outline of diagnostic imaging methods in quantifying molecular changes and early diagnostic aspects of cartilage degeneration are described. The sodium MRI section begins with a brief overview of the theory of sodium NMR of biological tissues and is followed by a section on multiple quantum filters that can be used to quantify both bi-exponential relaxation and residual quadrupolar interaction. Specifically, (i) the rationale behind the use of sodium MRI in quantifying proteoglycan (PG) changes, (ii) validation studies using biochemical assays, (iii) studies on human OA specimens, (iv) results on animal models and (v) clinical imaging protocols are reviewed. Results demonstrating the feasibility of quantifying PG in OA patients and comparison with that in healthy subjects are also presented. The section concludes with the discussion of advantages and potential issues with sodium MRI and the impact of new technological advancements (e.g. ultra-high field scanners and parallel imaging methods). In the theory section on T1ρ, a brief description of (i) principles of measuring T1ρ relaxation, (ii) pulse sequences for computing T1ρ relaxation maps, (iii) issues regarding radio frequency power deposition, (iv) mechanisms that contribute to T1ρ in biological tissues and (v) effects of exchange and dipolar interaction on T1ρ dispersion are discussed. Correlation of T1ρ relaxation rate with macromolecular content and biomechanical properties in cartilage specimens subjected to trypsin and cytokine-induced glycosaminoglycan depletion and validation against biochemical assay and histopathology are presented. Experimental T1ρ data from osteoarthritic specimens, animal models, healthy human

  3. Knee MRI scan

    MedlinePlus

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

  4. 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 ...

  5. 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 ...

  6. 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 ...

  7. MRI (Magnetic Resonance Imaging)

    MedlinePlus

    ... some MRI exams, intravenous (IV) drugs, such as gadolinium-based contrast agents (GBCAs) are used to change the contrast of the MR image. Gadolinium-based contrast agents are rare earth metals that ...

  8. MRI of the Breast

    MedlinePlus

    ... as a supplemental tool to breast screening with mammography or ultrasound. It may be used to screen ... following diagnosis, or further evaluate abnormalities seen on mammography. Breast MRI does not use ionizing radiation, and ...

  9. Towards MRI microarrays.

    PubMed

    Hall, Andrew; Mundell, Victoria J; Blanco-Andujar, Cristina; Bencsik, Martin; McHale, Glen; Newton, Michael I; Cave, Gareth W V

    2010-04-14

    Superparamagnetic iron oxide nanometre scale particles have been utilised as contrast agents to image staked target binding oligonucleotide arrays using MRI to correlate the signal intensity and T(2)* relaxation times in different NMR fluids. PMID:20379545

  10. Sinus MRI scan

    MedlinePlus

    ... Thomsen HS, Reimer P. Intravascular contrast media for radiology, CT, and MRI. In: Adam A, Dixon AK, ... JH, Schaefer-Prokop CM, eds. Grainger & Allison's Diagnostic Radiology: A Textbook of Medical Imaging . 6th ed. New ...

  11. 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 ...

  12. MO-C-17A-08: Evaluation of Lung Deformation Using Three Dimensional Strain Maps

    SciTech Connect

    Cui, T; Huang, Q; Miller, W; Zhong, X; Yin, F; Cai, J

    2014-06-15

    Purpose: To develop a systematic approach to generate three dimensional (3D) strain maps of lung using the displacement vector field (DVF) during the respiratory deformation, and to demonstrate its application in evaluating deformable image registration (DIR). Methods: A DVF based strain tensor at each voxel of interest (VOI) was calculated from the relative displacements between the VOI and each of the six nearest neighbors. The maximum and minimum stretches of a VOI can be determined by the principal strains (E{sub 1}, E{sub 2} and E{sub 3}), which are the eigenvalues and the corresponding strain tensors. Two healthy volunteers enrolled in this study under IRB-approved protocol, each was scanned using 3D Hyperpolarized He-3 tagging-MRI and 3D proton-MRI with TrueFISP sequence at the endof- inhalation (EOI) and the end-of-exhalation (EOE) phases. 3D DVFs of tagging- and proton-MRI were obtained by the direct measurements of the tagging grid trajectory and by the DIR method implemented in commercial software. Results: 3D strain maps were successfully generated for all DVFs. The principal strain E1s were calculated as 0.43±0.05 and 0.17±0.25 for tagging-MRI and proton-MRI, respectively. The large values of E{sub 1} indicate the predominant lung motion in the superior-inferior (SI) direction. Given that the DVFs from the tagging images are considered as the ground truth, the discrepancies in the DIR-based strain maps suggest the inaccuracy of the DIR algorithm. In the E{sub 1} maps of tagging-MRI for subject 1, the fissures were distinguishable by the larger values (0.49±0.02) from the adjacent tissues (0.41±0.03) due to the larger relative displacement between the lung lobes. Conclusion: We have successfully developed a methodology to generate DVF-based 3D strain maps of lung. It can potentially enable us to better understand the pulmonary biomechanics and to evaluate and improve the DIR algorithms for the lung deformation. We are currently studying more

  13. Current MRI Techniques for the Assessment of Renal Disease

    PubMed Central

    Takahashi, Takamune; Wang, Feng; Quarles, Christopher C.

    2015-01-01

    Purpose of review Over the past decade a variety of magnetic resonance imaging (MRI) methods have been developed and applied to many kidney diseases. These MRI techniques show great promise, enabling the noninvasive assessment of renal structure, function, and injury in individual subjects. This review will highlight current applications of functional MRI techniques for the assessment of renal disease and discuss future directions. Recent findings Many pathological (functional and structural) changes or factors in renal disease can be assessed by advanced MRI techniques. These include renal vascular structure and function (contrast-enhanced MRI, arterial spin labeling), tissue oxygenation (blood oxygen level-dependent MRI), renal tissue injury and fibrosis (diffusion or magnetization transfer imaging, MR elastography), renal metabolism (chemical exchange saturation transfer, spectroscopic imaging), nephron endowment (cationic-contrast imaging), sodium concentration (23Na-MRI), and molecular events (targeted-contrast imaging). Summary Current advances in MRI techniques have enabled the non-invasive investigation of renal disease. Further development, evaluation, and application of the MRI techniques should facilitate better understanding and assessment of renal disease and the development of new imaging biomarkers, enabling the intensified treatment to high-risk populations and a more rapid interrogation of novel therapeutic agents and protocols. PMID:26066472

  14. Optogenetic Functional MRI

    PubMed Central

    Lin, Peter; Fang, Zhongnan; Liu, Jia; Lee, Jin Hyung

    2016-01-01

    The investigation of the functional connectivity of precise neural circuits across the entire intact brain can be achieved through optogenetic functional magnetic resonance imaging (ofMRI), which is a novel technique that combines the relatively high spatial resolution of high-field fMRI with the precision of optogenetic stimulation. Fiber optics that enable delivery of specific wavelengths of light deep into the brain in vivo are implanted into regions of interest in order to specifically stimulate targeted cell types that have been genetically induced to express light-sensitive trans-membrane conductance channels, called opsins. fMRI is used to provide a non-invasive method of determining the brain's global dynamic response to optogenetic stimulation of specific neural circuits through measurement of the blood-oxygen-level-dependent (BOLD) signal, which provides an indirect measurement of neuronal activity. This protocol describes the construction of fiber optic implants, the implantation surgeries, the imaging with photostimulation and the data analysis required to successfully perform ofMRI. In summary, the precise stimulation and whole-brain monitoring ability of ofMRI are crucial factors in making ofMRI a powerful tool for the study of the connectomics of the brain in both healthy and diseased states. PMID:27167840

  15. Optogenetic Functional MRI.

    PubMed

    Lin, Peter; Fang, Zhongnan; Liu, Jia; Lee, Jin Hyung

    2016-01-01

    The investigation of the functional connectivity of precise neural circuits across the entire intact brain can be achieved through optogenetic functional magnetic resonance imaging (ofMRI), which is a novel technique that combines the relatively high spatial resolution of high-field fMRI with the precision of optogenetic stimulation. Fiber optics that enable delivery of specific wavelengths of light deep into the brain in vivo are implanted into regions of interest in order to specifically stimulate targeted cell types that have been genetically induced to express light-sensitive trans-membrane conductance channels, called opsins. fMRI is used to provide a non-invasive method of determining the brain's global dynamic response to optogenetic stimulation of specific neural circuits through measurement of the blood-oxygen-level-dependent (BOLD) signal, which provides an indirect measurement of neuronal activity. This protocol describes the construction of fiber optic implants, the implantation surgeries, the imaging with photostimulation and the data analysis required to successfully perform ofMRI. In summary, the precise stimulation and whole-brain monitoring ability of ofMRI are crucial factors in making ofMRI a powerful tool for the study of the connectomics of the brain in both healthy and diseased states. PMID:27167840

  16. Reliability of Task-Based fMRI for Preoperative Planning: A Test-Retest Study in Brain Tumor Patients and Healthy Controls

    PubMed Central

    Morrison, Melanie A.; Churchill, Nathan W.; Cusimano, Michael D.; Schweizer, Tom A.; Das, Sunit; Graham, Simon J.

    2016-01-01

    Background Functional magnetic resonance imaging (fMRI) continues to develop as a clinical tool for patients with brain cancer, offering data that may directly influence surgical decisions. Unfortunately, routine integration of preoperative fMRI has been limited by concerns about reliability. Many pertinent studies have been undertaken involving healthy controls, but work involving brain tumor patients has been limited. To develop fMRI fully as a clinical tool, it will be critical to examine these reliability issues among patients with brain tumors. The present work is the first to extensively characterize differences in activation map quality between brain tumor patients and healthy controls, including the effects of tumor grade and the chosen behavioral testing paradigm on reliability outcomes. Method Test-retest data were collected for a group of low-grade (n = 6) and high-grade glioma (n = 6) patients, and for matched healthy controls (n = 12), who performed motor and language tasks during a single fMRI session. Reliability was characterized by the spatial overlap and displacement of brain activity clusters, BOLD signal stability, and the laterality index. Significance testing was performed to assess differences in reliability between the patients and controls, and low-grade and high-grade patients; as well as between different fMRI testing paradigms. Results There were few significant differences in fMRI reliability measures between patients and controls. Reliability was significantly lower when comparing high-grade tumor patients to controls, or to low-grade tumor patients. The motor task produced more reliable activation patterns than the language tasks, as did the rhyming task in comparison to the phonemic fluency task. Conclusion In low-grade glioma patients, fMRI data are as reliable as healthy control subjects. For high-grade glioma patients, further investigation is required to determine the underlying causes of reduced reliability. To maximize

  17. Biomedical Applications of Sodium MRI In Vivo

    PubMed Central

    Madelin, Guillaume; Regatte, Ravinder R.

    2013-01-01

    In this article, we present an up-to-date overview of the potential biomedical applications of sodium MRI in vivo. Sodium MRI is a subject of increasing interest in translational imaging research as it can give some direct and quantitative biochemical information on the tissue viability, cell integrity and function, and therefore not only help the diagnosis but also the prognosis of diseases and treatment outcomes. It has already been applied in vivo in most of human tissues, such as brain for stroke or tumor detection and therapeutic response, in breast cancer, in articular cartilage, in muscle and in kidney, and it was shown in some studies that it could provide very useful new information not available through standard proton MRI. However, this technique is still very challenging due to the low detectable sodium signal in biological tissue with MRI and hardware/software limitations of the clinical scanners. The article is divided in three parts: (1) the role of sodium in biological tissues, (2) a short review on sodium magnetic resonance, and (3) a review of some studies on sodium MRI on different organs/diseases to date. PMID:23722972

  18. Mapping the epitopes of a neutralizing antibody fragment directed against the lethal factor of Bacillus anthracis and cross-reacting with the homologous edema factor.

    PubMed

    Thullier, Philippe; Avril, Arnaud; Mathieu, Jacques; Behrens, Christian K; Pellequer, Jean-Luc; Pelat, Thibaut

    2013-01-01

    The lethal toxin (LT) of Bacillus anthracis, composed of the protective antigen (PA) and the lethal factor (LF), plays an essential role in anthrax pathogenesis. PA also interacts with the edema factor (EF, 20% identity with LF) to form the edema toxin (ET), which has a lesser role in anthrax pathogenesis. The first recombinant antibody fragment directed against LF was scFv 2LF; it neutralizes LT by blocking the interaction between PA and LF. Here, we report that scFv 2LF cross-reacts with EF and cross-neutralizes ET, and we present an in silico method taking advantage of this cross-reactivity to map the epitope of scFv 2LF on both LF and EF. This method identified five epitope candidates on LF, constituted of a total of 32 residues, which were tested experimentally by mutating the residues to alanine. This combined approach precisely identified the epitope of scFv 2LF on LF as five residues (H229, R230, Q234, L235 and Y236), of which three were missed by the consensus epitope candidate identified by pre-existing in silico methods. The homolog of this epitope on EF (H253, R254, E258, L259 and Y260) was experimentally confirmed to constitute the epitope of scFv 2LF on EF. Other inhibitors, including synthetic molecules, could be used to target these epitopes for therapeutic purposes. The in silico method presented here may be of more general interest. PMID:23741517

  19. Direct interaction and functional coupling between human 5-HT6 receptor and the light chain 1 subunit of the microtubule-associated protein 1B (MAP1B-LC1).

    PubMed

    Kim, Soon-Hee; Kim, Dong Hyuk; Lee, Kang Ho; Im, Sun-Kyoung; Hur, Eun-Mi; Chung, Kwang Chul; Rhim, Hyewhon

    2014-01-01

    Serotonin (5-HT) receptors of type 6 (5-HT6R) play important roles in mood, psychosis, and eating disorders. Recently, a growing number of studies support the use of 5-HT6R-targeting compounds as promising drug candidates for treating cognitive dysfunction associated with Alzheimer's disease. However, the mechanistic linkage between 5-HT6R and such functions remains poorly understood. By using yeast two-hybrid, GST pull-down, and co-immunoprecipitation assays, here we show that human 5-HT6R interacts with the light chain 1 (LC1) subunit of MAP1B protein (MAP1B-LC1), a classical microtubule-associated protein highly expressed in the brain. Functionally, we have found that expression of MAP1B-LC1 regulates serotonin signaling in a receptor subtype-specific manner, specifically controlling the activities of 5-HT6R, but not those of 5-HT4R and 5-HT7R. In addition, we have demonstrated that MAP1B-LC1 increases the surface expression of 5-HT6R and decreases its endocytosis, suggesting that MAP1B-LC1 is involved in the desensitization and trafficking of 5-HT6R via a direct interaction. Together, we suggest that signal transduction pathways downstream of 5-HT6R are regulated by MAP1B, which might play a role in 5-HT6R-mediated signaling in the brain. PMID:24614691

  20. Direct Interaction and Functional Coupling between Human 5-HT6 Receptor and the Light Chain 1 Subunit of the Microtubule-Associated Protein 1B (MAP1B-LC1)

    PubMed Central

    Kim, Soon-Hee; Kim, Dong Hyuk; Lee, Kang Ho; Im, Sun-Kyoung; Hur, Eun-Mi; Chung, Kwang Chul; Rhim, Hyewhon

    2014-01-01

    Serotonin (5-HT) receptors of type 6 (5-HT6R) play important roles in mood, psychosis, and eating disorders. Recently, a growing number of studies support the use of 5-HT6R-targeting compounds as promising drug candidates for treating cognitive dysfunction associated with Alzheimer’s disease. However, the mechanistic linkage between 5-HT6R and such functions remains poorly understood. By using yeast two-hybrid, GST pull-down, and co-immunoprecipitation assays, here we show that human 5-HT6R interacts with the light chain 1 (LC1) subunit of MAP1B protein (MAP1B-LC1), a classical microtubule-associated protein highly expressed in the brain. Functionally, we have found that expression of MAP1B-LC1 regulates serotonin signaling in a receptor subtype-specific manner, specifically controlling the activities of 5-HT6R, but not those of 5-HT4R and 5-HT7R. In addition, we have demonstrated that MAP1B-LC1 increases the surface expression of 5-HT6R and decreases its endocytosis, suggesting that MAP1B-LC1 is involved in the desensitization and trafficking of 5-HT6R via a direct interaction. Together, we suggest that signal transduction pathways downstream of 5-HT6R are regulated by MAP1B, which might play a role in 5-HT6R-mediated signaling in the brain. PMID:24614691

  1. Inference of biological networks using Bi-directional Random Forest Granger causality.

    PubMed

    Furqan, Mohammad Shaheryar; Siyal, Mohammad Yakoob

    2016-01-01

    The standard ordinary least squares based Granger causality is one of the widely used methods for detecting causal interactions between time series data. However, recent developments in technology limit the utilization of some existing implementations due to the availability of high dimensional data. In this paper, we are proposing a technique called Bi-directional Random Forest Granger causality. This technique uses the random forest regularization together with the idea of reusing the time series data by reversing the time stamp to extract more causal information. We have demonstrated the effectiveness of our proposed method by applying it to simulated data and then applied it to two real biological datasets, i.e., fMRI and HeLa cell. fMRI data was used to map brain network involved in deductive reasoning while HeLa cell dataset was used to map gene network involved in cancer. PMID:27186478

  2. Tissue-point motion tracking in the tongue from cine MRI and tagged MRI.

    PubMed

    Woo, Jonghye; Stone, Maureen; Suo, Yuanming; Murano, Emi Z; Prince, Jerry L

    2014-04-01

    PURPOSE Accurate tissue motion tracking within the tongue can help professionals diagnose and treat vocal tract-related disorders, evaluate speech quality before and after surgery, and conduct various scientific studies. The authors compared tissue tracking results from 4 widely used deformable registration (DR) methods applied to cine magnetic resonance imaging (MRI) with harmonic phase (HARP)-based tracking applied to tagged MRI. METHOD Ten subjects repeated the phrase "a geese" multiple times while sagittal images of the head were collected at 26 Hz, first in a tagged MRI data set and then in a cine MRI data set. HARP tracked the motion of 8 specified tissue points in the tagged data set. Four DR methods including diffeomorphic demons and free-form deformations based on cubic B-spline with 3 different similarity measures were used to track the same 8 points in the cine MRI data set. Individual points were tracked and length changes of several muscles were calculated using the DR- and HARP-based tracking methods. RESULTS The results showed that the DR tracking errors were nonsystematic and varied in direction, amount, and timing across speakers and within speakers. Comparison of HARP and DR tracking with manual tracking showed better tracking results for HARP except at the tongue surface, where mistracking caused greater errors in HARP than DR. CONCLUSIONS Tissue point tracking using DR tracking methods contains nonsystematic tracking errors within and across subjects, making it less successful than tagged MRI tracking within the tongue. However, HARP sometimes mistracks points at the tongue surface of tagged MRI because of its limited bandpass filter and tag pattern fading, so that DR has better success measuring surface tissue points on cine MRI than HARP does. Therefore, a hybrid method is being explored. PMID:24686470

  3. Triaxial fiber optic magnetic field sensor for MRI applications

    NASA Astrophysics Data System (ADS)

    Filograno, Massimo L.; Pisco, Marco; Catalano, Angelo; Forte, Ernesto; Aiello, Marco; Soricelli, Andrea; Davino, Daniele; Visone, Ciro; Cutolo, Antonello; Cusano, Andrea

    2016-05-01

    In this paper, we report a fiber-optic triaxial magnetic field sensor, based on Fiber Bragg Gratings (FBGs) integrated with giant magnetostrictive material, the Terfenol-D. The realized sensor has been designed and engineered for Magnetic Resonance Imaging (MRI) applications. A full magneto-optical characterization of the triaxial sensing probe has been carried out, providing the complex relationship among the FBGs wavelength shift and the applied magnetostatic field vector. Finally, the developed fiber optic sensors have been arranged in a sensor network composed of 20 triaxial sensors for mapping the magnetic field distribution in a MRI-room at a diagnostic center in Naples (SDN), equipped with Positron emission tomography/magnetic resonance (PET/MR) instrumentation. Experimental results reveal that the proposed sensor network can be efficiently used in MRI centers for performing quality assurance tests, paving the way for novel integrated tools to measure the magnetic dose accumulated day by day by MRI operators.

  4. Functional MRI compliance in children with attention deficit hyperactivity disorder

    PubMed Central

    Karakaş, Sirel; Dinçer, Elvin Doğutepe; Ceylan, Arzu Özkan; Tileylioğlu, Emre; Karakaş, Hakkı Muammer; Talı, E. Turgut

    2015-01-01

    PURPOSE We aimed to test the effect of prescan training and orientation in functional magnetic resonance imaging (fMRI) in children with attention deficit hyperactivity disorder (ADHD) and to investigate whether fMRI compliance was modified by state anxiety. METHODS Subjects included 77 males aged 6–12 years; there were 53 patients in the ADHD group and 24 participants in the healthy control group. Exclusion criteria included neurological and/or psychiatric comorbidities (other than ADHD), the use of psychoactive drugs, and an intelligence quotient outside the normal range. Children were individually subjected to prescan orientation and training. Data were acquired using a 1.5 Tesla scanner and an 8-channel head coil. Functional scans were performed using a standard neurocognitive task. RESULTS The neurocognitive task led to reliable fMRI maps. Compliance was not significantly different between ADHD and control groups based on success, failure, and repetition rates of fMRI. Compliance of ADHD patients with extreme levels of anxiety was also not significantly different. CONCLUSION The fMRI compliance of ADHD children is typically lower than that of healthy children. However, compliance can be increased to the level of age-matched healthy control children by addressing concerns about the technical and procedural aspects of fMRI, providing orientation programs, and performing on-task training. In patients thus trained, compliance does not change with the level of state anxiety suggesting that the anxiety hypothesis of fMRI compliance is not supported. PMID:25519454

  5. Inverse field-based approach for simultaneous B₁ mapping at high fields - a phantom based study.

    PubMed

    Jin, Jin; Liu, Feng; Zuo, Zhentao; Xue, Rong; Li, Mingyan; Li, Yu; Weber, Ewald; Crozier, Stuart

    2012-04-01

    Based on computational electromagnetics and multi-level optimization, an inverse approach of attaining accurate mapping of both transmit and receive sensitivity of radiofrequency coils is presented. This paper extends our previous study of inverse methods of receptivity mapping at low fields, to allow accurate mapping of RF magnetic fields (B(1)) for high-field applications. Accurate receive sensitivity mapping is essential to image domain parallel imaging methods, such as sensitivity encoding (SENSE), to reconstruct high quality images. Accurate transmit sensitivity mapping will facilitate RF-shimming and parallel transmission techniques that directly address the RF inhomogeneity issue, arguably the most challenging issue of high-field magnetic resonance imaging (MRI). The inverse field-based approach proposed herein is based on computational electromagnetics and iterative optimization. It fits an experimental image to the numerically calculated signal intensity by iteratively optimizing the coil-subject geometry to better resemble the experiments. Accurate transmit and receive sensitivities are derived as intermediate results of the optimization process. The method is validated by imaging studies using homogeneous saline phantom at 7T. A simulation study at 300MHz demonstrates that the proposed method is able to obtain receptivity mapping with errors an order of magnitude less than that of the conventional method. The more accurate receptivity mapping and simultaneously obtained transmit sensitivity mapping could enable artefact-reduced and intensity-corrected image reconstructions. It is hoped that by providing an approach to the accurate mapping of both transmit and receive sensitivity, the proposed method will facilitate a range of applications in high-field MRI and parallel imaging. PMID:22391489

  6. Fast and robust 3D T1 mapping using spiral encoding and steady RF excitation at 7 T: application to cardiac manganese enhanced MRI (MEMRI) in mice.

    PubMed

    Castets, Charles R; Ribot, Emeline J; Lefrançois, William; Trotier, Aurélien J; Thiaudière, Eric; Franconi, Jean-Michel; Miraux, Sylvain

    2015-07-01

    Mapping longitudinal relaxation times in 3D is a promising quantitative and non-invasive imaging tool to assess cardiac remodeling. Few methods are proposed in the literature allowing us to perform 3D T1 mapping. These methods often require long scan times and use a low number of 3D images to calculate T1 . In this project, a fast 3D T1 mapping method using a stack-of-spirals sampling scheme and regular RF pulse excitation at 7 T is presented. This sequence, combined with a newly developed fitting procedure, allowed us to quantify T1 of the whole mouse heart with a high spatial resolution of 208 × 208 × 315 µm(3) in 10-12 min acquisition time. The sensitivity of this method for measuring T1 variations was demonstrated on mouse hearts after several injections of manganese chloride (doses from 25 to 150 µmol kg(-1) ). T1 values were measured in vivo in both pre- and post-contrast experiments. This protocol was also validated on ischemic mice to demonstrate its efficiency to visualize tissue damage induced by a myocardial infarction. This study showed that combining spiral gradient shape and steady RF excitation enabled fast and robust 3D T1 mapping of the entire heart with a high spatial resolution. PMID:25989986

  7. Extrastriate projections in human optic radiation revealed by fMRI-informed tractography.

    PubMed

    Alvarez, Ivan; Schwarzkopf, D Samuel; Clark, Chris A

    2015-09-01

    The human optic radiation (OR) is the main pathway for conveying visual input to occipital cortex, but it is unclear whether it projects beyond primary visual cortex (V1). In this study, we used functional MRI mapping to delineate early visual areas in 30 healthy volunteers and determined the termination area of the OR as reconstructed with diffusion tractography. Direct thalamo-cortical projections to areas V2 and V3 were found in all hemispheres tested, with a distinct anatomical arrangement of superior-inferior fiber placement for dorsal and ventral projections, respectively, and a medio-lateral nesting arrangement for projections to V1, V2 and V3. Finally, segment-specific microstructure was examined, revealing sub-fascicular information. This is to date the first in vivo demonstration of direct extrastriate projections of the OR in humans. PMID:24903826

  8. Radiotherapy planning using MRI

    NASA Astrophysics Data System (ADS)

    Schmidt, Maria A.; Payne, Geoffrey S.

    2015-11-01

    The use of magnetic resonance imaging (MRI) in radiotherapy (RT) planning is rapidly expanding. We review the wide range of image contrast mechanisms available to MRI and the way they are exploited for RT planning. However a number of challenges are also considered: the requirements that MR images are acquired in the RT treatment position, that they are geometrically accurate, that effects of patient motion during the scan are minimized, that tissue markers are clearly demonstrated, that an estimate of electron density can be obtained. These issues are discussed in detail, prior to the consideration of a number of specific clinical applications. This is followed by a brief discussion on the development of real-time MRI-guided RT.

  9. Map reading tools for map libraries.

    USGS Publications Warehouse

    Greenberg, G.L.

    1982-01-01

    Engineers, navigators and military strategists employ a broad array of mechanical devices to facilitate map use. A larger number of map users such as educators, students, tourists, journalists, historians, politicians, economists and librarians are unaware of the available variety of tools which can be used with maps to increase the speed and efficiency of their application and interpretation. This paper identifies map reading tools such as coordinate readers, protractors, dividers, planimeters, and symbol-templets according to a functional classification. Particularly, arrays of tools are suggested for use in determining position, direction, distance, area and form (perimeter-shape-pattern-relief). -from Author

  10. Co-registration of high resolution MRI sub-volumes in non-human primates

    NASA Astrophysics Data System (ADS)

    Lecoeur, Jérémy; Wang, Feng; Chen, Li Min; Li, Rui; Avison, Malcom J.; Dawant, Benoit M.

    2011-03-01

    Dynamic structural and functional remodeling of the Central Nervous System occurs throughout the lifespan of the organism from the molecular to the systems level. MRI offers several advantages to observe this phenomenon: it is non-invasive and non-destructive, the contrast can be tuned to interrogate different tissue properties and imaging resolution can range from cortical columns to whole brain networks in the same session. To measure these changes reliably, functional maps generated over time with high resolution fMRI need to be registered accurately. This article presents a new method for registering automatically thin cortical MR volumes that are aligned with the functional maps. These acquisitions focus on the primary somato-sensory cortex, a region in the anterior parietal part of the brain, responsible for fine touch and proprioception. Currently, these slabs are acquired in approximately the same orientation from acquisition to acquisition and then registered by hand. Because they only cover a small portion of the cortex, their direct automatic registration is difficult. To address this issue, we propose a method relying on an intermediate image, acquired with a surface coil that covers a larger portion of the head to which the slabs can be registered. Because images acquired with surface coils suffer from severe intensity attenuation artifact, we also propose a method to register these. The results from data sets obtained with three squirrel monkeys show a registration accuracy of thirty micrometers.

  11. microRNA-206 impairs c-Myc-driven cancer in a synthetic lethal manner by directly inhibiting MAP3K13

    PubMed Central

    Han, Han; Chen, Yuxing; Cheng, Li; Prochownik, Edward V.; Li, Youjun

    2016-01-01

    c-Myc (Myc) is one of the most frequently dysregulated oncogenic transcription factors in human cancer. By functionally screening a microRNA (miR) library, we identified miR-206 as being a synthetic lethal in Myc over-expressing human cancer cells. miR-206 inhibited MAP3K13, which resulted in Myc protein de-stabilization, and an inhibition of anchorage-independent growth and in vivo tumorigenesis by Myc over-expressing human cancer cells. Eliminating MAP3K13 by shRNA recapitulated the effects caused by miR-206, thus supporting the idea that miR-206's effect on Myc was mediated through MAP3K13. Conversely, enforced expression of MAP3K13 stabilized Myc by promoting its N-terminal phosphorylation and enhancing its transcriptional activity. Gene expression analyses of breast cancers expressing high levels of Myc indicated that low miR-206 expression and high MAP3K13 expression correlated with poor patient survival. The critical link between miR-206 and MAP3K13 in the development of Myc over-expressing human cancers suggests potential points of therapeutic intervention for this molecular sub-category. PMID:26918941

  12. MRI Catheterization in Cardiopulmonary Disease

    PubMed Central

    Rogers, Toby; Ratnayaka, Kanishka

    2014-01-01

    Diagnosis and prognostication in patients with complex cardiopulmonary disease can be a clinical challenge. A new procedure, MRI catheterization, involves invasive right-sided heart catheterization performed inside the MRI scanner using MRI instead of traditional radiographic fluoroscopic guidance. MRI catheterization combines simultaneous invasive hemodynamic and MRI functional assessment in a single radiation-free procedure. By combining both modalities, the many individual limitations of invasive catheterization and noninvasive imaging can be overcome, and additional clinical questions can be addressed. Today, MRI catheterization is a clinical reality in specialist centers in the United States and Europe. Advances in medical device design for the MRI environment will enable not only diagnostic but also interventional MRI procedures to be performed within the next few years. PMID:24394821

  13. Gadofullerene MRI contrast agents.

    PubMed

    Bolskar, Robert D

    2008-04-01

    A promising new class of MRI contrast-enhancing agents with high relaxivities is based on gadolinium-containing metallofullerenes, which are also termed gadofullerenes. Detailed study of the water-proton relaxivity properties and intermolecular nanoclustering behavior of gadofullerene derivatives has revealed valuable information about their relaxivity mechanisms and given a deeper understanding of this new class of paramagnetic contrast agent. Here, the latest findings on water-solubilized gadofullerene materials and how these findings relate to their future applications in MRI are reviewed and discussed. PMID:18373426

  14. Convex-Optimization-Based Compartmental Pharmacokinetic Analysis for Prostate Tumor Characterization Using DCE-MRI.

    PubMed

    Ambikapathi, ArulMurugan; Chan, Tsung-Han; Lin, Chia-Hsiang; Yang, Fei-Shih; Chi, Chong-Yung; Wang, Yue

    2016-04-01

    Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a powerful imaging modality to study the pharmacokinetics in a suspected cancer/tumor tissue. The pharmacokinetic (PK) analysis of prostate cancer includes the estimation of time activity curves (TACs), and thereby, the corresponding kinetic parameters (KPs), and plays a pivotal role in diagnosis and prognosis of prostate cancer. In this paper, we endeavor to develop a blind source separation algorithm, namely convex-optimization-based KPs estimation (COKE) algorithm for PK analysis based on compartmental modeling of DCE-MRI data, for effective prostate tumor detection and its quantification. The COKE algorithm first identifies the best three representative pixels in the DCE-MRI data, corresponding to the plasma, fast-flow, and slow-flow TACs, respectively. The estimation accuracy of the flux rate constants (FRCs) of the fast-flow and slow-flow TACs directly affects the estimation accuracy of the KPs that provide the cancer and normal tissue distribution maps in the prostate region. The COKE algorithm wisely exploits the matrix structure (Toeplitz, lower triangular, and exponential decay) of the original nonconvex FRCs estimation problem, and reformulates it into two convex optimization problems that can reliably estimate the FRCs. After estimation of the FRCs, the KPs can be effectively estimated by solving a pixel-wise constrained curve-fitting (convex) problem. Simulation results demonstrate the efficacy of the proposed COKE algorithm. The COKE algorithm is also evaluated with DCE-MRI data of four different patients with prostate cancer and the obtained results are consistent with clinical observations. PMID:26292336

  15. Use of affinity-directed liquid chromatography-mass spectrometry to map the epitopes of a factor VIII inhibitor antibody fraction

    PubMed Central

    Griffiths, Amy E.; Wang, Wensheng; Hagen, Fred K.; Fay, Philip J.

    2011-01-01

    Summary Background Neutralizing factor (F) VIII antibodies develop in ~30% of individuals with hemophilia A and show specificity to multiple sites in the FVIII protein. Methods Reactive epitopes to an immobilized IgG fraction prepared from a high-titer, FVIII inhibitor plasma were determined following immuno-precipitation (IP) of tryptic and chymotryptic peptides derived from digests of the A1 and A2 subunits of FVIIIa and FVIII light chain. Peptides were detected and identified using highly sensitive liquid chromatography-mass spectrometry (LC-MS). Results Coverage maps of the A1 subunit, A2 subunit and light chain represented 79%, 69% and 90%, respectively, of the protein sequences. Dot blots indicated that the inhibitor IgG reacted with epitopes contained within each subunit of FVIIIa. IP coupled with LC-MS identified 19 peptides representing epitopes from all FVIII A and C domains. The majority of peptides (10) were derived from the A2 domain. Three peptides mapped to the C2 domain, while two mapped to the A1 and A3 domains, and single peptides mapped to the a1 segment and C1 domain. Epitopes were typically defined by peptide sequences of <12 residues. Conclusions IP coupled with LC-MS identified extensive antibody reactivity at high resolution over the entire functional FVIII molecule and yielded sequence lengths of less than 15 residues. A number of the peptides identified mapped to known sequences involved in functionally important protein-protein and protein-membrane interactions. PMID:21668738

  16. Preoperative Evaluation with fMRI of Patients with Intracranial Gliomas

    PubMed Central

    Kapsalakis, Ioannis Z.; Kapsalaki, Eftychia Z.; Gotsis, Efstathios D.; Verganelakis, Dimitrios; Toulas, Panagiotis; Hadjigeorgiou, Georgios; Chung, Indug; Fezoulidis, Ioannis; Papadimitriou, Alexandros; Robinson, Joe Sam; Lee, Gregory P.; Fountas, Kostas N.

    2012-01-01

    Introduction. Aggressive surgical resection constitutes the optimal treatment for intracranial gliomas. However, the proximity of a tumor to eloquent areas requires exact knowledge of its anatomic relationships to functional cortex. The purpose of our study was to evaluate fMRI's accuracy by comparing it to intraoperative cortical stimulation (DCS) mapping. Material and Methods. Eighty-seven patients, with presumed glioma diagnosis, underwent preoperative fMRI and intraoperative DCS for cortical mapping during tumor resection. Findings of fMRI and DCS were considered concordant if the identified cortical centers were less than 5 mm apart. Pre and postoperative Karnofsky Performance Scale and Spitzer scores were recorded. A postoperative MRI was obtained for assessing the extent of resection. Results. The areas of interest were identified by fMRI and DCS in all participants. The concordance between fMRI and DCS was 91.9% regarding sensory-motor cortex, 100% for visual cortex, and 85.4% for language. Data analysis showed that patients with better functional condition demonstrated higher concordance rates, while there also was a weak association between tumor grade and concordance rate. The mean extent of tumor resection was 96.7%. Conclusions. Functional MRI is a highly accurate preoperative methodology for sensory-motor mapping. However, in language mapping, DCS remains necessary for accurate localization. PMID:22848821

  17. Virtual Electrophysiologic Study in a Three-dimensional Cardiac MRI Model of Porcine Myocardial Infarction

    PubMed Central

    Ng, Jason; Jacobson, Jason T; Ng, Justin K; Gordon, David; Lee, Daniel C; Carr, James C.; Goldberger, Jeffrey J

    2012-01-01

    Objective This study sought to test the hypothesis that “virtual” electrophysiologic studies (EPS) on an anatomic platform generated by 3D MRI reconstruction of the left ventricle (LV) can reproduce the reentrant circuits of induced ventricular tachycardia (VT) in a porcine model of myocardial infarction (MI). Background Delayed-enhancement MRI has been used to characterize MI and “gray zones”, which are thought to reflect heterogeneous regions of viable and non-viable myocytes. Methods MI by coronary artery occlusion was induced in eight pigs. After a recovery period, 3D cardiac MRIs were obtained from each pig in-vivo. Normal areas, gray zones, and infarct cores were classified based on voxel intensity. In the computer model, gray zones were assigned slower conduction and longer action potential durations than those for normal myocardium. Virtual EPS was performed and was compared to results of actual in vivo programmed stimulation and non-contact mapping. Results The LV volumes ranged from 97.8 to 166.2 cm3 with 4.9 to 17.5% of voxels classified as infarct zones. Six of the seven pigs that developed VT during actual EPS were also inducible with virtual EPS. Four of the six pigs that had simulated VT had reentrant circuits that approximated the circuits seen with non-contact mapping, while the remaining two had similar circuits but propagating in opposite directions. Conclusions This initial study demonstrates the feasibility of applying a mathematical model to MRI reconstructions of the LV to predict VT circuits. Virtual EPS may be helpful to plan catheter ablation strategies or to identify patients who are at risk for future episodes of VT. PMID:22633654

  18. MRI driven magnetic microswimmers.

    PubMed

    Kósa, Gábor; Jakab, Péter; Székely, Gábor; Hata, Nobuhiko

    2012-02-01

    Capsule endoscopy is a promising technique for diagnosing diseases in the digestive system. Here we design and characterize a miniature swimming mechanism that uses the magnetic fields of the MRI for both propulsion and wireless powering of the capsule. Our method uses both the static and the radio frequency (RF) magnetic fields inherently available in MRI to generate a propulsive force. Our study focuses on the evaluation of the propulsive force for different swimming tails and experimental estimation of the parameters that influence its magnitude. We have found that an approximately 20 mm long, 5 mm wide swimming tail is capable of producing 0.21 mN propulsive force in water when driven by a 20 Hz signal providing 0.85 mW power and the tail located within the homogeneous field of a 3 T MRI scanner. We also analyze the parallel operation of the swimming mechanism and the scanner imaging. We characterize the size of artifacts caused by the propulsion system. We show that while the magnetic micro swimmer is propelling the capsule endoscope, the operator can locate the capsule on the image of an interventional scene without being obscured by significant artifacts. Although this swimming method does not scale down favorably, the high magnetic field of the MRI allows self propulsion speed on the order of several millimeter per second and can propel an endoscopic capsule in the stomach. PMID:22037673

  19. Teratoma - MRI scan (image)

    MedlinePlus

    This MRI scan shows a tumor (teratoma) at the base of the spine (seen on the left lower edge of the screen), located in the sacrum and coccyx (sacrococcygeal) area. Teratomas are present at birth and may contain hair, teeth, and other tissues.

  20. PCA-based groupwise image registration for quantitative MRI.

    PubMed

    Huizinga, W; Poot, D H J; Guyader, J-M; Klaassen, R; Coolen, B F; van Kranenburg, M; van Geuns, R J M; Uitterdijk, A; Polfliet, M; Vandemeulebroucke, J; Leemans, A; Niessen, W J; Klein, S

    2016-04-01

    Quantitative magnetic resonance imaging (qMRI) is a technique for estimating quantitative tissue properties, such as the T1 and T2 relaxation times, apparent diffusion coefficient (ADC), and various perfusion measures. This estimation is achieved by acquiring multiple images with different acquisition parameters (or at multiple time points after injection of a contrast agent) and by fitting a qMRI signal model to the image intensities. Image registration is often necessary to compensate for misalignments due to subject motion and/or geometric distortions caused by the acquisition. However, large differences in image appearance make accurate image registration challenging. In this work, we propose a groupwise image registration method for compensating misalignment in qMRI. The groupwise formulation of the method eliminates the requirement of choosing a reference image, thus avoiding a registration bias. The method minimizes a cost function that is based on principal component analysis (PCA), exploiting the fact that intensity changes in qMRI can be described by a low-dimensional signal model, but not requiring knowledge on the specific acquisition model. The method was evaluated on 4D CT data of the lungs, and both real and synthetic images of five different qMRI applications: T1 mapping in a porcine heart, combined T1 and T2 mapping in carotid arteries, ADC mapping in the abdomen, diffusion tensor mapping in the brain, and dynamic contrast-enhanced mapping in the abdomen. Each application is based on a different acquisition model. The method is compared to a mutual information-based pairwise registration method and four other state-of-the-art groupwise registration methods. Registration accuracy is evaluated in terms of the precision of the estimated qMRI parameters, overlap of segmented structures, distance between corresponding landmarks, and smoothness of the deformation. In all qMRI applications the proposed method performed better than or equally well as

  1. Co-Registration of MEG and ULF MRI using a 7 channel low-Tc SQUID system

    SciTech Connect

    Magnelind, Per E; Sandin, Jan H; Volegov, Petr L; Matlashov, Andrei N; Owens, Tuba; Gomez, John J; Espy, Michelle A

    2010-01-01

    In human brain imaging, e.g. pre-surgical mapping, it is highly desired to obtain images with high spatial and temporal resolution. However, no single imaging device is capable of producing both a high spatial resolution anatomical image and a high temporal resolution functional image. During the last couple of years significant efforts have been directed towards magnetic resonance imaging (MRI) in fields comparable to the Earth's field, i.e. microtesla fields, or lower fields. The fields in this range are called ultra-low fields (ULF). Interestingly, the idea of magnetic resonance at microtesla fields is more than 50 years old. In ULF MR it is essential to use pre-polarization to increase the signal-to-noise ratio of the signal from the precessing spins, since the magnetization from the measurement field alone is very small. Even with the present level of prepolarization the ULF images are not as highly resolved as their high-field counterparts. By using a 7 channel system equipped with low transition temperature (T{sub c}) Superconducting QUantum Interference Devices (SQUIDs) to perform both ULF MRI and magnetoencephalography (MEG), it is possible to coregister a lower resolution ULF MR image and an MEG image obtained during one run. Thereby, the MEG data is aligned to the ULF MR image after performing a calibration run with a phantom. The ULF MR image can then be used to align the MEG data onto a high-field MR image. Recently, our group presented the first brain images obtained by ULF MRI. The MR imaging was combined with an MEG session performed a posteriori. The subject's head was moved in between the MRI run and the MEG run and no reference coils were used to quantify the translation. The main reason for the translation of the head was to improve the coverage of the auditory evoked response. In this paper, we report interleaved ULF MRI and MEG measurements co-registered in the same system.

  2. Threats to ultra-high-field MRI

    NASA Astrophysics Data System (ADS)

    Le Bihan, Denis

    2009-08-01

    In 2004 the European Commission (EC) adopted a directive restricting occupational exposure to electromagnetic fields. This directive (2004/40/CE), which examines the possible health risks of the electromagnetic fields from mobile phones, Wi-Fi, Bluetooth and other devices, concluded that upper limits on radiation and applied electromagnetic fields are necessary to prevent workers from suffering any undue acute health effects. But although not initially intended, the biggest impact of the directive could be on magnetic resonance imaging (MRI), which is used in hospitals worldwide to produce images of unrivalled quality of the brain and other soft tissues.

  3. MR Scanner Systems Should Be Adequately Characterized in Diffusion-MRI of the Breast

    PubMed Central

    Giannelli, Marco; Sghedoni, Roberto; Iacconi, Chiara; Iori, Mauro; Traino, Antonio Claudio; Guerrisi, Maria; Mascalchi, Mario; Toschi, Nicola; Diciotti, Stefano

    2014-01-01

    Breast imaging represents a relatively recent and promising field of application of quantitative diffusion-MRI techniques. In view of the importance of guaranteeing and assessing its reliability in clinical as well as research settings, the aim of this study was to specifically characterize how the main MR scanner system-related factors affect quantitative measurements in diffusion-MRI of the breast. In particular, phantom acquisitions were performed on three 1.5 T MR scanner systems by different manufacturers, all equipped with a dedicated multi-channel breast coil as well as acquisition sequences for diffusion-MRI of the breast. We assessed the accuracy, inter-scan and inter-scanner reproducibility of the mean apparent diffusion coefficient measured along the main orthogonal directions () as well as of diffusion-tensor imaging (DTI)-derived mean diffusivity (MD) measurements. Additionally, we estimated spatial non-uniformity of (NU) and MD (NUMD) maps. We showed that the signal-to-noise ratio as well as overall calibration of high strength diffusion gradients system in typical acquisition sequences for diffusion-MRI of the breast varied across MR scanner systems, introducing systematic bias in the measurements of diffusion indices. While and MD values were not appreciably different from each other, they substantially varied across MR scanner systems. The mean of the accuracies of measured and MD was in the range [−2.3%,11.9%], and the mean of the coefficients of variation for and MD measurements across MR scanner systems was 6.8%. The coefficient of variation for repeated measurements of both and MD was < 1%, while NU and NUMD values were <4%. Our results highlight that MR scanner system-related factors can substantially affect quantitative diffusion-MRI of the breast. Therefore, a specific quality control program for assessing and monitoring the performance of MR scanner systems for diffusion-MRI of the breast is

  4. Technical Note: MRI only prostate radiotherapy planning using the statistical decomposition algorithm

    SciTech Connect

    Siversson, Carl; Nordström, Fredrik; Nilsson, Terese; Nyholm, Tufve; Jonsson, Joakim; Gunnlaugsson, Adalsteinn; Olsson, Lars E.

    2015-10-15

    Purpose: In order to enable a magnetic resonance imaging (MRI) only workflow in radiotherapy treatment planning, methods are required for generating Hounsfield unit (HU) maps (i.e., synthetic computed tomography, sCT) for dose calculations, directly from MRI. The Statistical Decomposition Algorithm (SDA) is a method for automatically generating sCT images from a single MR image volume, based on automatic tissue classification in combination with a model trained using a multimodal template material. This study compares dose calculations between sCT generated by the SDA and conventional CT in the male pelvic region. Methods: The study comprised ten prostate cancer patients, for whom a 3D T2 weighted MRI and a conventional planning CT were acquired. For each patient, sCT images were generated from the acquired MRI using the SDA. In order to decouple the effect of variations in patient geometry between imaging modalities from the effect of uncertainties in the SDA, the conventional CT was nonrigidly registered to the MRI to assure that their geometries were well aligned. For each patient, a volumetric modulated arc therapy plan was created for the registered CT (rCT) and recalculated for both the sCT and the conventional CT. The results were evaluated using several methods, including mean average error (MAE), a set of dose-volume histogram parameters, and a restrictive gamma criterion (2% local dose/1 mm). Results: The MAE within the body contour was 36.5 ± 4.1 (1 s.d.) HU between sCT and rCT. Average mean absorbed dose difference to target was 0.0% ± 0.2% (1 s.d.) between sCT and rCT, whereas it was −0.3% ± 0.3% (1 s.d.) between CT and rCT. The average gamma pass rate was 99.9% for sCT vs rCT, whereas it was 90.3% for CT vs rCT. Conclusions: The SDA enables a highly accurate MRI only workflow in prostate radiotherapy planning. The dosimetric uncertainties originating from the SDA appear negligible and are notably lower than the uncertainties

  5. Linking contemporary high resolution magnetic resonance imaging to the von Economo legacy: A study on the comparison of MRI cortical thickness and histological measurements of cortical structure.

    PubMed

    Scholtens, Lianne H; de Reus, Marcel A; van den Heuvel, Martijn P

    2015-08-01

    The cerebral cortex is a distinctive part of the mammalian nervous system, displaying a spatial variety in cyto-, chemico-, and myelinoarchitecture. As part of a rich history of histological findings, pioneering anatomists von Economo and Koskinas provided detailed mappings on the cellular structure of the human cortex, reporting on quantitative aspects of cytoarchitecture of cortical areas. Current day investigations into the structure of human cortex have embraced technological advances in Magnetic Resonance Imaging (MRI) to assess macroscale thickness and organization of the cortical mantle in vivo. However, direct comparisons between current day MRI estimates and the quantitative measurements of early anatomists have been limited. Here, we report on a simple, but nevertheless important cross-analysis between the histological reports of von Economo and Koskinas on variation in thickness of the cortical mantle and MRI derived measurements of cortical thickness. We translated the von Economo cortical atlas to a subdivision of the commonly used Desikan-Killiany atlas (as part of the FreeSurfer Software package and a commonly used parcellation atlas in studies examining MRI cortical thickness). Next, values of "width of the cortical mantle" as provided by the measurements of von Economo and Koskinas were correlated to cortical thickness measurements derived from high-resolution anatomical MRI T1 data of 200+ subjects of the Human Connectome Project (HCP). Cross-correlation revealed a significant association between group-averaged MRI measurements of cortical thickness and histological recordings (r = 0.54, P < 0.001). Further validating such a correlation, we manually segmented the von Economo parcellation atlas on the standardized Colin27 brain dataset and applied the obtained three-dimensional von Economo segmentation atlas to the T1 data of each of the HCP subjects. Highly consistent with our findings for the mapping to the Desikan-Killiany regions, cross

  6. A review of MRI evaluation of demyelination in cuprizone murine model

    NASA Astrophysics Data System (ADS)

    Krutenkova, E.; Pan, E.; Khodanovich, M.

    2015-11-01

    The cuprizone mouse model of non-autoimmune demyelination reproduces some phenomena of multiple sclerosis and is appropriate for validation and specification of a new method of non-invasive diagnostics. In the review new data which are collected using the new MRI method are compared with one or more conventional MRI tools. Also the paper reviewed the validation of MRI approaches using histological or immunohistochemical methods. Luxol fast blue histological staining and myelin basic protein immunostaining is widespread. To improve the accuracy of non-invasive conventional MRI, multimodal scanning could be applied. The new quantitative MRI method of fast mapping of the macromolecular proton fraction is a reliable biomarker of myelin in the brain and can be used for research of demyelination in animals. To date, a validation of MPF method on the CPZ mouse model of demyelination is not performed, although this method is probably the best way to evaluate demyelination using MRI.

  7. A review of MRI evaluation of demyelination in cuprizone murine model

    SciTech Connect

    Krutenkova, E. Pan, E.; Khodanovich, M.

    2015-11-17

    The cuprizone mouse model of non-autoimmune demyelination reproduces some phenomena of multiple sclerosis and is appropriate for validation and specification of a new method of non-invasive diagnostics. In the review new data which are collected using the new MRI method are compared with one or more conventional MRI tools. Also the paper reviewed the validation of MRI approaches using histological or immunohistochemical methods. Luxol fast blue histological staining and myelin basic protein immunostaining is widespread. To improve the accuracy of non-invasive conventional MRI, multimodal scanning could be applied. The new quantitative MRI method of fast mapping of the macromolecular proton fraction is a reliable biomarker of myelin in the brain and can be used for research of demyelination in animals. To date, a validation of MPF method on the CPZ mouse model of demyelination is not performed, although this method is probably the best way to evaluate demyelination using MRI.

  8. Mapping the semantic structure of cognitive neuroscience.

    PubMed

    Beam, Elizabeth; Appelbaum, L Gregory; Jack, Jordynn; Moody, James; Huettel, Scott A

    2014-09-01

    Cognitive neuroscience, as a discipline, links the biological systems studied by neuroscience to the processing constructs studied by psychology. By mapping these relations throughout the literature of cognitive neuroscience, we visualize the semantic structure of the discipline and point to directions for future research that will advance its integrative goal. For this purpose, network text analyses were applied to an exhaustive corpus of abstracts collected from five major journals over a 30-month period, including every study that used fMRI to investigate psychological processes. From this, we generate network maps that illustrate the relationships among psychological and anatomical terms, along with centrality statistics that guide inferences about network structure. Three terms--prefrontal cortex, amygdala, and anterior cingulate cortex--dominate the network structure with their high frequency in the literature and the density of their connections with other neuroanatomical terms. From network statistics, we identify terms that are understudied compared with their importance in the network (e.g., insula and thalamus), are underspecified in the language of the discipline (e.g., terms associated with executive function), or are imperfectly integrated with other concepts (e.g., subdisciplines like decision neuroscience that are disconnected from the main network). Taking these results as the basis for prescriptive recommendations, we conclude that semantic analyses provide useful guidance for cognitive neuroscience as a discipline, both by illustrating systematic biases in the conduct and presentation of research and by identifying directions that may be most productive for future research. PMID:24666126

  9. Electrophysiological correlates of the BOLD signal for EEG-informed fMRI

    PubMed Central

    Murta, Teresa; Leite, Marco; Carmichael, David W; Figueiredo, Patrícia; Lemieux, Louis

    2015-01-01

    Electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) are important tools in cognitive and clinical neuroscience. Combined EEG–fMRI has been shown to help to characterise brain networks involved in epileptic activity, as well as in different sensory, motor and cognitive functions. A good understanding of the electrophysiological correlates of the blood oxygen level-dependent (BOLD) signal is necessary to interpret fMRI maps, particularly when obtained in combination with EEG. We review the current understanding of electrophysiological–haemodynamic correlates, during different types of brain activity. We start by describing the basic mechanisms underlying EEG and BOLD signals and proceed by reviewing EEG-informed fMRI studies using fMRI to map specific EEG phenomena over the entire brain (EEG–fMRI mapping), or exploring a range of EEG-derived quantities to determine which best explain colocalised BOLD fluctuations (local EEG–fMRI coupling). While reviewing studies of different forms of brain activity (epileptic and nonepileptic spontaneous activity; cognitive, sensory and motor functions), a significant attention is given to epilepsy because the investigation of its haemodynamic correlates is the most common application of EEG-informed fMRI. Our review is focused on EEG-informed fMRI, an asymmetric approach of data integration. We give special attention to the invasiveness of electrophysiological measurements and the simultaneity of multimodal acquisitions because these methodological aspects determine the nature of the conclusions that can be drawn from EEG-informed fMRI studies. We emphasise the advantages of, and need for, simultaneous intracranial EEG–fMRI studies in humans, which recently became available and hold great potential to improve our understanding of the electrophysiological correlates of BOLD fluctuations. PMID:25277370

  10. High-quality breast MRI.

    PubMed

    Hendrick, R Edward

    2014-05-01

    Breast magnetic resonance imaging (MRI) demands the competing factors of high spatial resolution, good temporal resolution, high signal-to-noise ratios, and complete bilateral breast coverage. Achieving these competing factors requires modern MRI equipment with high magnetic field strength and homogeneity, high maximum gradient strength with short rise times, dedicated multichannel bilateral breast coils with prone patient positioning, and 3D (volume) gradient-echo MRI pulse sequences with short TR, short TE, high spatial resolution, and reasonably short acquisition times. This article discusses the equipment and pulse sequences needed to achieve high-quality breast MRI and summarizes requirements of the ACR Breast MRI Accreditation Program. PMID:24792656

  11. Human brain functional MRI and DTI visualization with virtual reality.

    PubMed

    Chen, Bin; Moreland, John; Zhang, Jingyu

    2011-12-01

    Magnetic resonance diffusion tensor imaging (DTI) and functional MRI (fMRI) are two active research areas in neuroimaging. DTI is sensitive to the anisotropic diffusion of water exerted by its macromolecular environment and has been shown useful in characterizing structures of ordered tissues such as the brain white matter, myocardium, and cartilage. The diffusion tensor provides two new types of information of water diffusion: the magnitude and the spatial orientation of water diffusivity inside the tissue. This information has been used for white matter fiber tracking to review physical neuronal pathways inside the brain. Functional MRI measures brain activations using the hemodynamic response. The statistically derived activation map corresponds to human brain functional activities caused by neuronal activities. The combination of these two methods provides a new way to understand human brain from the anatomical neuronal fiber connectivity to functional activities between different brain regions. In this study, virtual reality (VR) based MR DTI and fMRI visualization with high resolution anatomical image segmentation and registration, ROI definition and neuronal white matter fiber tractography visualization and fMRI activation map integration is proposed. Rationale and methods for producing and distributing stereoscopic videos are also discussed. PMID:23256049

  12. A Parametric Empirical Bayesian framework for fMRI-constrained MEG/EEG source reconstruction

    PubMed Central

    Henson, Richard N; Flandin, Guillaume; Friston, Karl J; Mattout, Jérémie

    2010-01-01

    We describe an asymmetric approach to fMRI and MEG/EEG fusion in which fMRI data are treated as empirical priors on electromagnetic sources, such that their influence depends on the MEG/EEG data, by virtue of maximizing the model evidence. This is important if the causes of the MEG/EEG signals differ from those of the fMRI signal. Furthermore, each suprathreshold fMRI cluster is treated as a separate prior, which is important if fMRI data reflect neural activity arising at different times within the EEG/MEG data. We present methodological considerations when mapping from a 3D fMRI Statistical Parametric Map to a 2D cortical surface and thence to the covariance components used within our Parametric Empirical Bayesian framework. Our previous introduction of a canonical (inverse-normalized) cortical mesh also allows deployment of fMRI priors that live in a template space; for example, from a group analysis of different individuals. We evaluate the ensuing scheme with MEG and EEG data recorded simultaneously from 12 participants, using the same face-processing paradigm under which independent fMRI data were obtained. Because the fMRI priors become part of the generative model, we use the model evidence to compare (i) multiple versus single, (ii) valid versus invalid, (iii) binary versus continuous, and (iv) variance versus covariance fMRI priors. For these data, multiple, valid, binary, and variance fMRI priors proved best for a standard Minimum Norm inversion. Interestingly, however, inversion using Multiple Sparse Priors benefited little from additional fMRI priors, suggesting that they already provide a sufficiently flexible generative model. Hum Brain Mapp, 2010. © 2010 Wiley-Liss, Inc. PMID:20091791

  13. Orientation decoding depends on maps, not columns

    PubMed Central

    Freeman, Jeremy; Brouwer, Gijs Joost; Heeger, David J.; Merriam, Elisha P.

    2011-01-01

    The representation of orientation in primary visual cortex (V1) has been examined at a fine spatial scale corresponding to the columnar architecture. We present functional magnetic resonance imaging (fMRI) measurements providing evidence for a topographic map of orientation preference in human V1 at a much coarser scale, in register with the angular-position component of the retinotopic map of V1. This coarse-scale orientation map provides a parsimonious explanation for why multivariate pattern analysis methods succeed in decoding stimulus orientation from fMRI measurements, challenging the widely-held assumption that decoding results reflect sampling of spatial irregularities in the fine-scale columnar architecture. Decoding stimulus attributes and cognitive states from fMRI measurements has proven useful for a number of applications, but our results demonstrate that the interpretation cannot assume decoding reflects or exploits columnar organization. PMID:21451017

  14. Cortex-based inter-subject analysis of iEEG and fMRI data sets: application to sustained task-related BOLD and gamma responses.

    PubMed

    Esposito, Fabrizio; Singer, Neomi; Podlipsky, Ilana; Fried, Itzhak; Hendler, Talma; Goebel, Rainer

    2013-02-01

    Linking regional metabolic changes with fluctuations in the local electromagnetic fields directly on the surface of the human cerebral cortex is of tremendous importance for a better understanding of detailed brain processes. Functional magnetic resonance imaging (fMRI) and intra-cranial electro-encephalography (iEEG) measure two technically unrelated but spatially and temporally complementary sets of functional descriptions of human brain activity. In order to allow fine-grained spatio-temporal human brain mapping at the population-level, an effective comparative framework for the cortex-based inter-subject analysis of iEEG and fMRI data sets is needed. We combined fMRI and iEEG recordings of the same patients with epilepsy during alternated intervals of passive movie viewing and music listening to explore the degree of local spatial correspondence and temporal coupling between blood oxygen level dependent (BOLD) fMRI changes and iEEG spectral power modulations across the cortical surface after cortex-based inter-subject alignment. To this purpose, we applied a simple model of the iEEG activity spread around each electrode location and the cortex-based inter-subject alignment procedure to transform discrete iEEG measurements into cortically distributed group patterns by establishing a fine anatomic correspondence of many iEEG cortical sites across multiple subjects. Our results demonstrate the feasibility of a multi-modal inter-subject cortex-based distributed analysis for combining iEEG and fMRI data sets acquired from multiple subjects with the same experimental paradigm but with different iEEG electrode coverage. The proposed iEEG-fMRI framework allows for improved group statistics in a common anatomical space and preserves the dynamic link between the temporal features of the two modalities. PMID:23138047

  15. Quantitative fMRI and oxidative neuroenergetics

    PubMed Central

    Hyder, Fahmeed; Rothman, Douglas L.

    2012-01-01

    The discovery of functional magnetic resonance imaging (fMRI) has greatly impacted neuroscience. The blood oxygenation level-dependent (BOLD) signal, using deoxyhemoglobin as an endogenous paramagnetic contrast agent, exposes regions of interest in task-based and resting-state paradigms. However the BOLD contrast is at best a partial measure of neuronal activity, because the functional maps obtained by differencing or correlations ignore the total neuronal activity in the baseline state. Here we describe how studies of brain energy metabolism at Yale, especially with 13C magnetic resonance spectroscopy and related techniques, contributed to development of quantitative functional brain imaging with fMRI by providing a reliable measurement of baseline energy. This narrative takes us on a journey, from molecules to mind, with illuminating insights about neuronal-glial activities in relation to energy demand of synaptic activity. These results, along with key contributions from laboratories worldwide, comprise the energetic basis for quantitative interpretation of fMRI data. PMID:22542993

  16. Use of Cationized Ferritin Nanoparticles to Measure Renal Glomerular Microstructure with MRI.

    PubMed

    Bennett, Kevin M; Beeman, Scott C; Baldelomar, Edwin J; Zhang, Min; Wu, Teresa; Hann, Bradley D; Bertram, John F; Charlton, Jennifer R

    2016-01-01

    Magnetic resonance imaging (MRI) is becoming important for whole-kidney assessment of glomerular morphology, both in vivo and ex vivo. MRI-based renal morphological measurements can be made in intact organs and allow direct measurements of every perfused glomerulus. Cationic ferritin (CF) is used as a superparamagnetic contrast agent for MRI. CF binds to the glomerular basement membrane after intravenous injection, allowing direct, whole-kidney measurements of glomerular number, volume, and volume distribution. Here we describe the production, testing, and use of CF as an MRI contrast agent for quantitative glomerular morphology in intact mouse, rat, and human kidneys. PMID:26676128

  17. MRI of the penis

    PubMed Central

    Kirkham, A

    2012-01-01

    MRI of the penis is an expensive test that is not always superior to clinical examination or ultrasound. However, it shows many of the important structures, and in particular the combination of tumescence from intracavernosal alprostadil, and high-resolution T2 sequences show the glans, corpora and the tunica albuginea well. In this paper we summarise the radiological anatomy and discuss the indications for MRI. For penile cancer, it may be useful in cases where the local stage is not apparent clinically. In priapism, it is an emerging technique for assessing corporal viability, and in fracture it can in most cases make the diagnosis and locate the injury. In some cases of penile fibrosis and Peyronie's disease, it may aid surgical planning, and in complex pelvic fracture may replace or augment conventional urethrography. It is an excellent investigation for the malfunctioning penile prosthesis. PMID:23118102

  18. Thoughts turned into high-level commands: Proof-of-concept study of a vision-guided robot arm driven by functional MRI (fMRI) signals.

    PubMed

    Minati, Ludovico; Nigri, Anna; Rosazza, Cristina; Bruzzone, Maria Grazia

    2012-06-01

    Previous studies have demonstrated the possibility of using functional MRI to control a robot arm through a brain-machine interface by directly coupling haemodynamic activity in the sensory-motor cortex to the position of two axes. Here, we extend this work by implementing interaction at a more abstract level, whereby imagined actions deliver structured commands to a robot arm guided by a machine vision system. Rather than extracting signals from a small number of pre-selected regions, the proposed system adaptively determines at individual level how to map representative brain areas to the input nodes of a classifier network. In this initial study, a median action recognition accuracy of 90% was attained on five volunteers performing a game consisting of collecting randomly positioned coloured pawns and placing them into cups. The "pawn" and "cup" instructions were imparted through four mental imaginery tasks, linked to robot arm actions by a state machine. With the current implementation in MatLab language the median action recognition time was 24.3s and the robot execution time was 17.7s. We demonstrate the notion of combining haemodynamic brain-machine interfacing with computer vision to implement interaction at the level of high-level commands rather than individual movements, which may find application in future fMRI approaches relevant to brain-lesioned patients, and provide source code supporting further work on larger command sets and real-time processing. PMID:22405803

  19. Mapping Earth Science Concepts.

    ERIC Educational Resources Information Center

    McDuffie, Thomas E., Jr.; Van Dine, William E.

    1978-01-01

    Presents two experiments concerned with mapping skills. Directions are given for calculating the circumference of the earth and for developing a model of the solar system using familiar territory as a frame of reference. (MA)

  20. enceladus_stress_map

    NASA Video Gallery

    This is a map of the changing stress on the surface of Enceladus' icy crust from the wobble and gravitational tides. Blue lines show the direction of forces pulling the crust apart, and red lines s...

  1. [MRI in coma survivors].

    PubMed

    Tshibanda, L; Vanhaudenhuyse, A; Bruno, M A; Boly, M; Soddu, A; Laureys, S; Moonen, G

    2009-01-01

    Traumatic and non-traumatic brain injured disorders of consciousness patients are still challenging for diagnosis, prognosis, ethical and socio-economic reasons. Currently, there remains a high rate of misdiagnosis of the vegetative state (Schnakers, et al. 2009). Recent advances in MRI techniques (diffusion tensor, magnetic resonance spectroscopy and functional imaging) provide data that could improve the diagnostic and prognostic evaluation and management of these patients. PMID:20085015

  2. MRI Anatomy of Schizophrenia

    PubMed Central

    McCarley, Robert W.; Wible, Cynthia G.; Frumin, Melissa; Hirayasu, Yoshio; Levitt, James J.; Fischer, Iris A.; Shenton, Martha E.

    2010-01-01

    Structural magnetic resonance imaging (MRI) data have provided much evidence in support of our current view that schizophrenia is a brain disorder with altered brain structure, and consequently involving more than a simple disturbance in neurotransmission. This review surveys 118 peer–reviewed studies with control group from 1987 to May 1998. Most studies (81%) do not find abnormalities of whole brain/intracranial contents, while lateral ventricle enlargement is reported in 77%, and third ventricle enlargement in 67%. The temporal lobe was the brain parenchymal region with the most consistently documented abnormalities. Volume decreases were found in 62% of 37 studies of whole temporal lobe, and in 81% of 16 studies of the superior temporal gyrus (and in 100% with gray matter separately evaluated). Fully 77% of the 30 studies of the medial temporal lobe reported volume reduction in one or more of its constituent structures (hippocampus, amygdala, parahippocampal gyrus). Despite evidence for frontal lobe functional abnormalities, structural MRI investigations less consistently found abnormalities, with 55% describing volume reduction. It may be that frontal lobe volume changes are small, and near the threshold for MRI detection. The parietal and occipital lobes were much less studied; about half of the studies showed positive findings. Most studies of cortical gray matter (86%) found volume reductions were not diffuse, but more pronounced in certain areas. About two thirds of the studies of subcortical structures of thalamus, corpus callosum and basal ganglia (which tend to increase volume with typical neuroleptics), show positive findings, as do almost all (91%) studies of cavum septi pellucidi (CSP). Most data were consistent with a developmental model, but growing evidence was compatible also with progressive, neurodegenerative features, suggesting a “two– hit” model of schizophrenia, for which a cellular hypothesis is discussed. The relationship of

  3. MRI Findings in Neuroferritinopathy

    PubMed Central

    Ohta, Emiko; Takiyama, Yoshihisa

    2012-01-01

    Neuroferritinopathy is a neurodegenerative disease which demonstrates brain iron accumulation caused by the mutations in the ferritin light chain gene. On brain MRI in neuroferritinopathy, iron deposits are observed as low-intensity areas on T2WI and as signal loss on T2∗WI. On T2WI, hyperintense abnormalities reflecting tissue edema and gliosis are also seen. Another characteristic finding is the presence of symmetrical cystic changes in the basal ganglia, which are seen in the advanced stages of this disorder. Atrophy is sometimes noted in the cerebellar and cerebral cortices. The variety in the MRI findings is specific to neuroferritinopathy. Based on observations of an excessive iron content in patients with chronic neurologic disorders, such as Parkinson disease and Alzheimer disease, the presence of excess iron is therefore recognized as a major risk factor for neurodegenerative diseases. The future development of multimodal and advanced MRI techniques is thus expected to play an important role in accurately measuring the brain iron content and thereby further elucidating the neurodegenerative process. PMID:21808735

  4. Nonlinear functional connectivity network recovery in the human brain with mutual connectivity analysis (MCA): convergent cross-mapping and non-metric clustering

    NASA Astrophysics Data System (ADS)

    Wismüller, Axel; Abidin, Anas Z.; D'Souza, Adora M.; Wang, Xixi; Hobbs, Susan K.; Leistritz, Lutz; Nagarajan, Mahesh B.

    2015-03-01

    We explore a computational framework for functional connectivity analysis in resting-state functional MRI (fMRI) data acquired from the human brain for recovering the underlying network structure and understanding causality between network components. Termed mutual connectivity analysis (MCA), this framework involves two steps, the first of which is to evaluate the pair-wise cross-prediction performance between fMRI pixel time series within the brain. In a second step, the underlying network structure is subsequently recovered from the affinity matrix using non-metric network clustering approaches, such as the so-called Louvain method. Finally, we use convergent cross-mapping (CCM) to study causality between different network components. We demonstrate our MCA framework in the problem of recovering the motor cortex network associated with hand movement from resting state fMRI data. Results are compared with a ground truth of active motor cortex regions as identified by a task-based fMRI sequence involving a finger-tapping stimulation experiment. Our results regarding causation between regions of the motor cortex revealed a significant directional variability and were not readily interpretable in a consistent manner across subjects. However, our results on whole-slice fMRI analysis demonstrate that MCA-based model-free recovery of regions associated with the primary motor cortex and supplementary motor area are in close agreement with localization of similar regions achieved with a task-based fMRI acquisition. Thus, we conclude that our MCA methodology can extract and visualize valuable information concerning the underlying network structure between different regions of the brain in resting state fMRI.

  5. Pharmacokinetics of Chiral Dendrimer-Triamine-Coordinated Gd-MRI Contrast Agents Evaluated by in Vivo MRI and Estimated by in Vitro QCM

    PubMed Central

    Miyake, Yuka; Ishikawa, Syungo; Kimura, Yu; Son, Aoi; Imai, Hirohiko; Matsuda, Tetsuya; Yamada, Hisatsugu; Toshimitsu, Akio; Kondo, Teruyuki

    2015-01-01

    Recently, we developed novel chiral dendrimer-triamine-coordinated Gd-MRI contrast agents (Gd-MRI CAs), which showed longitudinal relaxivity (r1) values about four times higher than that of clinically used Gd-DTPA (Magnevist®, Bayer). In our continuing study of pharmacokinetic differences derived from both the chirality and generation of Gd-MRI CAs, we found that the ability of chiral dendrimer Gd-MRI CAs to circulate within the body can be directly evaluated by in vitro MRI (7 T). In this study, the association constants (Ka) of chiral dendrimer Gd-MRI CAs to bovine serum albumin (BSA), measured and calculated with a quartz crystal microbalance (QCM) in vitro, were found to be an extremely easy means for evaluating the body-circulation ability of chiral dendrimer Gd-MRI CAs. The Ka values of S-isomeric dendrimer Gd-MRI CAs were generally greater than those of R-isomeric dendrimer Gd-MRI CAs, which is consistent with the results of our previous MRI study in vivo. PMID:26694418

  6. Functional magnetic resonance imaging of category-specific cortical activation: evidence for semantic maps.

    PubMed

    Spitzer, M; Kischka, U; Gückel, F; Bellemann, M E; Kammer, T; Seyyedi, S; Weisbrod, M; Schwartz, A; Brix, G

    1998-04-01

    Functional magnetic resonance imaging (fMRI) was used to examine the pattern of cortical activity during a picture naming task. Subjects (n=12) had to covertly name either animals or furniture items. Functional scanning was performed using a conventional 1.5-Tesla whole-body MRI system. Images obtained during naming the two categories were compared using a non-parametric test. The study revealed evidence for domain-specific lexical regions in left middle, right middle and inferior frontal areas, as well as in superior and middle temporal areas. The results corroborate neuropsychological data and demonstrate directly and non-invasively in human volunteers that semantic representations in frontal and temporal areas are, to some degree, localized and possibly implemented as multiple maps. A completely distributed storage of semantic information is rendered unlikely. PMID:9593960

  7. Harmonic analysis for the characterization and correction of geometric distortion in MRI

    SciTech Connect

    Tadic, Tony Stanescu, Teodor; Jaffray, David A.

    2014-11-01

    Purpose: Magnetic resonance imaging (MRI) is gaining widespread use in radiation therapy planning, patient setup verification, and real-time guidance of radiation delivery. Successful implementation of these technologies relies on the development of simple and efficient methods to characterize and monitor the geometric distortions arising due to system imperfections and gradient nonlinearities. To this end, the authors present the theory and validation of a novel harmonic approach to the quantification of system-related distortions in MRI. Methods: The theory of spatial encoding in MRI is applied to demonstrate that the 3D distortion vector field (DVF) is given by the solution of a second-order boundary value problem (BVP). This BVP is comprised of Laplace’s equation and a limited measurement of the distortion on the boundary of a specified region of interest (ROI). An analytical series expansion solving this BVP within a spherical ROI is obtained, and a statistical uncertainty analysis is performed to determine how random errors in the boundary measurements propagate to the ROI interior. This series expansion is then evaluated to obtain volumetric DVF mappings that are compared to reference data obtained on a 3 T full-body scanner. This validation is performed within two spheres of 20 cm diameter (one centered at the scanner origin and the other offset +3 cm along each of the transverse directions). Initially, a high-order mapping requiring measurements at 5810 boundary points is used. Then, after exploring the impact of the boundary sampling density and the effect of series truncation, a reduced-order mapping requiring measurements at 302 boundary points is evaluated. Results: The volumetric DVF mappings obtained from the harmonic analysis are in good agreement with the reference data. Following distortion correction using the high-order mapping, the authors estimate a reduction in the mean distortion magnitude from 0.86 to 0.42 mm and from 0.93 to 0.39 mm

  8. XTC MRI: sensitivity improvement through parameter optimization.

    PubMed

    Ruppert, Kai; Mata, Jaime F; Wang, Hsuan-Tsung J; Tobias, William A; Cates, Gordon D; Brookeman, James R; Hagspiel, Klaus D; Mugler, John P

    2007-06-01

    Xenon polarization Transfer Contrast (XTC) MRI pulse sequences permit the gas exchange of hyperpolarized xenon-129 in the lung to be measured quantitatively. However, the pulse sequence parameter values employed in previously published work were determined empirically without considering the now-known gas exchange rates and the underlying lung physiology. By using a theoretical model for the consumption of magnetization during data acquisition, the noise intensity in the computed gas-phase depolarization maps was minimized as a function of the gas-phase depolarization rate. With such optimization the theoretical model predicted an up to threefold improvement in precision. Experiments in rabbits demonstrated that for typical imaging parameter values the optimized XTC pulse sequence yielded a median noise intensity of only about 3% in the depolarization maps. Consequently, the reliable detection of variations in the average alveolar wall thickness of as little as 300 nm can be expected. This improvement in the precision of the XTC MRI technique should lead to a substantial increase in its sensitivity for detecting pathological changes in lung function. PMID:17534927

  9. Cardiopulmonary exercise testing in the MRI environment.

    PubMed

    Lafountain, Richard A; da Silveira, Juliana Serafim; Varghese, Juliet; Mihai, Georgeta; Scandling, Debbie; Craft, Jason; Swain, Carmen B; Franco, Veronica; Raman, Subha V; Devor, Steven T; Simonetti, Orlando P

    2016-04-01

     =  0.505, P  =  0.137). [Formula: see text]max CPX testing can be effectively performed in the MRI environment, enabling direct combination of physiological data with advanced post-exercise imaging in the same test session. PMID:26987361

  10. One-year test-retest reliability of intrinsic connectivity network fMRI in older adults

    PubMed Central

    Guo, Cong C.; Kurth, Florian; Zhou, Juan; Mayer, Emeran A.; Eickhoff, Simon B; Kramer, Joel H.; Seeley, William W.

    2014-01-01

    “Resting-state” or task-free fMRI can assess intrinsic connectivity network (ICN) integrity in health and disease, suggesting a potential for use of these methods as disease-monitoring biomarkers. Numerous analytical options are available, including model-driven ROI-based correlation analysis and model-free, independent component analysis (ICA). High test-retest reliability will be a necessary feature of a successful ICN biomarker, yet available reliability data remains limited. Here, we examined ICN fMRI test-retest reliability in 24 healthy older subjects scanned roughly one year apart. We focused on the salience network, a disease-relevant ICN not previously subjected to reliability analysis. Most ICN analytical methods proved reliable (intraclass coefficients > 0.4) and could be further improved by wavelet analysis. Seed-based ROI correlation analysis showed high map-wise reliability, whereas graph theoretical measures and temporal concatenation group ICA produced the most reliable individual unit-wise outcomes. Including global signal regression in ROI-based correlation analyses reduced reliability. Our study provides a direct comparison between the most commonly used ICN fMRI methods and potential guidelines for measuring intrinsic connectivity in aging control and patient populations over time. PMID:22446491

  11. MRI-based biomechanical parameters for carotid artery plaque vulnerability assessment.

    PubMed

    Speelman, Lambert; Teng, Zhongzhao; Nederveen, Aart J; van der Lugt, Aad; Gillard, Jonathan H

    2016-02-29

    Carotid atherosclerotic plaques are a major cause of ischaemic stroke. The biomechanical environment to which the arterial wall and plaque is subjected to plays an important role in the initiation, progression and rupture of carotid plaques. MRI is frequently used to characterize the morphology o