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Reproducible White Matter Tract Segmentation Using 3D U-Net on a Large-scale DTI Dataset
[article]
2019
arXiv
pre-print
Preserved Fulltext
We therefore developed a novel convolutional neural network based method to directly segment white matter tract trained on a low-resolution dataset of 9149 DTI images. ...
As a consequence, there is a large interest in the automatic segmentation of white matter tract in diffusion tensor MRI data. ...
This is the first deep learning based method of WM tract segmentation developed on such a large-scale dataset. ...
arXiv:1908.10219v1
fatcat:fvjzisxtdfa5rjyfutoa7guila
Neuro4Neuro: A neural network approach for neural tract segmentation using large-scale population-based diffusion imaging
2020
NeuroImage
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In conclusion, we presented a highly reproducible and fast method for WM tract segmentation that has the potential of being used in large-scale studies and clinical practice. ...
This 3D end-to-end method is trained to segment 25 WM tracts in aging individuals from a large population-based study (N=9752, 1.5T MRI). ...
In addition, M. de Groot has a financial interest in the GSK company. The GSK had no role in this study. ...
doi:10.1016/j.neuroimage.2020.116993
pmid:32492510
fatcat:ropm3a5nb5ao5lf65iaagunedu
Neuro4Neuro: A neural network approach for neural tract segmentation using large-scale population-based diffusion imaging
[article]
2020
arXiv
pre-print
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In conclusion, we presented a highly reproducible and fast method for WM tract segmentation that has the potential of being used in large-scale studies and clinical practice. ...
This 3D end-to-end method is trained to segment 25 WM tracts in aging individuals from a large population-based study (N=9752, 1.5T MRI). ...
In addition, M. de Groot has a financial interest in the GSK company. The GSK had no role in this study. ...
arXiv:2005.12838v1
fatcat:k7riidy5k5e4dmczja5ld4cmwa
Longitudinal diffusion MRI analysis using Segis-Net: a single-step deep-learning framework for simultaneous segmentation and registration
2021
NeuroImage
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We applied Segis-Net to the analysis of white matter tracts from N=8045 longitudinal brain MRI datasets of 3249 elderly individuals. ...
Segis-Net approach showed a significant increase in registration accuracy, spatio-temporal segmentation consistency, and reproducibility compared with two multistage pipelines. ...
Application to diffusion MRI The performance of Segis-Net is demonstrated by analyzing white matter tracts in a large diffusion MRI dataset, and compared to that of two multi-stage pipelines, in which ...
doi:10.1016/j.neuroimage.2021.118004
pmid:33794359
fatcat:q3qotochh5gy7fivri3grky3x4
Longitudinal diffusion MRI analysis using Segis-Net: a single-step deep-learning framework for simultaneous segmentation and registration
[article]
2020
arXiv
pre-print
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2021 accepted arXiv:2012.14230v2 fatcat:xtbsy7jokjftrmjfpuwwrjvoau
We applied Segis-Net to the analysis of white matter tracts from N=8045 longitudinal brain MRI datasets of 3249 elderly individuals. ...
Segis-Net approach showed a significant increase in registration accuracy, spatio-temporal segmentation consistency, and reproducibility comparing with two multistage pipelines. ...
Application to diffusion MRI The performance of Segis-Net is demonstrated by analyzing white matter tracts in a large diffusion MRI dataset, and compared to that of two multi-stage pipelines, in which ...
arXiv:2012.14230v1
fatcat:kieonl7vnvhhfdmmamrjdb5ag4
Informative and Reliable Tract Segmentation for Preoperative Planning
2022
Frontiers in Radiology
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We use a 3D U-Net to segment white matter tracts. We then estimate model and data uncertainty using test time dropout and test time augmentation, respectively. ...
Identifying white matter (WM) tracts to locate eloquent areas for preoperative surgical planning is a challenging task. ...
ACKNOWLEDGMENTS We thank NVIDIA for providing the Titan V GPU used in this work. ...
doi:10.3389/fradi.2022.866974
fatcat:bqrh3oxsnrbhheja325hdhxpny
A hybrid deep learning framework for integrated segmentation and registration: evaluation on longitudinal white matter tract changes
[article]
2019
arXiv
pre-print
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We applied this method to the segmentation of white matter tracts, describing functionally grouped axonal fibers, using N=8045 longitudinal brain MRI data of 3249 individuals. ...
Registration between time-points is used either as a prior for segmentation in a subsequent time point or to perform segmentation in a common space. ...
The framework was evaluated on longitudinal white matter tracts analysis using a large-scale diffusion MRI dataset. ...
arXiv:1908.10221v1
fatcat:vphuywjrhndflj7vopd7szsl74
Methods and considerations for longitudinal structural brain imaging analysis across development
2014
Developmental Cognitive Neuroscience
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We focus on measurements of brain morphometry (e.g., volume, cortical thickness, surface area, folding patterns), as well as measurements derived from diffusion tensor imaging (DTI). ...
Results from these studies have given us a glimpse into the remarkably extended and multifaceted development of our brain, converging with evidence from anatomical and histological studies. ...
Anne-Lise Goddings for providing the initial inspiration for this review, as well as for many helpful conversations on the topic. ...
doi:10.1016/j.dcn.2014.04.004
pmid:24879112
pmcid:PMC6989768
fatcat:bz4k6rrmlfacbbgiqfutax6zwi
Mean apparent propagator (MAP) MRI: A novel diffusion imaging method for mapping tissue microstructure
2013
NeuroImage
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The lowest order term in this expansion contains a diffusion tensor that characterizes the Gaussian displacement distribution, equivalent to diffusion tensor MRI (DTI). ...
We also define and map novel quantitative descriptors of diffusion that can be computed robustly using this MAP-MRI framework. ...
A diffusion-weighted multislice spin echo EPI pulse sequence with 4 segments was used. ...
doi:10.1016/j.neuroimage.2013.04.016
pmid:23587694
pmcid:PMC4059870
fatcat:ihzvrgdp7nf5lillgo4occbrra
A framework for spatial normalization and voxelwise analysis of diffusion propagators in multiple MAP-MRI data sets
[article]
2019
bioRxiv
pre-print
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First, we compute a DTI study template which provides the reference frame and scaling parameters needed to construct a standardized set of MAP-MRI basis functions at each voxel in template space. ...
We illustrate the application of this method by generating a template of MAP propagators for a cohort of healthy volunteers and show a proof-of-principle example of how this pipeline may be used to detect ...
We identified white matter structures based on the International Consortium of Brain Mapping (ICBM)-DTI-81 atlas. ...
doi:10.1101/697284
fatcat:tpczdf43qbgcddf6txr7om4mty
From Diffusion MRI to Brain Connectomics
[chapter]
2012
Modeling in Computational Biology and Biomedicine
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We reproduce here only the final example. 675 Using the affine invariant Riemannian metric on Sym + 3 , which also forms a Riemannian metric on 676 the space of 3D Gaussian distributions N (x, r), it is ...
segmentation framework using this metric for DTI. ...
doi:10.1007/978-3-642-31208-3_6
fatcat:yie47qd3ezc4jivnqpyfo62rju
On the Viability of Diffusion MRI-Based Microstructural Biomarkers in Ischemic Stroke
2018
Frontiers in Neuroscience
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Recent tract-based analyses provided evidence for the exploitability of 3D-SHORE microstructural descriptors derived from diffusion MRI (dMRI) in revealing white matter (WM) plasticity. ...
Reproducibility of all the indices on both WM and GM was quantitatively proved on controls. ...
In particular, both 3D-SHORE-based and DTI indices exhibited high reproducibility, as quantified by ICC, and high stability, as quantified by intra/inter-subject CV parameters, on both tract and region-based ...
doi:10.3389/fnins.2018.00092
pmid:29515362
pmcid:PMC5826355
fatcat:6dlax2nflffuhj5emk534ym6s4
Diffusion-Weighted Imaging of the Spinal Cord
[chapter]
2014
Quantitative MRI of the Spinal Cord
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TRACTOGRAPHY Fiber tracking or tractography uses information from DWI data to obtain a 3D representation of fiber architecture in the white matter. ...
assess specific white matter tracts. ...
doi:10.1016/b978-0-12-396973-6.00009-5
fatcat:2pzz7ydv2rcvhmn7zuhsows7si
Tracking white-matter brain modifications in chronic non-bothersome acoustic trauma tinnitus
2021
NeuroImage: Clinical
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We conducted a deep-learning based tractography segmentation and mapped Apparent Fiber Density (AFD) on the bundles of interest. ...
To date, the specific role of white matter abnormalities related to tinnitus reaches no consensus in the literature. ...
This study was performed on the IRMaGe platform member of France Life Imaging network (Grant ANR-11-INBS-0006). ...
doi:10.1016/j.nicl.2021.102696
pmid:34029920
fatcat:sm2is3djf5f6pfldhrpu4seq4y
Enhancing the Estimation of Fiber Orientation Distributions using Convolutional Neural Networks
2021
Computers in Biology and Medicine
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We evaluate U-Net and High-Resolution Network (HighResNet) 3D CNN architectures on data from the Human Connectome Project and an in-house dataset. ...
than used to train the CNN; and 3) when testing on a dataset with a fewer number of gradient directions than used to train the CNN. ...
We evaluate U-Net and High-Resolution Network (HighResNet) 3D CNN architectures on data from the Human Connectome Project and an in-house dataset. ...
doi:10.1016/j.compbiomed.2021.104643
pmid:34280774
fatcat:76tw73wenfcarfov4se3apklbe
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