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Sample records for direct mri mapping

  1. Direct estimation of tracer-kinetic parameter maps from highly undersampled brain dynamic contrast enhanced MRI.

    PubMed

    Guo, Yi; Lingala, Sajan Goud; Zhu, Yinghua; Lebel, R Marc; Nayak, Krishna S

    2017-10-01

    The purpose of this work was to develop and evaluate a T1 -weighted dynamic contrast enhanced (DCE) MRI methodology where tracer-kinetic (TK) parameter maps are directly estimated from undersampled (k,t)-space data. The proposed reconstruction involves solving a nonlinear least squares optimization problem that includes explicit use of a full forward model to convert parameter maps to (k,t)-space, utilizing the Patlak TK model. The proposed scheme is compared against an indirect method that creates intermediate images by parallel imaging and compressed sensing before to TK modeling. Thirteen fully sampled brain tumor DCE-MRI scans with 5-second temporal resolution are retrospectively undersampled at rates R = 20, 40, 60, 80, and 100 for each dynamic frame. TK maps are quantitatively compared based on root mean-squared-error (rMSE) and Bland-Altman analysis. The approach is also applied to four prospectively R = 30 undersampled whole-brain DCE-MRI data sets. In the retrospective study, the proposed method performed statistically better than indirect method at R ≥ 80 for all 13 cases. This approach provided restoration of TK parameter values with less errors in tumor regions of interest, an improvement compared to a state-of-the-art indirect method. Applied prospectively, the proposed method provided whole-brain, high-resolution TK maps with good image quality. Model-based direct estimation of TK maps from k,t-space DCE-MRI data is feasible and is compatible up to 100-fold undersampling. Magn Reson Med 78:1566-1578, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  2. Combined noninvasive language mapping by navigated transcranial magnetic stimulation and functional MRI and its comparison with direct cortical stimulation.

    PubMed

    Ille, Sebastian; Sollmann, Nico; Hauck, Theresa; Maurer, Stefanie; Tanigawa, Noriko; Obermueller, Thomas; Negwer, Chiara; Droese, Doris; Zimmer, Claus; Meyer, Bernhard; Ringel, Florian; Krieg, Sandro M

    2015-07-01

    Repetitive navigated transcranial magnetic stimulation (rTMS) is now increasingly used for preoperative language mapping in patients with lesions in language-related areas of the brain. Yet its correlation with intraoperative direct cortical stimulation (DCS) has to be improved. To increase rTMS's specificity and positive predictive value, the authors aim to provide thresholds for rTMS's positive language areas. Moreover, they propose a protocol for combining rTMS with functional MRI (fMRI) to combine the strength of both methods. The authors performed multimodal language mapping in 35 patients with left-sided perisylvian lesions by using rTMS, fMRI, and DCS. The rTMS mappings were conducted with a picture-to-trigger interval (PTI, time between stimulus presentation and stimulation onset) of either 0 or 300 msec. The error rates (ERs; that is, the number of errors per number of stimulations) were calculated for each region of the cortical parcellation system (CPS). Subsequently, the rTMS mappings were analyzed through different error rate thresholds (ERT; that is, the ER at which a CPS region was defined as language positive in terms of rTMS), and the 2-out-of-3 rule (a stimulation site was defined as language positive in terms of rTMS if at least 2 out of 3 stimulations caused an error). As a second step, the authors combined the results of fMRI and rTMS in a predefined protocol of combined noninvasive mapping. To validate this noninvasive protocol, they correlated its results to DCS during awake surgery. The analysis by different rTMS ERTs obtained the highest correlation regarding sensitivity and a low rate of false positives for the ERTs of 15%, 20%, 25%, and the 2-out-of-3 rule. However, when comparing the combined fMRI and rTMS results with DCS, the authors observed an overall specificity of 83%, a positive predictive value of 51%, a sensitivity of 98%, and a negative predictive value of 95%. In comparison with fMRI, rTMS is a more sensitive but less specific

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

    PubMed Central

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

    2016-01-01

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

  4. MRI Technologies in Recent Human Brain Mapping

    NASA Astrophysics Data System (ADS)

    Sasaki, Yuka

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

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

    NASA Astrophysics Data System (ADS)

    Gaur, Pooja; Grissom, William A.

    2017-03-01

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

  6. Temperature mapping of thermal ablation using MRI.

    PubMed

    Samset, Eigil

    2006-01-01

    MRI is a unique tool for minimally invasive thermal ablation in that it can provide both targeting, monitoring and control during the procedure. Monitoring is achieved by using MRI temperature mapping. In this review the relevant physics is explained as a background to the state-of-the-art methods for computing temperature maps as well as the more cutting edge methods. The review covers both methods to monitor heating and cooling of tissue and explains temperature mapping using Proton Resonance Frequency shift, T1 mapping, diffusion mapping, R2* mapping and thermal models.

  7. MRI temperature mapping during thermal balloon angioplasty.

    PubMed

    Shmatukha, Andriy V; Bakker, Chris J G

    2006-04-21

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

  8. Clinical applications and future directions of functional MRI.

    PubMed

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

    2012-09-01

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

  9. Simulated field maps for susceptibility artefact correction in interventional MRI.

    PubMed

    Kochan, Martin; Daga, Pankaj; Burgos, Ninon; White, Mark; Cardoso, M Jorge; Mancini, Laura; Winston, Gavin P; McEvoy, Andrew W; Thornton, John; Yousry, Tarek; Duncan, John S; Stoyanov, Danail; Ourselin, Sébastien

    2015-09-01

    Intraoperative MRI (iMRI) is a powerful modality for acquiring images of the brain to facilitate precise image-guided neurosurgery. Diffusion-weighted MRI (DW-MRI) provides critical information about location, orientation and structure of nerve fibre tracts, but suffers from the "susceptibility artefact" stemming from magnetic field perturbations due to the step change in magnetic susceptibility at air-tissue boundaries in the head. An existing approach to correcting the artefact is to acquire a field map by means of an additional MRI scan. However, to recover true field maps from the acquired field maps near air-tissue boundaries is challenging, and acquired field maps are unavailable in historical MRI data sets. This paper reports a detailed account of our method to simulate field maps from structural MRI scans that was first presented at IPCAI 2014 and provides a thorough experimental and analysis section to quantitatively validate our technique. We perform automatic air-tissue segmentation of intraoperative MRI scans, feed the segmentation into a field map simulation step and apply the acquired and the simulated field maps to correct DW-MRI data sets. We report results for 12 patient data sets acquired during anterior temporal lobe resection surgery for the surgical management of focal epilepsy. We find a close agreement between acquired and simulated field maps and observe a statistically significant reduction in the susceptibility artefact in DW-MRI data sets corrected using simulated field maps in the vicinity of the resection. The artefact reduction obtained using acquired field maps remains better than that using the simulated field maps in all evaluated regions of the brain. The proposed simulated field maps facilitate susceptibility artefact reduction near the resection. Accurate air-tissue segmentation is key to achieving accurate simulation. The proposed simulation approach is adaptable to different iMRI and neurosurgical applications.

  10. 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

  11. Neuroethics and fMRI: mapping a fledgling relationship.

    PubMed

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

    2011-04-22

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

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

    PubMed Central

    Papanastassiou, Alex M.; DiCarlo, James J.

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2000-06-01

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

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

    PubMed

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

    2016-02-01

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

  15. 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

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

    PubMed Central

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

    2016-01-01

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

  17. NOTE: MRI temperature mapping during thermal balloon angioplasty

    NASA Astrophysics Data System (ADS)

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

    2006-04-01

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

  18. Computed inverse MRI for magnetic susceptibility map reconstruction

    PubMed Central

    Chen, Zikuan; Calhoun, Vince

    2015-01-01

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

  19. 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.

  20. 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.

  1. 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.

  2. Ex vivo quantitative multiparametric MRI mapping of human meniscus degeneration.

    PubMed

    Nebelung, Sven; Tingart, Markus; Pufe, Thomas; Kuhl, Christiane; Jahr, Holger; Truhn, Daniel

    2016-12-01

    To evaluate the diagnostic performance of T1, T1ρ, T2, T2*, and UTE-T2* (ultrashort-echo time-enhanced T2*) mapping in the refined graduation of human meniscus degeneration with histology serving as standard-of-reference. This IRB-approved intra-individual comparative ex vivo study was performed on 24 lateral meniscus body samples obtained from 24 patients undergoing total knee replacement. Samples were assessed on a 3.0-T MRI scanner using inversion-recovery (T1), spin-lock multi-gradient-echo (T1ρ), multi-spin-echo (T2) and multi-gradient-echo (T2* and UTE-T2*) sequences to determine relaxation times of quantitative MRI (qMRI) parameters. Relaxation times were calculated on the respective maps, averaged to the entire meniscus and to its zones. Histologically, samples were analyzed on a four-point score according to Williams (0-III). QMRI results and Williams (sub)scores were correlated using Spearman's ρ, while Williams grade-dependent differences were assessed using Kruskal-Wallis and Dunn's tests. Sensitivities and specificities in the detection of intact (Williams grade [WG]-0) and severely degenerate meniscus (WG-II-III) were calculated. Except for T2*, significant increases in qMRI parameters with increasing Williams grades were observed. T1, T1ρ, T2, and UTE-T2* exhibited high sensitivity and variable specificity rates. Significant marked-to-strong correlations were observed for these parameters with each other, with histological WGs and the subscores tissue integrity and cellularity. QMRI mapping holds promise in the objective evaluation of human meniscus. Although sufficient discriminatory power of T1, T1ρ, T2, and UTE-T2* was only demonstrated for the histological extremes, these data may aid in the future MRI-based parameterization and quantification of human meniscus degeneration.

  3. Apparent exchange rate mapping with diffusion MRI.

    PubMed

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

    2011-08-01

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

  4. Mapping Directly Imaged Giant Exoplanets

    NASA Astrophysics Data System (ADS)

    Kostov, Veselin; Apai, Dániel

    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 H2O, CH4, 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, cloud cover

  5. 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

  6. In vivo manganese-enhanced MRI for visuotopic brain mapping.

    PubMed

    Chan, Kevin C; Wu, Ed X

    2012-01-01

    This study explored the feasibility of localized manganese-enhanced MRI (MEMRI) via 3 different routes of Mn(2+) administrations for visuotopic brain mapping of retinal, callosal, cortico-subcortical, transsynaptic and horizontal connections in normal adult rats. Upon fractionated intravitreal Mn(2+) injection, Mn enhancements were observed in the contralateral superior colliculus (SC) and lateral geniculate nucleus (LGN) by 45-60% at 1-3 days after initial Mn(2+) injection and in the contralateral primary visual cortex (V1) by about 10% at 2-3 days after initial Mn(2+) injection. Direct, single-dose Mn(2+) injection to the LGN resulted in Mn enhancement by 13-21% in V1 and 8-11% in SC of the ipsilateral hemisphere at 8 to 24 hours after Mn(2+) administration. Intracortical, single-dose Mn(2+) injection to the visual cortex resulted in Mn enhancement by 53-65% in ipsilateral LGN, 15-26% in ipsilateral SC, 32-34% in the splenium of corpus callosum and 17-25% in contralateral V1/V2 transition zone at 8 to 24 hours after Mn(2+) administration. Notably, some patchy patterns were apparent near the V1/V2 border of the contralateral hemisphere. Laminar-specific horizontal cortical connections were also observed in the ipsilateral hemisphere. The current results demonstrated the sensitivity of MEMRI for assessing the neuroarchitecture of the visual brains in vivo without depth-limitation, and may possess great potentials for studying the basic neural components and connections in the visual system longitudinally during development, plasticity, pharmacological interventions and genetic modifications.

  7. In vivo Visuotopic Brain Mapping with Manganese-Enhanced MRI and Resting-State Functional Connectivity MRI

    PubMed Central

    Chan, Kevin C.; Fan, Shu-Juan; Chan, Russell W.; Cheng, Joe S.; Zhou, Iris Y.; Wu, Ed X.

    2014-01-01

    The rodents are an increasingly important model for understanding the mechanisms of development, plasticity, functional specialization and disease in the visual system. However, limited tools have been available for assessing the structural and functional connectivity of the visual brain network globally, in vivo and longitudinally. There are also ongoing debates on whether functional brain connectivity directly reflects structural brain connectivity. In this study, we explored the feasibility of manganese-enhanced MRI (MEMRI) via 3 different routes of Mn2+ administration for visuotopic brain mapping and understanding of physiological transport in normal and visually deprived adult rats. In addition, resting-state functional connectivity MRI (RSfcMRI) was performed to evaluate the intrinsic functional network and structural-functional relationships in the corresponding anatomical visual brain connections traced by MEMRI. Upon intravitreal, subcortical, and intracortical Mn2+ injection, different topographic and layer-specific Mn enhancement patterns could be revealed in the visual cortex and subcortical visual nuclei along retinal, callosal, cortico-subcortical, transsynaptic and intracortical horizontal connections. Loss of visual input upon monocular enucleation to adult rats appeared to reduce interhemispheric polysynaptic Mn2+ transfer but not intra- or inter-hemispheric monosynaptic Mn2+ transport after Mn2+ injection into visual cortex. In normal adults, both structural and functional connectivity by MEMRI and RSfcMRI was stronger interhemispherically between bilateral primary/secondary visual cortex (V1/V2) transition zones (TZ) than between V1/V2 TZ and other cortical nuclei. Intrahemispherically, structural and functional connectivity was stronger between visual cortex and subcortical visual nuclei than between visual cortex and other subcortical nuclei. The current results demonstrated the sensitivity of MEMRI and RSfcMRI for assessing the

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

    PubMed

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

    2014-12-01

    In this study we validate passive language fMRI protocols designed for clinical application in pediatric epilepsy surgical planning as they do not require overt participation from patients. We introduced a set of quality checks that assess reliability of noninvasive fMRI mappings utilized for clinical purposes. We initially compared two fMRI language mapping paradigms, one active in nature (requiring participation from the patient) and the other passive in nature (requiring no participation from the patient). Group-level analysis in a healthy control cohort demonstrated similar activation of the putative language centers of the brain in the inferior frontal (IFG) and temporoparietal (TPG) regions. Additionally, we showed that passive language fMRI produced more left-lateralized activation in TPG (LI=+0.45) compared to the active task; with similarly robust left-lateralized IFG (LI=+0.24) activations using the passive task. We validated our recommended fMRI mapping protocols in a cohort of 15 pediatric epilepsy patients by direct comparison against the invasive clinical gold-standards. We found that language-specific TPG activation by fMRI agreed to within 9.2mm to subdural localizations by invasive functional mapping in the same patients, and language dominance by fMRI agreed with Wada test results at 80% congruency in TPG and 73% congruency in IFG. Lastly, we tested the recommended passive language fMRI protocols in a cohort of very young patients and confirmed reliable language-specific activation patterns in that challenging cohort. We concluded that language activation maps can be reliably achieved using the passive language fMRI protocols we proposed even in very young (average 7.5 years old) or sedated pediatric epilepsy patients. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    PubMed

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

    2014-11-01

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

  10. Direct SAR mapping by thermoacoustic imaging: A feasibility study.

    PubMed

    Winkler, Simone A; Picot, Paul A; Thornton, Michael M; Rutt, Brian K

    2016-10-25

    To develop a new method capable of directly measuring specific absorption rate (SAR) deposited in tissue using the thermoacoustic signal induced by short radiofrequency (RF) pulse excitation. A detailed model based on the thermoacoustic wave generation and propagation is presented. We propose a new concept for direct measurement of SAR, to be used as a safety assessment/monitoring tool for MRI. The concept involves the use of short bursts of RF energy and the measurement of the resulting thermoacoustic excitation pattern by an array of ultrasound transducers, followed by image reconstruction to yield the 3D SAR distribution. We developed a simulation framework to model this thermoacoustic SAR mapping concept and verified the concept in vitro. Simulations show good agreement between reconstructed and original SAR distributions with an error of 4.2, 7.2, and 8.4% of the mean SAR values in axial, sagittal, and coronal planes and support the feasibility of direct experimental mapping of SAR distributions in vivo. The in vitro experiments show good agreement with theory (r(2)  = 0.52). A novel thermoacoustic method for in vivo mapping of local SAR patterns in MRI has been proposed and verified in simulation and in a phantom experiment. Magn Reson Med, 2016. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  11. An atlas-based electron density mapping method for magnetic resonance imaging (MRI)-alone treatment planning and adaptive MRI-based prostate radiation therapy.

    PubMed

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

    2012-05-01

    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. 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. 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. The electron-density atlas method provides the ability to

  12. 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

  13. 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.

  14. 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.

  15. 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. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Fast MRI of RF Heating Via Phase Difference Mapping

    PubMed Central

    Shapiro, Erik M.; Borthakur, Arijitt; Shapiro, Michael J.; Reddy, Ravinder; Leigh, John S.

    2010-01-01

    A method is presented for the rapid acquisition of temperature maps derived from phase difference maps. The temperature-dependent chemical shift coefficients (TDCSCs) of various concentrations of aqueous cobalt and dysprosium-based compounds were measured. The largest TDCSC calculated was for 100 mM DyEDTA, which had a TDCSC of −0.09 PPM/K; 160 mM CoCl2 had a TDCSC of −0.04 PPM/K. These temperature-dependent chemical shifts (TDCSs) result in phase changes in the MR signal with changing temperature. Agarose phantoms were constructed with each paramagnetic metal. A fast gradientecho (FGRE) MR image was acquired to serve as the baseline image. A “test” MRI procedure was then performed on the phantom. Immediately afterwards, a second FGRE MR image was acquired, serving as the probing image. Proper image processing as a phase difference map between the probing image and the baseline image resulted in an image which quantitatively described the temperature increase of the phantom in response to a particular “test” imaging experiment. Applications of this technique in assessing the safety of pulse sequences and MR coils are discussed. PMID:11870836

  17. Reading sequence-directed computational nucleosome maps.

    PubMed

    Nibhani, Reshma; Trifonov, Edward N

    2015-01-01

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

  18. 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

  19. Three-directional acceleration phase mapping of myocardial function.

    PubMed

    Staehle, Felix; Jung, Bernd A; Bauer, Simon; Leupold, Jochen; Bock, Jelena; Lorenz, Ramona; Föll, Daniela; Markl, Michael

    2011-05-01

    An optimized acceleration encoded phase contrast method termed "acceleration phase mapping" for the assessment of regional myocardial function is presented. Based on an efficient gradient waveform design using two-sided encoding for in vivo three-directional acceleration mapping, echo and repetition times TE = 12-14 ms and TR = 15-17 ms for low accelerations sensitivity aenc = 5-8 m/s(2) were achieved. In addition to phantom validation, the technique was applied in a study with 10 healthy volunteers at 1.5T and 3T to evaluate its feasibility to assess regional myocardial acceleration at 1.5T and 3T. Results of the acceleration measurements were compared with the temporal derivative of myocardial velocities from three-directional velocity encoded standard phase contrast MRI in the same volunteers. The feasibility to assess myocardial acceleration along the radial, circumferential, and longitudinal direction of the left ventricle was demonstrated. Despite improved signal-to-noise-ratio at 3T (34% increase compared with 1.5T), image quality with respect to susceptibility artifacts was better 1.5T compared with 3T. Analysis of global and regional left ventricular acceleration showed characteristic patterns of systolic and diastolic acceleration and deceleration. Comparisons of directly measured and derived myocardial acceleration dynamics over the cardiac cycle revealed good correlation (r = 0.45-0.68, P < 0.01) between both methods. Copyright © 2010 Wiley-Liss, Inc.

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

    PubMed

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

    2008-08-01

    Conductive implants are in most cases a strict contraindication for MRI examinations, as RF pulses applied during the MRI measurement can lead to severe heating of the surrounding tissue. Understanding and mapping of these heating effects is therefore crucial for determining the circumstances under which patient examinations are safe. The use of fluoroptic probes is the standard procedure for monitoring these heating effects. However, the observed temperature increase is highly dependent on the positioning of such a probe, as it can only determine the temperature locally. Temperature mapping with MRI after RF heating can be used, but cooling effects during imaging lead to a significant underestimation of the heating effect. In this work, an MRI thermometry method was combined with an MRI heating sequence, allowing for temperature mapping during RF heating. This technique may provide new opportunities for implant safety investigations. (c) 2008 Wiley-Liss, Inc.

  1. 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

  2. Language mapping using high gamma electrocorticography, fMRI, and TMS versus electrocortical stimulation.

    PubMed

    Babajani-Feremi, Abbas; Narayana, Shalini; Rezaie, Roozbeh; Choudhri, Asim F; Fulton, Stephen P; Boop, Frederick A; Wheless, James W; Papanicolaou, Andrew C

    2016-03-01

    The aim of the present study was to compare localization of the language cortex using cortical stimulation mapping (CSM), high gamma electrocorticography (hgECoG), functional magnetic resonance imaging (fMRI), and transcranial magnetic stimulation (TMS). Language mapping using CSM, hgECoG, fMRI, and TMS were compared in nine patients with epilepsy. Considering CSM as reference, we compared language mapping approaches based on hgECoG, fMRI, and TMS using their sensitivity, specificity, and the results of receiver operating characteristic (ROC) analyses. Our results show that areas involved in language processing can be identified by hgECoG, fMRI, and TMS. The average sensitivity/specificity of hgECoG, fMRI, and TMS across all patients was 100%/85%, 50%/80%, and 67%/66%, respectively. The average area under the ROC curve of hgECoG, fMRI, and TMS across CSM-positive patients was 0.98, 0.76, and 0.68, respectively. There is considerable concordance between CSM, hgECoG, fMRI, and TMS language mapping. Our results reveal that hgECoG, fMRI, and TMS are valuable tools for presurgical language mapping. Language mapping on the basis of hgECoG, fMRI, and TMS can provide important additional information, therefore, these methods can be used in conjunction with CSM or as an alternative, when the latter is deemed impractical. Copyright © 2015 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

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

    PubMed

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

    2001-07-01

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

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

    PubMed

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

    2014-01-01

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

  5. Three-tesla functional MR language mapping: comparison with direct cortical stimulation in gliomas.

    PubMed

    Kuchcinski, Grégory; Mellerio, Charles; Pallud, Johan; Dezamis, Edouard; Turc, Guillaume; Rigaux-Viodé, Odile; Malherbe, Caroline; Roca, Pauline; Leclerc, Xavier; Varlet, Pascale; Chrétien, Fabrice; Devaux, Bertrand; Meder, Jean-Francois; Oppenheim, Catherine

    2015-02-10

    To evaluate the accuracy of functional MRI (fMRI) at 3T, as currently used in the preoperative mapping of language areas, compared with direct cortical stimulation (DCS) during awake surgery, in patients with supratentorial gliomas; and to identify clinical, histopathologic,and radiologic factors associated with fMRI/DCS discrepancies. Language mapping with fMRI and DCS of 40 consecutive patients with gliomas(24 low-grade, 16 high-grade) in functional areas were retrospectively analyzed. Three block designed tasks were performed during fMRI (letter word generation, category word generation,semantic association). During awake surgery, eloquent areas were mapped using DCS, blinded to fMRI. A site-by-site comparison of the 2 techniques was performed using a cortical grid. fMRI sensitivity and specificity were calculated using DCS as the reference. Associations of clinical,histopathologic, and radiologic features (including relative cerebral blood volume [rCBV] measured with dynamic susceptibility contrast MRI) with fMRI false-positive and false-negative occurrence were assessed using hierarchical logistic regressions. Of 2,114 stimulated cortical sites, 103 were positive for language during DCS. Sensitivity and specificity of language fMRI combining the 3 tasks reached 37.1% (95% confidence interval [CI] 20.7–57.2) and 83.4% (95% CI 77.1–88.3), respectively. Astrocytoma subtype(odds ratio [OR] 2.50 [1.32–4.76]; p 5 0.007), tumor rCBV ,1.5 (OR 2.17 [1.08–4.35]; p 50.03), higher cortical rCBV (OR 2.22 [1.15–4.17]; p 5 0.02), and distance to tumor .1 cm (OR2.46 [1.82–3.32]; p # 0.001) were independently associated with fMRI false-positive occurrence. There are pitfalls in preoperative fMRI as currently used in preoperative language mapping in glioma patients, made more complicated when high-grade and hyperperfused tumors are evaluated.

  6. A New Paradigm for Individual Subject Language Mapping: Movie-Watching fMRI.

    PubMed

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

    2015-01-01

    Functional MRI (fMRI) based on language tasks has been used in presurgical language mapping in patients with lesions in or near putative language areas. However, if patients have difficulty performing the tasks due to neurological deficits, it leads to unreliable or noninterpretable results. In this study, we investigate the feasibility of using a movie-watching fMRI for language mapping. A 7-minute movie clip with contrasting speech and nonspeech segments was shown to 22 right-handed healthy subjects. Based on all subjects' language functional regions-of-interest, 6 language response areas were defined, within which a language response model (LRM) was derived by extracting the main temporal activation profile. Using a leave-one-out procedure, individuals' language areas were identified as the areas that expressed highly correlated temporal responses with the LRM derived from an independent group of subjects. Compared with an antonym generation task-based fMRI, the movie-watching fMRI generated language maps with more localized activations in the left frontal language area, larger activations in the left temporoparietal language area, and significant activations in their right-hemisphere homologues. Results of 2 brain tumor patients' movie-watching fMRI using the LRM derived from the healthy subjects indicated its ability to map putative language areas; while their task-based fMRI maps were less robust and noisier. These results suggest that it is feasible to use this novel "task-free" paradigm as a complementary tool for fMRI language mapping when patients cannot perform the tasks. Its deployment in more neurosurgical patients and validation against gold-standard techniques need further investigation. Copyright © 2015 by the American Society of Neuroimaging.

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

    PubMed Central

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

    2015-01-01

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

  8. Quantitative pixelwise myocardial perfusion maps from first-pass perfusion MRI.

    PubMed

    Weng, A M; Ritter, C O; Beer, M; Hahn, D; Köstler, H

    2014-07-01

    To calculate and evaluate absolute quantitative myocardial perfusion maps from rest first-pass perfusion MRI. 10 patients after revascularization of myocardial infarction underwent cardiac rest first-pass perfusion MRI. Additionally, perfusion examinations were performed in 12 healthy volunteers. Quantitative myocardial perfusion maps were calculated by using a deconvolution technique, and results were compared were the findings of a sector-based quantification. Maps were typically calculated within 3 min per slice. For the volunteers, myocardial blood flow values of the maps were 0.51 ± 0.16 ml g(-1) per minute, whereas sector-based evaluation delivered 0.52 ± 0.15 ml g(-1) per minute. A t-test revealed no statistical difference between the two sets of values. For the patients, all perfusion defects visually detected in the dynamic perfusion series could be correctly reproduced in the maps. Calculation of quantitative perfusion maps from myocardial perfusion MRI examinations is feasible. The absolute quantitative maps provide additional information on the transmurality of perfusion defects compared with the visual evaluation of the perfusion series and offer a convenient way to present perfusion MRI findings. Voxelwise analysis of myocardial perfusion helps clinicians to assess the degree of tissue damage, and the resulting maps are a good tool to present findings to patients.

  9. Correlation analysis of dual-energy CT iodine maps with quantitative pulmonary perfusion MRI

    PubMed Central

    Hansmann, Jan; Apfaltrer, Paul; Zoellner, Frank G; Henzler, Thomas; Meyer, Mathias; Weisser, Gerald; Schoenberg, Stefan O; Attenberger, Ulrike I

    2013-01-01

    AIM: To correlate dual-energy computed tomography (DECT) pulmonary angiography derived iodine maps with parameter maps of quantitative pulmonary perfusion magnetic resonance imaging (MRI). METHODS: Eighteen patients with pulmonary perfusion defects detected on DECT derived iodine maps were included in this prospective study and additionally underwent time-resolved contrast-enhanced pulmonary MRI [dynamic contrast enhanced (DCE)-MRI]. DCE-MRI data were quantitatively analyzed using a pixel-by-pixel deconvolution analysis calculating regional pulmonary blood flow (PBF), pulmonary blood volume (PBV) and mean transit time (MTT) in visually normal lung parenchyma and perfusion defects. Perfusion parameters were correlated to mean attenuation values of normal lung and perfusion defects on DECT iodine maps. Two readers rated the concordance of perfusion defects in a visual analysis using a 5-point Likert-scale (1 = no correlation, 5 = excellent correlation). RESULTS: In visually normal pulmonary tissue mean DECT and MRI values were: 22.6 ± 8.3 Hounsfield units (HU); PBF: 58.8 ± 36.0 mL/100 mL per minute; PBV: 16.6 ± 8.5 mL; MTT: 17.1 ± 10.3 s. In areas with restricted perfusion mean DECT and MRI values were: 4.0 ± 3.9 HU; PBF: 10.3 ± 5.5 mL/100 mL per minute, PBV: 5 ± 4 mL, MTT: 21.6 ± 14.0 s. The differences between visually normal parenchyma and areas of restricted perfusion were statistically significant for PBF, PBV and DECT (P < 0.0001). No linear correlation was found between MRI perfusion parameters and attenuation values of DECT iodine maps (PBF: r = 0.35, P = 0.15; PBV: r = 0.34, P = 0.16; MTT: r = 0.41, P = 0.08). Visual analysis revealed a moderate correlation between perfusion defects on DECT iodine maps and the parameter maps of DCE-MRI (mean score 3.6, κ 0.45). CONCLUSION: There is a moderate visual but not statistically significant correlation between DECT iodine maps and perfusion parameter maps of DCE-MRI. PMID:23805370

  10. Correlation analysis of dual-energy CT iodine maps with quantitative pulmonary perfusion MRI.

    PubMed

    Hansmann, Jan; Apfaltrer, Paul; Zoellner, Frank G; Henzler, Thomas; Meyer, Mathias; Weisser, Gerald; Schoenberg, Stefan O; Attenberger, Ulrike I

    2013-05-28

    To correlate dual-energy computed tomography (DECT) pulmonary angiography derived iodine maps with parameter maps of quantitative pulmonary perfusion magnetic resonance imaging (MRI). Eighteen patients with pulmonary perfusion defects detected on DECT derived iodine maps were included in this prospective study and additionally underwent time-resolved contrast-enhanced pulmonary MRI [dynamic contrast enhanced (DCE)-MRI]. DCE-MRI data were quantitatively analyzed using a pixel-by-pixel deconvolution analysis calculating regional pulmonary blood flow (PBF), pulmonary blood volume (PBV) and mean transit time (MTT) in visually normal lung parenchyma and perfusion defects. Perfusion parameters were correlated to mean attenuation values of normal lung and perfusion defects on DECT iodine maps. Two readers rated the concordance of perfusion defects in a visual analysis using a 5-point Likert-scale (1 = no correlation, 5 = excellent correlation). In visually normal pulmonary tissue mean DECT and MRI values were: 22.6 ± 8.3 Hounsfield units (HU); PBF: 58.8 ± 36.0 mL/100 mL per minute; PBV: 16.6 ± 8.5 mL; MTT: 17.1 ± 10.3 s. In areas with restricted perfusion mean DECT and MRI values were: 4.0 ± 3.9 HU; PBF: 10.3 ± 5.5 mL/100 mL per minute, PBV: 5 ± 4 mL, MTT: 21.6 ± 14.0 s. The differences between visually normal parenchyma and areas of restricted perfusion were statistically significant for PBF, PBV and DECT (P < 0.0001). No linear correlation was found between MRI perfusion parameters and attenuation values of DECT iodine maps (PBF: r = 0.35, P = 0.15; PBV: r = 0.34, P = 0.16; MTT: r = 0.41, P = 0.08). Visual analysis revealed a moderate correlation between perfusion defects on DECT iodine maps and the parameter maps of DCE-MRI (mean score 3.6, κ 0.45). There is a moderate visual but not statistically significant correlation between DECT iodine maps and perfusion parameter maps of DCE-MRI.

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

    PubMed

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

    2014-10-01

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

  12. 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

  13. Fast and accurate multi-channel B1+ mapping based on the TIAMO technique for 7T UHF body MRI.

    PubMed

    Brunheim, Sascha; Gratz, Marcel; Johst, Sören; Bitz, Andreas Karsten; Fiedler, Thomas M; Ladd, Mark Edward; Quick, Harald Hartmut; Orzada, Stephan

    2017-10-09

    Current methods for mitigation of transmit field B1+ inhomogeneities at ultrahigh field (UHF) MRI by multi-channel radiofrequency (RF) shimming rely on accurate B1+ mapping. This can be time consuming when many RF channels have to be mapped for in vivo body MRI, where the B1 maps should ideally be acquired within a single breath-hold. Therefore, a new B1+ mapping technique (B1TIAMO) is proposed. The performance of this technique is validated against an established method (DREAM) in phantom measurements for a cylindrical head phantom with an 8-channel transmit/receive (Tx/Rx) array. Furthermore, measurements for a 32-channel Tx/Rx remote array are conducted in a large body phantom and the |B1+| map reliability is validated against simulations of the transmit RF field distribution. Finally, in vivo results of this new mapping technique for human abdomen are presented. For the head phantom (8-channel Tx/Rx coil), the single |B1+| comparison between B1 TIAMO, the direct DREAM measurements, and simulation data showed good agreement with 10-19% difference. For the large body phantom (32-channel Tx/Rx coil), B1TIAMO matched the RF field simulations well. The results demonstrate the potential to acquire 32 accurate single-channel B1+ maps for large field-of-view body imaging within only a single breath-hold of 16 s at 7T UHF MRI. Magn Reson Med, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

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

    PubMed

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

    2017-02-01

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

  15. Cerebrovascular reactivity mapping in patients with low grade gliomas undergoing presurgical sensorimotor mapping with BOLD fMRI.

    PubMed

    Zacà, Domenico; Jovicich, Jorge; Nadar, Sreenivasan R; Voyvodic, James T; Pillai, Jay J

    2014-08-01

    (i) to validate blood oxygenation level dependent (BOLD) breathhold cerebrovascular reactivity (BH CVR) mapping as an effective technique for potential detection of neurovascular uncoupling (NVU) in a cohort of patients with perirolandic low grade gliomas undergoing presurgical functional MRI (fMRI) for sensorimotor mapping, and (ii) to determine whether NVU potential, as assessed by BH CVR mapping, is prevalent in this tumor group. We retrospectively evaluated 12 patients, with histological diagnosis of grade II glioma, who performed multiple motor tasks and a BH task. Sensorimotor activation maps and BH CVR maps were compared in two automatically defined regions of interest (ROIs), ipsilateral to the lesion (i.e., ipsilesional) and contralateral to the lesion (i.e., contralesional). Motor task mean T-value was significantly higher in the contralesional ROIs (6.00 ± 1.74 versus 4.34 ± 1.68; P = 0.00004) as well as the BH mean T-value (4.74 ± 2.30 versus 4.09 ± 2.50; P = 0.009). The number of active voxels was significantly higher in the contralesional ROIs (Z = 2.99; P = 0.03). Actual NVU prevalence was 75%. Presurgical sensorimotor fMRI mapping can be affected by NVU-related false negative activation in low grade gliomas (76% of analyzed tasks). © 2013 Wiley Periodicals, Inc.

  16. Interpreting fMRI data: maps, modules and dimensions.

    PubMed

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

    2008-02-01

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

  17. Interpreting fMRI data: maps, modules and dimensions

    PubMed Central

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

    2009-01-01

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

  18. “Awake” intraoperative functional MRI (ai-fMRI) for mapping the eloquent cortex: Is it possible in awake craniotomy?☆

    PubMed Central

    Lu, Jun-Feng; Zhang, Han; Wu, Jin-Song; Yao, Cheng-Jun; Zhuang, Dong-Xiao; Qiu, Tian-Ming; Jia, Wen-Bin; Mao, Ying; Zhou, Liang-Fu

    2012-01-01

    As a promising noninvasive imaging technique, functional MRI (fMRI) has been extensively adopted as a functional localization procedure for surgical planning. However, the information provided by preoperative fMRI (pre-fMRI) is hampered by the brain deformation that is secondary to surgical procedures. Therefore, intraoperative fMRI (i-fMRI) becomes a potential alternative that can compensate for brain shifts by updating the functional localization information during craniotomy. However, previous i-fMRI studies required that patients be under general anesthesia, preventing the wider application of such a technique as the patients cannot perform tasks unless they are awake. In this study, we propose a new technique that combines awake surgery and i-fMRI, named “awake” i-fMRI (ai-fMRI). We introduced ai-fMRI to the real-time localization of sensorimotor areas during awake craniotomy in seven patients. The results showed that ai-fMRI could successfully detect activations in the bilateral primary sensorimotor areas and supplementary motor areas for all patients, indicating the feasibility of this technique in eloquent area localization. The reliability of ai-fMRI was further validated using intraoperative stimulation mapping (ISM) in two of the seven patients. Comparisons between the pre-fMRI-derived localization result and the ai-fMRI derived result showed that the former was subject to a heavy brain shift and led to incorrect localization, while the latter solved that problem. Additionally, the approaches for the acquisition and processing of the ai-fMRI data were fully illustrated and described. Some practical issues on employing ai-fMRI in awake craniotomy were systemically discussed, and guidelines were provided. PMID:24179766

  19. 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

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

    NASA Astrophysics Data System (ADS)

    Singh, Manbir; Sungkarat, Witaya

    2005-04-01

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

  1. Directional disorientation following left retrosplenial hemorrhage: a case report with fMRI studies.

    PubMed

    Ino, Tadashi; Doi, Toshiki; Hirose, Syuichi; Kimura, Toru; Ito, Jin; Fukuyama, Hidenao

    2007-02-01

    We report a 55-year-old right-handed man who presented with topographical disorientation following left retrosplenial hemorrhage. His directional information about familiar places, encoded by previous navigation, was severely impaired, and he could not learn the direction to new places in large-scale spaces beyond the range of visual surveillance. By contrast, he had no difficulties with directional information encoded in a tabletop manner: he could locate major cities or countries on a map, and he also could memorize the spatial relationship of objects in a room. Six months after the ictus, when he had recovered from his directional disorientation, a functional magnetic resonance imaging (fMRI) study of mental navigation demonstrated prominent activation in the retrosplenial area along the right parieto-occipital sulcus and the circumference of the injured area on the left side. The present study, together with previous investigations including clinical case reports, functional neuroimaging, and anatomical and physiological studies on monkeys, suggests that the 'sense of direction' in a large-scale locomotor environment is subserved by the visual area along the parieto-occipital sulcus, and that bilateral deterioration of this function causes directional disorientation.

  2. 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

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

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

  4. Velocity Gradient Maps Directly Measured by PLF

    NASA Astrophysics Data System (ADS)

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

    2000-11-01

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

  5. Real-Time Motor Cortex Mapping for the Safe Resection of Glioma: An Intraoperative Resting-State fMRI Study.

    PubMed

    Qiu, T-M; Gong, F-Y; Gong, X; Wu, J-S; Lin, C-P; Biswal, B B; Zhuang, D-X; Yao, C-J; Zhang, X-L; Lu, J-F; Zhu, F-P; Mao, Y; Zhou, L-F

    2017-09-07

    Resting-state functional MR imaging has been used for motor mapping in presurgical planning but never used intraoperatively. This study aimed to investigate the feasibility of applying intraoperative resting-state functional MR imaging for the safe resection of gliomas using real-time motor cortex mapping during an operation. Using interventional MR imaging, we conducted preoperative and intraoperative resting-state intrinsic functional connectivity analyses of the motor cortex in 30 patients with brain tumors. Factors that may influence intraoperative imaging quality, including anesthesia type (general or awake anesthesia) and tumor cavity (filled with normal saline or not), were studied to investigate image quality. Additionally, direct cortical stimulation was used to validate the accuracy of intraoperative resting-state fMRI in mapping the motor cortex. Preoperative and intraoperative resting-state fMRI scans were acquired for all patients. Fourteen patients who successfully completed both sufficient intraoperative resting-state fMRI and direct cortical stimulation were used for further analysis of sensitivity and specificity. Compared with those subjected to direct cortical stimulation, the sensitivity and specificity of intraoperative resting-state fMRI in localizing the motor area were 61.7% and 93.7%, respectively. The image quality of intraoperative resting-state fMRI was better when the tumor cavity was filled with normal saline (P = .049). However, no significant difference between the anesthesia types was observed (P = .102). This study demonstrates the feasibility of using intraoperative resting-state fMRI for real-time localization of functional areas during a neurologic operation. The findings suggest that using intraoperative resting-state fMRI can avoid the risk of intraoperative seizures due to direct cortical stimulation and may provide neurosurgeons with valuable information to facilitate the safe resection of gliomas. © 2017 American Society

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

    PubMed

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

    2011-01-25

    The concept of a topographical map of the corpus callosum (CC) has emerged from human lesion studies and from anatomical tracing investigations in other mammals. Over the last few years, a rising number of researchers have been reporting functional magnetic resonance imaging (fMRI) activation in white matter, particularly the CC. In this study, the scope for describing CC topography with fMRI was explored by evoking activation through simple sensory stimulation and motor tasks. We reviewed our published and unpublished fMRI data on the cortical representation of tactile, gustatory, and visual sensitivity and of motor activation, obtained in 36 volunteers. Activation foci were consistently detected in discrete CC regions: anterior (taste stimuli), central (motor tasks), central and posterior (tactile stimuli), and splenium (visual stimuli). These findings demonstrate that the functional topography of the CC can be explored with fMRI.

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

    PubMed Central

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

    2014-01-01

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

  8. Mapping Informative Clusters in a Hierarchial Framework of fMRI Multivariate Analysis

    PubMed Central

    Xu, Rui; Zhen, Zonglei; Liu, Jia

    2010-01-01

    Pattern recognition methods have become increasingly popular in fMRI data analysis, which are powerful in discriminating between multi-voxel patterns of brain activities associated with different mental states. However, when they are used in functional brain mapping, the location of discriminative voxels varies significantly, raising difficulties in interpreting the locus of the effect. Here we proposed a hierarchical framework of multivariate approach that maps informative clusters rather than voxels to achieve reliable functional brain mapping without compromising the discriminative power. In particular, we first searched for local homogeneous clusters that consisted of voxels with similar response profiles. Then, a multi-voxel classifier was built for each cluster to extract discriminative information from the multi-voxel patterns. Finally, through multivariate ranking, outputs from the classifiers were served as a multi-cluster pattern to identify informative clusters by examining interactions among clusters. Results from both simulated and real fMRI data demonstrated that this hierarchical approach showed better performance in the robustness of functional brain mapping than traditional voxel-based multivariate methods. In addition, the mapped clusters were highly overlapped for two perceptually equivalent object categories, further confirming the validity of our approach. In short, the hierarchical framework of multivariate approach is suitable for both pattern classification and brain mapping in fMRI studies. PMID:21152081

  9. Cerebrovascular reactivity mapping in patients with low grade gliomas undergoing presurgical sensorimotor mapping with BOLD fMRI

    PubMed Central

    Zacà, Domenico; Jovicich, Jorge; Nadar, Sreenivasan R.; Voyvodic, James T.; Pillai, Jay J.

    2013-01-01

    Purpose i) to validate Blood Oxygenation Level Dependent (BOLD) breath hold cerebrovascular reactivity mapping (BH CVR) as an effective technique for potential detection of neurovascular uncoupling (NVU) in a cohort of patients with perirolandic low grade gliomas undergoing presurgical functional magnetic resonance imaging (fMRI) for sensorimotor mapping, and ii) to determine whether NVU potential, as assessed by BH CVR mapping, is prevalent in this tumor group. Materials and Methods We retrospectively evaluated 12 patients, with histological diagnosis of grade II glioma, who performed multiple motor tasks and a BH task. Sensorimotor activation maps and BH CVR maps were compared in two automatically defined regions of interest (ROIs), ipsilateral to the lesion (i.e., ipsilesional) and contralateral to the lesion (i.e., contralesional). Results Motor task mean T-value was significantly higher in the contralesional ROIs (6.00±1.74 vs 4.34±1.68, p=0.00004) as well as the BH mean T-value (4.74±2.30 vs 4.09±2.50, p=0.009). The number of active voxels was significantly higher in the contralesional ROIs (Z=2.99, p=0.03). Actual NVU prevalence was 75%. Conclusion Presurgical sensorimotor fMRI mapping can be affected by NVU-related false negative activation in low grade gliomas (76% of analyzed tasks). PMID:24338845

  10. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  12. Mapping the MRI voxel volume in which thermal noise matches physiological noise--implications for fMRI.

    PubMed

    Bodurka, J; Ye, F; Petridou, N; Murphy, K; Bandettini, P A

    2007-01-15

    This work addresses the choice of the imaging voxel volume in blood oxygen level dependent (BOLD) functional magnetic resonance imaging (fMRI). Noise of physiological origin that is present in the voxel time course is a prohibitive factor in the detection of small activation-induced BOLD signal changes. If the physiological noise contribution dominates over the temporal fluctuation contribution in the imaging voxel, further increases in the voxel signal-to-noise ratio (SNR) will have diminished corresponding increases in temporal signal-to-noise (TSNR), resulting in reduced corresponding increases in the ability to detect activation induced signal changes. On the other hand, if the thermal and system noise dominate (suggesting a relatively low SNR) further decreases in SNR can prohibit detection of activation-induced signal changes. Here we have proposed and called the "suggested" voxel volume for fMRI the volume where thermal plus system-related and physiological noise variances are equal. Based on this condition we have created maps of fMRI suggested voxel volume from our experimental data at 3T, since this value will spatially vary depending on the contribution of physiologic noise in each voxel. Based on our fast EPI segmentation technique we have found that for gray matter (GM), white matter (WM), and cerebral spinal fluid (CSF) brain compartments the mean suggested cubical voxel volume is: (1.8 mm)3, (2.1 mm)3 and (1.4 mm)3, respectively. Serendipitously, (1.8 mm)3 cubical voxel volume for GM approximately matches the cortical thickness, thus optimizing BOLD contrast by minimizing partial volume averaging. The introduced suggested fMRI voxel volume can be a useful parameter for choice of imaging volume for functional studies.

  13. Mapping between fMRI responses to movies and their natural language annotations.

    PubMed

    Vodrahalli, Kiran; Chen, Po-Hsuan; Liang, Yingyu; Baldassano, Christopher; Chen, Janice; Yong, Esther; Honey, Christopher; Hasson, Uri; Ramadge, Peter; Norman, Kenneth A; Arora, Sanjeev

    2017-06-23

    Several research groups have shown how to map fMRI responses to the meanings of presented stimuli. This paper presents new methods for doing so when only a natural language annotation is available as the description of the stimulus. We study fMRI data gathered from subjects watching an episode of BBCs Sherlock (Chen et al., 2017), and learn bidirectional mappings between fMRI responses and natural language representations. By leveraging data from multiple subjects watching the same movie, we were able to perform scene classification with 72% accuracy (random guessing would give 4%) and scene ranking with average rank in the top 4% (random guessing would give 50%). The key ingredients underlying this high level of performance are (a) the use of the Shared Response Model (SRM) and its variant SRM-ICA (Chen et al., 2015; Zhang et al., 2016) to aggregate fMRI data from multiple subjects, both of which are shown to be superior to standard PCA in producing low-dimensional representations for the tasks in this paper; (b) a sentence embedding technique adapted from the natural language processing (NLP) literature (Arora et al., 2017) that produces semantic vector representation of the annotations; (c) using previous timestep information in the featurization of the predictor data. These optimizations in how we featurize the fMRI data and text annotations provide a substantial improvement in classification performance, relative to standard approaches. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

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

    PubMed Central

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

    2016-01-01

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

  15. New directions in the design of MRI gradient coils

    NASA Astrophysics Data System (ADS)

    Baig, Tanvir Noor

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

  16. Electromechanical Mapping With MRI Tagging and Epicardial Sock Electrodes

    PubMed Central

    McVeigh, Elliot; Faris, Owen; Ennis, Dan; Helm, Patrick; Evans, Frank

    2005-01-01

    Methods currently exist for the precise measurement of local three-dimensional myocardial motion noninvasivly with magnetic resonace imaging tagging. From these motion estimates, strain images representing the local deformation of the myocardium can be formed to show local myocardial contraction. These images clearly show the sequence of mechanical events during the activation and relaxation of the heart, making them ideal to visualize abnormalities caused by asynchronous electrical activation or ischemia. Coupled with the near simultaneous mapping of electrical depolarization with a sock electrode array, we can investigate the relationship between electical activity and mechanical function on a local level in the in vivo heart. Registered fiber angle maps can be also be obtained in the same heart with diffusion magnetic resonance imaging to assist in the construction of the electromechanical model of the whole heart. PMID:12539100

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

    PubMed

    Whitlock, Jonathan R; Derdikman, Dori

    2012-01-01

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

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

    ERIC Educational Resources Information Center

    Ungar, S.; And Others

    1994-01-01

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

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

    PubMed

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

    2017-04-01

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

  20. 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

  1. Head direction maps remain stable despite grid map fragmentation

    PubMed Central

    Whitlock, Jonathan R.; Derdikman, Dori

    2012-01-01

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

  2. 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

  3. 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

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

    PubMed

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

    2011-10-01

    The projection of vagina, uterine cervix, and nipple to the sensory cortex in humans has not been reported. The aim of this study was to map the sensory cortical fields of the clitoris, vagina, cervix, and nipple, toward an elucidation of the neural systems underlying sexual response. 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. The main outcome measures used for this study were the fMRI of brain regions activated by the various sensory stimuli. Clitoral, vaginal, and cervical self-stimulation activated 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. 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. © 2011 International Society for Sexual Medicine.

  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. National Mapping Division Strategic Direction 1997

    USGS Publications Warehouse

    ,

    1997-01-01

    The mission of the U.S. Geological Survey's (USGS) National Mapping Division (NMD) is to meet the Nation's need for basic geopspatial data, ensuring access to and advancing the application of these data and other related earth science information for users worldwide.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  9. Object naming is a more sensitive measure of speech localization than number counting: Converging evidence from direct cortical stimulation and fMRI.

    PubMed

    Petrovich Brennan, Nicole M; Whalen, Stephen; de Morales Branco, Daniel; O'shea, James P; Norton, Isaiah H; Golby, Alexandra J

    2007-01-01

    Using direct cortical stimulation to map language function during awake craniotomy is a well-described and useful technique. However, the optimum neuropsychological tasks to use have not been detailed. We used both functional MRI (fMRI) and direct cortical stimulation to compare the sensitivity of two behavioral paradigms, number counting and object naming, in the demonstration of eloquent cortical language areas. Fifteen patients with left hemisphere lesions and seven healthy control subjects participated. Patients had both preoperative fMRI at 3 T and direct cortical stimulation. Patients and controls performed object naming and number counting during fMRI at 3 T. Laterality indices were calculated from the fMRI maps for the Number-counting>Object-naming and Object-naming>Number-counting contrasts. The same number-counting and object-naming paradigms were tested during awake craniotomy and assessed for sensitivity to speech disruption. In all patients during intraoperative cortical stimulation, speech disruption occurred at more sites during object naming than during number counting. Subtle speech errors were only elicited with the object-naming paradigm, whereas only speech arrest and/or hypophonia were measured using the number counting paradigm. In both patients and controls, fMRI activation maps demonstrated greater left lateralization for object naming as compared to number counting in both frontal and temporal language areas. Number counting resulted in a more bihemispheric distribution of activations than object naming. Both cortical stimulation testing and fMRI suggest that automated speech tasks such as number counting may not fully engage putative language networks and therefore are not optimal for language localization for surgical planning.

  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. Sodium Mapping in Focal Cerebral Ischemia in the Rat by Quantitative 23Na MRI

    PubMed Central

    Yushmanov, Victor E.; Yanovski, Boris; Kharlamov, Alexander; LaVerde, George; Boada, Fernando E.; Jones, Stephen C.

    2009-01-01

    Purpose To validate 23Na twisted projection magnetic resonance imaging (MRI) as a quantitative technique to assess local brain sodium concentration ([Na+]br) during rat focal ischemia every 5.3 minutes. Materials and Methods The MRI protocol included an ultrashort echo-time (0.4 msec), a correction of radiofrequency (RF) inhomogeneities by B1 mapping, and the use of 0–154 mM NaCl calibration standards. To compare MRI [Na+]br values with those obtained by emission flame photometry in precision-punched brain samples of about 0.5 mm3 size, MR images were aligned with a histological three-dimensional reconstruction of the punched brain and regions of interest (ROIs) were placed precisely over the punch voids. Results The Bland–Altman analysis of [Na+]br in normal and ischemic cortex and caudate putamen of seven rats quantitated by 23Na MRI and flame photometry yielded a mean bias and limits of agreement (at ±1.96 SD) of 2% and 43% of average, respectively. A linear increase in [Na+]br was observed between 1 and 6 hours after middle cerebral artery occlusion. Conclusion 23Na MRI provides accurate and reliable results within the whole range of [Na+]br in ischemia with a temporal resolution of 5.3 minutes and precisely targeted submicroliter ROIs in selected brain structures. PMID:19306443

  12. 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. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. 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.

  14. Linking retinotopic fMRI mapping and anatomical probability maps of human occipital areas V1 and V2.

    PubMed

    Wohlschläger, A M; Specht, K; Lie, C; Mohlberg, H; Wohlschläger, A; Bente, K; Pietrzyk, U; Stöcker, T; Zilles, K; Amunts, K; Fink, G R

    2005-05-15

    Using functional MRI, we characterized field sign maps of the occipital cortex and created three-dimensional maps of these areas. By averaging the individual maps into group maps, probability maps of functionally defined V1 or V2 were determined and compared to anatomical probability maps of Brodmann areas BA17 and BA18 derived from cytoarchitectonic analysis (Amunts, K., Malikovic, A., Mohlberg, H., Schormann, T., Zilles, K., 2000. Brodmann's areas 17 and 18 brought into stereotaxic space-where and how variable? NeuroImage 11, 66-84). Comparison of areas BA17/V1 and BA18/V2 revealed good agreement of the anatomical and functional probability maps. Taking into account that our functional stimulation (due to constraints of the visual angle of stimulation achievable in the MR scanner) only identified parts of V1 and V2, for statistical evaluation of the spatial correlation of V1 and BA17, or V2 and BA18, respectively, the a priori measure kappa was calculated testing the hypothesis that a region can only be part of functionally defined V1 or V2 if it is also in anatomically defined BA17 or BA18, respectively. kappa = 1 means the hypothesis is fully true, kappa = 0 means functionally and anatomically defined visual areas are independent. When applying this measure to the probability maps, kappa was equal to 0.84 for both V1/BA17 and V2/BA18. The data thus show a good correspondence of functionally and anatomically derived segregations of early visual processing areas and serve as a basis for employing anatomical probability maps of V1 and V2 in group analyses to characterize functional activations of early visual processing areas.

  15. 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).

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

    PubMed

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

    2016-03-22

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

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

    PubMed Central

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

    2016-01-01

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

  18. 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

  19. 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.

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

    PubMed Central

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

    2007-01-01

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

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

    PubMed

    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 3T 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 3T; 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. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. 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.

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

    PubMed

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

    2011-09-01

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

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

    PubMed

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

    2014-12-01

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

  5. 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

  6. Validation of a new global 30-min drainage direction map

    NASA Astrophysics Data System (ADS)

    Döll, Petra; Lehner, Bernhard

    2002-02-01

    Digital drainage direction maps are a prerequisite for analyzing the flow of water on the land surface of the Earth. For continental or global studies, the most appropriate and most frequently used resolution for such data sets appears to be 30‧ (longitude-by-latitude). In this paper we present the new global drainage direction map DDM30, a 30‧ raster map of surface drainage directions, which organizes the Earth's land area into drainage basins and provides the river network topology. DDM30 was generated by first upscaling two drainage direction maps (DDMs) at higher resolutions. The resulting map was then extensively corrected in an iterative manner by comparison against vectorized, high resolution river maps and other geographic information. Finally, it was co-referenced to the locations of 935 gauging stations (provided by the Global Runoff Data Centre GRDC), which again involved manual corrections. DDM30 was validated against drainage basin areas from the literature, against the given upstream areas of the GRDC stations and, most importantly, against information from HYDRO1k, a data set based on a hydrologically corrected 1-km digital elevation model which is thought to afford the best information on surface drainage currently available at the global scale. In the course of the validation, the quality of DDM30 was compared to three other 30‧ DDMs. The validation results show that DDM30 provides a more accurate representation of drainage directions and river network topology than the other 30‧ DDMs.

  7. BOLD fMRI mapping of brain responses to nociceptive stimuli in rats under ketamine anesthesia.

    PubMed

    Shih, Yen-Yu I; Chang, Chen; Chen, Jyh-Cheng; Jaw, Fu-Shan

    2008-10-01

    Ketamine is one of the most commonly used anesthetics, but its effects on nociceptive responses are not clearly defined. This study used blood-oxygenation-level-dependent (BOLD) functional magnetic resonance imaging (fMRI) to hemodynamically map responses to formalin stimuli under ketamine anesthesia. All imaging was performed on a 4.7-T fMRI system. During dynamic image acquisition, formalin was injected into the rat hindpaw as a painful stimulant. Correlation coefficients were calculated, and each image was registered and fused with the corresponding rat brain atlas so as to avoid inaccuracies arising from manual definition of the brain area and to achieve atlas-based normalization among subjects. Formalin injections were found to increase BOLD signals in the cingulate cortex, sensory-motor cortices, insular cortex, striatum, nucleus accumbens, medial thalamus, ventrolateral thalamic group, and hippocampus. Moreover, in contrast to previous pain investigations, the frontal subcortical regions were strongly activated in ketamine-anesthetized rats.

  8. Presurgical brain mapping of the language network in patients with brain tumors using resting-state fMRI: Comparison with task fMRI.

    PubMed

    Sair, Haris I; Yahyavi-Firouz-Abadi, Noushin; Calhoun, Vince D; Airan, Raag D; Agarwal, Shruti; Intrapiromkul, Jarunee; Choe, Ann S; Gujar, Sachin K; Caffo, Brian; Lindquist, Martin A; Pillai, Jay J

    2016-03-01

    To compare language networks derived from resting-state fMRI (rs-fMRI) with task-fMRI in patients with brain tumors and investigate variables that affect rs-fMRI vs task-fMRI concordance. Independent component analysis (ICA) of rs-fMRI was performed with 20, 30, 40, and 50 target components (ICA20 to ICA50) and language networks identified for patients presenting for presurgical fMRI mapping between 1/1/2009 and 7/1/2015. 49 patients were analyzed fulfilling criteria for presence of brain tumors, no prior brain surgery, and adequate task-fMRI performance. Rs-vs-task-fMRI concordance was measured using Dice coefficients across varying fMRI thresholds before and after noise removal. Multi-thresholded Dice coefficient volume under the surface (DiceVUS) and maximum Dice coefficient (MaxDice) were calculated. One-way Analysis of Variance (ANOVA) was performed to determine significance of DiceVUS and MaxDice between the four ICA order groups. Age, Sex, Handedness, Tumor Side, Tumor Size, WHO Grade, number of scrubbed volumes, image intensity root mean square (iRMS), and mean framewise displacement (FD) were used as predictors for VUS in a linear regression. Artificial elevation of rs-fMRI vs task-fMRI concordance is seen at low thresholds due to noise. Noise-removed group-mean DiceVUS and MaxDice improved as ICA order increased, however ANOVA demonstrated no statistically significant difference between the four groups. Linear regression demonstrated an association between iRMS and DiceVUS for ICA30-50, and iRMS and MaxDice for ICA50. Overall there is moderate group level rs-vs-task fMRI language network concordance, however substantial subject-level variability exists; iRMS may be used to determine reliability of rs-fMRI derived language networks. © 2015 Wiley Periodicals, Inc.

  9. 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

  10. 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

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

    PubMed

    Zhang, Xiaotong; Zhu, Shanan; He, Bin

    2010-02-01

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

  12. Arterial spin labeling for motor activation mapping at 3T with a 32-channel coil: reproducibility and spatial accuracy in comparison with BOLD fMRI.

    PubMed

    Raoult, Hélène; Petr, Jan; Bannier, Elise; Stamm, Aymeric; Gauvrit, Jean-Yves; Barillot, Christian; Ferré, Jean-Christophe

    2011-09-01

    Functional arterial spin labeling (fASL) is an innovative biomarker of neuronal activation that allows direct and absolute quantification of activation-related CBF and is less sensitive to venous contamination than BOLD fMRI. This study evaluated fASL for motor activation mapping in comparison with BOLD fMRI in terms of involved anatomical area localization, intra-individual reproducibility of location, quantification of neuronal activation, and spatial accuracy. Imaging was performed at 3T with a 32-channel coil and dedicated post-processing tools were used. Twelve healthy right-handed subjects underwent fASL and BOLD fMRI while performing a right hand motor activation task. Three sessions were performed 7days apart in similar physiological conditions. Our results showed an activation in the left primary hand motor area for all 36 sessions in both fASL and BOLD fMRI. The individual functional maps for fASL demonstrated activation in ipsilateral secondary motor areas more often than the BOLD fMRI maps. This finding was corroborated by the group maps. In terms of activation location, fASL reproducibility was comparable to BOLD fMRI, with a distance between activated volumes of 2.1mm and an overlap ratio for activated volumes of 0.76, over the 3 sessions. In terms of activation quantification, fASL reproducibility was higher, although not significantly, with a CVintra of 11.6% and an ICC value of 0.75. Functional ASL detected smaller activation volumes than BOLD fMRI but the areas had a high degree of co-localization. In terms of spatial accuracy in detecting activation in the hand motor area, fASL had a higher specificity (43.5%) and a higher positive predictive value (69.8%) than BOLD fMRI while maintaining high sensitivity (90.7%). The high intra-individual reproducibility and spatial accuracy of fASL revealed in the present study will subsequently be applied to pathological subjects. Copyright © 2011 Elsevier Inc. All rights reserved.

  13. A Motion Direction Map in Macaque V2

    PubMed Central

    Lu, Haidong D.; Chen, Gang; Tanigawa, Hisashi; Roe, Anna W.

    2010-01-01

    SUMMARY In mammals, the perception of motion starts with direction-selective neurons in the visual cortex. Despite numerous studies in monkey V1 and V2 (primary and second visual cortex), there has been no evidence of direction maps in these areas. In the present study, we used optical imaging methods to study the organization of motion response in Macaque monkey V1 and V2. In contrast to the findings in other mammals (e.g. cats and ferrets), we found no direction maps in macaque V1. Robust direction maps, however, were found in V2 thick/pale stripes and avoided thin stripes. In many cases direction maps were located within thick stripes and exhibited pinwheel or linear organizations. The presence of motion maps in V2 points to a new found prominence of V2 in motion processing, either for contributing to motion perception in the dorsal pathway and/or for motion-cue dependent form perception in the ventral pathway. PMID:21145011

  14. 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

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

    PubMed

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

    2016-01-01

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

  16. Improving language mapping in clinical fMRI through assessment of grammar.

    PubMed

    Połczyńska, Monika; Japardi, Kevin; Curtiss, Susan; Moody, Teena; Benjamin, Christopher; Cho, Andrew; Vigil, Celia; Kuhn, Taylor; Jones, Michael; Bookheimer, Susan

    2017-01-01

    Brain surgery in the language dominant hemisphere remains challenging due to unintended post-surgical language deficits, despite using pre-surgical functional magnetic resonance (fMRI) and intraoperative cortical stimulation. Moreover, patients are often recommended not to undergo surgery if the accompanying risk to language appears to be too high. While standard fMRI language mapping protocols may have relatively good predictive value at the group level, they remain sub-optimal on an individual level. The standard tests used typically assess lexico-semantic aspects of language, and they do not accurately reflect the complexity of language either in comprehension or production at the sentence level. Among patients who had left hemisphere language dominance we assessed which tests are best at activating language areas in the brain. We compared grammar tests (items testing word order in actives and passives, wh-subject and object questions, relativized subject and object clauses and past tense marking) with standard tests (object naming, auditory and visual responsive naming), using pre-operative fMRI. Twenty-five surgical candidates (13 females) participated in this study. Sixteen patients presented with a brain tumor, and nine with epilepsy. All participants underwent two pre-operative fMRI protocols: one including CYCLE-N grammar tests (items testing word order in actives and passives, wh-subject and object questions, relativized subject and object clauses and past tense marking); and a second one with standard fMRI tests (object naming, auditory and visual responsive naming). fMRI activations during performance in both protocols were compared at the group level, as well as in individual candidates. The grammar tests generated more volume of activation in the left hemisphere (left/right angular gyrus, right anterior/posterior superior temporal gyrus) and identified additional language regions not shown by the standard tests (e.g., left anterior

  17. 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.

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

    PubMed

    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 0.3T 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.

  19. Brain MRI in global hypoxia-ischemia: a map of selective vulnerability.

    PubMed

    Luigetti, Marco; Goldsberry, Grant T; Cianfoni, Alessandro

    2012-03-01

    Hypoxic-ischemic injury to the brain is a devastating occurrence that frequently results in death or profound long-term neurologic disability. In this report, we describe the neuroradiological findings of a patient suffering from a global brain hypoxic-ischemic injury. Our findings clearly display that the areas of the brain with the highest metabolic activity, such as basal ganglia, thalami, and occipital and perirolandic cortex, are most susceptible to hypoxic injury. The MRI images delineate a map of the brain areas with selective vulnerability to hypoxia.

  20. Pore Diameter Mapping Using Double Pulsed-Field Gradient MRI and its Validation Using a Novel Glass Capillary Array Phantom

    PubMed Central

    Komlosh, Michal E.; Özarslan, Evren; Lizak, Martin J.; Horkay, Ferenc; Schram, Vincent; Shemesh, Noam; Cohen, Yoram; Basser, Peter J.

    2010-01-01

    Double Pulsed Field Gradient (d-PFG) MRI can provide quantitative maps of microstructural quantities and features within porous media and tissues. We propose and describe a novel MRI phantom, consisting of wafers of highly ordered glass capillary arrays (GCA), and its use to validate and calibrate a d-PFG MRI method to measure and map the local pore diameter. Specifically, we employ d-PFG Spin-Echo Filtered MRI in conjunction with a recently introduced theoretical framework, to estimate a mean pore diameter in each voxel within the imaging volume. This simulation scheme accounts for all diffusion and imaging gradients within the diffusion weighted MRI (DWI) sequence, and admits the violation of the short gradient pulse approximation. These diameter maps agree well with pore sizes measured using both optical microscopy and single PFG diffusion diffraction NMR spectroscopy using the same phantom. Pixel-by-pixel analysis shows that the local pore diameter can be mapped precisely and accurately within a specimen using d-PFG MRI. PMID:21084204

  1. Pore diameter mapping using double pulsed-field gradient MRI and its validation using a novel glass capillary array phantom.

    PubMed

    Komlosh, Michal E; Özarslan, Evren; Lizak, Martin J; Horkay, Ferenc; Schram, Vincent; Shemesh, Noam; Cohen, Yoram; Basser, Peter J

    2011-01-01

    Double pulsed-field gradient (d-PFG) MRI can provide quantitative maps of microstructural quantities and features within porous media and tissues. We propose and describe a novel MRI phantom, consisting of wafers of highly ordered glass capillary arrays (GCA), and its use to validate and calibrate a d-PFG MRI method to measure and map the local pore diameter. Specifically, we employ d-PFG Spin-Echo Filtered MRI in conjunction with a recently introduced theoretical framework, to estimate a mean pore diameter in each voxel within the imaging volume. This simulation scheme accounts for all diffusion and imaging gradients within the diffusion weighted MRI (DWI) sequence, and admits the violation of the short gradient pulse approximation. These diameter maps agree well with pore sizes measured using both optical microscopy and single PFG diffusion diffraction NMR spectroscopy using the same phantom. Pixel-by-pixel analysis shows that the local pore diameter can be mapped precisely and accurately within a specimen using d-PFG MRI. Copyright © 2010. Published by Elsevier Inc.

  2. Contribution of large scale biases in decoding of direction-of-motion from high-resolution fMRI data in human early visual cortex.

    PubMed

    Beckett, A; Peirce, J W; Sanchez-Panchuelo, R-M; Francis, S; Schluppeck, D

    2012-11-15

    Previous studies have demonstrated that the perceived direction of motion of a visual stimulus can be decoded from the pattern of functional magnetic resonance imaging (fMRI) responses in occipital cortex using multivariate analysis methods (Kamitani and Tong, 2006). One possible mechanism for this is a difference in the sampling of direction selective cortical columns between voxels, implying that information at a level smaller than the voxel size might be accessible with fMRI. Alternatively, multivariate analysis methods might be driven by the organization of neurons into clusters or even orderly maps at a much larger scale. To assess the possible sources of the direction selectivity observed in fMRI data, we tested how classification accuracy varied across different visual areas and subsets of voxels for classification of motion-direction. To enable high spatial resolution functional MRI measurements (1.5mm isotropic voxels), data were collected at 7T. To test whether information about the direction of motion is represented at the scale of retinotopic maps, we looked at classification performance after combining data across different voxels within visual areas (V1-3 and MT+/V5) before training the multivariate classifier. A recent study has shown that orientation biases in V1 are both necessary and sufficient to explain classification of stimulus orientation (Freeman et al., 2011). Here, we combined voxels with similar visual field preference as determined in separate retinotopy measurements and observed that classification accuracy was preserved when averaging in this 'retinotopically restricted' way, compared to random averaging of voxels. This insensitivity to averaging of voxels (with similar visual angle preference) across substantial distances in cortical space suggests that there are large-scale biases at the level of retinotopic maps underlying our ability to classify direction of motion. Copyright © 2012 Elsevier Inc. All rights reserved.

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

    PubMed Central

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

    2017-01-01

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

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

    SciTech Connect

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

    1996-12-31

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

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

    PubMed

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

    2006-08-15

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

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

    PubMed

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

    2016-11-15

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

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

    PubMed

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

    2016-03-29

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

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

    PubMed

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

    2016-09-01

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

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

    PubMed Central

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

    2016-01-01

    Electrical conductivity and permittivity of biological tissues are important diagnostic parameters and are useful for calculating subject-specific specific absorption rate distribution. On the other hand, water proton density also has clinical relevance for diagnosis purposes. These two kinds of tissue properties are inevitably associated in the technique of electrical properties tomography (EPT), which can be used to map in vivo electrical properties based on the measured B1 field distribution at Larmor frequency using magnetic resonance imaging (MRI). The signal magnitude in MR images is locally proportional to both the proton density of tissue and the receive B1 field; this is a source of artifact in receive B1-based EPT reconstruction because these two quantities cannot easily be disentangled. In this study, a new method was proposed for simultaneously extracting quantitative conductivity, permittivity and proton density from the measured magnitude of transmit B1 field, proton density-weighted receive B1 field, and transceiver phase, in a multi-channel radiofrequency (RF) coil using MRI, without specific assumptions to derive the proton density distribution. We evaluated the spatial resolution, sensitivity to contrast, and accuracy of the method using numerical simulations of B1 field in a phantom and in a realistic human head model. Using the proposed method, conductivity, permittivity and proton density were then experimentally obtained ex vivo in a pork tissue sample on a 7T MRI scanner equipped with a 16-channel microstrip transceiver RF coil. PMID:28005010

  10. Fast Multiclass Dictionaries Learning With Geometrical Directions in MRI Reconstruction.

    PubMed

    Zhan, Zhifang; Cai, Jian-Feng; Guo, Di; Liu, Yunsong; Chen, Zhong; Qu, Xiaobo

    2016-09-01

    Improve the reconstructed image with fast and multiclass dictionaries learning when magnetic resonance imaging is accelerated by undersampling the k-space data. A fast orthogonal dictionary learning method is introduced into magnetic resonance image reconstruction to provide adaptive sparse representation of images. To enhance the sparsity, image is divided into classified patches according to the same geometrical direction and dictionary is trained within each class. A new sparse reconstruction model with the multiclass dictionaries is proposed and solved using a fast alternating direction method of multipliers. Experiments on phantom and brain imaging data with acceleration factor up to 10 and various undersampling patterns are conducted. The proposed method is compared with state-of-the-art magnetic resonance image reconstruction methods. Artifacts are better suppressed and image edges are better preserved than the compared methods. Besides, the computation of the proposed approach is much faster than the typical K-SVD dictionary learning method in magnetic resonance image reconstruction. The proposed method can be exploited in undersampled magnetic resonance imaging to reduce data acquisition time and reconstruct images with better image quality.

  11. Reversed scan direction reduces electron beam damage in EBSD maps.

    PubMed

    Kidder, S; Prior, D

    2014-08-01

    The deleterious effects of electron beam damage on high-resolution electron backscatter diffraction (EBSD) maps of undeformed quartz are significantly reduced by scanning in the direction opposite to that dictated by widely used EBSD acquisition software. Higher quality electron backscatter patterns are produced when the electron beam moves progressively down the sample (the apparent 'up' direction in the resulting maps) for all step sizes where beam damage affects EBSD map quality (≤ ∼0.4 μm in this study). The relative improvement associated with downward scanning increases as step size is reduced. A comparison of high-resolution maps made in experimentally deformed quartz demonstrates that downward scanning reduces by a factor of ∼2 the lower limit in step size relative to maps scanned in the conventional direction. The electron beam damages quartz at its point of entry, forming ∼0.1-μm diameter bumps visible in Scanning electron microscope (SEM) images. Downward scanning produces better results because it minimizes the flux of electrons through these loci of damaged crystal. © 2014 The Authors Journal of Microscopy © 2014 Royal Microscopical Society.

  12. Direct and accelerated parameter mapping using the unscented Kalman filter.

    PubMed

    Zhao, Li; Feng, Xue; Meyer, Craig H

    2016-05-01

    To accelerate parameter mapping using a new paradigm that combines image reconstruction and model regression as a parameter state-tracking problem. In T2 mapping, the T2 map is first encoded in parameter space by multi-TE measurements and then encoded by Fourier transformation with readout/phase encoding gradients. Using a state transition function and a measurement function, the unscented Kalman filter can describe T2 mapping as a dynamic system and directly estimate the T2 map from the k-space data. The proposed method was validated with a numerical brain phantom and volunteer experiments with a multiple-contrast spin echo sequence. Its performance was compared with a conjugate-gradient nonlinear inversion method at undersampling factors of 2 to 8. An accelerated pulse sequence was developed based on this method to achieve prospective undersampling. Compared with the nonlinear inversion reconstruction, the proposed method had higher precision, improved structural similarity and reduced normalized root mean squared error, with acceleration factors up to 8 in numerical phantom and volunteer studies. This work describes a new perspective on parameter mapping by state tracking. The unscented Kalman filter provides a highly accelerated and efficient paradigm for T2 mapping. © 2015 Wiley Periodicals, Inc.

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

    PubMed Central

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

    2016-01-01

    Noninvasive localization of brain function is used to understand and treat neurological disease, exemplified by pre-operative fMRI mapping prior to neurosurgical intervention. The principal approach for generating these maps relies on brain responses evoked by a task and, despite known limitations, has dominated clinical practice for over 20 years. Recently, pre-operative fMRI mapping based on correlations in spontaneous brain activity has been demonstrated, however this approach has its own limitations and has not seen widespread clinical use. Here we show that spontaneous and task-based mapping can be performed together using the same pre-operative fMRI data, provide complimentary information relevant for functional localization, and can be combined to improve identification of eloquent motor cortex. Accuracy, sensitivity, and specificity of our approach are quantified through comparison with electrical cortical stimulation mapping in eight patients with intractable epilepsy. Broad applicability and reproducibility of our approach is demonstrated through prospective replication in an independent dataset of six patients from a different center. In both cohorts and every individual patient, we see a significant improvement in signal to noise and mapping accuracy independent of threshold, quantified using receiver operating characteristic curves. Collectively, our results suggest that modifying the processing of fMRI data to incorporate both task-based and spontaneous activity significantly improves functional localization in pre-operative patients. Because this method requires no additional scan time or modification to conventional pre-operative data acquisition protocols it could have widespread utility. PMID:26408860

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

    PubMed

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

    2016-01-01

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

  15. Accuracy of the morphology enabled dipole inversion (MEDI) algorithm for quantitative susceptibility mapping in MRI.

    PubMed

    Liu, Tian; Xu, Weiyu; Spincemaille, Pascal; Avestimehr, A Salman; Wang, Yi

    2012-03-01

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

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

    PubMed Central

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

    2013-01-01

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

  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.

  18. Real-time functional mapping with electrocorticography in pediatric epilepsy: comparison with fMRI and ESM findings.

    PubMed

    Korostenskaja, Milena; Wilson, Adam J; Rose, Douglas F; Brunner, Peter; Schalk, Gerwin; Leach, James; Mangano, Francesco T; Fujiwara, Hisako; Rozhkov, Leonid; Harris, Elana; Chen, Po-Ching; Seo, Joo-Hee; Lee, Ki H

    2014-07-01

    SIGFRIED (SIGnal modeling For Real-time Identification and Event Detection) software provides real-time functional mapping (RTFM) of eloquent cortex for epilepsy patients preparing to undergo resective surgery. This study presents the first application of paradigms used in functional magnetic resonance (fMRI) and electrical cortical stimulation mapping (ESM) studies for shared functional cortical mapping in the context of RTFM. Results from the 3 modalities are compared. A left-handed 13-year-old male with intractable epilepsy participated in functional mapping for localization of eloquent language cortex with fMRI, ESM, and RTFM. For RTFM, data were acquired over the frontal and temporal cortex. Several paradigms were sequentially presented: passive (listening to stories) and active (picture naming and verb generation). For verb generation and story processing, fMRI showed atypical right lateralizing language activation within temporal lobe regions of interest and bilateral frontal activation with slight right lateralization. Left hemisphere ESM demonstrated no eloquent language areas. RTFM procedures using story processing and picture naming elicited activity in the right lateral and basal temporal regions. Verb generation elicited strong right lateral temporal lobe activation, as well as left frontal lobe activation. RTFM results confirmed atypical language lateralization evident from fMRI and ESM. We demonstrated the feasibility and usefulness of a new RTFM stimulation paradigm during presurgical evaluation. Block design paradigms used in fMRI may be optimal for this purpose. Further development is needed to create age-appropriate RTFM test batteries.

  19. 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

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

    PubMed Central

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

    2007-01-01

    Measures of brain change can be computed from sequential MRI scans, providing valuable information on disease progression, e.g., for patient monitoring and drug trials. Tensor-based morphometry (TBM) creates maps of these brain changes, visualizing the 3D profile and rates of tissue growth or atrophy, but its sensitivity depends on the contrast and geometric stability of the images. A s part of the Alzheimer’s Disease Neuroimaging Initiative (ADNI), 17 normal elderly subjects were scanned twice (at a 2-week interval) with several 3D 1.5 T MRI pulse sequences: high and low flip angle SPGR/FLASH (from which Synthetic T1 images were generated), MP-RAGE, IR-SPGR (N = 10) and MEDIC (N = 7) scans. For each subject and scan type, a 3D deformation map aligned baseline and follow-up scans, computed with a nonlinear, inverse-consistent elastic registration algorithm. Voxelwise statistics, in ICBM stereotaxic space, visualized the profile of mean absolute change and its cross-subject variance; these maps were then compared using permutation testing. Image stability depended on: (1) the pulse sequence; (2) the transmit/receive coil type (birdcage versus phased array); (3) spatial distortion corrections (using MEDIC sequence information); (4) B1-field intensity inhomogeneity correction (using N3). SPGR/FLASH images acquired using a birdcage coil had least overall deviation. N3 correction reduced coil type and pulse sequence differences and improved scan reproducibility, except for Synthetic T1 images (which were intrinsically corrected for B1-inhomogeneity). No strong evidence favored B0 correction. Although SPGR/FLASH images showed least deviation here, pulse sequence selection for the ADNI project was based on multiple additional image analyses, to be reported elsewhere. PMID:16480900

  1. 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/.

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

    PubMed

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

    2006-06-01

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

  3. 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. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Correlation of scar in cardiac MRI and high-resolution contact mapping of left ventricle in a chronic infarct model.

    PubMed

    Thajudeen, Anees; Jackman, Warren M; Stewart, Brian; Cokic, Ivan; Nakagawa, Hiroshi; Shehata, Michael; Amorn, Allen M; Kali, Avinash; Liu, Ezh; Harlev, Doron; Bennett, Nathan; Dharmakumar, Rohan; Chugh, Sumeet S; Wang, Xunzhang

    2015-06-01

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

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

    PubMed

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

    2013-12-01

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

  6. Mapping individual cosmid DNAs by direct AFM imaging.

    PubMed

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

    1997-05-01

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

  7. Impairment of preoperative language mapping by lesion location: a functional magnetic resonance imaging, navigated transcranial magnetic stimulation, and direct cortical stimulation study.

    PubMed

    Ille, Sebastian; Sollmann, Nico; Hauck, Theresa; Maurer, Stefanie; Tanigawa, Noriko; Obermueller, Thomas; Negwer, Chiara; Droese, Doris; Boeckh-Behrens, Tobias; Meyer, Bernhard; Ringel, Florian; Krieg, Sandro M

    2015-08-01

    Language mapping by repetitive navigated transcranial magnetic stimulation (rTMS) is increasingly used and has already replaced functional MRI (fMRI) in some institutions for preoperative mapping of neurosurgical patients. Yet some factors affect the concordance of both methods with direct cortical stimulation (DCS), most likely by lesions affecting cortical oxygenation levels. Therefore, the impairment of the accuracy of rTMS and fMRI was analyzed and compared with DCS during awake surgery in patients with intraparenchymal lesions. Language mapping was performed by DCS, rTMS, and fMRI using an object-naming task in 27 patients with left-sided perisylvian lesions, and the induced language errors of each method were assigned to the cortical parcellation system. Subsequently, the receiver operating characteristics were calculated for rTMS and fMRI and compared with DCS as ground truth for regions with (w/) and without (w/o) the lesion in the mapped regions. The w/ subgroup revealed a sensitivity of 100% (w/o 100%), a specificity of 8% (w/o 5%), a positive predictive value of 34% (w/o: 53%), and a negative predictive value (NPV) of 100% (w/o: 100%) for the comparison of rTMS versus DCS. Findings for the comparison of fMRI versus DCS within the w/ subgroup revealed a sensitivity of 32% (w/o: 62%), a specificity of 88% (w/o: 60%), a positive predictive value of 56% (w/o: 62%), and a NPV of 73% (w/o: 60%). Although strengths and weaknesses exist for both rTMS and fMRI, the results show that rTMS is less affected by a brain lesion than fMRI, especially when performing mapping of language-negative cortical regions based on sensitivity and NPV.

  8. Implementation of fast macromolecular proton fraction mapping on 1.5 and 3 Tesla clinical MRI scanners: preliminary experience

    NASA Astrophysics Data System (ADS)

    Yarnykh, V.; Korostyshevskaya, A.

    2017-08-01

    Macromolecular proton fraction (MPF) is a biophysical parameter describing the amount of macromolecular protons involved into magnetization exchange with water protons in tissues. MPF represents a significant interest as a magnetic resonance imaging (MRI) biomarker of myelin for clinical applications. A recent fast MPF mapping method enabled clinical translation of MPF measurements due to time-efficient acquisition based on the single-point constrained fit algorithm. However, previous MPF mapping applications utilized only 3 Tesla MRI scanners and modified pulse sequences, which are not commonly available. This study aimed to test the feasibility of MPF mapping implementation on a 1.5 Tesla clinical scanner using standard manufacturer’s sequences and compare the performance of this method between 1.5 and 3 Tesla scanners. MPF mapping was implemented on 1.5 and 3 Tesla MRI units of one manufacturer with either optimized custom-written or standard product pulse sequences. Whole-brain three-dimensional MPF maps obtained from a single volunteer were compared between field strengths and implementation options. MPF maps demonstrated similar quality at both field strengths. MPF values in segmented brain tissues and specific anatomic regions appeared in close agreement. This experiment demonstrates the feasibility of fast MPF mapping using standard sequences on 1.5 T and 3 T clinical scanners.

  9. 4-Dimensional MRI and Attenuation Map Generation in PET/MRI with 4-Dimensional PET-Derived Deformation Matrices: Study of Feasibility for Lung Cancer Applications.

    PubMed

    Fayad, Hadi; Schmidt, Holger; Küstner, Thomas; Visvikis, Dimitris

    2017-05-01

    Respiratory motion may reduce accuracy in the fusion of functional and anatomic images from combined PET/MRI systems. Methodologies for the correction of respiratory motion in PET acquisitions with such systems are mostly based on the use of respiration-synchronized MRI acquisitions to derive motion fields. Existing approaches based on tagging acquisitions may introduce artifacts in MR images, whereas motion model approaches require the acquisition of training datasets. The objective of this work was to investigate the possibility of generating 4-dimensional (4D) MR images and associated attenuation maps (AMs) from the combination of a single static MR image and motion fields obtained from simultaneously acquired 4D non-attenuation-corrected (NAC) PET images. Methods: Four-dimensional PET/MRI datasets were acquired for 11 patients on a simultaneous PET/MRI system. The 4D PET datasets were retrospectively binned into 4 motion amplitude frames corresponding to the simultaneously acquired T1-weighted 4D MR images. A T1-weighted 3-dimensional MRI sequence with Dixon-based fat and water separation was also acquired at the end of expiration for PET attenuation correction purposes. All reconstructed 4D NAC PET images were then elastically registered to the single end-of-expiration NAC PET image. The derived motion fields were subsequently applied to the end-of-expiration frame of the acquired 4D MRI volume and the AM derived from the Dixon MR image to generate respiration-synchronized MR images and corresponding AMs. Results: The accuracy of the proposed method was assessed by comparing the generated and acquired images according to metrics such as overall correlation coefficients and differences in distances of anatomic landmarks on the generated and acquired MRI datasets. High correlation coefficients (mean ± SD: 0.93 ± 0.03) and small differences (2.69 ± 0.5 mm) were obtained. Moreover, small tissue classification differences (2.23% ± 0.68%) between generated and 4

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

    PubMed

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

    2008-01-01

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

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

    PubMed

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

    2007-11-01

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

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  14. Comparison of blocked and event-related fMRI designs for pre-surgical language mapping.

    PubMed

    Tie, Yanmei; Suarez, Ralph O; Whalen, Stephen; Radmanesh, Alireza; Norton, Isaiah H; Golby, Alexandra J

    2009-08-01

    Language functional magnetic resonance imaging (fMRI) is a promising non-invasive technique for pre-surgical planning in patients whose lesions are adjacent to or within critical language areas. Most language fMRI studies in patients use blocked experimental design. In this study, we compared a blocked design and a rapid event-related design with a jittered inter-stimulus-interval (ISI) (or stochastic design) for language fMRI in six healthy controls, and eight brain tumor patients, using a vocalized antonym generation task. Comparisons were based on visual inspection of fMRI activation maps and degree of language lateralization, both of which were assessed at a constant statistical threshold for each design. The results indicated a relatively high degree of discordance between the two task designs. In general, the event-related design provided maps with more robust activations in the putative language areas than the blocked design, especially for brain tumor patients. Our results suggest that the rapid event-related design has potential for providing comparable or even higher detection power over the blocked design for localizing language function in brain tumor patients, and therefore may be able to generate more sensitive language maps. More patient studies, and further investigation and optimization of language fMRI paradigms will be needed to determine the utility and validity of this approach for pre-surgical planning.

  15. 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. Copyright © 2011 Wiley Periodicals, Inc.

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

    PubMed Central

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

    2012-01-01

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

  17. 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

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

    PubMed

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

    2017-03-31

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

  19. Nonlinear Regularization for Per Voxel Estimation of Magnetic Susceptibility Distributions from MRI Field Maps

    PubMed Central

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

    2010-01-01

    Magnetic susceptibility is an important physical property of tissues, and can be used as a contrast mechanism in magnetic resonance imaging. Recently, targeting contrast agents by conjugation with signaling molecules and labeling stem cells with contrast agents have become feasible. These contrast agents are strongly paramagnetic, and the ability to quantify magnetic susceptibility could allow accurate measurement of signaling and cell localization. Presented here is a technique to estimate arbitrary magnetic susceptibility distributions by solving an ill-posed inversion problem from field maps obtained in an MRI scanner. Two regularization strategies are considered, conventional Tikhonov regularization, and a sparsity promoting nonlinear regularization using the ℓ1 norm. Proof of concept is demonstrated using numerical simulations, phantoms, and in a stroke model mouse. Initial experience indicates that the nonlinear regularization better suppresses noise and streaking artifacts common in susceptibility estimation. PMID:19502123

  20. 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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  4. fMRI orientation decoding in V1 does not require global maps or globally coherent orientation stimuli.

    PubMed

    Alink, Arjen; Krugliak, Alexandra; Walther, Alexander; Kriegeskorte, Nikolaus

    2013-01-01

    The orientation of a large grating can be decoded from V1 functional magnetic resonance imaging (fMRI) data, even at low resolution (3-mm isotropic voxels). This finding has suggested that columnar-level neuronal information might be accessible to fMRI at 3T. However, orientation decodability might alternatively arise from global orientation-preference maps. Such global maps across V1 could result from bottom-up processing, if the preferences of V1 neurons were biased toward particular orientations (e.g., radial from fixation, or cardinal, i.e., vertical or horizontal). Global maps could also arise from local recurrent or top-down processing, reflecting pre-attentive perceptual grouping, attention spreading, or predictive coding of global form. Here we investigate whether fMRI orientation decoding with 2-mm voxels requires (a) globally coherent orientation stimuli and/or (b) global-scale patterns of V1 activity. We used opposite-orientation gratings (balanced about the cardinal orientations) and spirals (balanced about the radial orientation), along with novel patch-swapped variants of these stimuli. The two stimuli of a patch-swapped pair have opposite orientations everywhere (like their globally coherent parent stimuli). However, the two stimuli appear globally similar, a patchwork of opposite orientations. We find that all stimulus pairs are robustly decodable, demonstrating that fMRI orientation decoding does not require globally coherent orientation stimuli. Furthermore, decoding remained robust after spatial high-pass filtering for all stimuli, showing that fine-grained components of the fMRI patterns reflect visual orientations. Consistent with previous studies, we found evidence for global radial and vertical preference maps in V1. However, these were weak or absent for patch-swapped stimuli, suggesting that global preference maps depend on globally coherent orientations and might arise through recurrent or top-down processes related to the perception of

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

    PubMed

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

    2010-05-01

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

  6. Direct (17)O MRI with partial volume correction: first experiences in a glioblastoma patient.

    PubMed

    Hoffmann, Stefan H; Radbruch, Alexander; Bock, Michael; Semmler, Wolfhard; Nagel, Armin M

    2014-12-01

    In tumor cells the energy production is shifted from aerobic to anaerobic metabolization of glucose, which makes the cerebral metabolic rate of oxygen consumption (CMRO2) a diagnostic parameter for tissue viability. Direct oxygen-17 ((17)O) MRI during inhalation of (17)O gas allows for a non-invasive determination of the CMRO2. However, the low spatial resolution and the fast transverse relaxation of (17)O lead to partial volume effects that severely bias the quantification of signal intensities. The aim of this work was to determine the CMRO2 in a tumor patient by (17)O MRI in combination with a partial volume correction (PVC) scheme. Direct (17)O MRI was performed in a glioblastoma patient (F, 51 years) prior to surgery at 7 T. The 'geometric transfer matrix' algorithm for volume of interest based PVC was adapted to (17)O MRI to recover the true signal intensities. We determined the CMRO2 values of gray matter (GM), white matter (WM), cerebrospinal fluid (CSF) and the tumor areas of the contrast enhancing rim (CE), the necrotic center (NE), and the perifocal edema (PE) using a three-phase metabolic model. Large differences in the signal increase during (17)O2 inhalation were obtained ranging from less than 2% in the tumor center up to more than 20% in GM areas. After PVC of the signal time curves, we determined CMRO2 values of 0.67 ± 0.08 μmol/g/min (WM), 3.57 ± 0.67 μmol/g/min (GM), 0.35 ± 0.09 μmol/g/min (CE), and 0.42 ± 0.05 μmol/g/min (PE). In CSF and NE no oxygen uptake (i.e. CMRO2 = 0) was determined from the corrected signals, well in accordance with the underlying physiology in these regions. The results show that PVC has a strong effect on the resulting CMRO2 values obtained by (17)O MRI. We found substantial differences-especially in GM tissue-between corrected and non-corrected CMRO2 values. Additionally, we demonstrated the feasibility of CMRO2 assessment in a glioblastoma patient by (17)O MRI.

  7. White matter fiber tractography based on a directional diffusion field in diffusion tensor MRI

    NASA Astrophysics Data System (ADS)

    Kumazawa, S.; Yoshiura, T.; Arimura, H.; Mihara, F.; Honda, H.; Higashida, Y.; Toyofuku, F.

    2006-03-01

    Diffusion tensor (DT) MRI provides the directional information of water molecular diffusion, which can be utilized to estimate the connectivity of white matter tract pathways in the human brain. Several white matter tractography methods have been developed to reconstruct the white matter fiber tracts using DT-MRI. With conventional methods (e.g., streamline techniques), however, it would be very difficult to trace the white matter tracts passing through the fiber crossing and branching regions due to the ambiguous directional information with the partial volume effect. The purpose of this study was to develop a new white matter tractography method which permits fiber tract branching and passing through crossing regions. Our tractography method is based on a three-dimensional (3D) directional diffusion function (DDF), which was defined by three eigenvalues and their corresponding eigenvectors of DT in each voxel. The DDF-based tractography (DDFT) consists of the segmentation of white matter tract region and fiber tracking process. The white matter tract regions were segmented by thresholding the 3D directional diffusion field, which was generated by the DDF. In fiber tracking, the DDFT method estimated the local tract direction based on overlap of the DDFs instead of the principal eigenvector, which has been used in conventional methods, and reconstructed tract branching by means of a one-to-many relation model. To investigate the feasibility and usefulness of the DDFT method, we applied it to DT-MRI data of five normal subjects and seven patients with a brain tumor. With the DDFT method, the detailed anatomy of white matter tracts was depicted more appropriately than the conventional methods.

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

    PubMed Central

    Adams, Samantha V.; Harris, Chris M.

    2014-01-01

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

  9. Functional Subpopulations of Neurons in a Macaque Face Patch Revealed by Single-Unit fMRI Mapping.

    PubMed

    Park, Soo Hyun; Russ, Brian E; McMahon, David B T; Koyano, Kenji W; Berman, Rebecca A; Leopold, David A

    2017-08-16

    Neurons within fMRI-defined face patches of the macaque brain exhibit shared categorical responses to flashed images but diverge in their responses under more natural viewing conditions. Here we investigate functional diversity among neurons in the anterior fundus (AF) face patch, combining whole-brain fMRI with longitudinal single-unit recordings in a local population (<1 mm(3)). For each cell, we computed a whole-brain correlation map based on its shared time course with voxels throughout the brain during naturalistic movie viewing. Based on this mapping, neighboring neurons showed markedly different affiliation with distant visually responsive areas and fell coarsely into subpopulations. Of these, only one subpopulation (∼16% of neurons) yielded similar correlation maps to the local fMRI signal. The results employ the readout of large-scale fMRI networks and, by indicating multiple functional domains within a single voxel, present a new view of functional diversity within a local neural population. Published by Elsevier Inc.

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

    PubMed

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

    2016-06-10

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

  11. 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).

  12. A motion direction preference map in monkey V4.

    PubMed

    Li, Peichao; Zhu, Shude; Chen, Ming; Han, Chao; Xu, Haoran; Hu, Jiaming; Fang, Yang; Lu, Haidong D

    2013-04-24

    In the primate visual system, area V4 is located in the ventral pathway and is traditionally thought to be involved in processing color and form information. However, little is known about its functional role in processing motion information. Using intrinsic signal optical imaging over large fields of view in V1, V2, and V4, we mapped the direction of motion responses in anesthetized macaques. We found that V4 contains direction-preferring domains that are preferentially activated by stimuli moving in one direction. These direction-preferring domains normally occupy several restricted regions of V4 and tend to overlap with orientation- and color-preferring domains. Single-cell recordings targeting these direction-preferring domains also showed a clustering, as well as a columnar organization of V4 direction-selective neurons. These data suggest that, in contrast to the classical view, motion information is also processed in ventral pathway regions such as area V4. Copyright © 2013 Elsevier Inc. All rights reserved.

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

    PubMed Central

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

    2003-01-01

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

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

    PubMed Central

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

    2016-01-01

    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

  15. 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

  16. 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.

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

    PubMed Central

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

    2013-01-01

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

  18. Rapidly reversible myocardial edema in patients with acromegaly: assessment with ultrafast T2 mapping in a single-breath-hold MRI sequence.

    PubMed

    Gouya, Hervé; Vignaux, Olivier; Le Roux, Patrick; Chanson, Philippe; Bertherat, Jérome; Bertagna, Xavier; Legmann, Paul

    2008-06-01

    The purpose of this study was to use a single-breath-hold T2-mapping MRI sequence to evaluate the reversibility of myocardial edema in patients treated for acromegaly. Before and after treatment, 15 patients with acromegaly underwent myocardial T2 mapping with an experimental single-breath-hold black-blood fast spin-echo sequence. Myocardial T2 mapping with both a multiple-breath-hold fast spinecho sequence and the experimental sequence also was performed on 14 volunteers. T2 relaxation times were calculated with a standard linear least-squares fit applied to myocardial signal intensity. The T2 relaxation times of patients were compared with those of volunteers and correlated with levels of serum growth hormone and insulinlike growth factor 1. Left ventricular function and mass index were determined with cine MRI. T2 values before treatment were higher in patients (71 +/- 12 milliseconds) than in volunteers (55.9 +/- 3.6 milliseconds) (p = 0.0003). These T2 values in patients decreased soon after treatment (57.6 +/- 6.6 milliseconds, p = 0.0007). This reduction correlates with successful reduction of levels of serum growth hormone and insulinlike growth factor 1. In volunteers, myocardial T2 values did not vary significantly between the single-breath-hold sequence and the multiple-breath-hold fast spin-echo sequence. In patients, myocardial mass and left ventricular function did not differ significantly before and after treatment. Patients with acromegaly have increased myocardial T2 values, which decrease soon after treatment, reflecting reversible myocardial edema. T2 value is more sensitive than left ventricular mass index in the detection of early reversal of acromegalic cardiomyopathy. These results highlight the potential role of MRI in direct assessment of the tissular effects of growth hormone and insulinlike growth factor 1 and in evaluation of the efficacy of treatment.

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2009-01-01

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

  1. 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

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

    PubMed

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

    2015-01-01

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

  3. A five-colour colour-coded mapping method for DCE-MRI analysis of head and neck tumours.

    PubMed

    Yuan, J; Chow, S K K; Yeung, D K W; King, A D

    2012-03-01

    To devise a method to convert the time-intensity curves (TICs) of head and neck dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) data into a pixel-by-pixel colour-coded map for identifying normal tissues and tumours. Twenty-three patients with head and neck squamous cell carcinoma (HNSCC) underwent DCE-MRI. TIC patterns of primary tumours, metastatic nodes, and normal tissues were assessed and a program was devised to convert the patterns into a classified colour-coded map. The enhancement patterns of tumours and normal tissue structures were evaluated and categorized into nine grades (0-8) based on the predominance of coloured pixels on maps. Five identified TIC patterns were converted into a colour-coded map consisting of red (maximum enhancement), brown (continuous slow rise-up), yellow (rapid wash-in and wash-out), green (rapid wash-in and plateau), and blue (rapid wash-in and rise-up). The colour-coded map distinguished all 21 primary tumours and 15 metastatic nodes from normal structures. Primary tumours and metastatic nodes were colour coded as predominantly yellow (grades 1-2) in 17/21 and 6/15, green (grades 3-5) in 3/21 and 5/15, and blue (grades 6-7) in 1/21 and 4/15, respectively. Vessels were coded red in 46/46 (grade 0) and muscles were coded brown in 23/23 (grade 8). Salivary glands, thyroid glands, and palatine tonsils were coded into predominantly yellow (grade 1) in 46/46 and 10/10 and 18/22, respectively. DCE-MRI derived five-colour-coded mapping provides an objective easy-to-interpret method to assess the dynamic enhancement pattern of head and neck cancers. Copyright © 2011 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

  4. The Learning Curve in Prostate MRI Interpretation: Self-Directed Learning Versus Continual Reader Feedback.

    PubMed

    Rosenkrantz, Andrew B; Ayoola, Abimbola; Hoffman, David; Khasgiwala, Anunita; Prabhu, Vinay; Smereka, Paul; Somberg, Molly; Taneja, Samir S

    2017-03-01

    The purpose of this study is to evaluate the roles of self-directed learning and continual feedback in the learning curve for tumor detection by novice readers of prostate MRI. A total of 124 prostate MRI examinations classified as positive (n = 52; single Prostate Imaging Reporting and Data System [PI-RADS] category 3 or higher lesion showing Gleason score ≥ 7 tumor at MRI-targeted biopsy) or negative (n = 72; PI-RADS category 2 or lower and negative biopsy) for detectable tumor were included. These were divided into four equal-sized batches, each with matching numbers of positive and negative examinations. Six second-year radiology residents reviewed examinations to localize tumors. Three of the six readers received feedback after each examination showing the preceding case's solution. The learning curve, plotting accuracy over time, was assessed by the Akaike information criterion (AIC). Logistic regression and mixed-model ANOVA were performed. For readers with and without feedback, the learning curve exhibited an initial rapid improvement that slowed after 40 examinations (change in AIC > 0.2%). Accuracy improved from 58.1% (batch 1) to 71.0-75.3% (batches 2-4) without feedback and from 58.1% to 72.0-77.4% with feedback (p = 0.027-0.046), without a difference in the extent of improvement (p = 0.800). Specificity improved from 53.7% to 68.5-81.5% without feedback and from 55.6% to 74.1-81.5% with feedback (p = 0.006-0.010), without a difference in the extent of improvement (p = 0.891). Sensitivity improved from 59.0-61.5% (batches 1-2) to 71.8-76.9% (batches 3-4) with feedback (p = 0.052), though did not improve without feedback (p = 0.602). Sensitivity for transition zone tumors exhibited larger changes (p = 0.024) with feedback than without feedback. Sensitivity for peripheral zone tumors did not improve in either group (p > 0.3). Reader confidence increased only with feedback (p < 0.001). The learning curve in prostate tumor detection largely reflected self-directed

  5. MRI-based mismatch detection in acute ischemic stroke: Optimal PWI maps and thresholds validated with PET.

    PubMed

    Zaro-Weber, Olivier; Moeller-Hartmann, Walter; Siegmund, Dora; Kandziora, Alexandra; Schuster, Alexander; Heiss, Wolf-Dieter; Sobesky, Jan

    2017-09-01

    Perfusion-weighted (PW) magnetic resonance imaging (MRI) is used to detect penumbral tissue in acute stroke, but the selection of optimal PW-maps and thresholds for tissue at risk detection remains a matter of debate. We validated the performance of PW-maps with 15O-water-positron emission tomography (PET) in a large comparative PET-MR cohort of acute stroke patients. In acute and subacute stroke patients with back-to-back MRI and PET imaging, PW-maps were validated with 15O-water-PET. We pooled two different cerebral blood flow (CBF) PET-maps to define the critical flow (CF) threshold, (i) quantitative (q)CBF-PET with the CF threshold <20 ml/100 g/min and (ii) normalized non-quantitative (nq)CBF-PET with a CF threshold of <70% (corresponding to <20 ml/100 g/min according to a previously published normogram). A receiver operating characteristic (ROC) curve analysis was performed to specify the accuracy and the optimal critical flow threshold of each PW-map as defined by PET. In 53 patients, (stroke to imaging: 9.8 h; PET to MRI: 52 min) PW-time-to-maximum (Tmax) with a threshold >6.1 s (AUC = 0.94) and non-deconvolved PW-time-to-peak (TTP) >4.8 s (AUC = 0.93) showed the best performance to detect the CF threshold as defined by PET. PW-Tmax with a threshold >6.1 s and TTP with a threshold >4.8 s are the most predictive in detecting the CF threshold for MR-based mismatch definition.

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

    PubMed

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

    2015-02-01

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

  7. Decoding fMRI events in sensorimotor motor network using sparse paradigm free mapping and activation likelihood estimates.

    PubMed

    Tan, Francisca M; Caballero-Gaudes, César; Mullinger, Karen J; Cho, Siu-Yeung; Zhang, Yaping; Dryden, Ian L; Francis, Susan T; Gowland, Penny A

    2017-08-16

    Most functional MRI (fMRI) studies map task-driven brain activity using a block or event-related paradigm. Sparse paradigm free mapping (SPFM) can detect the onset and spatial distribution of BOLD events in the brain without prior timing information, but relating the detected events to brain function remains a challenge. In this study, we developed a decoding method for SPFM using a coordinate-based meta-analysis method of activation likelihood estimation (ALE). We defined meta-maps of statistically significant ALE values that correspond to types of events and calculated a summation overlap between the normalized meta-maps and SPFM maps. As a proof of concept, this framework was applied to relate SPFM-detected events in the sensorimotor network (SMN) to six motor functions (left/right fingers, left/right toes, swallowing, and eye blinks). We validated the framework using simultaneous electromyography (EMG)-fMRI experiments and motor tasks with short and long duration, and random interstimulus interval. The decoding scores were considerably lower for eye movements relative to other movement types tested. The average successful rate for short and long motor events were 77 ± 13% and 74 ± 16%, respectively, excluding eye movements. We found good agreement between the decoding results and EMG for most events and subjects, with a range in sensitivity between 55% and 100%, excluding eye movements. The proposed method was then used to classify the movement types of spontaneous single-trial events in the SMN during resting state, which produced an average successful rate of 22 ± 12%. Finally, this article discusses methodological implications and improvements to increase the decoding performance. Hum Brain Mapp, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

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

    PubMed

    Kwon, Yong Hyun; Jang, Sung Ho

    2012-08-25

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

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

    PubMed Central

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

    2015-01-01

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

  10. 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.

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

    PubMed

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

    2010-05-01

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

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

    PubMed

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

    2016-05-01

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

  13. 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.

  14. Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm

    PubMed Central

    Glunčić, Matko; Paar, Vladimir

    2013-01-01

    The main feature of global repeat map (GRM) algorithm (www.hazu.hr/grm/software/win/grm2012.exe) is its ability to identify a broad variety of repeats of unbounded length that can be arbitrarily distant in sequences as large as human chromosomes. The efficacy is due to the use of complete set of a K-string ensemble which enables a new method of direct mapping of symbolic DNA sequence into frequency domain, with straightforward identification of repeats as peaks in GRM diagram. In this way, we obtain very fast, efficient and highly automatized repeat finding tool. The method is robust to substitutions and insertions/deletions, as well as to various complexities of the sequence pattern. We present several case studies of GRM use, in order to illustrate its capabilities: identification of α-satellite tandem repeats and higher order repeats (HORs), identification of Alu dispersed repeats and of Alu tandems, identification of Period 3 pattern in exons, implementation of ‘magnifying glass’ effect, identification of complex HOR pattern, identification of inter-tandem transitional dispersed repeat sequences and identification of long segmental duplications. GRM algorithm is convenient for use, in particular, in cases of large repeat units, of highly mutated and/or complex repeats, and of global repeat maps for large genomic sequences (chromosomes and genomes). PMID:22977183

  15. 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.

  16. 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

  17. 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.

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

    PubMed Central

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

    2007-01-01

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

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

    PubMed

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

    2014-01-01

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

  20. 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. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  1. 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

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

    PubMed

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

    2017-04-01

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

  3. 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.

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

    PubMed

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

    2004-01-21

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

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

    PubMed

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

    2013-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2004-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

  8. 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.

  9. Cluster analysis of quantitative parametric maps from DCE-MRI: application in evaluating heterogeneity of tumor response to antiangiogenic treatment.

    PubMed

    Longo, Dario Livio; Dastrù, Walter; Consolino, Lorena; Espak, Miklos; Arigoni, Maddalena; Cavallo, Federica; Aime, Silvio

    2015-07-01

    The objective of this study was to compare a clustering approach to conventional analysis methods for assessing changes in pharmacokinetic parameters obtained from dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) during antiangiogenic treatment in a breast cancer model. BALB/c mice bearing established transplantable her2+ tumors were treated with a DNA-based antiangiogenic vaccine or with an empty plasmid (untreated group). DCE-MRI was carried out by administering a dose of 0.05 mmol/kg of Gadocoletic acid trisodium salt, a Gd-based blood pool contrast agent (CA) at 1T. Changes in pharmacokinetic estimates (K(trans) and vp) in a nine-day interval were compared between treated and untreated groups on a voxel-by-voxel analysis. The tumor response to therapy was assessed by a clustering approach and compared with conventional summary statistics, with sub-regions analysis and with histogram analysis. Both the K(trans) and vp estimates, following blood-pool CA injection, showed marked and spatial heterogeneous changes with antiangiogenic treatment. Averaged values for the whole tumor region, as well as from the rim/core sub-regions analysis were unable to assess the antiangiogenic response. Histogram analysis resulted in significant changes only in the vp estimates (p<0.05). The proposed clustering approach depicted marked changes in both the K(trans) and vp estimates, with significant spatial heterogeneity in vp maps in response to treatment (p<0.05), provided that DCE-MRI data are properly clustered in three or four sub-regions. This study demonstrated the value of cluster analysis applied to pharmacokinetic DCE-MRI parametric maps for assessing tumor response to antiangiogenic therapy. Copyright © 2015 Elsevier Inc. All rights reserved.

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

    PubMed

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

    2012-05-01

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

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

    PubMed

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

    2015-06-03

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

  12. Functional MRI mapping of visual function and selective attention for performance assessment and presurgical planning using conjunctive visual search

    PubMed Central

    Parker, Jason G; Zalusky, Eric J; Kirbas, Cemil

    2014-01-01

    Background Accurate mapping of visual function and selective attention using fMRI is important in the study of human performance as well as in presurgical treatment planning of lesions in or near visual centers of the brain. Conjunctive visual search (CVS) is a useful tool for mapping visual function during fMRI because of its greater activation extent compared with high-capacity parallel search processes. Aims The purpose of this work was to develop and evaluate a CVS that was capable of generating consistent activation in the basic and higher level visual areas of the brain by using a high number of distractors as well as an optimized contrast condition. Materials and methods Images from 10 healthy volunteers were analyzed and brain regions of greatest activation and deactivation were determined using a nonbiased decomposition of the results at the hemisphere, lobe, and gyrus levels. The results were quantified in terms of activation and deactivation extent and mean z-statistic. Results The proposed CVS was found to generate robust activation of the occipital lobe, as well as regions in the middle frontal gyrus associated with coordinating eye movements and in regions of the insula associated with task-level control and focal attention. As expected, the task demonstrated deactivation patterns commonly implicated in the default-mode network. Further deactivation was noted in the posterior region of the cerebellum, most likely associated with the formation of optimal search strategy. Conclusion We believe the task will be useful in studies of visual and selective attention in the neuroscience community as well as in mapping visual function in clinical fMRI. PMID:24683515

  13. Noninvasive pressure difference mapping derived from 4D flow MRI in patients with unrepaired and repaired aortic coarctation.

    PubMed

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

    2014-04-01

    To develop a method for computing and visualizing pressure differences derived from time-resolved velocity-encoded three-dimensional phase-contrast magnetic resonance imaging (4D flow MRI) and to compare pressure difference maps of patients with unrepaired and repaired aortic coarctation to young healthy volunteers. 4D flow MRI data of four patients with aortic coarctation either before or after repair (mean age 17 years, age range 3-28, one female, three males) and four young healthy volunteers without history of cardiovascular disease (mean age 24 years, age range 20-27, one female, three males) was acquired using a 1.5-T clinical MR scanner. Image analysis was performed with in-house developed image processing software. Relative pressures were computed based on the Navier-Stokes equation. A standardized method for intuitive visualization of pressure difference maps was developed and successfully applied to all included patients and volunteers. Young healthy volunteers exhibited smooth and regular distribution of relative pressures in the thoracic aorta at mid systole with very similar distribution in all analyzed volunteers. Patients demonstrated disturbed pressures compared to volunteers. Changes included a pressure drop at the aortic isthmus in all patients, increased relative pressures in the aortic arch in patients with residual narrowing after repair, and increased relative pressures in the descending aorta in a patient after patch aortoplasty. Pressure difference maps derived from 4D flow MRI can depict alterations of spatial pressure distribution in patients with repaired and unrepaired aortic coarctation. The technique might allow identifying pathophysiological conditions underlying complications after aortic coarctation repair.

  14. 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…

  15. 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…

  16. 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…

  17. 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…

  18. 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

  19. Cerebrospinal fluid volumetric MRI mapping as a simple measurement for evaluating brain atrophy.

    PubMed

    De Vis, J B; Zwanenburg, J J; van der Kleij, L A; Spijkerman, J M; Biessels, G J; Hendrikse, J; Petersen, E T

    2016-05-01

    To assess whether volumetric cerebrospinal fluid (CSF) MRI can be used as a surrogate for brain atrophy assessment and to evaluate how the T2 of the CSF relates to brain atrophy. Twenty-eight subjects [mean age 64 (sd 2) years] were included; T1-weighted and CSF MRI were performed. The first echo data of the CSF MRI sequence was used to obtain intracranial volume, CSF partial volume was measured voxel-wise to obtain CSF volume (VCSF) and the T2 of CSF (T2,CSF) was calculated. The correlation between VCSF/T2,CSF and brain atrophy scores [global cortical atrophy (GCA) and medial temporal lobe atrophy (MTA)] was evaluated. Relative total, peripheral subarachnoidal, and ventricular VCSF increased significantly with increased scores on the GCA and MTA (R = 0.83, 0.78 and 0.78 and R = 0.72, 0.62 and 0.86). Total, peripheral subarachnoidal, and ventricular T2 of the CSF increased significantly with higher scores on the GCA and MTA (R = 0.72, 0.70 and 0.49 and R = 0.60, 0.57 and 0.41). A fast, fully automated CSF MRI volumetric sequence is an alternative for qualitative atrophy scales. The T2 of the CSF is related to brain atrophy and could thus be a marker of neurodegenerative disease. • A 1:11 min CSF MRI volumetric sequence can evaluate brain atrophy. • CSF MRI provides accurate atrophy assessment without partial volume effects. • CSF MRI data can be processed quickly without user interaction. • The measured T 2 of the CSF is related to brain atrophy.

  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. 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. Copyright © 2016, American Association for the Advancement of Science.

  2. 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%.

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

    PubMed

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

    2017-02-06

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

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

    PubMed Central

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

    2009-01-01

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

  5. 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

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

    PubMed

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

    2016-02-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2011-01-01

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

  9. 3D gradient system for two B0 field directions in earth's field MRI.

    PubMed

    Lother, Steffen; Hoelscher, Uvo; Kampf, Thomas; Jakob, Peter; Fidler, Florian

    2013-12-01

    A new gradient system for earth's field magnetic resonance imaging (EFMRI) is presented that can be rotated relatively to the earth's field direction while maintaining the ability to encode images. Orthogonal components of the gradient field are exploited to reduce the number of gradient coils. Two favorable orientations of the gradient system relative to the earth's magnetic field (parallel and perpendicular) are discussed. We introduce the theory for the magnetic fields of the new gradient system and illustrate the design of the coil geometries which were worked out with the help of simulations and a numerical optimization algorithm. Field mapping measurements and imaging experiments in the two different orientations of the gradient system were carried out. Orthogonal components of the gradient field take over the role of the additionally needed gradient fields when the gradient system is rotated relative to the earth's magnetic field. The results from the field mapping and imaging experiments verify the presented theory and show the functionality of the new gradient system. The presented system demonstrates that gradient coils can be used for image encoding in multiple directions. This fact can be exploited to realize an EFMRI setup for parallel and perpendicular prepolarization with a single set of gradient coils.

  10. 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.

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

    PubMed

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

    2012-04-01

    Two-dimensional (2D)-SE, 2D-GE and tri-dimensional (3D)-GE two-point T(1)-weighted MRI methods were evaluated in this study in order to maximize the accuracy of temperature mapping of bread dough during thermal processing. Uncertainties were propagated throughout each protocol of measurement, and comparisons demonstrated that all the methods with comparable acquisition times minimized the temperature uncertainty to similar extent. The experimental uncertainties obtained with low-field MRI were also compared to the theoretical estimations. Some discrepancies were reported between experimental and theoretical values of uncertainties of temperature; however, experimental and theoretical trends with varying parameters agreed to a large extent for both SE and GE methods. The 2D-SE method was chosen for further applications on prefermented dough because of its lower sensitivity to susceptibility differences in porous media. It was applied for temperature mapping in prefermented dough during chilling prior to freezing and compared locally to optical fiber measurements. Copyright © 2012 Elsevier Inc. All rights reserved.

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

    PubMed

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

    2017-02-28

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

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

    PubMed

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

    2017-03-01

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

  14. Direct, intraoperative observation of ∼0.1 Hz hemodynamic oscillations in awake human cortex: Implications for fMRI

    PubMed Central

    Rayshubskiy, Aleksandr; Wojtasiewicz, Teresa J.; Mikell, Charles B.; Bouchard, Matthew B.; Timerman, Dmitriy; Youngerman, Brett E.; McGovern, Robert A.; Otten, Marc L.; Canoll, Peter D.; McKhann, Guy M.; Hillman, Elizabeth M.C.

    2014-01-01

    An almost sinusoidal, large amplitude ∼0.1 Hz oscillation in cortical hemodynamics has been repeatedly observed in species ranging from mice to humans. However, the occurrence of ‘slow sinusoidal hemodynamic oscillations’ (SSHOs) in human functional magnetic resonance imaging (fMRI) studies is rarely noted or considered. As a result, little investigation into the cause of SSHOs has been undertaken, and their potential to confound fMRI analysis, as well as their possible value as a functional biomarker has been largely overlooked. Here, we report direct observation of large-amplitude, sinusoidal ∼0.1 Hz hemodynamic oscillations in the cortex of an awake human undergoing surgical resection of a brain tumor. Intraoperative multispectral optical intrinsic signal imaging (MS-OISI) revealed that SSHOs were spatially localized to distinct regions of the cortex, exhibited wave-like propagation, and involved oscillations in the diameter of specific pial arterioles, confirming that the effect was not the result of systemic blood pressure oscillations. fMRI data collected from the same subject 4 days prior to surgery demonstrates that ∼0.1 Hz oscillations in the BOLD signal can be detected around the same region. Intraoperative optical imaging data from a patient undergoing epilepsy surgery, in whom sinusoidal oscillations were not observed, is shown for comparison. This direct observation of the ‘0.1 Hz wave’ in the awake human brain, using both intraoperative imaging and pre-operative fMRI, confirms that SSHOs occur in the human brain, and can be detected by fMRI. We discuss the possible physiological basis of this oscillation and its potential link to brain pathologies, highlighting its relevance to resting-state fMRI and its potential as a novel target for functional diagnosis and delineation of neurological disease. PMID:24185013

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

    PubMed

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

    2013-01-01

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

  16. Compressed sensing MRI via fast linearized preconditioned alternating direction method of multipliers.

    PubMed

    Chen, Shanshan; Du, Hongwei; Wu, Linna; Jin, Jiaquan; Qiu, Bensheng

    2017-04-27

    The challenge of reconstructing a sparse medical magnetic resonance image based on compressed sensing from undersampled k-space data has been investigated within recent years. As total variation (TV) performs well in preserving edge, one type of approach considers TV-regularization as a sparse structure to solve a convex optimization problem. Nevertheless, this convex optimization problem is both nonlinear and nonsmooth, and thus difficult to handle, especially for a large-scale problem. Therefore, it is essential to develop efficient algorithms to solve a very broad class of TV-regularized problems. In this paper, we propose an efficient algorithm referred to as the fast linearized preconditioned alternating direction method of multipliers (FLPADMM), to solve an augmented TV-regularized model that adds a quadratic term to enforce image smoothness. Because of the separable structure of this model, FLPADMM decomposes the convex problem into two subproblems. Each subproblem can be alternatively minimized by augmented Lagrangian function. Furthermore, a linearized strategy and multistep weighted scheme can be easily combined for more effective image recovery. The method of the present study showed improved accuracy and efficiency, in comparison to other methods. Furthermore, the experiments conducted on in vivo data showed that our algorithm achieved a higher signal-to-noise ratio (SNR), lower relative error (Rel.Err), and better structural similarity (SSIM) index in comparison to other state-of-the-art algorithms. Extensive experiments demonstrate that the proposed algorithm exhibits superior performance in accuracy and efficiency than conventional compressed sensing MRI algorithms.

  17. 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.

  18. A 4-channel coil array interconnection by analog direct modulation optical link for 1.5-T MRI.

    PubMed

    Yuan, Jing; Wei, Juan; Shen, Gary X

    2008-10-01

    Optical glass fiber shows great advantages over coaxial cables in terms of electromagnetic interference, thus, it should be considered a potential alternative for magnetic resonance imaging (MRI) receive coil interconnection, especially for a large number coil array at high field. In this paper, we propose a 4-channel analog direct modulation optical link for a 1.5-T MRI coil array interconnection. First, a general direct modulated optical link is compared to an external modulated optical link. And then the link performances of the proposed direct modulated optical link, including power gain, frequency response, and dynamic range, are analyzed and measured. Phantom and in vivo head images obtained using this optical link are demonstrated for comparison with those obtained by cable connections. The signal-to-noise (SNR) analysis shows that the optical link achieves 6%-8% SNR a improvement over coaxial cables by elimination of electrical interference between cables during MR signal transmission.

  19. Comparative neuroimaging in children with cerebral palsy using fMRI and a novel EEG-based brain mapping during a motor task--a preliminary investigation.

    PubMed

    Lee, Jae Jin; Lee, Dong Ryul; Shin, Yoon Kyum; Lee, Nam Gi; Han, Bong S; You, Sung Joshua Hyun

    2013-01-01

    The purpose of this study was to compare topographical maps using a novel EEG-based brain mapping system with fMRI in normal and children with cerebral palsy (CP) during a grasping motor task. A normal child (mean ± SD = 13 ± 0 yrs) and four children with CP (mean ± SD = 10.25 ± 2.86 yrs) were recruited from a local community school and medical center. A novel EEG-based brain mapping system with 30 scalp sites (an extension of the 10-20 system) and a 3T MR scanner were used to observe cortical activation patterns during a grasping motor task. Descriptive analysis. In the EEG brain mapping data, the sensorimotor cortex (SMC) and inferior parietal cortex (IPC) were activated in all of the children. The children with CP showed additional activation areas in the premotor cortex (PMC), superior parietal cortex (SPC), and prefrontal cortex (PFC). In the fMRI brain mapping data, SMC activation was observed in all of the children, and the children with CP showed additional activation areas in the PMC and primary somatosensory cortex (PSC). The EEG-based topographical maps were equivalent to the maps obtained from fMRI during the grasping motor task. The results indicate that our novel EEG-based brain mapping system is useful for probing cortical activation patterns in normal children and children with CP.

  20. 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

  1. 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.

  2. Time-resolved resting state fMRI analysis: current status, challenges, and new directions.

    PubMed

    Keilholz, Shella Dawn; Caballero-Gaudes, Cesar; Bandettini, Peter; Deco, Gustavo; Calhoun, Vince D

    2017-09-06

    Time-resolved analysis of resting state fMRI data allows researchers to extract more information about brain function than traditional functional connectivity analysis, yet a number of challenges in data analysis and interpretation remain. This manuscript briefly summarizes common methods for time-resolved analysis and presents some of the pressing issues and opportunities in the field. From there, the discussion moves to the interpretation of the network dynamics observed with resting state fMRI and the role that resting state fMRI can play in elucidating the large-scale organization of brain activity.

  3. Quantitative T1 and T2 mapping in recurrent glioblastomas under bevacizumab: earlier detection of tumor progression compared to conventional MRI.

    PubMed

    Lescher, Stephanie; Jurcoane, Alina; Veit, Andreas; Bähr, Oliver; Deichmann, Ralf; Hattingen, Elke

    2015-01-01

    Treatment with the humanized anti-vascular endothelial growth factor (VEGF) antibody bevacizumab in glioblastoma patients suppresses contrast enhancement via the reduction of vascular permeability, which does not necessarily indicate real reduction of tumor cell mass. Therefore, other imaging criteria are needed to recognize tumor growth under bevacizumab more reliably. It is still unknown, whether quantitative T1 mapping is useful to monitor the effects of anti-angiogenic therapy or to indicate a tumor progression earlier and more reliable compared to conventional magnetic resonance imaging (MRI) sequences. This raised the question whether quantitative T1 mapping is more suitable to monitor treatment effects of bevacizumab. Conventional and quantitative MRI was performed on six consecutive patients with recurrent glioblastoma before treatment with bevacizumab and every 8 weeks thereafter until further tumor progression. Quantitative T1 maps before and after intravenous application of contrast agent and quantitative T2 maps were performed to calculate serial differential maps and subtraction maps from one time point, subtracting contrast-enhanced T1 maps from non-contrast T1 maps. In five illustrative cases, tumor progression was documented earlier in differential T1 relaxation time (DiffT1) and T2 relaxation time (DiffT2) maps before changes in the conventional MRI studies were obvious. Four patients showed previous prolongation of T1 relaxation time in the DiffT1 maps, suggesting tumor progression, and subtraction maps revealed faint contrast enhancement matching with the areas of T1 prolongation. Our results emphasize that quantitative relaxation time mapping could be a promising method for tumor monitoring in glioblastoma patients under anti-angiogenic therapy. Quantitative T1 mapping seems to detect enhancing tumor earlier than conventional contrast-enhanced T1-weighted images.

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

    PubMed Central

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

    2015-01-01

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

  5. Cortical and subcortical mapping of language areas: correlation of functional MRI and tractography in a 3T scanner with intraoperative cortical and subcortical stimulation in patients with brain tumors located in eloquent areas.

    PubMed

    Jiménez de la Peña, M; Gil Robles, S; Recio Rodríguez, M; Ruiz Ocaña, C; Martínez de Vega, V

    2013-01-01

    To describe the detection of cortical areas and subcortical pathways involved in language observed in MRI activation studies and tractography in a 3T MRI scanner and to correlate the findings of these functional studies with direct intraoperative cortical and subcortical stimulation. We present a series of 14 patients with focal brain tumors adjacent to eloquent brain areas. All patients underwent neuropsychological evaluation before and after surgery. All patients underwent MRI examination including structural sequences, perfusion imaging, spectroscopy, functional imaging to determine activation of motor and language areas, and 3D tractography. All patients underwent cortical mapping through cortical and subcortical stimulation during the operation to resect the tumor. Postoperative follow-up studies were done 24 hours after surgery. The correlation of motor function and of the corticospinal tract determined by functional MRI and tractography with intraoperative mapping of cortical and subcortical motor areas was complete. The eloquent brain areas of language expression and reception were strongly correlated with intraoperative cortical mapping in all but two cases (a high grade infiltrating glioma and a low grade glioma located in the frontal lobe). 3D tractography identified the arcuate fasciculus, the lateral part of the superior longitudinal fasciculus, the subcallosal fasciculus, the inferior fronto-occipital fasciculus, and the optic radiations, which made it possible to mark the limits of the resection. The correlation with the subcortical mapping of the anatomic arrangement of the fasciculi with respect to the lesions was complete. The best treatment for brain tumors is maximum resection without associated deficits, so high quality functional studies are necessary for preoperative planning. Copyright © 2011 SERAM. Published by Elsevier Espana. All rights reserved.

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

    PubMed

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

    2012-01-01

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

  7. 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

  8. Direct comparison of multiparametric magnetic resonance imaging (MRI) results with final histopathology in patients with proven prostate cancer in MRI/ultrasonography-fusion biopsy.

    PubMed

    Borkowetz, Angelika; Platzek, Ivan; Toma, Marieta; Renner, Theresa; Herout, Roman; Baunacke, Martin; Laniado, Michael; Baretton, Gustavo; Froehner, Michael; Zastrow, Stefan; Wirth, Manfred

    2016-08-01

    To compare multiparametric magnetic resonance imaging (mpMRI) of the prostate and histological findings of both targeted MRI/ultrasonography-fusion prostate biopsy (PBx) and systematic PBx with final histology of the radical prostatectomy (RP) specimen. A total of 105 patients with prostate cancer (PCa) histopathologically proven using a combination of fusion Pbx and systematic PBx, who underwent RP, were investigated. All patients had been examined using mpMRI, applying the European Society of Urogenital Radiology criteria. Histological findings from the RP specimen were compared with those from the PBx. Whole-mount RP specimen and mpMRI results were directly compared by a uro-pathologist and a uro-radiologist in step-section analysis. In the 105 patients with histopathologically proven PCa by combination of fusion PBx and systematic PBx, the detection rate of PCa was 90% (94/105) in fusion PBx alone and 68% (72/105) in systematic PBx alone (P = 0.001). The combination PBx detected 23 (22%) Gleason score (GS) 6, 69 (66%) GS 7 and 13 (12%) GS ≥8 tumours. Fusion PBx alone detected 25 (26%) GS 6, 57 (61%) GS 7 and 12 (13%) GS ≥8 tumours. Systematic PBx alone detected 17 (24%) GS 6, 49 (68%) GS 7 and 6 (8%) GS ≥8 tumours. Fusion PBx alone would have missed 11 tumours (4% [4/105] of GS 6, 6% [6/105] of GS 7 and 1% [1/105] of GS ≥8 tumours). Systematic PBx alone would have missed 33 tumours (10% [10/105] of GS 6, 20% [21/105] of GS 7 and 2% [2/105] of GS ≥8 tumours). The rates of concordance with regard to GS between the PBx and RP specimen were 63% (n = 65), 54% (n = 56) and 75% (n = 78) in fusion, systematic and combination PBx (fusion and systematic PBx combined), respectively. Upgrading of the GS between PBx and RP specimen occurred in 33% (n = 34), 44% (n = 46) and 18% (n = 19) in fusion, systematic and combination PBx, respectively. γ-correlation for detection of any cancer was 0.76 for combination PBx, 0.68 for fusion PBx alone and 0.23 for systematic

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

    PubMed

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

    2016-11-15

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

  10. 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.

  11. 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.

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

    PubMed

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

    2016-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

  14. 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

  15. Multiacquisition T1-mapping MRI during tidal respiration for quantification of myocardial T1 in swine with heart failure.

    PubMed

    Hood, Maureen N; Song, Ting; Bedocs, Peter; Capacchione, John F; Kasper, Christine E; Haigney, Mark C; Ho, Vincent B

    2013-10-01

    The purpose of this article is to evaluate a free-breathing pulse sequence to quantify myocardial T1 changes in a swine model of tachycardia-induced heart failure. Yorkshire swine were implanted with pacemakers and were ventricularly paced at 200 beats/min to induce heart failure. Animals were scanned twice with a 1.5-T MRI scanner, once at baseline and once at heart failure. A T1-mapping sequence was performed during tidal respiration before and 5 minutes after the administration of a gadolinium-chelate contrast agent. T1-mapping values were compared between the baseline and heart failure scans. The percentage of fibrosis of heart failure myocardial tissue was compared with similar left ventricular tissue from control animals using trichrome blue histologic analysis. In the study cohort, differences were found between the baseline and heart failure T1-mapping values before the administration of contrast agent (960 ± 96 and 726 ± 94 ms, respectively; p = 0.02) and after contrast agent administration (546 ± 180 and 300 ± 171 ms, respectively; p = 0.005). The animals with heart failure also had a difference histologically in the percentage of myocardial collagen compared with tissue from healthy control animals (control, 5.4% ± 1.0%; heart failure, 9.4% ± 1.6%; p < 0.001). The proposed T1-mapping technique can quantify diffuse myocardial changes associated with heart failure without the use of a contrast agent and without breath-holding. These T1 changes appear to be associated with increases in the percentage of myocardial collagen that in this study were not detected by traditional myocardial delayed enhancement imaging. T1 mapping may be a useful technique for detecting early but clinically significant myocardial fibrosis.

  16. Naturalistic fMRI Mapping Reveals Superior Temporal Sulcus as the Hub for the Distributed Brain Network for Social Perception

    PubMed Central

    Lahnakoski, Juha M.; Glerean, Enrico; Salmi, Juha; Jääskeläinen, Iiro P.; Sams, Mikko; Hari, Riitta; Nummenmaa, Lauri

    2012-01-01

    Despite the abundant data on brain networks processing static social signals, such as pictures of faces, the neural systems supporting social perception in naturalistic conditions are still poorly understood. Here we delineated brain networks subserving social perception under naturalistic conditions in 19 healthy humans who watched, during 3-T functional magnetic resonance imaging (fMRI), a set of 137 short (approximately 16 s each, total 27 min) audiovisual movie clips depicting pre-selected social signals. Two independent raters estimated how well each clip represented eight social features (faces, human bodies, biological motion, goal-oriented actions, emotion, social interaction, pain, and speech) and six filler features (places, objects, rigid motion, people not in social interaction, non-goal-oriented action, and non-human sounds) lacking social content. These ratings were used as predictors in the fMRI analysis. The posterior superior temporal sulcus (STS) responded to all social features but not to any non-social features, and the anterior STS responded to all social features except bodies and biological motion. We also found four partially segregated, extended networks for processing of specific social signals: (1) a fronto-temporal network responding to multiple social categories, (2) a fronto-parietal network preferentially activated to bodies, motion, and pain, (3) a temporo-amygdalar network responding to faces, social interaction, and speech, and (4) a fronto-insular network responding to pain, emotions, social interactions, and speech. Our results highlight the role of the pSTS in processing multiple aspects of social information, as well as the feasibility and efficiency of fMRI mapping under conditions that resemble the complexity of real life. PMID:22905026

  17. [MRI-based radiotherapy planning].

    PubMed

    Largent, A; Nunes, J-C; Lafond, C; Périchon, N; Castelli, J; Rolland, Y; Acosta, O; de Crevoisier, R

    2017-07-06

    MRI-based radiotherapy planning is a topical subject due to the introduction of a new generation of treatment machines combining a linear accelerator and a MRI. One of the issues for introducing MRI in this task is the lack of information to provide tissue density information required for dose calculation. To cope with this issue, two strategies may be distinguished from the literature. Either a synthetic CT scan is generated from the MRI to plan the dose, or a dose is generated from the MRI based on physical underpinnings. Within the first group, three approaches appear: bulk density mapping assign a homogeneous density to different volumes of interest manually defined on a patient MRI; machine learning-based approaches model local relationship between CT and MRI image intensities from multiple data, then applying the model to a new MRI; atlas-based approaches use a co-registered training data set (CT-MRI) which are registered to a new MRI to create a pseudo CT from spatial correspondences in a final fusion step. Within the second group, physics-based approaches aim at computing the dose directly from the hydrogen contained within the tissues, quantified by MRI. Excepting the physics approach, all these methods generate a synthetic CT called "pseudo CT", on which radiotherapy planning will be finally realized. This literature review shows that atlas- and machine learning-based approaches appear more accurate dosimetrically. Bulk density approaches are not appropriate for bone localization. The fastest methods are machine learning and the slowest are atlas-based approaches. The less automatized are bulk density assignation methods. The physical approaches appear very promising methods. Finally, the validation of these methods is crucial for a clinical practice, in particular in the perspective of adaptive radiotherapy delivered by a linear accelerator combined with an MRI scanner. Copyright © 2017. Published by Elsevier SAS.

  18. 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.

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

    PubMed

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

    2017-01-01

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

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2010-02-01

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

  2. Mapping Tumor Hypoxia In Vivo Using Pattern Recognition of Dynamic Contrast-enhanced MRI Data12

    PubMed Central

    Stoyanova, Radka; Huang, Kris; Sandler, Kiri; Cho, HyungJoon; Carlin, Sean; Zanzonico, Pat B; Koutcher, Jason A; Ackerstaff, Ellen

    2012-01-01

    In solid tumors, hypoxia contributes significantly to radiation and chemotherapy resistance and to poor outcomes. The “gold standard” pO2 electrode measurements of hypoxia in vivo are unsatisfactory because they are invasive and have limited spatial coverage. Here, we present an approach to identify areas of tumor hypoxia using the signal versus time curves of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) data as a surrogate marker of hypoxia. We apply an unsupervised pattern recognition (PR) technique to determine the differential signal versus time curves associated with different tumor microenvironmental characteristics in DCE-MRI data of a preclinical cancer model. Well-perfused tumor areas are identified by rapid contrast uptake followed by rapid washout; hypoxic areas, which are regions of reduced vascularization, are identified by delayed contrast signal buildup and washout; and necrotic areas exhibit slow or no contrast uptake and no discernible washout over the experimental observation. The strength of the PR concept is that it captures the pixel-enhancing behavior in its entirety—during both contrast agent uptake and washout—and thus, subtleties in the temporal behavior of contrast enhancement related to features of the tumor microenvironment (driven by vascular changes) may be detected. The assignment of the tumor compartments/microenvironment to well vascularized, hypoxic, and necrotic is validated by comparison to data previously obtained using complementary imaging modalities. The proposed novel analysis approach has the advantage that it can be readily translated to the clinic, as DCE-MRI is used routinely for the identification of tumors in patients, is widely available, and easily implemented on any clinical magnet. PMID:23326621

  3. 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

  4. Prognostic value of dynamic MRI positive enhancement integral color mapping in osteosynthesis of undisplaced femoral neck fractures.

    PubMed

    Morimoto, Masatoshi; Takahashi, Yoshinori; Kubo, Takahiro; Sugiura, Kosuke; Tamaki, Yasuaki; Toki, Shunichi; Suganuma, Katsuyoshi; Inoue, Kazumasa; Adachi, Keisuke; Chikawa, Takashi; Sairyo, Koichi; Nagamachi, Akihiro

    2017-07-01

    The common treatment for an undisplaced femoral neck fracture is osteosynthesis. Two major complications of osteosynthesis are non-union and late collapse of the femoral head. We speculated that femoral head perfusion is one of the most important factors that affect the outcome of osteosynthesis after femoral neck fracture. We have preoperatively estimated femoral head perfusion by dynamic MRI positive enhancement integral color mapping (PEICM). The purpose of this study was to evaluate the outcomes of undisplaced femoral neck fractures based on PEICM. Sixty-eight patients participated in this prospective study. All patients underwent PEICM in a 1.5-Tesla MRI machine using coronal fast spoiled gradient echo imaging sequences with gadopentetate dimeglumine as the contrast agent. Femoral head perfusion was displayed via color mapping using PEICM. Three types were distinguished. For type A, the color was identical to unaffected side indicated normal perfusion. For type B, the color was darker than unaffected side indicated decreased perfusion. For type C, the color was black indicated complete absence of perfusion. All patients underwent osteosynthesis with three cannulated screws. The rates of non-union and late collapse for each type were calculated. Sixteen patients were classified as Type A, 43 as Type B, and 6 as Type C. The non-union rates were 0% for Type A, 6.7% for Type B, and 50.0% for Type C. The late collapse rates were 0% for Type A, 4.4% for Type B, and 0% for Type C. PEICM precisely detected femoral head perfusion. Primary prosthetic replacement should be considered for older patients with Type C to minimize the chances of revision surgery, even in undisplaced femoral neck fractures. Copyright © 2017 The Japanese Orthopaedic Association. Published by Elsevier B.V. All rights reserved.

  5. Deep Learning for Brain MRI Segmentation: State of the Art and Future Directions.

    PubMed

    Akkus, Zeynettin; Galimzianova, Alfiia; Hoogi, Assaf; Rubin, Daniel L; Erickson, Bradley J

    2017-08-01

    Quantitative analysis of brain MRI is routine for many neurological diseases and conditions and relies on accurate segmentation of structures of interest. Deep learning-based segmentation approaches for brain MRI are gaining interest due to their self-learning and generalization ability over large amounts of data. As the deep learning architectures are becoming more mature, they gradually outperform previous state-of-the-art classical machine learning algorithms. This review aims to provide an overview of current deep learning-based segmentation approaches for quantitative brain MRI. First we review the current deep learning architectures used for segmentation of anatomical brain structures and brain lesions. Next, the performance, speed, and properties of deep learning approaches are summarized and discussed. Finally, we provide a critical assessment of the current state and identify likely future developments and trends.

  6. Directional antennas for electromagnetic mapping in a borehole

    DOEpatents

    Reagor, David Wesley; Nguyen, Doan Ngoc; Ashworth, Stephen Paul

    2017-05-02

    A bottom hole assembly used for a field operation is disclosed herein. The bottom hole assembly can include at least one directional antenna disposed on an outer surface of a first tubing pipe of a tubing string, where the at least one directional antenna receives a first electric current from at least one power source, where the first electric current generates a first magnetic field that radiates from the at least one directional antenna into a formation. The bottom hole assembly can also include at least one receiver disposed on a second tubing pipe of the tubing string, where the at least one receiver receives the first magnetic field returning from the formation.

  7. 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.

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

    PubMed

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

    2008-02-15

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

  9. Mapping the Bilateral Visual Integration by EEG and fMRI

    PubMed Central

    Liu, Zhongming; Zhang, Nanyin; Chen, Wei; He, Bin

    2009-01-01

    In the human visual system, the internal representation of the left and right visual hemifields is split at the midline of the two cerebral hemispheres. The present study aims to address the questions of when and where the lateralized cortical visual representations are merged to form an intact percept by using a multimodal neuroimaging approach. Visual evoked potential (VEP) and functional magnetic resonance imaging (fMRI) data were acquired from a group of healthy subjects presented with unilateral versus bilateral visual stimuli. Cortical activities involved in processing bilateral visual information are expected to be equally responsive to ipsilateral and contralateral stimuli, and demonstrate spatial nonlinearity in the response to bilateral stimuli. Utilizing these features, we performed integrative as well as separate analyses for both VEP and fMRI data. The present results suggest that i) the majority of cortical activity that integrates visual information across hemifields takes place at extrastriate areas during late visual processing, and that ii) the lateral occipito-temporal (LOT) regions (likely the MT+ complex) and the medial occipital cortex (i.e. V1) may contribute to bilateral visual integration during early visual processing. Our findings are generally in agreement with the bottom-up visual hierarchy, with the exception of the evidence suggesting an early activation of the higher-tier LOT areas and the influence from ipsilateral visual inputs upon the V1 response. PMID:19306933

  10. Analysis of event-related fMRI data using diffusion maps.

    PubMed

    Shen, Xilin; Meyer, François G

    2005-01-01

    The blood oxygen level-dependent (BOLD) signal in response to brief periods of stimulus can be detected using event-related functional magnetic resonance imaging (ER-fMRI). In this paper, we propose a new approach for the analysis of ER-fMRI data. We regard the time series as vectors in a high dimensional space (the dimension is the number of time samples). We believe that all activated times series share a common structure and all belong to a low dimensional manifold. On the other hand, we expect the background time series (after detrending) to form a cloud around the origin. We construct an embedding that reveals the organization of the data into an activated manifold and a cluster of non-activated time series. We use a graph partitioning technique-the normalized cut to find the separation between the activated manifold and the background time series. We have conducted several experiments with synthetic and in-vivo data that demonstrate the performance of our approach.

  11. Direct comparison of high-temporal-resolution CINE MRI with Doppler ultrasound for assessment of diastolic dysfunction in mice.

    PubMed

    Roberts, Thomas A; Price, Anthony N; Jackson, Laurence H; Taylor, Valerie; David, Anna L; Lythgoe, Mark F; Stuckey, Daniel J

    2017-10-01

    Diastolic dysfunction is a sensitive early indicator of heart failure and can provide additional data to conventional measures of systolic function. Transmitral Doppler ultrasound, which measures the one-dimensional flow of blood through the mitral valve, is currently the preferred method for the measurement of diastolic function, but the measurement of the left ventricular volume changes using high-temporal-resolution cinematic magnetic resonance imaging (CINE MRI) is an alternative approach which is emerging as a potentially more robust and user-independent technique. Here, we investigated the performance of high-temporal-resolution CINE MRI and compared it with ultrasound for the detection of diastolic dysfunction in a mouse model of myocardial infarction. An in-house, high-temporal-resolution, retrospectively gated CINE sequence was developed with a temporal resolution of 1 ms. Diastolic function in mice was assessed using a custom-made, open-source reconstruction package. Early (E) and late (A) left ventricular filling phases were easily identifiable, and these measurements were compared directly with high-frequency, pulsed-wave, Doppler ultrasound measurements of mitral valve inflow. A repeatability study established that high-temporal-resolution CINE MRI and Doppler ultrasound showed comparable accuracy when measuring E/A in normal control mice. However, when applied in a mouse model of myocardial infarction, high-temporal-resolution CINE MRI indicated diastolic heart failure (E/A = 0.94 ± 0.11), whereas ultrasound falsely detected normal cardiac function (E/A = 1.21 ± 0.11). The addition of high-temporal-resolution CINE MRI to preclinical imaging studies enhances the library of sequences available to cardiac researchers and potentially identifies diastolic heart failure early in disease progression. © 2017 The Authors. NMR in Biomedicine published by John Wiley & Sons Ltd.

  12. Quantitative susceptibility mapping using principles of echo shifting with a train of observations sequence on 1.5T MRI.

    PubMed

    Kan, Hirohito; Arai, Nobuyuki; Kasai, Harumasa; Kunitomo, Hiroshi; Hirose, Yasujiro; Shibamoto, Yuta

    2017-10-01

    To evaluate the accuracy of susceptibility estimated from the principles of echo shifting with a train of observations (PRESTO) sequence using a 1.5T MRI system, we conducted experiments on the human brain using the PRESTO sequence and compared our results with the susceptibility obtained from spoiled gradient-recalled echo (GRE) sequence with flow compensation using quantitative susceptibility mapping (QSM) reconstruction. Experiments on the human brain were conducted on 12 healthy volunteers (27±4years) using PRESTO and spoiled GRE sequences on a 1.5T scanner. The PRESTO sequence is an echo-shifted gradient echo sequence that allows high susceptibility sensitivity and rapid acquisition because of TE>TR compared with the spoiled GRE sequence. QSM analysis was performed on the obtained phase images using the iLSQR method. Estimated susceptibility maps were used for region of interest analyses and estimation of line profiles through iron-rich tissue and major vessels. Our results demonstrated that susceptibility maps were accurately estimated, without error, by QSM analysis of PRESTO and spoiled GRE sequences. Acquisition time in the PRESTO sequence was reduced by 43% compared with that in the spoiled GRE sequence. Differences did exist between susceptibility maps in PRESTO and spoiled GRE sequences for visualization and quantitative values of major blood vessels and the areas around them CONCLUSION: The PRESTO sequence enables correct estimation of tissue susceptibility with rapid acquisition and may be useful for QSM analysis of clinical use of 1.5T scanners. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Fast direct fourier reconstruction of radial and PROPELLER MRI data using the chirp transform algorithm on graphics hardware.

    PubMed

    Feng, Yanqiu; Song, Yanli; Wang, Cong; Xin, Xuegang; Feng, Qianjin; Chen, Wufan

    2013-10-01

    To develop and test a new algorithm for fast direct Fourier transform (DrFT) reconstruction of MR data on non-Cartesian trajectories composed of lines with equally spaced points. The DrFT, which is normally used as a reference in evaluating the accuracy of other reconstruction methods, can reconstruct images directly from non-Cartesian MR data without interpolation. However, DrFT reconstruction involves substantially intensive computation, which makes the DrFT impractical for clinical routine applications. In this article, the Chirp transform algorithm was introduced to accelerate the DrFT reconstruction of radial and Periodically Rotated Overlapping ParallEL Lines with Enhanced Reconstruction (PROPELLER) MRI data located on the trajectories that are composed of lines with equally spaced points. The performance of the proposed Chirp transform algorithm-DrFT algorithm was evaluated by using simulation and in vivo MRI data. After implementing the algorithm on a graphics processing unit, the proposed Chirp transform algorithm-DrFT algorithm achieved an acceleration of approximately one order of magnitude, and the speed-up factor was further increased to approximately three orders of magnitude compared with the traditional single-thread DrFT reconstruction. Implementation the Chirp transform algorithm-DrFT algorithm on the graphics processing unit can efficiently calculate the DrFT reconstruction of the radial and PROPELLER MRI data. Copyright © 2012 Wiley Periodicals, Inc.

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

    PubMed

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

    2011-07-20

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

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

    USGS Publications Warehouse

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

    2015-01-01

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

  16. 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

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

    PubMed

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

    2016-01-01

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

  18. Synthetic quantitative MRI through relaxometry modelling.

    PubMed

    Callaghan, Martina F; Mohammadi, Siawoosh; Weiskopf, Nikolaus

    2016-12-01

    Quantitative MRI (qMRI) provides standardized measures of specific physical parameters that are sensitive to the underlying tissue microstructure and are a first step towards achieving maps of biologically relevant metrics through in vivo histology using MRI. Recently proposed models have described the interdependence of qMRI parameters. Combining such models with the concept of image synthesis points towards a novel approach to synthetic qMRI, in which maps of fundamentally different physical properties are constructed through the use of biophysical models. In this study, the utility of synthetic qMRI is investigated within the context of a recently proposed linear relaxometry model. Two neuroimaging applications are considered. In the first, artefact-free quantitative maps are synthesized from motion-corrupted data by exploiting the over-determined nature of the relaxometry model and the fact that the artefact is inconsistent across the data. In the second application, a map of magnetization transfer (MT) saturation is synthesized without the need to acquire an MT-weighted volume, which directly leads to a reduction in the specific absorption rate of the acquisition. This feature would be particularly important for ultra-high field applications. The synthetic MT map is shown to provide improved segmentation of deep grey matter structures, relative to segmentation using T1 -weighted images or R1 maps. The proposed approach of synthetic qMRI shows promise for maximizing the extraction of high quality information related to tissue microstructure from qMRI protocols and furthering our understanding of the interrelation of these qMRI parameters. © 2016 The Authors. NMR in Biomedicine published by John Wiley & Sons Ltd.

  19. Synthetic quantitative MRI through relaxometry modelling

    PubMed Central

    Mohammadi, Siawoosh; Weiskopf, Nikolaus

    2016-01-01

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

  20. 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.

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

    PubMed

    Bergen, Benjamin K; Chan Lau, Ting Ting

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Seghier, Mohamed L.; Price, Cathy J.

    2016-02-01

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

  3. 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

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

    PubMed Central

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

    2012-01-01

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

  5. Integration of myocardial scar identified by preoperative delayed contrast-enhanced MRI into a high-resolution mapping system for planning and guidance of VT ablation procedures

    NASA Astrophysics Data System (ADS)

    Rettmann, M. E.; Suzuki, A.; Wang, S.; Pottinger, N.; Arter, J.; Netzer, A.; Parker, K.; Viker, K.; Packer, D. L.

    2017-03-01

    Myocardial scarring creates a substrate for reentrant circuits which can lead to ventricular tachycardia. In ventricular catheter ablation therapy, regions of myocardial scarring are targeted to interrupt arrhythmic electrical pathways. Low voltage regions are a surrogate for myocardial scar and are identified by generating an electro anatomic map at the start of the procedure. Recent efforts have focussed on integration of preoperative scar information generated from delayed contrast-enhanced MR imaging to augment intraprocedural information. In this work, we describe an initial feasibility study of integration of a preoperative MRI derived scar maps into a high-resolution mapping system to improve planning and guidance of VT ablation procedures.

  6. In Vivo Lung Morphometry With Hyperpolarized 3He Diffusion MRI: Reproducibility and the Role of Diffusion Sensitizing Gradient Direction

    PubMed Central

    Quirk, James D.; Chang, Yulin V.; Yablonskiy, Dmitriy A.

    2014-01-01

    Purpose Lung morphometry with hyperpolarized gas diffusion MRI is a highly sensitive technique for the non-invasive measurement of acinar microstructural parameters traditionally only accessible by histology. The goal of this work is to establish the reproducibility of these measurements in healthy volunteers and their dependence upon the direction of the applied diffusion-sensitizing gradient. Methods Helium-3 lung morphometry MRI was performed on a total of five healthy subjects. Two subjects received duplicate imaging on the same day and three after a four or twenty-seven month delay to assess reproducibility. Four subjects repeated the measurement during the same session with different diffusion-sensitizing gradient directions to determine the effect on the parameter estimates. Results The helium-3 lung morphometry measurements were reproducible over the short and long term (e.g. % coefficient of variation (CV) of mean chord length, Lm = 2.1% and 2.9% respectively) and across different diffusion gradient directions (Lm % CV = 2.6%). Results also show independence of field inhomogeneity effects at 1.5T. Conclusion Helium-3 lung morphometry is a reproducible technique for measuring acinar microstructure and is effectively independent of the choice of diffusion gradient direction. This provides confidence for the use of this technique to compare populations and treatment efficacy. PMID:24752926

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

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

    PubMed

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

    2011-09-01

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

  9. 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

  10. 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.

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2016-12-01

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

  13. 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.

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

    PubMed

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

    2012-09-07

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2008-01-01

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

  18. MRI-guided transurethral ultrasound therapy of the prostate gland using real-time thermal mapping: initial studies.

    PubMed

    Siddiqui, Kashif; Chopra, Rajiv; Vedula, Siddharth; Sugar, Linda; Haider, Masoom; Boyes, Aaron; Musquera, Mireia; Bronskill, Michael; Klotz, Laurence

    2010-12-01

    To confirm the correlation between planning and thermal injury of the prostate as determined by magnetic resonance imaging (MRI) and histology in canine and humans treated with transurethral ultrasound. Canine studies: 2 sets of in vivo studies were performed under general anesthesia in 1.5 T clinical MRI. Nine dogs were treated using single transducer; 8 dogs were treated using urethral applicator with multiple transducers. Rectal cooling was maintained. After initial imaging, a target boundary was selected and high-intensity ultrasound energy delivered. The spatial temperature distribution was measured continuously every 5 seconds with MR thermometry using the proton-resonant frequency shift method. The goal was to achieve 55 °C at the target boundary. After treatment, the prostate was harvested and fixed with adjoining tissue, including rectum. Temperature maps, anatomical images, and histologic sections were registered to each other and compared. Human studies: To date, 5 patients with localized prostate cancer have been treated immediately before radical prostatectomy. Approximately 30% of the gland volume was targeted. A continuous pattern of thermal coagulation was successfully achieved within the target region, with an average spatial precision of 1-2 mm. Radical prostatectomy was routine, with an uncomplicated postoperative course in all patients. The correlation between anatomical, thermal, and histologic images was ≤3 mm. Treatment time was <30 minutes. No thermal damage to rectal tissue was observed. Thermal ablation within the prescribed target of the prostate has been successfully demonstrated in canine studies. The treatment is also feasible in humans. Copyright © 2010 Elsevier Inc. All rights reserved.

  19. 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.

  20. Direct MRI fistulography with hydrogen peroxide in patients with recurrent perianal fistulas: a new proposal of extended diagnostics.

    PubMed

    Waniczek, Dariusz; Adamczyk, Tomasz; Arendt, Jerzy; Kluczewska, Ewa

    2015-02-10

    Perianal fistulas are malformations of the anorectal area. Accurate preoperative assessment of perianal fistula tract is a main assumption in diagnosis of the disease, affecting the operation efficiency. The aim of the study was to present our experience in application of a new diagnostic protocol based on the magnetic resonance imaging (MRI) examination using a mixture of hydrogen peroxide (HP) and gadolinium as a direct contrast medium in evaluation of recurrent fistulas tract. The method is referred to as HPMRI. The study group consisted of 12 subjects operated on from 2011. Direct HPMRI fistulography was performed in all subjects before the operation. All types of fistulas were precisely evaluated by HPMRI examination. Intraoperative state confirmed complete course of fistulas in 11 cases. In 1 case, an internal opening was not found. We suggest that this new method of direct HPMRI fistulography may improve visualization of the tracts of recurrent fistulas and improve efficacy of surgical procedures.

  1. Motility mapping as evaluation tool for bowel motility: initial results on the development of an automated color-coding algorithm in cine MRI.

    PubMed

    Hahnemann, Maria L; Nensa, Felix; Kinner, Sonja; Gerken, Guido; Lauenstein, Thomas C

    2015-02-01

    To develop and implement an automated algorithm for visualizing and quantifying bowel motility using cine magnetic resonance imaging (MRI). Four healthy volunteers as well as eight patients with suspected or diagnosed inflammatory bowel disease (IBD) underwent MR examinations on a 1.5T scanner. Coronal T2-weighted cine MR images were acquired in healthy volunteers without and with intravenous (i.v.) administration of butylscopolamine. In patients with IBD, cine MRI sequences were collected prior to standard bowel MRI. Bowel motility was assessed using an optical flow algorithm. The resulting motion vector magnitudes were presented as bowel motility maps. Motility changes after i.v. administration of butylscopolamine were measured in healthy volunteers. Inflamed bowel segments in patients were correlated with motility map findings. The acquisition of bowel motility maps was feasible in all subjects examined. In healthy volunteers butylscopolamine led to quantitatively measurable decrease in bowel motility (mean decrease of 59%; P = 0.171). In patients with IBD, visualization of bowel movement by color-coded motility mapping allowed for the detection of segments with abnormal bowel motility. Inflamed bowel segments could be identified by exhibiting a decreased motility. Our method is a feasible and promising approach for the assessment of bowel motility disorders. © 2014 Wiley Periodicals, Inc.

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

    PubMed Central

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

    2013-01-01

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

  3. Mapping of verbal working memory in nonfluent Chinese-English bilinguals with functional MRI.

    PubMed

    Xue, Gui; Dong, Qi; Jin, Zhen; Chen, Chuansheng

    2004-05-01

    Existing cognitive and neural imaging studies have suggested a frontoparietal network of multiple, cooperative components for verbal working memory (WM). We used functional MRI to investigate whether this neural network is also involved in the processing of second language by nonfluent bilinguals. Twelve (five males, seven females) native Chinese speakers who had limited English proficiency were scanned while performing working memory tasks in Chinese and English. They were asked to make judgment continuously whether the word presented on the screen was semantically related to (i.e., the semantic tasks) another word presented two words earlier. On a different task (i.e., the phonological tasks), they were asked to make judgment whether the target word rhymed with the other word. A naming and judgment task in each language was adopted to control for the visual process, initial lexical process, and motor responses. Behavioral data showed that subjects performed better at tasks in their native language (Chinese, L1) than in English (L2). Imaging results showed that all working memory tasks in both L1 and L2 elicited a very similar pattern of left-hemisphere-dominated activation in the dorsolateral prefrontal cortex, pars opercularis region, pars triangularis region, precentral cortex, and parietal lobule. Consistent with the behavioral data, the volume of activation in the left opercularis region, left parietal lobule, and right precentral region was greater for L2 than for L1. These results suggest that working memory in L1 and L2 is mediated by a unitary neural system (i.e., frontoparietal region), which is capable of recruiting surrounding cortical resources to meet the increased computational demand caused by low L2 proficiency.

  4. 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

  5. Scattered PET data for attenuation-map reconstruction in PET/MRI.

    PubMed

    Berker, Yannick; Kiessling, Fabian; Schulz, Volkmar

    2014-10-01

    In hybrid medical imaging devices combining positron emission tomography (PET) with magnetic resonance imaging, PET attenuation correction remains challenging. Known approaches to estimating attenuation (μ-)maps from PET emission data, especially maximum-likelihood reconstruction of activity and attenuation (MLAA), take into account true coincidences only and exhibit two kinds of ambiguities: First, the attenuation sinogram can only be determined up to a constant offset (sinogram ambiguity). Second, the attenuation sinogram is unknown outside of the support of the activity sinogram and does not completely define a μ-map (image-space ambiguity). In this work, the authors aim at using additional information from scattered coincidences to resolve these ambiguities--information that is unavailable using true coincidences. The authors propose a two-level scheme for combining measurements of true and scattered coincidences. On the top level, scatter-to-attenuation (S2A) reconstruction recovers the μ-map from a measurement of scattered coincidences and results available from trues-based algorithms. On the lower level, S2A reconstruction is implemented by iterative scatter simulation and a proposed (simplified) S2A back-projection. The S2A back-projection is based on determining possible scattering locations in image space from energy measurements (via Compton-scattering angles) and summing contributions from scattered coincidences in image space. S2A back-projection is validated with GATE simulations of activity-attenuation configurations with both sinogram and image-space ambiguities. The authors further evaluate the impact of asymmetric source and activity distributions, extended source distributions, and energy uncertainty to demonstrate the limitations of the simplified noniterative S2A back-projection approach. Feasibility of the iterative S2A reconstruction is evaluated in a low-resolution, analytical 2D problem. S2A back-projection of scattered coincidences with

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

    PubMed Central

    Habeck, Christian G.

    2006-01-01

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

  7. 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

  8. 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

  9. Integration of fMRI and MEG functional maps into a CyberKnife planning system: feasibility study for motor activity localization and dose planning.

    PubMed

    De Martin, Elena; Duran, Dunja; Ghielmetti, Francesco; Visani, Elisa; Aquino, Domenico; Marchetti, Marcello; Rossi Sebastiano, Davide; Cusumano, Davide; Bruzzone, Maria Grazia; Panzica, Ferruccio; Fariselli, Laura

    2017-09-20

    Magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI) provide non-invasive localization of eloquent brain areas for pre-surgical planning. The aim of this study is the integration of MEG and fMRI maps into a CyberKnife (CK) system to optimize dose planning. Four patients with brain metastases in the motor area underwent functional imaging study of the hand motor cortex prior radiosurgery. MEG data were acquired during a visually cued hand motor-task. Motor activations were identified also using an fMRI block-designed paradigm. MEG and fMRI maps were then integrated into a CK system and contoured as organs at risk (OARs) for treatment planning optimization. The integration of fMRI data into the CK system was achieved for all patients by means of a standardized protocol. We also implemented an ad hoc pipeline to convert the MEG signal into DICOM standard, to make sure that it was readable by our CyberKnife treatment planning system. Inclusion of the activation areas into the optimization plan allowed the creation of treatment plans which reduced the irradiation of the motor cortex while not affecting the brain peripheral dose. The availability of advanced neuroimaging techniques is playing a more and more important role in radiosurgical planning strategy. We successfully imported MEG and fMRI activations into a CyberKnife system. This additional information can improve dose sparing of eloquent areas, allowing a more comprehensive investigation of the related dose-volume constraints which in theory could translate into a gain in tumor local control and reduction of neurological complications. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Mapping the Organization of Axis of Motion Selective Features in Human Area MT Using High-Field fMRI

    PubMed Central

    De Martino, Federico; van de Moortele, Pierre-Francois; Feinberg, David; Adriany, Gregor; Chaimow, Denis; Shmuel, Amir; Uğurbil, Kamil; Yacoub, Essa

    2011-01-01

    Functional magnetic resonance imaging (fMRI) at high magnetic fields has made it possible to investigate the columnar organization of the human brain in vivo with high degrees of accuracy and sensitivity. Until now, these results have been limited to the organization principles of early visual cortex (V1). While the middle temporal area (MT) has been the first identified extra-striate visual area shown to exhibit a columnar organization in monkeys, evidence of MT's columnar response properties and topographic layout in humans has remained elusive. Research using various approaches suggests similar response properties as in monkeys but failed to provide direct evidence for direction or axis of motion selectivity in human area MT. By combining state of the art pulse sequence design, high spatial resolution in all three dimensions (0.8 mm isotropic), optimized coil design, ultrahigh field magnets (7 Tesla) and novel high resolution cortical grid sampling analysis tools, we provide the first direct evidence for large-scale axis of motion selective feature organization in human area MT closely matching predictions from topographic columnar-level simulations. PMID:22163328

  11. Attenuation correction methods suitable for brain imaging with a PET/MRI scanner: a comparison of tissue atlas and template attenuation map approaches.

    PubMed

    Malone, Ian B; Ansorge, Richard E; Williams, Guy B; Nestor, Peter J; Carpenter, T Adrian; Fryer, Tim D

    2011-07-01

    Modeled attenuation correction (AC) will be necessary for combined PET/MRI scanners not equipped with transmission scanning hardware. We compared 2 modeled AC approaches that use nonrigid registration with rotating (68)Ge rod-based measured AC for 10 subjects scanned with (18)F-FDG. Two MRI and attenuation map pairs were evaluated: tissue atlas-based and measured templates. The tissue atlas approach used a composite of the BrainWeb and Zubal digital phantoms, whereas the measured templates were produced by averaging spatially normalized measured MR image and coregistered attenuation maps. The composite digital phantom was manually edited to include 2 additional tissue classes (paranasal sinuses, and ethmoidal air cells or nasal cavity). In addition, 3 attenuation values for bone were compared. The MRI and attenuation map pairs were used to generate subject-specific attenuation maps via nonrigid registration of the MRI to the MR image of the subject. SPM2 and a B-spline free-form deformation algorithm were used for the nonrigid registration. To determine the accuracy of the modeled AC approaches, radioactivity concentration was assessed on a voxelwise and regional basis. The template approach produced better spatial consistency than the phantom-based atlas, with an average percentage error in radioactivity concentration across the regions, compared with measured AC, of -1.2% ± 1.2% and -1.5% ± 1.9% for B-spline and SPM2 registration, respectively. In comparison, the tissue atlas method with B-spline registration produced average percentage errors of 0.0% ± 3.0%, 0.9% ± 2.9%, and 2.9% ± 2.8% for bone attenuation values of 0.143 cm(-1), 0.152 cm(-1), and 0.172 cm(-1), respectively. The largest errors for the template AC method were found in parts of the frontal cortex (-3%) and the cerebellar vermis (-5%). Intersubject variability was higher with SPM2 than with B-spline. Compared with measured AC, template AC with B-spline and SPM2 achieved a correlation

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

    PubMed

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

    2014-04-15

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

  13. Validation of Sodium MRI of Intervertebral Disc

    PubMed Central

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

    2009-01-01

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

  14. 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.

  15. 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

  16. Mapping strain exerted on blood vessel walls using deuterium double-quantum-filtered MRI

    PubMed Central

    Sharf, Yehuda; Seo, Yoshiteru; Eliav, Uzi; Akselrod, Solang; Navon, Gil

    1998-01-01

    A technique is described for displaying distinct tissue layers of large blood vessel walls as well as measuring their mechanical strain. The technique is based on deuterium double-quantum-filtered (DQF) spectroscopic imaging. The effectiveness of the double-quantum filtration in suppressing the signal of bulk water is demonstrated on a phantom consisting of rat tail tendon fibers. Only intrafibrillar water is displayed, excluding all other signals of water molecules that reorient isotropically. One- and two-dimensional spectroscopic imaging of bovine aorta and coronary arteries show the characteristic DQF spectrum of each of the tissue layers. This property is used to obtain separate images of the outer layer, the tunica adventitia, or the intermediate layer, the tunica media, or both. To visualize the effect of elongation, the average residual quadrupole splitting <Δνq> is calculated for each pixel. Two-dimensional deuterium quadrupolar splitting images are obtained for a fully relaxed and a 55% elongated sample of bovine coronary artery. These images indicate that the strong effect of strain is associated with water molecules in the tunica adventitia whereas the DQF NMR signal of water in the tunica media is apparently strain-insensitive. After appropriate calibration, these average quadrupolar splitting images can be interpreted as strain maps. PMID:9539698

  17. Mapping strain exerted on blood vessel walls using deuterium double-quantum-filtered MRI.

    PubMed

    Sharf, Y; Seo, Y; Eliav, U; Akselrod, S; Navon, G

    1998-04-14

    A technique is described for displaying distinct tissue layers of large blood vessel walls as well as measuring their mechanical strain. The technique is based on deuterium double-quantum-filtered (DQF) spectroscopic imaging. The effectiveness of the double-quantum filtration in suppressing the signal of bulk water is demonstrated on a phantom consisting of rat tail tendon fibers. Only intrafibrillar water is displayed, excluding all other signals of water molecules that reorient isotropically. One- and two-dimensional spectroscopic imaging of bovine aorta and coronary arteries show the characteristic DQF spectrum of each of the tissue layers. This property is used to obtain separate images of the outer layer, the tunica adventitia, or the intermediate layer, the tunica media, or both. To visualize the effect of elongation, the average residual quadrupole splitting is calculated for each pixel. Two-dimensional deuterium quadrupolar splitting images are obtained for a fully relaxed and a 55% elongated sample of bovine coronary artery. These images indicate that the strong effect of strain is associated with water molecules in the tunica adventitia whereas the DQF NMR signal of water in the tunica media is apparently strain-insensitive. After appropriate calibration, these average quadrupolar splitting images can be interpreted as strain maps.

  18. Variance decomposition of MRI-based covariance maps using genetically informative samples and structural equation modeling.

    PubMed

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

    2009-08-01

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

  19. PET/MRI in the Presence of Metal Implants: Completion of the Attenuation Map from PET Emission Data.

    PubMed

    Fuin, Niccolo; Pedemonte, Stefano; Catalano, Onofrio A; Izquierdo-Garcia, David; Soricelli, Andrea; Salvatore, Marco; Heberlein, Keith; Hooker, Jacob M; Van Leemput, Koen; Catana, Ciprian

    2017-05-01

    We present a novel technique for accurate whole-body attenuation correction in the presence of metallic endoprosthesis, on integrated non-time-of-flight (non-TOF) PET/MRI scanners. The proposed implant PET-based attenuation map completion (IPAC) method performs a joint reconstruction of radioactivity and attenuation from the emission data to determine the position, shape, and linear attenuation coefficient (LAC) of metallic implants. Methods: The initial estimate of the attenuation map was obtained using the MR Dixon method currently available on the Siemens Biograph mMR scanner. The attenuation coefficients in the area of the MR image subjected to metal susceptibility artifacts are then reconstructed from the PET emission data using the IPAC algorithm. The method was tested on 11 subjects presenting 13 different metallic implants, who underwent CT and PET/MR scans. Relative mean LACs and Dice similarity coefficients were calculated to determine the accuracy of the reconstructed attenuation values and the shape of the metal implant, respectively. The reconstructed PET images were compared with those obtained using the reference CT-based approach and the Dixon-based method. Absolute relative change (aRC) images were generated in each case, and voxel-based analyses were performed. Results: The error in implant LAC estimation, using the proposed IPAC algorithm, was 15.7% ± 7.8%, which was significantly smaller than the Dixon- (100%) and CT- (39%) derived values. A mean Dice similarity coefficient of 73% ± 9% was obtained when comparing the IPAC- with the CT-derived implant shape. The voxel-based analysis of the reconstructed PET images revealed quantification errors (aRC) of 13.2% ± 22.1% for the IPAC- with respect to CT-corrected images. The Dixon-based method performed substantially worse, with a mean aRC of 23.1% ± 38.4%. Conclusion: We have presented a non-TOF emission-based approach for estimating the attenuation map in the presence of metallic implants, to

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

    PubMed Central

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

    1995-01-01

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

  1. Mental maze solving: directional fMRI tuning and population coding in the superior parietal lobule.

    PubMed

    Gourtzelidis, Pavlos; Tzagarakis, Charidimos; Lewis, Scott M; Crowe, David A; Auerbach, Edward; Jerde, Trenton A; Uğurbil, Kâmil; Georgopoulos, Apostolos P

    2005-09-01

    The superior parietal lobule (SPL) of six human subjects was imaged at 4 T during mental traversing of a directed maze path. Here we demonstrate the orderly involvement of the SPL in this function, as follows. Forty-two percent of the voxels were tuned with respect to the direction of the maze path. This suggests a coherent tuning of local neuronal populations contributing to the change of the single-voxel BOLD signal. Preferred directions ranged throughout the directional continuum of 360 degrees. Voxels with similar preferred directions tended to cluster together: on average there were seven same-direction clusters per slice, with an average cluster membership of five voxels/cluster and an average nearest-neighbor same-direction intercluster distance of 13.1 mm. On the other hand, the average nearest-neighbor intercluster distance between a given direction and all other directions was 3.1 mm. This suggests a patchy arrangement such that patches of directionally tuned voxels, containing voxels with different preferred directions, alternate with patches of non-tuned voxels. Finally, the population vector predicted accurately the direction of the maze path (with an error of 12.7 degrees), and provided good estimates (with an error of 29 degrees) when calculated within parts of the SPL. Altogether, these findings document a new, orderly functional organization of the SPL with respect to mental tracing.

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

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  3. Stimulus-response mappings shape inhibition processes: a combined EEG-fMRI study of contextual stopping.

    PubMed

    Lavallee, Christina F; Herrmann, Christoph S; Weerda, Riklef; Huster, René J

    2014-01-01

    Humans are rarely faced with one simple task, but are typically confronted with complex stimulus constellations and varying stimulus-relevance in a given situation. Through modifying the prototypical stop-signal task and by combined recording and analysis of electroencephalography (EEG) and functional magnetic resonance imaging (fMRI), we studied the effects of stimulus relevance for the generation of a response or its inhibition. Stimulus response mappings were modified by contextual cues, indicating which of two different stimuli following a go stimulus was relevant for stopping. Overall, response inhibition, that is comparing successful stopping to a stop-signal against go-signal related processes, was associated with increased activity in right inferior and left midfrontal regions, as well as increased EEG delta and theta power; however, stimulus-response conditions in which the most infrequent stop-signal was relevant for inhibition, were associated with decreased activity in regions typically involved in response inhibition, as well as decreased activity in the delta and theta bands as compared to conditions wherein the relevant stop-signal frequency was higher. Behaviorally, this (aforementioned) condition, which demanded inhibition only from the most infrequent stimulus, was also associated with reduced reaction times and lower error rates. This pattern of results does not align with typical stimulus frequency-driven findings and suggests interplay between task relevance and stimulus frequency of the stop-signal. Moreover, with a multimodal EEG-fMRI analysis, we demonstrated significant parameterization for response inhibition with delta, theta and beta time-frequency values, which may be interpreted as reflecting conflict monitoring, evaluative and/or motor processes as suggested by previous work (Huster et al., 2013; Aron, 2011). Further multimodal results suggest a possible neurophysiological and behavioral benefit under conditions whereby the most

  4. Effects of b-value and number of gradient directions on diffusion MRI measures obtained with Q-ball imaging

    NASA Astrophysics Data System (ADS)

    Schilling, Kurt G.; Nath, Vishwesh; Blaber, Justin; Harrigan, Robert L.; Ding, Zhaohua; Anderson, Adam W.; Landman, Bennett A.

    2017-02-01

    High-angular-resolution diffusion-weighted imaging (HARDI) MRI acquisitions have become common for use with higher order models of diffusion. Despite successes in resolving complex fiber configurations and probing microstructural properties of brain tissue, there is no common consensus on the optimal b-value and number of diffusion directions to use for these HARDI methods. While this question has been addressed by analysis of the diffusion-weighted signal directly, it is unclear how this translates to the information and metrics derived from the HARDI models themselves. Using a high angular resolution data set acquired at a range of b-values, and repeated 11 times on a single subject, we study how the b-value and number of diffusion directions impacts the reproducibility and precision of metrics derived from Q-ball imaging, a popular HARDI technique. We find that Q-ball metrics associated with tissue microstructure and white matter fiber orientation are sensitive to both the number of diffusion directions and the spherical harmonic representation of the Q-ball, and often are biased when under sampled. These results can advise researchers on appropriate acquisition and processing schemes, particularly when it comes to optimizing the number of diffusion directions needed for metrics derived from Q-ball imaging.

  5. 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.

  6. Force-activatable biosensor enables single platelet force mapping directly by fluorescence imaging.

    PubMed

    Wang, Yongliang; LeVine, Dana N; Gannon, Margaret; Zhao, Yuanchang; Sarkar, Anwesha; Hoch, Bailey; Wang, Xuefeng

    2017-09-08

    Integrin-transmitted cellular forces are critical for platelet adhesion, activation, aggregation and contraction during hemostasis and thrombosis. Measuring and mapping single platelet forces are desired in both research and clinical applications. Conventional force-to-strain based cell traction force microscopies have low resolution which is not ideal for cellular force mapping in small platelets. To enable platelet force mapping with submicron resolution, we developed a force-activatable biosensor named integrative tension sensor (ITS) which directly converts molecular tensions to fluorescent signals, therefore enabling cellular force mapping directly by fluorescence imaging. With ITS, we mapped cellular forces in single platelets at 0.4µm resolution. We found that platelet force distribution has strong polarization which is sensitive to treatment with the anti-platelet drug tirofiban, suggesting that the ITS force map can report anti-platelet drug efficacy. The ITS also calibrated integrin molecular tensions in platelets and revealed two distinct tension levels: 12-54 piconewton (nominal values) tensions generated during platelet adhesion and tensions above 54 piconewton generated during platelet contraction. Overall, the ITS is a powerful biosensor for the study of platelet mechanobiology, and holds great potential in antithrombotic drug development and assessing platelet activity in health and disease. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Investigating Focal Connectivity Deficits in Alzheimer's Disease Using Directional Brain Networks Derived from Resting-State fMRI

    PubMed Central

    Zhao, Sinan; Rangaprakash, D; Venkataraman, Archana; Liang, Peipeng; Deshpande, Gopikrishna

    2017-01-01

    Connectivity analysis of resting-state fMRI has been widely used to identify biomarkers of Alzheimer's disease (AD) based on brain network aberrations. However, it is not straightforward to interpret such connectivity results since our understanding of brain functioning relies on regional properties (activations and morphometric changes) more than connections. Further, from an interventional standpoint, it is easier to modulate the activity of regions (using brain stimulation, neurofeedback, etc.) rather than connections. Therefore, we employed a novel approach for identifying focal directed connectivity deficits in AD compared to healthy controls. In brief, we present a model of directed connectivity (using Granger causality) that characterizes the coupling among different regions in healthy controls and Alzheimer's disease. We then characterized group differences using a (between-subject) generative model of pathology, which generates latent connectivity variables that best explain the (within-subject) directed connectivity. Crucially, our generative model at the second (between-subject) level explains connectivity in terms of local or regionally specific abnormalities. This allows one to explain disconnections among multiple regions in terms of regionally specific pathology; thereby offering a target for therapeutic intervention. Two foci were identified, locus coeruleus in the brain stem and right orbitofrontal cortex. Corresponding disrupted connectivity network associated with the foci showed that the brainstem is the critical focus of disruption in AD. We further partitioned the aberrant connectomic network into four unique sub-networks, which likely leads to symptoms commonly observed in AD. Our findings suggest that fMRI studies of AD, which have been largely cortico-centric, could in future investigate the role of brain stem in AD. PMID:28729831

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

    PubMed

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

    2017-02-14

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

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

    PubMed

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

    2016-10-01

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

  10. 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

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

    PubMed

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

    2015-04-01

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

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

    PubMed

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

    2014-04-15

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

  13. 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

  14. 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

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

    PubMed

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

    2014-09-01

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

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

    PubMed

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

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

  17. Direct method for video-based navigation using a digital terrain map.

    PubMed

    Lerner, Ronen; Rivlin, Ehud

    2011-02-01

    A novel vision-based navigation algorithm is proposed. The gray levels of two images, together with a Digital Terrain Map (DTM), are directly utilized to define constraints on the navigation parameters. The feasibility of the algorithm is examined both under a simulated environment and using real flight data.

  18. Direction-specific fMRI adaptation reveals the visual cortical network underlying the "Rotating Snakes" illusion.

    PubMed

    Ashida, Hiroshi; Kuriki, Ichiro; Murakami, Ikuya; Hisakata, Rumi; Kitaoka, Akiyoshi

    2012-07-16

    The "Rotating Snakes" figure elicits a clear sense of anomalous motion in stationary repetitive patterns. We used an event-related fMRI adaptation paradigm to investigate cortical mechanisms underlying the illusory motion. Following an adapting stimulus (S1) and a blank period, a probe stimulus (S2) that elicited illusory motion either in the same or in the opposite direction was presented. Attention was controlled by a fixation task, and control experiments precluded explanations in terms of artefacts of local adaptation, afterimages, or involuntary eye movements. Recorded BOLD responses were smaller for S2 in the same direction than S2 in the opposite direction in V1-V4, V3A, and MT+, indicating direction-selective adaptation. Adaptation in MT+ was correlated with adaptation in V1 but not in V4. With possible downstream inheritance of adaptation, it is most likely that adaptation predominantly occurred in V1. The results extend our previous findings of activation in MT+ (I. Kuriki, H. Ashida, I. Murakami, and A. Kitaoka, 2008), revealing the activity of the cortical network for motion processing from V1 towards MT+. This provides evidence for the role of front-end motion detectors, which has been assumed in proposed models of the illusion. Copyright © 2012 Elsevier Inc. All rights reserved.

  19. Diffusion-direction-dependent imaging: a novel MRI approach for peripheral nerve imaging.

    PubMed

    Skorpil, Mikael; Engström, Mathias; Nordell, Anders

    2007-04-01

    A novel magnetic resonance imaging approach, called diffusion-direction-dependent imaging (DDI), is introduced. Due to inherent anisotropic diffusion properties, peripheral nerves can be visualized on diffusion tensor imaging (DTI). The largest signal attenuation on DTI correlates with the direction of a nerve fiber, and the least signal attenuation correlates with the direction perpendicular to the nerve fiber. Since low signal-to-noise ratio is a concern in peripheral nerve DTI, we explored a new approach focusing on the perpendicular diffusion direction. A 36-gradient diffusion direction scheme was used. A mean expected curve specific for peripheral nerves was calculated based on the sciatic nerve and its division into the common peroneal nerve and the tibial nerve in three healthy volunteers. By a simple postprocessing method, a comparison of the mean expected curve and the measured curve was made voxel by voxel, and the sciatic nerve and its division were reconstructed, excluding other tissues. More studies are needed to investigate whether other postprocessing methods or other diffusion direction schemes are more suited for peripheral nerve imaging with DDI. Further studies may also be of interest to investigate whether DDI can be a complementary method to conventional T(1)-weighted and T(2)-weighted sequences in the imaging of peripheral nerve pathology or even in the visualization of other tissues, possibly with different diffusion direction schemes.

  20. Heart MRI

    MedlinePlus

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

  1. 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.

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

    PubMed

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

    2016-08-12

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

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

    PubMed

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

    2011-01-01

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

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

    PubMed Central

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

    2011-01-01

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

  5. 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.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2007-11-01

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

  8. MAPS – a Magic Angle Positioning System for Enhanced Imaging in High-Field Small-Bore MRI

    PubMed Central

    Squires, Alexander; Chan, Kevin C.; Ho, Leon C.; Sigal, Ian A.; Jan, Ning-Jiun

    2016-01-01

    The “magic angle” MRI effect can enhance signal intensity in aligned collagenous structures oriented at approximately 55° with respect to the main magnetic field. The difficulty of positioning tissue inside closed-bore scanners has hampered magic angle use in research and clinics. An MRI-conditional mechatronic system has been developed to control sample orientation inside a 9.4T small bore MRI scanner. The system orients samples to within 0.5° and enables a 600% increase in tendon signal intensity. PMID:28713864

  9. MAPS - a Magic Angle Positioning System for Enhanced Imaging in High-Field Small-Bore MRI.

    PubMed

    Squires, Alexander; Chan, Kevin C; Ho, Leon C; Sigal, Ian A; Jan, Ning-Jiun; Tse, Zion Tsz Ho

    2016-03-01

    The "magic angle" MRI effect can enhance signal intensity in aligned collagenous structures oriented at approximately 55° with respect to the main magnetic field. The difficulty of positioning tissue inside closed-bore scanners has hampered magic angle use in research and clinics. An MRI-conditional mechatronic system has been developed to control sample orientation inside a 9.4T small bore MRI scanner. The system orients samples to within 0.5° and enables a 600% increase in tendon signal intensity.

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

    PubMed

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

    2017-07-15

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

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

    PubMed

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

    2013-03-01

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

  12. Population average T2 MRI maps reveal quantitative regional transformations in the degenerating rabbit intervertebral disc that vary by lumbar level.

    PubMed

    Martin, John T; Collins, Christopher M; Ikuta, Kensuke; Mauck, Robert L; 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 fitting the NP region of the T2 maps with modified 2-D and 3-D Gaussian distribution functions. 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. © 2014 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

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

    PubMed Central

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

    2014-01-01

    Abstract The aim of this study was to evaluate the efficacy of mosaicplasty with tissue-engineered cartilage for the treatment of osteochondral defects in a pig model with advanced MR technique. Eight adolescent miniature pigs were used. The right knee underwent mosaicplasty with tissue-engineered cartilage for treatment of focal osteochondral defects, while the left knee was repaired via single mosaicplasty as controls. At 6, 12, 18 and 26 weeks after surgery, repair tissue was evaluated by magnetic resonance imaging (MRI) with the cartilage repair tissue (MOCART) scoring system and T2 mapping. Then, the results of MRI for 26 weeks were compared with findings of macroscopic and histologic studies. The MOCART scores showed that the repaired tissue of the tissue-engineered cartilage group was statistically better than that of controls (P < 0.001). A significant correlation was found between macroscopic and MOCART scores (P < 0.001). Comparable mean T2 values were found between adjacent cartilage and repair tissue in the experimental group (P > 0.05). For zonal T2 value evaluation, there were no significant zonal T2 differences for repair tissue in controls (P > 0.05). For the experimental group, zonal T2 variation was found in repair tissue (P < 0.05). MRI, macroscopy and histology showed better repair results and bony incorporation in mosaicplasty with the tissue-engineered cartilage group than those of the single mosaicplasty group. Mosaicplasty with the tissue-engineered cartilage is a promising approach to repair osteochodndral defects. Morphological MRI and T2 mapping provide a non-invasive method for monitoring the maturation and integration of cartilage repair tissue in vivo. PMID:25050115

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

    PubMed

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

    2014-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

  16. Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry

    PubMed Central

    Vranken, Charlotte; Deen, Jochem; Dirix, Lieve; Stakenborg, Tim; Dehaen, Wim; Leen, Volker; Hofkens, Johan; Neely, Robert K.

    2014-01-01

    We demonstrate an approach to optical DNA mapping, which enables near single-molecule characterization of whole bacteriophage genomes. Our approach uses a DNA methyltransferase enzyme to target labelling to specific sites and copper-catalysed azide-alkyne cycloaddition to couple a fluorophore to the DNA. We achieve a labelling efficiency of ∼70% with an average labelling density approaching one site every 500 bp. Such labelling density bridges the gap between the output of a typical DNA sequencing experiment and the long-range information derived from traditional optical DNA mapping. We lay the foundations for a wider-scale adoption of DNA mapping by screening 11 methyltransferases for their ability to direct sequence-specific DNA transalkylation; the first step of the DNA labelling process and by optimizing reaction conditions for fluorophore coupling via a click reaction. Three of 11 enzymes transalkylate DNA with the cofactor we tested (a readily prepared s-adenosyl-l-methionine analogue). PMID:24452797

  17. Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry.

    PubMed

    Vranken, Charlotte; Deen, Jochem; Dirix, Lieve; Stakenborg, Tim; Dehaen, Wim; Leen, Volker; Hofkens, Johan; Neely, Robert K

    2014-04-01

    We demonstrate an approach to optical DNA mapping, which enables near single-molecule characterization of whole bacteriophage genomes. Our approach uses a DNA methyltransferase enzyme to target labelling to specific sites and copper-catalysed azide-alkyne cycloaddition to couple a fluorophore to the DNA. We achieve a labelling efficiency of ∼70% with an average labelling density approaching one site every 500 bp. Such labelling density bridges the gap between the output of a typical DNA sequencing experiment and the long-range information derived from traditional optical DNA mapping. We lay the foundations for a wider-scale adoption of DNA mapping by screening 11 methyltransferases for their ability to direct sequence-specific DNA transalkylation; the first step of the DNA labelling process and by optimizing reaction conditions for fluorophore coupling via a click reaction. Three of 11 enzymes transalkylate DNA with the cofactor we tested (a readily prepared s-adenosyl-l-methionine analogue).

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

    SciTech Connect

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

    2015-06-15

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

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

    PubMed Central

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

    2000-01-01

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

 PMID:10990503

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

    PubMed

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

    2015-09-01

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

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

    PubMed

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

    2003-11-01

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

  3. A novel, general-purpose, MR-compatible, manually actuated robotic manipulation system for minimally invasive interventions under direct MRI guidance.

    PubMed

    Christoforou, Eftychios G; Seimenis, Ioannis; Andreou, Eleni; Eracleous, Eleni; Tsekos, Nikolaos V

    2014-03-01

    Performing minimally invasive interventions under direct MRI guidance offers significant advantages. Required accessibility to the patient inside the MRI scanner is fairly limited, and employment of robotic assistance has been proposed. The development of MR-compatible robotic systems entails engineering challenges related to geometric constraints and the magnetic nature of the scanning environment. A novel, general-purpose, MR-compatible robotic manipulation system has been developed for the performance of minimally invasive interventions inside a cylindrical scanner under direct MRI guidance. The system is endowed with five degrees of freedom (DOF), is characterized by a unique kinematics structure and is manually actuated. The prototype system was shown to exhibit the required MR-compatibility characteristics and a task-space positioning ability of approximately 5 mm. Needle targeting testing demonstrated a 93% success rate in acquiring a 5 mm spherical target. Phantom testing was performed inside a 3 T scanner and results are reported for an experimental study simulating MRI-guided, manipulator-assisted, MR arthrography. Robotic assistance provided by the developed manipulator may effectively facilitate the performance of various MRI-guided, minimally invasive interventions inside a cylindrical scanner. Copyright © 2013 John Wiley & Sons, Ltd.

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

    NASA Astrophysics Data System (ADS)

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

    2003-01-01

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

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

    PubMed

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

    2013-11-27

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

  6. 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

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

    PubMed

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

    2012-11-01

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

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

    SciTech Connect

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

    2006-10-15

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

  9. Direct Push Optical Screening Tool for High-Resolution, Real-Time Mapping of Chlorinated Solvent DNAPL Architecture

    DTIC Science & Technology

    2016-04-01

    FINAL REPORT Direct Push Optical Screening Tool for High-Resolution, Real- Time Mapping of Chlorinated Solvent DNAPL Architecture ESTCP Project ER...Direct Push Optical Screening Tool for High Resolution, Real-time Mapping of Chlorinated Solvent DNAPL Architecture Murray Einarson Haley...for real-time, high-resolution mapping of petroleum hydrocarbon and coal tar-based NAPL source zones. The objective of this project is to demonstrate

  10. Direct Push Optical Screening Tool for High Resolution, Real-Time Mapping of Chlorinated Solvent DNAPL Architecture

    DTIC Science & Technology

    2016-07-01

    ER-201121) Direct Push Optical Screening Tool for High- Resolution, Real-Time Mapping of Chlorinated Solvent DNAPL Architecture July 2016 This...Report April 2011 - March 2016 Direct Push Optical Screening Tool for High Resolution, Real-time Mapping of Chlorinated Solvent DNAPL Architecture...tools are currently available for real-time, high-resolution mapping of petroleum hydrocarbon and coal tar-based NAPL source zones. The objective of

  11. Head MRI

    MedlinePlus

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

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

    PubMed

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

    2014-01-01

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

  13. 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

  14. Mapping and direct valuation: do they give equivalent EQ-5D-5L index scores?

    PubMed

    Luo, Nan; Cheung, Yin Bun; Ng, Raymond; Lee, Chun Fan

    2015-10-05

    Utility values of health states defined by health-related quality of life instruments can be derived from either direct valuation ('valuation-derived') or mapping ('mapping-derived'). This study aimed to compare the utility-based EQ-5D-5L index scores derived from the two approaches as a means to validating the mapping function developed by van Hout et al for the EQ-5D-5L instrument. This was an observational study of 269 breast cancer patients whose EQ-5D-5L index scores were derived from both methods. For comparing discriminatory ability and responsiveness to change, multivariable regression models were used to estimate the effect sizes of various health indicators on the index scores. Agreement and test-retest reliability were examined using intraclass correlation coefficient (ICC). Whenever appropriate, the 90% confidence intervals (90% CI) were compared to predefined equivalence margins. The mean difference in and ICC between the valuation- and mapping-derived EQ-5D-5L index scores were 0.015 (90% CI = 0.006 to 0.024) and 0.915, respectively. Discriminatory ability and responsiveness of the two indices were equivalent in 13 of 15 regression analyses. However, the mapping-derived index score was lower than the valuation-derived index score in patients experiencing extreme health problems, and the test-retest reliability of the former was lower than the latter, for example, their ICCs differed by 0.121 (90% CI = 0.051 to 0.198) in patients who reported no change in performance status in the follow-up survey. This study provided the first evidence supporting the validity of the mapping function for converting EQ-5D-5L profile data into a utility-based index score.

  15. A Non-Parametric Approach for the Activation Detection of Block Design fMRI Simulated Data Using Self-Organizing Maps and Support Vector Machine

    PubMed Central

    Bahrami, Sheyda; Shamsi, Mousa

    2017-01-01

    Functional magnetic resonance imaging (fMRI) is a popular method to probe the functional organization of the brain using hemodynamic responses. In this method, volume images of the entire brain are obtained with a very good spatial resolution and low temporal resolution. However, they always suffer from high dimensionality in the face of classification algorithms. In this work, we combine a support vector machine (SVM) with a self-organizing map (SOM) for having a feature-based classification by using SVM. Then, a linear kernel SVM is used for detecting the active areas. Here, we use SOM for feature extracting and labeling the datasets. SOM has two major advances: (i) it reduces dimension of data sets for having less computational complexity and (ii) it is useful for identifying brain regions with small onset differences in hemodynamic responses. Our non-parametric model is compared with parametric and non-parametric methods. We use simulated fMRI data sets and block design inputs in this paper and consider the contrast to noise ratio (CNR) value equal to 0.6 for simulated datasets. fMRI simulated dataset has contrast 1–4% in active areas. The accuracy of our proposed method is 93.63% and the error rate is 6.37%. PMID:28840116

  16. A Non-Parametric Approach for the Activation Detection of Block Design fMRI Simulated Data Using Self-Organizing Maps and Support Vector Machine.

    PubMed

    Bahrami, Sheyda; Shamsi, Mousa

    2017-01-01

    Functional magnetic resonance imaging (fMRI) is a popular method to probe the functional organization of the brain using hemodynamic responses. In this method, volume images of the entire brain are obtained with a very good spatial resolution and low temporal resolution. However, they always suffer from high dimensionality in the face of classification algorithms. In this work, we combine a support vector machine (SVM) with a self-organizing map (SOM) for having a feature-based classification by using SVM. Then, a linear kernel SVM is used for detecting the active areas. Here, we use SOM for feature extracting and labeling the datasets. SOM has two major advances: (i) it reduces dimension of data sets for having less computational complexity and (ii) it is useful for identifying brain regions with small onset differences in hemodynamic responses. Our non-parametric model is compared with parametric and non-parametric methods. We use simulated fMRI data sets and block design inputs in this paper and consider the contrast to noise ratio (CNR) value equal to 0.6 for simulated datasets. fMRI simulated dataset has contrast 1-4% in active areas. The accuracy of our proposed method is 93.63% and the error rate is 6.37%.

  17. Characterization and mapping of dipolar interactions within macromolecules in tissues using a combination of DQF, MT and UTE MRI.

    PubMed

    Eliav, Uzi; Komlosh, Michal; Basser, Peter J; Navon, Gil

    2012-10-01

    This study shows that by combining a double-quantum filtered magnetization transfer (DQF-MT) with an ultra-short TE (UTE) MRI that it is possible to obtain contrast between tissue compartments based on the following characteristics: (a) the residual dipolar coupling interaction within the biomacromolecules, which depends on their structure, (b) residual dipolar interactions within water molecules, and (c) the magnetization exchange rate between biomacromolecules and water. The technique is demonstrated in rat-tail specimens, where the collagenous tissue such as tendons and the annulus pulposus of the disc are highlighted in these images, and their macromolecular properties along with those of bones and muscles can be characterized. DQF-MT UTE MRI also holds promise because collagenous tissues that are typically invisible in conventional MRI experiments produce significant signal intensities using this approach. Copyright © 2012 John Wiley & Sons, Ltd.

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

    PubMed Central

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

    2016-01-01

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

  19. fMRI activities in the emotional cerebellum: a preference for negative stimuli and goal-directed behavior.

    PubMed

    Schraa-Tam, Caroline K L; Rietdijk, Willem J R; Verbeke, Willem J M I; Dietvorst, Roeland C; van den Berg, Wouter E; Bagozzi, Richard P; De Zeeuw, Chris I

    2012-03-01

    Several studies indicate that the cerebellum might play a role in experiencing and/or controlling emphatic emotions, but it remains to be determined whether there is a distinction between positive and negative emotions, and, if so, which specific parts of the cerebellum are involved in these types of emotions. Here, we visualized activations of the cerebellum and extracerebellar regions using high-field fMRI, while we asked participants to observe and imitate images with pictures of human faces expressing different emotional states or with moving geometric shapes as control. The state of the emotions could be positive (happiness and surprise), negative (anger and disgust), or neutral. The positive emotional faces only evoked mild activations of crus 2 in the cerebellum, whereas the negative emotional faces evoked prominent activations in lobules VI and VIIa in its hemispheres and lobules VIII and IX in the vermis. The cerebellar activations associated with negative emotions occurred concomitantly with activations of mirror neuron domains such as the insula and amygdala. These data suggest that the potential role of the cerebellum in control of emotions may be particularly relevant for goal-directed behavior that is required for observing and reacting to another person's (negative) expressions.

  20. [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.

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

    PubMed

    Wixted, John T; Mickes, Laura

    2013-01-01

    In this article, we ask about the contribution of fMRI data to our understanding of theories of cognition and about the contribution of theories of cognition to our understanding of fMRI data. Experiments using fMRI can contribute to our understanding of cognition when they are designed to test the predictions of a particular cognitive theory. Although not all cognitive theories make clear predictions about patterns of activity in the brain fMRI experiments are often well suited to testing the predictions of those that do. However, many fMRI studies that are concerned with cognitive functional neuroanatomy are not designed to test predictions of cognitive theories but are instead designed to investigate the role played by different regions of the brain in cognitive activity. These fMRI studies do not shed light on cognitive theories but instead depend on cognitive theories to interpret the data-an interpretation that is only as valid as the cognitive theory on which it is based. These considerations suggest that the relationship between fMRI and theories of cognition is a two-way street. © The Author(s) 2013.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  4. Visual attention and action: How cueing, direct mapping, and social interactions drive orienting.

    PubMed

    Atkinson, Mark A; Simpson, Andrew A; Cole, Geoff G

    2017-08-14

    Despite considerable interest in both action perception and social attention over the last 2 decades, there has been surprisingly little investigation concerning how the manual actions of other humans orient visual attention. The present review draws together studies that have measured the orienting of attention, following observation of another's goal-directed action. Our review proposes that, in line with the literature on eye gaze, action is a particularly strong orienting cue for the visual system. However, we additionally suggest that action may orient visual attention using mechanisms, which gaze direction does not (i.e., neural direct mapping and corepresentation). Finally, we review the implications of these gaze-independent mechanisms for the study of attention to action. We suggest that our understanding of attention to action may benefit from being studied in the context of joint action paradigms, where the role of higher level action goals and social factors can be investigated.

  5. 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.

  6. FreeSurfer-Initiated Fully-Automated Subcortical Brain Segmentation in MRI Using Large Deformation Diffeomorphic Metric Mapping

    PubMed Central

    Khan, Ali R.; Wang, Lei

    2010-01-01

    Fully-automated brain segmentation methods have not been widely adopted for clinical use because of issues related to reliability, accuracy, and limitations of delineation protocol. By combining the probabilistic-based FreeSurfer (FS) method with the Large Deformation Diffeomorphic Metric Mapping (LDDMM) based label propagation method, we are able to increase reliability and accuracy, and allow for flexibility in template choice. Our method uses the automated FreeSurfer subcortical labeling to provide a coarse to fine introduction of information in the LDDMM template-based segmentation resulting in a fully-automated subcortical brain segmentation method (FS+LDDMM). One major advantage of the FS+LDDMM-based approach is that the automatically generated segmentations generated are inherently smooth, thus subsequent steps in shape analysis can directly follow without manual post-processing or loss of detail. We have evaluated our new FS+LDDMM method on several databases containing a total of 50 subjects with different pathologies, scan sequences and manual delineation protocols for labeling the basal ganglia, thalamus, and hippocampus. In healthy controls we report Dice overlap measures of 0.81, 0.83, 0.74, 0.86 and 0.75 for the right caudate nucleus, putamen, pallidum, thalamus and hippocampus respectively. We also find statistically significant improvement of accuracy in FS+LDDMM over FreeSurfer for the caudate nucleus and putamen of Huntington’s disease and Tourette’s syndrome subjects, and the right hippocampus of Schizophrenia subjects. PMID:18455931

  7. Mapping the order and pattern of brain structural MRI changes using change-point analysis in premanifest Huntington's disease.

    PubMed

    Wu, Dan; Faria, Andreia V; Younes, Laurent; Mori, Susumu; Brown, Timothy; Johnson, Hans; Paulsen, Jane S; Ross, Christopher A; Miller, Michael I

    2017-10-01

    Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder that progressively affects motor, cognitive, and emotional functions. Structural MRI studies have demonstrated brain atrophy beginning many years prior to clinical onset ("premanifest" period), but the order and pattern of brain structural changes have not been fully characterized. In this study, we investigated brain regional volumes and diffusion tensor imaging (DTI) measurements in premanifest HD, and we aim to determine (1) the extent of MRI changes in a large number of structures across the brain by atlas-based analysis, and (2) the initiation points of structural MRI changes in these brain regions. We adopted a novel multivariate linear regression model to detect the inflection points at which the MRI changes begin (namely, "change-points"), with respect to the CAG-age product (CAP, an indicator of extent of exposure to the effects of CAG repeat expansion). We used approximately 300 T1-weighted and DTI data from premanifest HD and control subjects in the PREDICT-HD study, with atlas-based whole brain segmentation and change-point analysis. The results indicated a distinct topology of structural MRI changes: the change-points of the volumetric measurements suggested a central-to-peripheral pattern of atrophy from the striatum to the deep white matter; and the change points of DTI measurements indicated the earliest changes in mean diffusivity in the deep white matter and posterior white matter. While interpretation needs to be cautious given the cross-sectional nature of the data, these findings suggest a spatial and temporal pattern of spread of structural changes within the HD brain. Hum Brain Mapp 38:5035-5050, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  8. 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

  9. 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

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed

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

    2013-09-18

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

  12. 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)

  13. Bimodal Modulation and Continuous Stimulation in Optical Imaging to Map Direction Selectivity

    PubMed Central

    Vanni, M. P.; Provost, J.; Casanova, C.; Lesage, F.

    2009-01-01

    In the visual system, neurons with similar functional properties such as orientation and direction selectivity are clustered together to form modules. Optical imaging recordings in combination with episodic paradigms have been previously used to estimate direction selectivity, a fundamental property of visual neurons. The major drawback of the episodic approach is that the extraction of the signal from various forms of physiological noise is difficult, leading to a poor estimation of direction. Recent work, based on periodic stimulation and Fourier decomposition improved the extraction of periodic stimulus responses from noise and thus, reduced the recording time considerably. Given the success of this new paradigm in mapping orientation, the present study evaluated its reliability to measure direction selectivity in the visual cortex of anesthetised cats. Here, a model that exploits the harmonics of the Fourier decomposition is proposed where the first harmonic is related to direction responses, and the second to orientation. As expected, the first harmonic was absent when a static stimulus was presented. Contrarily, the first harmonic was present when moving stimuli were presented and the amplitude was greater with random dots kinematograms than with drifting gratings. The phase of the first harmonic showed a good agreement with direction preference measured by episodic paradigm. The ratio of the first/the second harmonic amplitude, related to a direction index, was weaker in fracture. It was also weaker in areas of the ventral pathway (areas 17 and 21a) where direction selectivity is known to be reduced. These results indicate that a periodic paradigm can be easily used to measure specific parameters in optical signals, particularly in situations when short acquisition periods are needed. PMID:19782756

  14. Neurocognitive Effects of Transcranial Direct Current Stimulation in Arithmetic Learning and Performance: A Simultaneous tDCS-fMRI Study.

    PubMed

    Hauser, Tobias U; Rütsche, Bruno; Wurmitzer, Karoline; Brem, Silvia; Ruff, Christian C; Grabner, Roland H

    A small but increasing number of studies suggest that non-invasive brain stimulation by means of transcranial direct current stimulation (tDCS) can modulate arithmetic processes that are essential for higher-order mathematical skills and that are impaired in dyscalculic individuals. However, little is known about the neural mechanisms underlying such stimulation effects, and whether they are specific to cognitive processes involved in different arithmetic tasks. We addressed these questions by applying tDCS during simultaneous functional magnetic resonance imaging (fMRI) while participants were solving two types of complex subtraction problems: repeated problems, relying on arithmetic fact learning and problem-solving by fact retrieval, and novel problems, requiring calculation procedures. Twenty participants receiving left parietal anodal plus right frontal cathodal stimulation were compared with 20 participants in a sham condition. We found a strong cognitive and neural dissociation between repeated and novel problems. Repeated problems were solved more accurately and elicited increased activity in the bilateral angular gyri and medial plus lateral prefrontal cortices. Solving novel problems, in contrast, was accompanied by stronger activation in the bilateral intraparietal sulci and the dorsomedial prefrontal cortex. Most importantly, tDCS decreased the activation of the right inferior frontal cortex while solving novel (compared to repeated) problems, suggesting that the cathodal stimulation rendered this region unable to respond to the task-specific cognitive demand. The present study revealed that tDCS during arithmetic problem-solving can modulate the neural activity in proximity to the electrodes specifically when the current demands lead to an engagement of this area. Copyright © 2016 Elsevier Inc. All rights reserved.

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

    PubMed

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

    2013-01-01

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

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

    PubMed

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

    2014-01-01

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

  17. 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.

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

    PubMed

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

    2002-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Parsons, Olga

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

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

    PubMed

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

    2005-11-01

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

  1. The evaluation of non-ischemic dilated cardiomyopathy with T1 mapping and ECV methods using 3T cardiac MRI.

    PubMed

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

    2017-02-01

    The aim of this study was to examine the correlation between ventricular function and the extracellular volume fraction (ECV) in patients with non-ischemic dilated cardiomyopathy (NIDCM) using 3.0 T magnetic resonance imaging (MRI). We also hypothesized that native T1 and ECV values would be increased in patients with NIDCM, independent of the left ventricular ejection fraction (LVEF). The findings of our study could lead to further studies of the follow-up protocols. In total, 53 consecutive dilated cardiomyopathy patients who had undergone cardiac MRI were functionally evaluated and underwent tissue characterization. The mean native T1 value was 1235 ± 10 ms, and the mean ECV value was 35.4 ± 2.7% in the myocardia. The LVEF values ranged from 29 to 44%. No significant correlations were observed between functional analysis measurements and native T1 or ECV values. Our results showed that myocardial fibrosis is unrelated to cardiac functional findings in NIDCM patients. Therefore, we propose that these patients should be evaluated using MRI and tissue characterization techniques, in addition to cardiac functional analysis.

  2. Direct measurement and microscale mapping of nanoNewton to milliNewton magnetic forces

    NASA Astrophysics Data System (ADS)

    Velez, Camilo; Carroll, Robin E.; Arnold, David P.

    2017-05-01

    This paper describes the direct measurement and mapping of magnetic forces/fields with microscale spatial resolution by combining a commercial microforce sensing probe with a thin-film permanent micromagnet. The main motivation of this work is to fill a critical metrology gap with a technology for direct measurement of magnetic forces from nN to 10's of mN with sub-millimeter spatial resolution. This capability is ideal for measuring forces (which are linked to magnetic field gradients) produced by small-scale magnetic and electromagnetic devices including sensors, actuators, MEMS, micromotors, microfluidics, biomedical devices. This new measuring technique is validated by comparison of measured forces from small permanent magnets with the analytical models.

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

    PubMed

    Qin, Huaizhen; Zhu, Xiaofeng

    2012-04-01

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

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

    SciTech Connect

    Yee, Seonghwan; Gao, Jia-Hong

    2014-12-15

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

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

    PubMed

    Chen, Shuang; Wang, Lin; Yang, Yufang

    2014-04-01

    This study examined the semantic representation of novel words learnt in two conditions: directly mapping a novel word to a concept (Direct mapping: DM) and inferring the concept from provided features (Inferred learning: IF). A condition where no definite concept could be inferred (No basic-level meaning: NM) served as a baseline. The semantic representation of the novel word was assessed via a semantic-relatedness judgment task. In this task, the learned novel word served as a prime, while the corresponding concept, an unlearned feature of the concept, and an unrelated word served as targets. ERP responses to the targets, primed by the novel words in the three learning conditions, were compared. For the corresponding concept, smaller N400s were elicited in the DM and IF conditions than in the NM condition, indicating that the concept could be obtained in both learning conditions. However, for the unlearned feature, the targets in the IF condition produced an N400 effect while in the DM condition elicited an LPC effect relative to the NM learning condition. No ERP difference was observed among the three learning conditions for the unrelated words. The results indicate that conditions of learning affect the semantic representation of novel word, and that the unlearned feature was only activated by the novel word in the IF learning condition. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

    NASA Astrophysics Data System (ADS)

    Rizaldy, A.; Firdaus, W.

    2012-07-01

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

  7. 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.

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

    PubMed

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

    2015-01-01

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

  9. 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

  10. 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

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

    PubMed

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

    2005-01-01

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

  12. 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

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

    PubMed

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

    2009-01-01

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

  14. 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

    2014-08-07

    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.

  15. Quantitative assessment of the supraspinatus tendon on MRI using T2/T2* mapping and shear-wave ultrasound elastography: a pilot study.

    PubMed

    Krepkin, Konstantin; Bruno, Mary; Raya, José G; Adler, Ronald S; Gyftopoulos, Soterios

    2017-02-01

    To determine whether there is an association between T2/T2* mapping and supraspinatus tendon mechanical properties as assessed by shear-wave ultrasound elastography (SWE). This HIPAA-compliant prospective pilot study received approval from our hospital's institutional review board. Eight patients (3 males/5 females; age range 44-72 years) and nine shoulders underwent conventional shoulder MRI, T2/T2* mapping on a 3-T scanner, and SWE. Two musculoskeletal radiologists reviewed the MRI examinations in consensus for evidence of supraspinatus tendon pathology, with tear size measured for full-thickness tears. T2/T2* values and ultrasound shear-wave velocities (SWV) were calculated in three corresponding equidistant regions of interest (ROIs) within the insertional 1-2 cm of the supraspinatus tendon (medial, middle, lateral). Pearson correlation coefficients between T2/T2* values and SWV, as well as among T2, T2*, SWV and tear size, were calculated. There was a significant negative correlation between T2* and SWV in the lateral ROI (r = -0.86, p = 0.013) and overall mean ROI (r = -0.90, p = 0.006). There was significant positive correlation between T2 and measures of tear size in the lateral and mean ROIs (r range 0.71-0.77, p range 0.016-0.034). There was significant negative correlation between SWV and tear size in the middle and mean ROIs (r range -0.79--0.68, p range 0.011-0.046). Our pilot study demonstrated a potential relationship between T2* values and shear wave velocity values in the supraspinatus tendon, a finding that could lead to an improved, more quantitative evaluation of the rotator cuff tendons.

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

    PubMed Central

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

    2017-01-01

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

  17. 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. Copyright © 2013 IPEM. Published by Elsevier Ltd. All rights reserved.

  18. 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

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

    PubMed

    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.

  20. 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.

  1. 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

  2. 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.

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

    PubMed Central

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

    2009-01-01

    As one of the earliest structures to degenerate in Alzheimer’s disease (AD), the hippocampus is the target of many studies of factors that influence rates of brain degeneration in the elderly. In one of the largest brain mapping studies to date, we mapped the 3D profile of hippocampal degeneration over time in 490 subjects scanned twice with brain MRI over a 1-year interval (980 scans). We examined baseline and 1-year follow-up scans of 97 AD subjects (49 males/48 females), 148 healthy control subjects (75 males/73 females), and 245 subjects with mild cognitive impairment (MCI; 160 males/85 females). We used our previously validated automated segmentation method, based on AdaBoost, to create 3D hippocampal surface models in all 980 scans. Hippocampal volume loss rates increased with worsening diagnosis (normal=0.66%/year; MCI=3.12%/year; AD=5.59%/year), and correlated with both baseline and interval changes in Mini-Mental State Examination (MMSE) scores and global and sum-of-boxes Clinical Dementia Rating scale (CDR) scores. Surface-based statistical maps visualized a selective profile of ongoing atrophy in all three diagnostic groups. Healthy controls carrying the ApoE4 gene atrophied faster than non-carriers, while more educated controls atrophied more slowly; converters from MCI to AD showed faster atrophy than non-converters. Hippocampal loss rates can be rapidly mapped, and they track cognitive decline closely enough to be used as surrogate markers of Alzheimer’s disease in drug trials. They also reveal genetically greater atrophy in cognitively intact subjects. PMID:19041724

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

    PubMed

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