arXiv subjects

Abrar Faiyaz

Publications and source records attributed to Abrar Faiyaz.

4 recordsLinked to original sources

arXiv2026

Theoretical derivation of blood velocity from TOF-MRA based artery centerline

Time-of-flight magnetic resonance angiography (TOF-MRA) is widely used for nonin-vasive visualization of arterial anatomy, but extracting hemodynamics like blood velocity typically requires supplementary phase-contrast scans, tagging or multi-TE images. This study proposes a novel, physics-informed computational framework to extract variable fluid velocity directly from standard TOF-MRA signal profiles. We analytically expand the approach-to-steady-state Bloch equations to include convective flow, establishing a mathematical relationship between the spatial decay of longitudinal magnetization and fluid velocity. The velocity derivation was further extended to pointwise estimation over a 1-D centerline, overcoming the limitations of constant-velocity assumptions. To validate and solve this problem, a MATLAB (R2025b) simulation framework was developed to model fluid flow in two variable-geometry flowing tube cases, i.e., continuous narrowing and focal stenosis, under synthetic scanner noise. A global inverse optimization approach utilizing Dual-Tikhonov regularization was applied to stably invert the ill-posed transit time integral, actively penalizing high-frequency numerical ringing while preserving structural curves. The computational simulations successfully recovered ground-truth point-wise velocities, tracking gradual hemodynamic accelerations and sharp stenotic jets. This theoretical framework and the example centerline TOF-MRA signal intensity pro-vide a robust mathematical proof-of-concept that quantitative, localized functional he-modynamic metrics can be extracted from standard structural MRA imaging, establishing a foundation for advanced flow quantification without requiring additional scan time.

physics.med-ph↗

arXiv2025

ArteryX: A Reliable End-to-End Toolbox for Standardized Intracranial Artery Feature Extraction from 3D TOF-MRA

Cerebrovascular research heavily relies on quantitative analysis of intracranial arteries from time-of-flight magnetic resonance angiography, yet existing processing pipelines remain limited by inconsistent artery labeling and a high manual correction burden. We present ArteryX, a toolbox for extracting features that standardizes artery classification across proximal and distal vascular territories. It integrates segmentation handling, isotropic processing, vessel-fused graph construction, and constrained landmark-based classification within a unified artery-specific feature reporting and reproducible workflow. The toolbox extracts morphological, topological, and complexity features including total length, mean radius, volume, surface area, branch count, tortuosity, and fractal dimensionality for standardized artery-segments. Test-and-validation were performed using three complementary datasets: (1)TopBrain-Challenge benchmarking with annotated arteries, (2)synthetic known-reference validation, and (3)exploratory in-vivo cohort of cerebral small vessel disease. In TopBrain analyses, ArteryX with supervised nnUnet segmentation showed minimal bias, while iCafe showed the highest bias and a large limit-of-agreement. ArteryX consistently demonstrated robust downstream quantification performance across segmentation sources (unsupervised/supervised). Agreement analyses showed minimal bias for radius and good sensitivity of extent-dependent metrics throughout the noisier segmentations compared to the state-of-the-art iCafe-toolbox. Furthermore, a stage-wise human-in-the-loop protocol showed lower intervention time than iCafe. In an in-vivo-cohort (48CSVD+, 20CSVD-), ArteryX-derived distal and territory-level features showed group-level differences, not evident with iCafe. To facilitate adoption-and-reproducibility, ArteryX is designed with versioned builds, tutorials, and documentation.

eess.IV↗

arXiv2022

Angular upsampling in diffusion MRI using contextual HemiHex sub-sampling in q-space

Artificial Intelligence (Deep Learning(DL)/ Machine Learning(ML)) techniques are widely being used to address and overcome all kinds of ill-posed problems in medical imaging which was or in fact is seemingly impossible. Reducing gradient directions but harnessing high angular resolution(HAR) diffusion data in MR that retains clinical features is an important and challenging problem in the field. While the DL/ML approaches are promising, it is important to incorporate relevant context for the data to ensure that maximum prior information is provided for the AI model to infer the posterior. In this paper, we introduce HemiHex (HH) subsampling to suggestively address training data sampling on q-space geometry, followed by a nearest neighbor regression training on the HH-samples to finally upsample the dMRI data. Earlier studies has tried to use regression for up-sampling dMRI data but yields performance issues as it fails to provide structured geometrical measures for inference. Our proposed approach is a geometrically optimized regression technique which infers the unknown q-space thus addressing the limitations in the earlier studies.

eess.IV↗

arXiv2021

Single-Shell NODDI Using Dictionary Learner Estimated Isotropic Volume Fraction

Neurite orientation dispersion and density imaging (NODDI) enables the assessment of intracellular, extracellular and free water signals from multi-shell diffusion MRI data. It is an insightful approach to characterize brain tissue microstructure. Single-shell reconstruction for NODDI parameters has been discouraged in previous studies caused by failure when fitting, especially for the neurite density index (NDI). Here, we investigated the possibility of creating robust NODDI parameter maps with single-shell data, using the isotropic volume fraction (fISO) as prior. Prior estimation was made independent of the NODDI model constraint using a dictionary learning approach. First, we used a stochastic sparse dictionary-based network (DictNet) in predicting fISO which is trained with data obtained from in vivo and simulated diffusion MRI data. In single-shell cases, the mean diffusivity (MD) and raw T2 signal with no diffusion weighting (S0) was incorporated in the dictionary for the fISO estimation. Then, the NODDI framework was used with the known fISO to estimate the NDI and orientation dispersion index (ODI). The fISO estimated by our model was compared with other fISO estimators in the simulation. Further, using both synthetic data simulation and human data collected on a 3T scanner, we compared the performance of our dictionary-based learning prior NODDI (DLpN) with the original NODDI for both single-shell and multi-shell data. Our results suggest that DLpN derived NDI and ODI parameters for single-shell protocols are comparable with original multi-shell NODDI, and protocol with b=2000 s/mm2 performs the best (error ~5% in white and grey matter). This may allow NODDI evaluation of studies on single-shell data by multi-shell scanning of two subjects for DictNet fISO training.

physics.med-ph↗