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Symmetric block-matching registration for the distortion correction of Echo-Planar images

Renaud Hedouin, Olivier Commowick, Maxime Taquet, Elise Bannier, Benoit Scherrer, Simon K. Warfield, Christian Barillot
2015 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI)  
We introduce a new approach to correct geometric and intensity distortion of Echo Planar Images (EPI) from images acquired with opposite phase encoding directions.  ...  A new symmetric block-matching registration algorithm has been developed for this purpose relying on new adapted transformations between blocks and a symmetric optimization scheme to ensure an opposite  ...  Block-Matching for Distortion Correction In the distortion model, the corrected image C is unknown and can at best be estimated.  ... 
doi:10.1109/isbi.2015.7163973 dblp:conf/isbi/HedouinCTBSWB15 fatcat:fca45nv6ibdalp5vhetxdeesbi

Block-Matching Distortion Correction of Echo-Planar Images With Opposite Phase Encoding Directions

Renaud Hedouin, Olivier Commowick, Elise Bannier, Benoit Scherrer, Maxime Taquet, Simon K. Warfield, Christian Barillot
2017 IEEE Transactions on Medical Imaging  
By shortening the acquisition time of MRI, Echo Planar Imaging (EPI) enables the acquisition of a large number of images in a short time, compatible with clinical constraints as required for diffusion  ...  We propose a new block-matching registration method to perform EPI distortion correction based on the acquisition of two EPI with opposite phase encoding directions (PED).  ...  The grid phantom was developed by the UNIRS group from the CEA Neurospin for the CATI Consortium for image acquisition and processing.  ... 
doi:10.1109/tmi.2016.2646920 pmid:28092527 fatcat:337j4dthzvc2re7eeg7vfbc6c4

Evaluation of distortion correction methods in diffusion MRI of the spinal cord [article]

Haykel Snoussi, Julien Cohen-Adad, Olivier Commowick, Benoit Combes, Elise Bannier, Soizic Leguy, Anne Kerbrat, Christian Barillot, Emmanuel Caruyer
2021 arXiv   pre-print
Magnetic field inhomogeneities generate important geometric distortions in reconstructed echo-planar images.  ...  The cross-correlation with anatomical image is also improved by Hyperelastic Susceptibility Artefact Correction (HySCO) and block-matching.  ...  The pulse sequence used for diffusion MRI was a single-shot Echo-planar imaging (ss-EPI) using parallel imaging (GRAPPA, acceleration factor 2).  ... 
arXiv:2108.03817v1 fatcat:kzp6aej46fhhxlkiaznrbqctve


Neculai Archip, Olivier Clatz, Stephen Whalen, Simon P. DiMaio, Peter M. Black, Ferenc A. Jolesz, Alexandra Golby, Simon K. Warfield
2008 Operative Neurosurgery  
The geometry of intraoperative images (0.5 T) is changed so that the images match the preoperative MRI scans (3 T).  ...  application of nonrigid registration to compensate for geometric distortion during neurosurgery, 4) measurement of residual distortion after geometric distortion correction, and 5) phantom study to quantify  ...  Acknowledgments We thank GE for the research support.  ... 
doi:10.1227/01.neu.0000317395.08466.e6 pmid:18424988 fatcat:3ztq5yoobzfy7jjuutkgfwwzza

Modeling and Analysis of Ultrasonic Echoes Reflected from a Surface under Two Layers [chapter]

Joyoni Dey, Takeo Kanade
2000 Lecture Notes in Computer Science  
In this work, we describe a possible method to compensate or correct for these distortions in ultrasound images. This can be used as a pre-processing step before registration with other modalities.  ...  Novel ultrasonic applications such as registration between CT and ultrasound images, requiring comparable levels of accuracies between modalities could suffer from the distortions in ultrasound images.  ...  Acknowledgments: We would like to thank Rajesh Gopakumar and Farhana Kagalwala for many helpful discussions and suggestions.  ... 
doi:10.1007/978-3-540-40899-4_49 fatcat:r5dvhmaghfg3dmrluy6o7a24em

Distortion correction for diffusion-weighted MRI tractography and fMRI in the temporal lobes

Karl V. Embleton, Hamied A. Haroon, David M. Morris, Matthew A. Lambon Ralph, Geoff J.M. Parker
2010 Human Brain Mapping  
Single shot echo-planar imaging (EPI) sequences are currently the most commonly used sequences for diffusion-weighted imaging (DWI) and functional magnetic resonance imaging (fMRI) as they allow relatively  ...  We describe robust acquisition and processing methods for correcting such distortions in spin echo (SE) EPI using a variant of the reversed direction k space traversal method with a number of novel additions  ...  ACKNOWLEDGMENTS We acknowledge the help of Liz Moore of Philips Medical Systems for assistance with sequence development.  ... 
doi:10.1002/hbm.20959 pmid:20143387 fatcat:ivyr24upnbd7lpfiwswsnczhkq

Quantitative Assessment of the Impact of Geometric Distortions and Their Correction on fMRI Data Analyses

Rodolfo Abreu, João Valente Duarte
2021 Frontiers in Neuroscience  
Functional magnetic resonance imaging (fMRI) data is typically collected with gradient-echo echo-planar imaging (GE-EPI) sequences, which are particularly prone to the susceptibility artifact as a result  ...  TOPUP. fMRI data should thus be corrected for geometric distortions, with the choice of the approach having a modest, albeit positive, impact on the fMRI analyses.  ...  AUTHOR CONTRIBUTIONS Both authors coded the stimulus presentation and acquired the data. RA performed the data analyses and wrote the manuscript. JD reviewed the manuscript.  ... 
doi:10.3389/fnins.2021.642808 pmid:33767610 pmcid:PMC7985341 fatcat:wljdukdtlrekrkxa2uii3wijdy

Distortion Correction of Single-shot EPI Enabled by Deep-learning

Zhangxuan Hu, Yishi Wang, Zhe Zhang, Jieying Zhang, Huimao Zhang, Chunjie Guo, Yuejiao Sun, Hua Guo
2020 NeuroImage  
The PSF-EPI method can obtain distortion-free echo planar images.  ...  Through the correction of diffusion-weighted images, the proposed deep-learning based method was demonstrated to have the feasibility to correct for the distortion of EPI images.  ...  ., 2018) proposed to use the convolutional neural network (CNN) for gradient-echo EPI distortion correction.  ... 
doi:10.1016/j.neuroimage.2020.117170 pmid:32682096 fatcat:7hp4gdfqrbfr3am3ryvj6wn4ti

3-D Residual Eddy Current Field Characterisation: Applied to Diffusion Weighted Magnetic Resonance Imaging

Kieran O'Brien, Alessandro Daducci, Nils Kickler, Francois Lazeyras, Rolf Gruetter, Thorsten Feiweier, Gunnar Krueger
2013 IEEE Transactions on Medical Imaging  
Characterization of the 3-D eddy current field with linear response theory enables the prediction of the 3-D eddy current field required to correct eddy current induced geometric distortions for a wide  ...  The model's performance was tested on diffusion weighted images of four normal volunteers, following distortion correction, the quality of the Stejskal-Tanner diffusion-weighted images was found to have  ...  ACKNOWLEDGMENT The authors would like to acknowledge the assistance of Dr. C. Granzeria for assistance with interpretation of the tract based analysis.  ... 
doi:10.1109/tmi.2013.2259249 pmid:23674437 fatcat:tj3rbiosnrbd5arwjuc4drcnsi

Application of Cortical Unfolding Techniques to Functional MRI of the Human Hippocampal Region

Michael M. Zeineh, Stephen A. Engel, Susan Y. Bookheimer
2000 NeuroImage  
We describe a new application of cortical unfolding to high-resolution functional magnetic resonance imaging (fMRI) of the human hippocampal region.  ...  The application of these unfolding techniques greatly enhances the ability of fMRI to localize and characterize signal changes within the medial temporal lobe.  ...  Special thanks to Oi Lee Wong for her help in segmentation. We also acknowledge Brian Wandell for the use of his segmentation and unfolding software. Finally, we thank J. Mazziotta, M. Cohen, A.  ... 
doi:10.1006/nimg.2000.0561 pmid:10860795 fatcat:5z2kx55vxraqjfcn3rywl3jclm

Hemifield columns co-opt ocular dominance column structure in human achiasma

Cheryl A. Olman, Pinglei Bao, Stephen A. Engel, Andrea N. Grant, Chris Purington, Cheng Qiu, Michael-Paul Schallmo, Bosco S. Tjan
2018 NeuroImage  
T 2 -weighted 2D Spin Echo images were acquired at 0.8 mm isotropic resolution. The left eye was occluded.  ...  To the right eye, a presentation of flickering checkerboards alternated between the left and right visual fields in a blocked stimulus design.  ...  A custommade radio frequency head coil (4-channel transmit, 9-channel receive; Adriany et al., 2012) was used for T 2 -weighted (spin echo) echo-planar imaging (EPI) in the achiasmic participant and  ... 
doi:10.1016/j.neuroimage.2016.12.063 pmid:28017921 pmcid:PMC5481499 fatcat:rvtwj3k4x5d4vepmyijxffdwqm

Properties of a 2D fat navigator for prospective image domain correction of nodding motion in brain MRI

Stefan Skare, Axel Hartwig, Magnus Mårtensson, Enrico Avventi, Mathias Engström
2014 Magnetic Resonance in Medicine  
Magnetic resonance imaging is one of the fastest developing medical imaging techniques.  ...  One of the possible MR imaging contrasts is the ability to visualize diffusion processes.  ...  Echo Planar Imaging Echo Planar Imaging (EPI) is a fast image acquisition technique that was invented in 1977 by Sir Peter Mansfield (4) .  ... 
doi:10.1002/mrm.25234 pmid:24733744 fatcat:edimpyjaafad7bnjtfem4datrm

Scattered slice SHARD reconstruction for motion correction in multi-shell diffusion MRI [article]

Daan Christiaens, Lucilio Cordero-Grande, Maximilian Pietsch, Jana Hutter, Anthony N. Price, Emer J. Hughes, Katy Vecchiato, Maria Deprez, A. David Edwards, Joseph V. Hajnal, J-Donald Tournier
2020 arXiv   pre-print
Furthermore, the proposed framework integrates slice-level outlier rejection, distortion correction, and slice profile correction.  ...  Validation experiments demonstrate accurate slice-level motion correction across the age range and across the range of motion in the population.  ...  However, the vast majority of dMRI data are collected as stacks of slices using echo planar imaging (EPI) sequences (Turner et al., 1990) .  ... 
arXiv:1905.02996v2 fatcat:xtxreyf7gbaarodlfvv5peehuq

Abstracts (Continue in Part XXXIII)

1996 Proceedings of the International Society for Magnetic Resonance in Medicine  
However, it has been observed that the correction of gradient echo EP images is generally not as good as in spin echo images. This results from intra-voxel dephasing in the gradient echo experiments.  ...  This has the disadvantage of a greater minimum echo time than for a half Fourier or gradient echo EPI experiment of the same resolution, often leading to excessive T2 contrast.  ...  Acknowledgements This project was supported in part by a Special Opportunities Award from the Whitaker Foundation, and by NIH lP41 RRO7723-03.  ... 
doi:10.1002/mrmp.22419960133 fatcat:qeadomlnojcy7fzo4lmbpjl7oq

Semi-automatic deformable registration of prostate MR images to pathological slices

Yousef Mazaheri, Louisa Bokacheva, Dirk-Jan Kroon, Oguz Akin, Hedvig Hricak, Daniel Chamudot, Samson Fine, Jason A. Koutcher
2010 Journal of Magnetic Resonance Imaging  
For each patient, the T2w imaging containing the largest area of tumor was manually matched with the corresponding pathologic slice.  ...  Purpose-To present a semi-automatic deformable registration algorithm for co-registering T2weighted (T2w) images of the prostate with whole-mount pathological sections of prostatectomy specimens.  ...  Ada Muellner, BA, for editing this manuscript. Funded by: National Institutes of Health grant #R01 CA76423.  ... 
doi:10.1002/jmri.22347 pmid:21031521 pmcid:PMC2975408 fatcat:23ijbjglvzhubbejkwgs6hshhu
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