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Yogesh Rathi

Publications and source records attributed to Yogesh Rathi.

At least 19 recordsLinked to original sources

Prior-Guided Implicit Neural Representations for Single-Subject Diffusion MRI Super-Resolution

Resolving complex fiber geometries in brain white matter requires high-resolution diffusion MRI at the cost of long acquisition times. This leads many clinical protocols to opt for low-resolution scans, making downstream microstructure estimation and tractography challenging. Implicit neural representations (INRs) can model the diffusion signal continuously, enabling native single-subject super-resolution by querying the network at arbitrary spatial coordinates, yet existing methods often suffer from long training times and lack a mechanism to incorporate anatomical priors to regularize super-resolution by constraining the space of plausible reconstructions. To address these limitations, we propose a novel transfer-learning framework that pre-trains an INR on a high-resolution template and then adapts it to subject-specific scans via registration and fine-tuning. For $4\times$ through-plane super-resolution from 5 mm to 1.25 mm on Human Connectome Project (HCP) data, our method reduces NRMSE by 36-49% and increases FSIM by 24-43% over a recent baseline with $6\times$ faster training, outperforming competing INR-based methods across both image quality and domain-specific metrics. Code is available on the project page at https://abdulkaderghandoura.github.io/research/msc-thesis/ .

eess.IV

Vendor-Agnostic Joint Relaxometry and Myelin Water Fraction Mapping with B1 and Motion Correction

Obtaining consistent quantitative maps of myelin content and relaxation times across different sites and vendors is essential for advancing our understanding of brain development. Herein, we present a harmonized, vendor-agnostic magnetic resonance acquisition method designed for joint T1, T2, and myelin water fraction mapping, along with a method for rapid B1+ and B1- field estimation. We used our dictionary-based fitting and multi-compartment modeling for joint mapping of T1, T2 and myelin water fraction. Self-navigation-based retrospective motion correction was integrated with subspace reconstruction to track and correct rigid head motion during scanning, operating without the need for external hardware. Simulations, phantom and in vivo experiments confirmed the sensitivity and accuracy of the method, particularly for short T2 values corresponding to myelin, and demonstrated consistent performance across multiple scanner types. Coupled with the harmonized calibration scan, the proposed package offers a practical tool for multi-site, multi-vendor neuroimaging studies in both adult and pediatric populations.

physics.med-ph

SIINR: Structurally Informed Implicit Neural Representations for super-resolution with uncertainty quantification of clinical quality diffusion MRI datasets

Diffusion Magnetic Resonance Imaging (dMRI) is a powerful tool for probing brain microstructure, but clinical acquisitions are often limited by low out-of-plane resolution, resulting in degraded structural information and reduced utility for advanced analysis. We introduce SIINR (Structurally Informed Implicit Neural Representations), a general framework for super-resoltion of clinical dMRI datasets while quantifying uncertainty in the reconstructed outputs. SIINR utilizes a supervised 3D U-net as a prior and combines it with a self-supervised implicit neural representation (INR) that fuses the high-resolution prior and the original low-resolution data. The INR enables joint modeling across spatial and angular domains, enforces data consistency, and provides analytic approximate posterior distributions for downstream uncertainty quantification. We validate the framework on a diverse set of open-access dMRI datasets, demonstrating that SIINR outperforms standard interpolation methods in both quantitative error metrics and qualitative anatomical fidelity. Experiments on clinical cases, including subjects with multiple sclerosis and brain lesions, illustrate the framework its ability to propagate intensity changes and flag uncertain regions in challenging scenarios. SIINR is flexible, modular, and can be adapted to different upsampling ratios and downstream tasks, providing a principled approach for enhancing clinical dMRI and supporting robust interpretation of derived neuroimaging metrics.

cs.CV

Tractogram foundation model

Diffusion MRI (dMRI) tractography is the only noninvasive approach for mapping white-matter pathways in the living human brain. It represents each brain as a tractogram: a large, unordered set of three-dimensional streamlines that includes information about both local streamline geometry and whole-brain anatomical organization. This structure makes tractograms a natural but challenging target for representation learning. Existing methods treat streamline classification and subject-level prediction as separate problems: streamline classifiers focus on geometric patterns, whereas subject-level prediction often depends on hand-crafted features. As a result, current methods do not learn reusable representations that connect streamline anatomy with whole-brain inter-subject variation. Here we introduce TractFM, a tractogram foundation model that learns reusable representations directly from whole-brain streamline sets. TractFM combines a local streamline encoder with a permutation-equivariant tractogram encoder, allowing all streamlines from a subject to be contextualized jointly in a single forward pass. Pretraining on dense anatomical tract parcellation, i.e., assigning anatomical labels to individual streamlines, yields two complementary representations: contextualized streamline-level embeddings for tract parcellation and compact subject-level descriptors for downstream prediction of subject phenotypes. Across three tractography algorithms and five dMRI datasets, TractFM transfers to both streamline-level and subject-level tasks. Its frozen representations achieve accurate tract parcellation and predict age and sex across independent datasets. These results show that whole-brain geometric context, learned once, can generalize across tractography pipelines, datasets, and prediction tasks.

eess.IV

HARP: HARmonizing in-vivo diffusion MRI using Phantom-only training

Purpose: Combining multi-site diffusion MRI (dMRI) data is hindered by inter-scanner variability, which confounds subsequent analysis. Previous harmonization methods require large, matched or traveling human subjects from multiple sites, which are impractical to acquire in many situations. This study aims to develop a deep learning-based dMRI harmonization framework that eliminates the reliance on multi-site in-vivo traveling human data for training. Methods: HARP employs a voxel-wise 1D neural network trained on an easily transportable diffusion phantom. The model learns relationships between spherical harmonics coefficients of different sites without memorizing spatial structures. Results: HARP reduced inter-scanner variability levels significantly in various measures. Quantitatively, it decreased inter-scanner variability as measured by standard error in FA (12%), MD (10%), and GFA (30%) with scan-rescan standard error as the baseline, while preserving fiber orientations and tractography after harmonization. Conclusion: We believe that HARP represents an important first step toward dMRI harmonization using only phantom data, thereby obviating the need for complex, matched in vivo multi-site cohorts. This phantom-only strategy substantially enhances the feasibility and scalability of quantitative dMRI for large-scale clinical studies.

cs.CV

Cross-Population White Matter Atlas Creation for Concurrent Mapping of Brain Connections in Neonates and Adults with Diffusion MRI Tractography

Comparing white matter (WM) connections between adults and neonates using diffusion MRI (dMRI) can advance our understanding of typical brain development and potential biomarkers for neurological disorders. However, existing WM atlases are population-specific (adult or neonatal) and reside in separate spaces, preventing direct cross-population comparisons. A unified WM atlas spanning both neonates and adults is still lacking. In this study, we propose a neonatal/adult brain atlas (NABA), a WM tractography atlas built from dMRI data of both neonates and adults. NABA is constructed using a robust, data-driven fiber clustering pipeline, enabling group-wise WM atlasing across populations despite substantial anatomical variability. The atlas provides a standardized template for WM parcellation, allowing direct comparison of WM tracts between neonates and adults. Using NABA, we conduct four analyses: (1) evaluating the feasibility of joint WM mapping across populations, (2) characterizing WM development across neonatal ages relative to adults, (3) assessing sex-related differences in neonatal WM development, and (4) examining the effects of preterm birth. Our results show that NABA robustly identifies WM tracts in both populations. We observe rapid fractional anisotropy (FA) development in long-range association tracts, including the arcuate fasciculus and superior longitudinal fasciculus II, whereas intra-cerebellar tracts develop more slowly. Neonatal females exhibit faster overall FA development than males. Although preterm neonates show lower overall FA development rates, they demonstrate relatively higher FA growth in specific tracts, including the corticospinal tract, corona radiata-pontine pathway, and intracerebellar tracts. These findings demonstrate that NABA is a useful tool for investigating WM development across neonates and adults.

cs.NE

DMVFC: Deep Learning Based Functionally Consistent Tractography Fiber Clustering Using Multimodal Diffusion MRI and Functional MRI

Tractography fiber clustering using diffusion MRI (dMRI) is a crucial method for white matter (WM) parcellation to enable analysis of brains structural connectivity in health and disease. Current fiber clustering strategies primarily use the fiber geometric characteristics (i.e., the spatial trajectories) to group similar fibers into clusters, while neglecting the functional and microstructural information of the fiber tracts. There is increasing evidence that neural activity in the WM can be measured using functional MRI (fMRI), providing potentially valuable multimodal information for fiber clustering to enhance its functional coherence. Furthermore, microstructural features such as fractional anisotropy (FA) can be computed from dMRI as additional information to ensure the anatomical coherence of the clusters. In this paper, we develop a novel deep learning fiber clustering framework, namely Deep Multi-view Fiber Clustering (DMVFC), which uses joint multi-modal dMRI and fMRI data to enable functionally consistent WM parcellation. DMVFC can effectively integrate the geometric and microstructural characteristics of the WM fibers with the fMRI BOLD signals along the fiber tracts. DMVFC includes two major components: (1) a multi-view pretraining module to compute embedding features from each source of information separately, including fiber geometry, microstructure measures, and functional signals, and (2) a collaborative fine-tuning module to simultaneously refine the differences of embeddings. In the experiments, we compare DMVFC with two state-of-the-art fiber clustering methods and demonstrate superior performance in achieving functionally meaningful and consistent WM parcellation results.

eess.IV

Is the medical image segmentation problem solved? A survey of current developments and future directions

Medical image segmentation has advanced rapidly over the past two decades, largely driven by deep learning, which has enabled accurate and efficient delineation of cells, tissues, organs, and pathologies across diverse imaging modalities. This progress raises a fundamental question: to what extent have current models overcome persistent challenges, and what gaps remain? In this work, we provide an in-depth review of medical image segmentation, tracing its progress and key developments over the past decade. We examine core principles, including multiscale analysis, attention mechanisms, and the integration of prior knowledge, across the encoder, bottleneck, skip connections, and decoder components of segmentation networks. Our discussion is organized around seven key dimensions: (1) the shift from supervised to semi-/unsupervised learning, (2) the transition from organ segmentation to lesion-focused tasks, (3) advances in multi-modality integration and domain adaptation, (4) the role of foundation models and transfer learning, (5) the move from deterministic to probabilistic segmentation, (6) the progression from 2D to 3D and 4D segmentation, and (7) the trend from model invocation to segmentation agents. Together, these perspectives provide a holistic overview of the trajectory of deep learning-based medical image segmentation and aim to inspire future innovation. To support ongoing research, we maintain a continually updated repository of relevant literature and open-source resources at https://github.com/apple1986/medicalSegReview

eess.IV

DDTracking: A Deep Generative Framework for Diffusion MRI Tractography with Streamline Local-Global Spatiotemporal Modeling

This paper presents DDTracking, a novel deep generative framework for diffusion MRI tractography that formulates streamline propagation as a conditional denoising diffusion process. In DDTracking, we introduce a dual-pathway encoding network that jointly models local spatial encoding (capturing fine-scale structural details at each streamline point) and global temporal dependencies (ensuring long-range consistency across the entire streamline). Furthermore, we design a conditional diffusion model module, which leverages the learned local and global embeddings to predict streamline propagation orientations for tractography in an end-to-end trainable manner. We conduct a comprehensive evaluation across diverse, independently acquired dMRI datasets, including both synthetic and clinical data. Experiments on two well-established benchmarks with ground truth (ISMRM Challenge and TractoInferno) demonstrate that DDTracking largely outperforms current state-of-the-art tractography methods. Furthermore, our results highlight DDTracking's strong generalizability across heterogeneous datasets, spanning varying health conditions, age groups, imaging protocols, and scanner types. Collectively, DDTracking offers anatomically plausible and robust tractography, presenting a scalable, adaptable, and end-to-end learnable solution for broad dMRI applications. Code is available at: https://github.com/yishengpoxiao/DDtracking.git

cs.CV

Multishot Dual Polarity GRAPPA: Robust Nyquist Ghost Correction for multishot EPI

Purpose: This work aims to develop a robust Nyquist ghost correction method for multishot echo-planar imaging (EPI). The method helps correct challenging Nyquist ghosts, particularly on scanners with high-performance gradients or ultra-high fields. Methods: A method for multishot EPI ghost correction, called multishot dual-polarity GRAPPA (msDPG), is developed by extending the DPG concept to multishot readouts. msDPG employs tailored DPG kernels to address high-order phase differences between two EPI readout polarities, which cannot be fully addressed using linear phase correction (LPC). Advanced regularizers can be readily employed with the proposed msDPG for physiologic inter-shot phase variation correction during reconstruction. Additionally, a calibration refinement method is proposed to improve the quality of the DPG calibration data and enhance reconstruction performance. Results: Phantom and in vivo experiments on scanners with high-performance gradients and ultra-high fields demonstrated that msDPG achieved superior ghost correction performance than LPC, reducing the ghost-to-signal ratio (GSR) by over 50%. Compared to conventional DPG, msDPG provided images with lower noise amplification, particularly for acquisitions with large in-plane acceleration. Consequently, high-fidelity, submillimeter diffusion images were obtained using msDPG with regularized reconstruction. Conclusion: The proposed msDPG provides a robust Nyquist ghost correction method for multishot EPI, enabling submillimeter imaging with improved fidelity.

physics.med-ph

AGFS-Tractometry: A Novel Atlas-Guided Fine-Scale Tractometry Approach for Enhanced Along-Tract Group Statistical Comparison Using Diffusion MRI Tractography

Diffusion MRI (dMRI) tractography is currently the only method for in vivo mapping of the brain's white matter (WM) connections. Tractometry is an advanced tractography analysis technique for along-tract profiling to investigate the morphology and microstructural properties along the fiber tracts. Tractometry has become an essential tool for studying local along-tract differences between different populations (e.g., health vs disease). In this study, we propose a novel atlas-guided fine-scale tractometry method, namely AGFS-Tractometry, that leverages tract spatial information and permutation testing to enhance the along-tract statistical analysis between populations. There are two major contributions in AGFS-Tractometry. First, we create a novel atlas-guided tract profiling template that enables consistent, fine-scale, along-tract parcellation of subject-specific fiber tracts. Second, we propose a novel nonparametric permutation testing group comparison method to enable simultaneous analysis across all along-tract parcels while correcting for multiple comparisons. We perform experimental evaluations on synthetic datasets with known group differences and in vivo real data. We compare AGFS-Tractometry with two state-of-the-art tractometry methods, including Automated Fiber-tract Quantification (AFQ) and BUndle ANalytics (BUAN). Our results show that the proposed AGFS-Tractometry obtains enhanced sensitivity and specificity in detecting local WM differences. In the real data analysis experiments, AGFS-Tractometry can identify more regions with significant differences, which are anatomically consistent with the existing literature. Overall, these demonstrate the ability of AGFS-Tractometry to detect subtle or spatially localized WM group-level differences. The created tract profiling template and related code are available at: https://github.com/ZhengRuixi/AGFS-Tractometry.git.

q-bio.QM

A Multimodal Deep Learning Approach for White Matter Shape Prediction in Diffusion MRI Tractography

Shape measures have emerged as promising descriptors of white matter tractography, offering complementary insights into anatomical variability and associations with cognitive and clinical phenotypes. However, conventional methods for computing shape measures are computationally expensive and time-consuming for large-scale datasets due to reliance on voxel-based representations. We propose Tract2Shape, a novel multimodal deep learning framework that leverages geometric (point cloud) and scalar (tabular) features to predict ten white matter tractography shape measures. To enhance model efficiency, we utilize a dimensionality reduction algorithm for the model to predict five primary shape components. The model is trained and evaluated on two independently acquired datasets, the HCP-YA dataset, and the PPMI dataset. We evaluate the performance of Tract2Shape by training and testing it on the HCP-YA dataset and comparing the results with state-of-the-art models. To further assess its robustness and generalization ability, we also test Tract2Shape on the unseen PPMI dataset. Tract2Shape outperforms SOTA deep learning models across all ten shape measures, achieving the highest average Pearson's r and the lowest nMSE on the HCP-YA dataset. The ablation study shows that both multimodal input and PCA contribute to performance gains. On the unseen testing PPMI dataset, Tract2Shape maintains a high Pearson's r and low nMSE, demonstrating strong generalizability in cross-dataset evaluation. Tract2Shape enables fast, accurate, and generalizable prediction of white matter shape measures from tractography data, supporting scalable analysis across datasets. This framework lays a promising foundation for future large-scale white matter shape analysis.

eess.IV

DeepNuParc: A Novel Deep Clustering Framework for Fine-scale Parcellation of Brain Nuclei Using Diffusion MRI Tractography

Brain nuclei are clusters of anatomically distinct neurons that serve as important hubs for processing and relaying information in various neural circuits. Fine-scale parcellation of the brain nuclei is vital for a comprehensive understanding of its anatomico-functional correlations. Diffusion MRI tractography is an advanced imaging technique that can estimate the brain's white matter structural connectivity to potentially reveal the topography of the nuclei of interest for studying its subdivisions. In this work, we present a deep clustering pipeline, namely DeepNuParc, to perform automated, fine-scale parcellation of brain nuclei using diffusion MRI tractography. First, we incorporate a newly proposed deep learning approach to enable accurate segmentation of the nuclei of interest directly on the dMRI data. Next, we design a novel streamline clustering-based structural connectivity feature for a robust representation of voxels within the nuclei. Finally, we improve the popular joint dimensionality reduction and k-means clustering approach to enable nuclei parcellation at a finer scale. We demonstrate DeepNuParc on two important brain structures, i.e. the amygdala and the thalamus, that are known to have multiple anatomically and functionally distinct nuclei subdivisions. Experimental results show that DeepNuParc enables consistent parcellation of the nuclei into multiple parcels across multiple subjects and achieves good correspondence with the widely used coarse-scale atlases. Our codes are available at https://github.com/HarlandZZC/deep_nuclei_parcellation.

eess.IV

TractCloud-FOV: Deep Learning-based Robust Tractography Parcellation in Diffusion MRI with Incomplete Field of View

Tractography parcellation classifies streamlines reconstructed from diffusion MRI into anatomically defined fiber tracts for clinical and research applications. However, clinical scans often have incomplete fields of view (FOV) where brain regions are partially imaged, leading to partial or truncated fiber tracts. To address this challenge, we introduce TractCloud-FOV, a deep learning framework that robustly parcellates tractography under conditions of incomplete FOV. We propose a novel training strategy, FOV-Cut Augmentation (FOV-CA), in which we synthetically cut tractograms to simulate a spectrum of real-world inferior FOV cutoff scenarios. This data augmentation approach enriches the training set with realistic truncated streamlines, enabling the model to achieve superior generalization. We evaluate the proposed TractCloud-FOV on both synthetically cut tractography and two real-life datasets with incomplete FOV. TractCloud-FOV significantly outperforms several state-of-the-art methods on all testing datasets in terms of streamline classification accuracy, generalization ability, tract anatomical depiction, and computational efficiency. Overall, TractCloud-FOV achieves efficient and consistent tractography parcellation in diffusion MRI with incomplete FOV.

cs.CV

Rapid Whole Brain Motion-robust Mesoscale In-vivo MR Imaging using Multi-scale Implicit Neural Representation

High-resolution whole-brain in vivo MR imaging at mesoscale resolutions remains challenging due to long scan durations, motion artifacts, and limited signal-to-noise ratio (SNR). This study proposes Rotating-view super-resolution (ROVER)-MRI, an unsupervised framework based on multi-scale implicit neural representations (INR), enabling efficient recovery of fine anatomical details from multi-view thick-slice acquisitions. ROVER-MRI employs coordinate-based neural networks to implicitly and continuously encode image structures at multiple spatial scales, simultaneously modeling anatomical continuity and correcting inter-view motion through an integrated registration mechanism. Validation on ex-vivo monkey brain data and multiple in-vivo human datasets demonstrates substantially improved reconstruction performance compared to bicubic interpolation and state-of-the-art regularized least-squares super-resolution reconstruction (LS-SRR) with 2-fold reduction in scan time. Notably, ROVER-MRI achieves an unprecedented whole-brain in-vivo T2-weighted imaging at 180 micron isotropic resolution in only 17 minutes of scan time on a 7T scanner with 22.4% lower relative error compared to LS-SRR. We also demonstrate improved SNR using ROVER-MRI compared to a time-matched 3D GRE acquisition. Quantitative results on several datasets demonstrate better sharpness of the reconstructed images with ROVER-MRI for different super-resolution factors (5 to 11). These findings highlight ROVER-MRI's potential as a rapid, accurate, and motion-resilient mesoscale imaging solution, promising substantial advantages for neuroimaging studies.

eess.IV

MICCAI-CDMRI 2023 QuantConn Challenge Findings on Achieving Robust Quantitative Connectivity through Harmonized Preprocessing of Diffusion MRI

White matter alterations are increasingly implicated in neurological diseases and their progression. International-scale studies use diffusion-weighted magnetic resonance imaging (DW-MRI) to qualitatively identify changes in white matter microstructure and connectivity. Yet, quantitative analysis of DW-MRI data is hindered by inconsistencies stemming from varying acquisition protocols. There is a pressing need to harmonize the preprocessing of DW-MRI datasets to ensure the derivation of robust quantitative diffusion metrics across acquisitions. In the MICCAI-CDMRI 2023 QuantConn challenge, participants were provided raw data from the same individuals collected on the same scanner but with two different acquisitions and tasked with preprocessing the DW-MRI to minimize acquisition differences while retaining biological variation. Submissions are evaluated on the reproducibility and comparability of cross-acquisition bundle-wise microstructure measures, bundle shape features, and connectomics. The key innovations of the QuantConn challenge are that (1) we assess bundles and tractography in the context of harmonization for the first time, (2) we assess connectomics in the context of harmonization for the first time, and (3) we have 10x additional subjects over prior harmonization challenge, MUSHAC and 100x over SuperMUDI. We find that bundle surface area, fractional anisotropy, connectome assortativity, betweenness centrality, edge count, modularity, nodal strength, and participation coefficient measures are most biased by acquisition and that machine learning voxel-wise correction, RISH mapping, and NeSH methods effectively reduce these biases. In addition, microstructure measures AD, MD, RD, bundle length, connectome density, efficiency, and path length are least biased by these acquisition differences.

physics.med-ph

A Novel Deep Learning Tractography Fiber Clustering Framework for Functionally Consistent White Matter Parcellation Using Multimodal Diffusion MRI and Functional MRI

Tractography fiber clustering using diffusion MRI (dMRI) is a crucial strategy for white matter (WM) parcellation. Current methods primarily use the geometric information of fibers (i.e., the spatial trajectories) to group similar fibers into clusters, overlooking the important functional signals present along the fiber tracts. There is increasing evidence that neural activity in the WM can be measured using functional MRI (fMRI), offering potentially valuable multimodal information for fiber clustering. In this paper, we develop a novel deep learning fiber clustering framework, namely Deep Multi-view Fiber Clustering (DMVFC), that uses joint dMRI and fMRI data to enable functionally consistent WM parcellation. DMVFC can effectively integrate the geometric characteristics of the WM fibers with the fMRI BOLD signals along the fiber tracts. It includes two major components: 1) a multi-view pretraining module to compute embedding features from fiber geometric information and functional signals separately, and 2) a collaborative fine-tuning module to simultaneously refine the two kinds of embeddings. In the experiments, we compare DMVFC with two state-of-the-art fiber clustering methods and demonstrate superior performance in achieving functionally meaningful and consistent WM parcellation results.

eess.IV

TractShapeNet: Efficient Multi-Shape Learning with 3D Tractography Point Clouds

Brain imaging studies have demonstrated that diffusion MRI tractography geometric shape descriptors can inform the study of the brain's white matter pathways and their relationship to brain function. In this work, we investigate the possibility of utilizing a deep learning model to compute shape measures of the brain's white matter connections. We introduce a novel framework, TractShapeNet, that leverages a point cloud representation of tractography to compute five shape measures: length, span, volume, total surface area, and irregularity. We assess the performance of the method on a large dataset including 1065 healthy young adults. Experiments for shape measure computation demonstrate that our proposed TractShapeNet outperforms other point cloud-based neural network models in both the Pearson correlation coefficient and normalized error metrics. We compare the inference runtime results with the conventional shape computation tool DSI-Studio. Our results demonstrate that a deep learning approach enables faster and more efficient shape measure computation. We also conduct experiments on two downstream language cognition prediction tasks, showing that shape measures from TractShapeNet perform similarly to those computed by DSI-Studio. Our code will be available at: https://github.com/SlicerDMRI/TractShapeNet.

cs.CV