no code implementations • 6 Apr 2024 • Yijie Li, Wei zhang, Ye Wu, Li Yin, Ce Zhu, Yuqian Chen, Suheyla Cetin-Karayumak, Kang Ik K Cho, Leo R. Zekelman, Jarrett Rushmore, Yogesh Rathi, Nikos Makris, Lauren J. O'Donnell, Fan Zhang
However, a comprehensive investigation into WM fiber tracts between Eastern and Western populations is challenged due to the lack of a cross-population WM atlas and the large site-specific variability of dMRI data.
no code implementations • 27 Mar 2024 • Yui Lo, Yuqian Chen, Dongnan Liu, Wan Liu, Leo Zekelman, Fan Zhang, Yogesh Rathi, Nikos Makris, Alexandra J. Golby, Weidong Cai, Lauren J. O'Donnell
Overall, our results indicate that the shape of the brain's connections is predictive of human language function.
no code implementations • 9 Jan 2024 • Yuxiang Wei, Yuqian Chen, Tengfei Xue, Leo Zekelman, Nikos Makris, Yogesh Rathi, Weidong Cai, Fan Zhang, Lauren J. O' Donnell
We present an explainable multi-view network (EMV-Net) that can use different anatomical views to improve prediction performance.
no code implementations • 25 Nov 2023 • Haolin He, Ce Zhu, Le Zhang, Yipeng Liu, Xiao Xu, Yuqian Chen, Leo Zekelman, Jarrett Rushmore, Yogesh Rathi, Nikos Makris, Lauren J. O'Donnell, Fan Zhang
The amygdala plays a vital role in emotional processing and exhibits structural diversity that necessitates fine-scale parcellation for a comprehensive understanding of its anatomico-functional correlations.
no code implementations • 18 Jul 2023 • Tengfei Xue, Yuqian Chen, Chaoyi Zhang, Alexandra J. Golby, Nikos Makris, Yogesh Rathi, Weidong Cai, Fan Zhang, Lauren J. O'Donnell
TractCloud achieves efficient and consistent whole-brain white matter parcellation across the lifespan (from neonates to elderly subjects, including brain tumor patients) without the need for registration.
no code implementations • 16 Jul 2023 • William Consagra, Lipeng Ning, Yogesh Rathi
Inferring brain connectivity and structure \textit{in-vivo} requires accurate estimation of the orientation distribution function (ODF), which encodes key local tissue properties.
no code implementations • 8 Jul 2023 • Yuqian Chen, Leo R. Zekelman, Chaoyi Zhang, Tengfei Xue, Yang song, Nikos Makris, Yogesh Rathi, Alexandra J. Golby, Weidong Cai, Fan Zhang, Lauren J. O'Donnell
We evaluate the effectiveness of the proposed method by predicting individual performance on two neuropsychological assessments of language using a dataset of 20 association white matter fiber tracts from 806 subjects from the Human Connectome Project.
no code implementations • 9 Jun 2023 • Jianzhong He, Fan Zhang, Yiang Pan, Yuanjing Feng, Jarrett Rushmore, Erickson Torio, Yogesh Rathi, Nikos Makris, Ron Kikinis, Alexandra J. Golby, Lauren J. O'Donnell
The corticospinal tract (CST) is a critically important white matter fiber tract in the human brain that enables control of voluntary movements of the body.
1 code implementation • 10 May 2023 • Loraine Franke, Tae Young Park, Jie Luo, Yogesh Rathi, Steve Pieper, Lipeng Ning, Daniel Haehn
We present a real-time visualization system for Transcranial Magnetic Stimulation (TMS), a non-invasive neuromodulation technique for treating various brain disorders and mental health diseases.
no code implementations • 16 Mar 2023 • Wan Liu, Yuqian Chen, Chuyang Ye, Nikos Makris, Yogesh Rathi, Weidong Cai, Fan Zhang, Lauren J. O'Donnell
In this paper, we investigate the potential of fiber tract shape features for predicting non-imaging phenotypes, both individually and in combination with traditional features.
no code implementations • 5 Jan 2023 • Yuqian Chen, Fan Zhang, Leo R. Zekelman, Tengfei Xue, Chaoyi Zhang, Yang song, Nikos Makris, Yogesh Rathi, Weidong Cai, Lauren J. O'Donnell
This work shows the potential of incorporating anatomical information, especially known anatomical similarities between input features, to guide convolutions in neural networks.
no code implementations • 18 Nov 2022 • Xiao Xu, Yuqian Chen, Leo Zekelman, Yogesh Rathi, Nikos Makris, Fan Zhang, Lauren J. O'Donnell
In this paper, we investigate a deep nonnegative matrix factorization clustering method (DNMFC) for parcellation of the human DN based on its structural connectivity using diffusion MRI tractography.
no code implementations • 15 Nov 2022 • Sipei Li, Jianzhong He, Tengfei Xue, Guoqiang Xie, Shun Yao, Yuqian Chen, Erickson F. Torio, Yuanjing Feng, Dhiego CA Bastos, Yogesh Rathi, Nikos Makris, Ron Kikinis, Wenya Linda Bi, Alexandra J Golby, Lauren J O'Donnell, Fan Zhang
The retinogeniculate pathway (RGVP) is responsible for carrying visual information from the retina to the lateral geniculate nucleus.
no code implementations • 11 Nov 2022 • Yuxiang Wei, Tengfei Xue, Yogesh Rathi, Nikos Makris, Fan Zhang, Lauren J. O'Donnell
The brain's white matter (WM) undergoes developmental and degenerative processes during the human lifespan.
no code implementations • 13 Oct 2022 • Tengfei Xue, Fan Zhang, Leo R. Zekelman, Chaoyi Zhang, Yuqian Chen, Suheyla Cetin-Karayumak, Steve Pieper, William M. Wells, Yogesh Rathi, Nikos Makris, Weidong Cai, Lauren J. O'Donnell
We propose a novel deep regression method, namely TractoSCR, that allows full supervision for contrastive learning in regression tasks using diffusion MRI tractography.
1 code implementation • 24 Aug 2022 • Kyler Larsen, Arghya Pal, Yogesh Rathi
The model was evaluated through L1 loss, gradient normalization, and structural similarity values.
1 code implementation • 18 Jul 2022 • Tengfei Xue, Fan Zhang, Chaoyi Zhang, Yuqian Chen, Yang song, Alexandra J. Golby, Nikos Makris, Yogesh Rathi, Weidong Cai, Lauren J. O'Donnell
We propose a novel two-stage deep-learning-based framework, Superficial White Matter Analysis (SupWMA), that performs an efficient and consistent parcellation of 198 SWM clusters from whole-brain tractography.
no code implementations • 6 Jul 2022 • Yuqian Chen, Fan Zhang, Chaoyi Zhang, Tengfei Xue, Leo R. Zekelman, Jianzhong He, Yang song, Nikos Makris, Yogesh Rathi, Alexandra J. Golby, Weidong Cai, Lauren J. O'Donnell
In this paper, we propose a deep-learning-based framework for neuropsychological score prediction using microstructure measurements estimated from diffusion magnetic resonance imaging (dMRI) tractography, focusing on predicting performance on a receptive vocabulary assessment task based on a critical fiber tract for language, the arcuate fasciculus (AF).
no code implementations • 5 Jul 2022 • Fan Zhang, Tengfei Xue, Weidong Cai, Yogesh Rathi, Carl-Fredrik Westin, Lauren J O'Donnell
Whole brain tractography (WBT) data contains over hundreds of thousands of individual fiber streamlines (estimated brain connections), and this data is usually parcellated to create compact representations for data analysis applications such as disease classification.
1 code implementation • 2 May 2022 • Yuqian Chen, Chaoyi Zhang, Tengfei Xue, Yang song, Nikos Makris, Yogesh Rathi, Weidong Cai, Fan Zhang, Lauren J. O'Donnell
In this work, we propose a novel deep learning framework for white matter fiber clustering, Deep Fiber Clustering (DFC), which solves the unsupervised clustering problem as a self-supervised learning task with a domain-specific pretext task to predict pairwise fiber distances.
no code implementations • 8 Feb 2022 • Hao He, Fan Zhang, Steve Pieper, Nikos Makris, Yogesh Rathi, William Wells III, Lauren J. O'Donnell
The human brain's white matter (WM) structure is of immense interest to the scientific community.
1 code implementation • 29 Jan 2022 • Tengfei Xue, Fan Zhang, Chaoyi Zhang, Yuqian Chen, Yang song, Nikos Makris, Yogesh Rathi, Weidong Cai, Lauren J. O'Donnell
Most parcellation methods focus on the deep white matter (DWM), while fewer methods address the superficial white matter (SWM) due to its complexity.
no code implementations • 17 Sep 2021 • Arghya Pal, Yogesh Rathi
Given the rapidly growing nature of the field, it is imperative to consolidate and summarize the large number of deep learning methods that have been reported in the literature, to obtain a better understanding of the field in general.
no code implementations • 11 Jul 2021 • Yuqian Chen, Chaoyi Zhang, Yang song, Nikos Makris, Yogesh Rathi, Weidong Cai, Fan Zhang, Lauren J. O'Donnell
White matter fiber clustering (WMFC) enables parcellation of white matter tractography for applications such as disease classification and anatomical tract segmentation.
1 code implementation • 16 May 2020 • Loraine Franke, Daniel Karl I. Weidele, Fan Zhang, Suheyla Cetin-Karayumak, Steve Pieper, Lauren J. O'Donnell, Yogesh Rathi, Daniel Haehn
Tractography from high-dimensional diffusion magnetic resonance imaging (dMRI) data allows brain's structural connectivity analysis.
1 code implementation • 26 Apr 2020 • Daniel Haehn, Loraine Franke, Fan Zhang, Suheyla Cetin Karayumak, Steve Pieper, Lauren O'Donnell, Yogesh Rathi
Fiber tracking produces large tractography datasets that are tens of gigabytes in size consisting of millions of streamlines.