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Inter-subject Registration of Functional Images: Do We Need Anatomical Images?

Elvis Dohmatob, Gael Varoquaux, Bertrand Thirion
2018 Frontiers in Neuroscience  
In Echo-Planar Imaging (EPI)-based Magnetic Resonance Imaging (MRI), inter-subject registration typically uses the subject's T1-weighted (T1w) anatomical image to learn deformations of the subject's brain  ...  Residual uncorrected distortions induce non-rigid deformations between the EPI scans and the same subject's anatomical scan.  ...  This is especially true in functional Magnetic Resonance Imaging (fMRI) studies in which the activations might span just a few voxels in diameter.  ... 
doi:10.3389/fnins.2018.00064 pmid:29497357 pmcid:PMC5819565 fatcat:i5sy4sjzqvfklgd4dstar6kiie

Brainstem fMRI

Pengxu Wei, Zhi Lan, Zeping Lv, Yubo Fan
2020 Encyclopedia  
In comparison with brain functional magnetic resonance imaging (fMRI), only a few fMRI studies investigating the brainstem have been reported because of a number of technical challenges.  ...  The human brainstem plays important roles in maintaining basic vital functions.  ...  Conflicts of Interest: The authors declare no conflict of interest. Entry Link on the Encyclopedia Platform: https://encyclopedia.pub/4576.  ... 
doi:10.3390/encyclopedia1010003 fatcat:t2xtd6iy3jgahgsy5snuydw4uy

Sammba-MRI: A Library for Processing SmAll-MaMmal BrAin MRI Data in Python

Marina Celestine, Nachiket A. Nadkarni, Clément M. Garin, Salma Bougacha, Marc Dhenain
2020 Frontiers in Neuroinformatics  
Small-mammal neuroimaging offers incredible opportunities to investigate structural and functional aspects of the brain.  ...  Many tools have been developed in the last decade to analyse small animal data, but current softwares are less mature than the available tools that process human brain data.  ...  INTRODUCTION The use of magnetic resonance imaging (MRI) methods in animals provides considerable benefits for improving our understanding of brain structure and function in health and diseases.  ... 
doi:10.3389/fninf.2020.00024 pmid:32547380 pmcid:PMC7270712 fatcat:aki7us74nbam7mlx7dpsyjpnda

Spatiotemporal alignment of in utero BOLD-MRI series

Esra Abaci Turk, Jie Luo, Borjan Gagoski, Javier Pascau, Carolina Bibbo, Julian N. Robinson, P. Ellen Grant, Elfar Adalsteinsson, Polina Golland, Norberto Malpica
2017 Journal of Magnetic Resonance Imaging  
correction based on non-rigid registration, (iii) correction of motion and non-rigid deformations across volumes, and (iv) detection of the outlier volumes to be discarded from subsequent analysis.  ...  Abstract Purpose-To present a method for spatio-temporal alignment of in-utero magnetic resonance imaging (MRI) time series acquired during maternal hyperoxia for enabling improved quantitative tracking  ...  Acknowledgements We would like to thank Dr. Arvind Palanisamy, Dr. Clare Tempany, Dr. Carol Barnewolt, and Dr. Judy Estroff.  ... 
doi:10.1002/jmri.25585 pmid:28152240 pmcid:PMC5509493 fatcat:f2zyh5kaongznoi77zt7mrdi3q

Geometric distortion correction for echo planar images using nonrigid registration with spatially varying scale

Yong Li, Ning Xu, J. Michael Fitzpatrick, Benoit M. Dawant
2008 Magnetic Resonance Imaging  
One method used to correct geometric and intensity distortions in Echo Planar images is to register them to undistorted images via nonrigid deformations.  ...  This estimate is generated using knowledge of the physical processes that induce distortions in EPI images. We evaluate the method of spatially varying scale on both simulated and real data.  ...  Introduction Echo Planar Imaging (EPI) is known for its ability to acquire magnetic resonance (MR) images in a very short time.  ... 
doi:10.1016/j.mri.2008.03.004 pmid:18499382 pmcid:PMC3511831 fatcat:xbq7gv2phjbvjdvdsncyaygcc4

Motion correction in fMRI via registration of individual slices into an anatomical volume

Boklye Kim, Jennifer L. Boes, Peyton H. Bland, Thomas L. Chenevert, Charles R. Meyer
1999 Magnetic Resonance in Medicine  
An automated retrospective image registration based on mutual information is adapted to a multislice functional magnetic resonance imaging (fMRI) acquisition protocol to provide accurate motion correction  ...  Motion correction is performed by mapping each slice to an anatomic volume data set acquired in the same fMRI session to accommodate inter-slice head motion.  ...  Echoplanar functional magnetic images are susceptible to localized image distortion arising from cardiac and respiratory pulsation as well as local magnetic field change.  ... 
doi:10.1002/(sici)1522-2594(199905)41:5<964::aid-mrm16>3.0.co;2-d pmid:10332880 fatcat:kgjurixmjfeibdzk4j7hsad5ja

Motion correction in fMRI via registration of individual slices into an anatomical volume

Boklye Kim, Jennifer L. Boes, Peyton H. Bland, Thomas L. Chenevert, Charles R. Meyer
1999 Magnetic Resonance in Medicine  
An automated retrospective image registration based on mutual information is adapted to a multislice functional magnetic resonance imaging (fMRI) acquisition protocol to provide accurate motion correction  ...  Motion correction is performed by mapping each slice to an anatomic volume data set acquired in the same fMRI session to accommodate inter-slice head motion.  ...  Echoplanar functional magnetic images are susceptible to localized image distortion arising from cardiac and respiratory pulsation as well as local magnetic field change.  ... 
doi:10.1002/(sici)1522-2594(199905)41:5<964::aid-mrm16>3.3.co;2-4 fatcat:ye57cexyjramli5367lxb5sipi

Improved Precision in the Measurement of Longitudinal Global and Regional Volumetric Changes via a Novel MRI Gradient Distortion Characterization and Correction Technique [chapter]

Vladimir S. Fonov, Andrew Janke, Zografos Caramanos, Douglas L. Arnold, Sridar Narayanan, G. Bruce Pike, D. Louis Collins
2010 Lecture Notes in Computer Science  
The distortions are expressed in terms of spherical harmonic functions, which are then used to define the distortion correction field for the volume of interest.  ...  One source of measurement error in anatomical MR is magnetic field gradientinduced geometric distortion.  ...  Non-linear registration [10] was used to estimate the residual anatomical misalignment due to the geometric distortion inside the brain.  ... 
doi:10.1007/978-3-642-15699-1_34 fatcat:f7zln225ubddnl3qi62xlg3y2y

Comparison of EPI Distortion Correction Methods in Diffusion Tensor MRI Using a Novel Framework [chapter]

Minjie Wu, Lin-Ching Chang, Lindsay Walker, Herve Lemaitre, Alan S. Barnett, Stefano Marenco, Carlo Pierpaoli
2008 Lecture Notes in Computer Science  
Several strategies have been proposed to correct EPI distortions including B 0 field mapping (B 0 M) and image registration.  ...  In this study, an experimental framework is proposed to evaluation the performance of different EPI distortion correction methods in improving DTderived quantities.  ...  Resonance Imaging of the Brain software library (FSL, www.fmrib.ox.ac.uk/).  ... 
doi:10.1007/978-3-540-85990-1_39 fatcat:iazrqg4s5bh5bdmeya74fgmsky

Measuring geometric accuracy in magnetic resonance imaging with 3D-printed phantom and nonrigid image registration

Katri Nousiainen, Teemu Mäkelä
2019 Magnetic Resonance Materials in Physics, Biology and Medicine  
We aimed to develop a vendor-neutral and interaction-free quality assurance protocol for measuring geometric accuracy of head and brain magnetic resonance (MR) images.  ...  The maximum displacements varied from 0.50 to 1.35 mm or 0.89 to 2.30 mm, with vendors' distortion correction on or off, respectively.  ...  This project received a Research and Development grant from HUS Medical Imaging Center, Hospital District of Helsinki and Uusimaa.  ... 
doi:10.1007/s10334-019-00788-6 pmid:31646408 fatcat:cy7c7c3qz5g2raejqhezbf7loa

Automatic cortical surface reconstruction of high-resolution T 1 echo planar imaging data

Ville Renvall, Thomas Witzel, Lawrence L. Wald, Jonathan R. Polimeni
2016 NeuroImage  
Echo planar imaging (EPI) is the method of choice for the majority of functional magnetic resonance imaging (fMRI), yet EPI is prone to geometric distortions and thus misaligns with conventional anatomical  ...  In particular, the alignment near the regions vulnerable to distortion due to magnetic susceptibility differences was improved, and sampling of the adjacent tissue classes outside of the cortex was reduced  ...  Acknowledgements We wish to thank Dr. Himanshu Bhat and Prof. Bruce Fischl for helpful discussions.  ... 
doi:10.1016/j.neuroimage.2016.04.004 pmid:27079529 pmcid:PMC5234090 fatcat:m6xd66gnp5hmxh6h2gihc5p6de

Comparison of fMRI coregistration results between human experts and software solutions in patients and healthy subjects

Andreas Gartus, Alexander Geissler, Thomas Foki, Amir Reza Tahamtan, Gerald Pahs, Markus Barth, Katja Pinker, Siegfried Trattnig, Roland Beisteiner
2006 European Radiology  
Functional magnetic resonance imaging (fMRI) performed by echo-planar imaging (EPI) is often highly distorted, and it is therefore necessary to coregister the functional to undistorted anatomical images  ...  A reference point chosen at a characteristic anatomical location within the fMRI sensorimotor activations was transferred to the high resolution anatomical MRI images by three human fMRI experts and by  ...  The exact transfer of neuronal activation to the correct corresponding neuroanatomical structure of non-distorted anatomical images is especially difficult in the presence of brain pathology.  ... 
doi:10.1007/s00330-006-0459-z pmid:17036153 fatcat:bcoz5yo6zjagdfei7blt5pfs3y

Super‐resolution for upper abdominal MRI: Acquisition and post‐processing protocol optimization using brain MRI control data and expert reader validation

Michael Ebner, Premal A. Patel, David Atkinson, Lucy Caselton, Louisa Firmin, Zahir Amin, Alan Bainbridge, Paolo De Coppi, Stuart A. Taylor, Sébastien Ourselin, Manil D. Chouhan, Tom Vercauteren
2019 Magnetic Resonance in Medicine  
Magnetic resonance (MR) cholangiopancreatography (MRCP) is an established specialist method for imaging the upper abdomen and biliary/pancreatic ducts.  ...  Due to limitations of either MR image contrast or low through-plane resolution, patients may require further evaluation with contrast-enhanced computed tomography (CT) images.  ...  | INTRODUCTION Magnetic resonance (MR) cholangiopancreatography (MRCP) is an established method for imaging the upper abdomen and biliary/pancreatic ducts.  ... 
doi:10.1002/mrm.27852 pmid:31264270 pmcid:PMC6742507 fatcat:uxkic6wwvnfnfbqhyxou3qdx7m

Methodological Considerations for Neuroimaging in Deep Brain Stimulation of the Subthalamic Nucleus in Parkinson's Disease Patients

Bethany R. Isaacs, Max C. Keuken, Anneke Alkemade, Yasin Temel, Pierre-Louis Bazin, Birte U. Forstmann
2020 Journal of Clinical Medicine  
These negative responses to treatment can partly be attributed to suboptimal pre-operative planning procedures via direct targeting through low-field and low-resolution magnetic resonance imaging (MRI)  ...  Image registration, correction, and post-processing techniques may require combined expertise of traditional radiologists, clinicians, and fundamental researchers.  ...  For pre-operative planning, at least two sets of image registrations are required: (i) anatomical T2 to T1 and (ii) pre-registered anatomical T1 and T2 to stereotaxic space defined by the CT or MRI including  ... 
doi:10.3390/jcm9103124 pmid:32992558 pmcid:PMC7600568 fatcat:zaparmvmr5avbkibibn57citbm

Front Matter: Volume 9784

2016 Medical Imaging 2016: Image Processing  
morphometry for brain atrophy estimation [9784-5] SESSION 2 KEYNOTE AND DIFFUSION MRI 9784 07 Image-processing pipelines: applications in magnetic resonance histology (Keynote Paper) [9784-6] 9784 08  ...  correspondences [9784-25] 9784 0R Fast correspondences for statistical shape models of brain structures [9784-26] 9784 0S Robust group-wise rigid registration of point sets using t-mixture model [9784  ...  correction of longitudinal retinal OCT data 9784 0Y Effects of spatial resolution on image registration 9784 0Z Non-rigid contour-to-pixel registration of photographic and quantitative light-induced  ... 
doi:10.1117/12.2240619 fatcat:kot6cogf4rf6dcjhkzdrr5gahi
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