Search Results for author: Yogesh Rathi

Found 25 papers, 7 papers with code

A Novel Deep Clustering Framework for Fine-Scale Parcellation of Amygdala Using dMRI Tractography

no code implementations25 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.

Clustering Deep Clustering +1

TractCloud: Registration-free tractography parcellation with a novel local-global streamline point cloud representation

no code implementations18 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.

Anatomy

Neural Orientation Distribution Fields for Estimation and Uncertainty Quantification in Diffusion MRI

no code implementations16 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.

Uncertainty Quantification

TractGeoNet: A geometric deep learning framework for pointwise analysis of tract microstructure to predict language assessment performance

no code implementations8 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.

regression

SlicerTMS: Real-Time Visualization of Transcranial Magnetic Stimulation for Mental Health Treatment

1 code implementation10 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.

Computational Efficiency

Fiber Tract Shape Measures Inform Prediction of Non-Imaging Phenotypes

no code implementations16 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.

TractGraphCNN: anatomically informed graph CNN for classification using diffusion MRI tractography

no code implementations5 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.

Tractography-Based Parcellation of Cerebellar Dentate Nuclei via a Deep Nonnegative Matrix Factorization Clustering Method

no code implementations18 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.

Clustering

A Deep Learning Approach Using Masked Image Modeling for Reconstruction of Undersampled K-spaces

1 code implementation24 Aug 2022 Kyler Larsen, Arghya Pal, Yogesh Rathi

The model was evaluated through L1 loss, gradient normalization, and structural similarity values.

MRI Reconstruction

White Matter Tracts are Point Clouds: Neuropsychological Score Prediction and Critical Region Localization via Geometric Deep Learning

no code implementations6 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).

TractoFormer: A Novel Fiber-level Whole Brain Tractography Analysis Framework Using Spectral Embedding and Vision Transformers

no code implementations5 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.

Data Augmentation Ensemble Learning

Deep fiber clustering: Anatomically informed fiber clustering with self-supervised deep learning for fast and effective tractography parcellation

1 code implementation2 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.

Anatomy Clustering +3

SupWMA: Consistent and Efficient Tractography Parcellation of Superficial White Matter with Deep Learning

1 code implementation29 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.

Contrastive Learning

A review and experimental evaluation of deep learning methods for MRI reconstruction

no code implementations17 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.

MRI Reconstruction

Deep Fiber Clustering: Anatomically Informed Unsupervised Deep Learning for Fast and Effective White Matter Parcellation

no code implementations11 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.

Clustering Segmentation +1

TRAKO: Efficient Transmission of Tractography Data for Visualization

1 code implementation26 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.

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