Biology subjects

Chandio, B. Q.

Publications and source records attributed to Chandio, B. Q..

7 recordsLinked to original sources

bioRxiv2023

BundleCleaner: Unsupervised Denoising and Subsampling of Diffusion MRI-Derived Tractography Data

We present BundleCleaner, an unsupervised multi-step frame-work that can filter, denoise and subsample bundles derived from diffusion MRI-based whole-brain tractography. Our approach considers both the global bundle structure and local streamline-wise features. We apply BundleCleaner to bundles generated from single-shell diffusion MRI data in an independent clinical sample of older adults from India using probabilistic tractography and the resulting cleaned bundles can better align with the atlas bundles with reduced overreach. In a downstream tractometry analysis, we show that the cleaned bundles, represented with less than 20% of the original set of points, can robustly localize along-tract microstructural differences between 32 healthy controls and 34 participants with Alzheimers disease ranging in age from 55 to 84 years old. Our approach can help reduce memory burden and improving computational efficiency when working with tractography data, and shows promise for large-scale multi-site tractometry.

neuroscience↗

bioRxiv2023

Along-Tract Statistical Mapping of Microstructural Abnormalities in Bipolar Disorder: A Pilot Study

Investigating brain circuitry involved in bipolar disorder (BD) is key to discovering brain biomarkers for genetic and interventional studies of the disorder. Even so, prior research has not provided a fine-scale spatial mapping of brain microstructural differences in BD. In this pilot diffusion MRI dataset, we used BUndle ANalytics (BUAN), a recently developed analytic approach for tractography, to extract, map, and visualize the profile of microstructural abnormalities on a 3D model of fiber tracts in people with BD (N=38) and healthy controls (N=49), and investigate along-tract white matter (WM) microstructural differences between these groups. Using the BUAN pipeline, BD was associated with lower mean Fractional Anisotropy (FA) in fronto-limbic and interhemispheric pathways and higher mean FA in posterior bundles relative to controls. BUAN combines tractography and anatomical information to capture distinct along-tract effects on WM microstructure that may aid in classifying diseases based on anatomical differences.

neuroscience↗

bioRxiv2023

Variational Autoencoders for Generating Synthetic Tractography-Based Bundle Templates in a Low-Data Setting

White matter tracts generated from whole brain tractography are often processed using automatic segmentation methods with standard atlases. Atlases are generated from hundreds of subjects, which becomes time-consuming to create and difficult to apply to all populations. In this study, we extended our prior work on using a deep generative model a Convolutional Variational Autoencoder - to map complex and data-intensive streamlines to a low-dimensional latent space given a limited sample size of 50 subjects from the ADNI3 dataset, to generate synthetic population-specific bundle templates using Kernel Density Estimation (KDE) on streamline embeddings. We conducted a quantitative shape analysis by calculating bundle shape metrics, and found that our bundle templates better capture the shape distribution of the bundles than the atlas data used in the original segmentation derived from young healthy adults. We further demonstrated the use of our framework for direct bundle segmentation from whole-brain tractograms.

neuroscience↗

bioRxiv2023

BundleWarp, streamline-based nonlinear registration of white matter tracts

Tractometry analysis represents a significant advancement in neuroimaging, offering a detailed examination of the brains white matter at a micro level. Unlike traditional ROI or voxel-based methods, tractometry precisely reconstructs and characterizes white matter tracts. Using advanced diffusion MRI and tractography algorithms, it maps the trajectory, shape, and connectivity patterns of individual white matter bundles. Accurate alignment of these tracts across different groups is crucial for reliable and reproducible results. Nonlinear registration techniques are essential for achieving this alignment, harmonizing bundle shapes, and improving sensitivity to disease-related changes. However, nonlinear registration is complex, especially with tractography data, which digitally represents the brains white matter anatomy. Potential structural changes in the bundles shape during registration can lead to artifacts that obscure critical anatomical details needed for disease identification. We introduce BundleWarp, a streamline-based nonlinear deformable registration method designed specifically for white matter tracts. BundleWarp employs a sophisticated approach to align two white matter bundles while preserving their topological and anatomical features. It is formulated as a probability density estimation problem with motion coherence penalties, ensuring coherent movement of points along streamlines and maintaining the anatomical integrity of tracts through displacement field regularization. Additionally, we introduce a tract morphometry framework utilizing the displacement field generated by BundleWarp to analyze white matter tract shape differences. Our results show that BundleWarp effectively quantifies bundle shape differences and enhances structural harmonization in tractometry analysis for diverse subjects, including those with Alzheimers and Parkinsons disease. Test-retest experiments further demonstrate that BundleWarp substantially improves subject finger-printing by increasing within-subject reproducibility of both bundle shape and microstructural profiles (FA, MD, RD, AD). It precisely maps the brains neuronal pathways, offering a robust tractometry framework with enhanced sensitivity for detecting disease-related structural and microstructural changes in white matter tracts associated with Mild Cognitive Impairment (MCI), dementia, and early-stage Alzheimers biomarkers, including amyloid-beta plaques and tau neurofibrillary tangles.

neuroscience↗

bioRxiv2022

Learning Optimal White Matter Tract Representations from Tractography using a Deep Generative Model for Population Analyses

Whole brain tractography is commonly used to study the brains white matter fiber pathways, but the large number of streamlines generated - up to one million per brain - can be challenging for large-scale population studies. We propose a robust dimensionality reduction framework for tractography, using a Convolutional Variational Autoencoder (ConvVAE) to learn low-dimensional embeddings from white matter bundles. The resulting embeddings can be used to facilitate downstream tasks such as outlier and abnormality detection, and mapping of disease effects on white matter tracts in individuals or groups. We design experiments to evaluate how well embeddings of different dimensions preserve distances from the original high-dimensional dataset, using distance correlation methods. We find that streamline distances and inter-bundle distances are well preserved in the latent space, with a 6-dimensional optimal embedding space. The generative ConvVAE model allows fast inference on new data, and the smooth latent space enables meaningful decodings that can be used for downstream tasks. We demonstrate the use of a ConvVAE model trained on control subjects data to detect structural anomalies in white matter tracts in patients with Alzheimers disease (AD). Using ConvVAEs to facilitate population analyses, we identified 6 tracts with statistically significant differences between AD and controls after controlling for age and sex effect, visualizing specific locations along the tracts with high anomalies despite large inter-subject variations in fiber bundle geometry.

neuroscience↗

bioRxiv2021

FiberNeat: unsupervised streamline clustering and white matter tract filtering in latent space

Whole-brain tractograms generated from diffusion MRI digitally represent the white matter structure of the brain and are composed of millions of streamlines. Such tractograms can have false positive and anatomically implausible streamlines. To obtain anatomically relevant streamlines and tracts, supervised and unsupervised methods can be used for tractogram clustering and tract extraction. Here we propose FiberNeat, an unsupervised white matter tract filtering method. FiberNeat takes an input set of streamlines that could either be unlabeled clusters or labeled tracts. Individual clusters/tracts are projected into a latent space using nonlinear dimensionality reduction techniques, t-SNE and UMAP, to find spurious and outlier streamlines. In addition, outlier streamline clusters are detected using DBSCAN and then removed from the data in streamline space. We performed quantitative comparisons with expertly delineated tracts. We ran FiberNeat on 131 participants data from the ADNI3 dataset. We show that applying FiberNeat as a filtering step after bundle segmentation improves the quality of extracted tracts and helps improve tractometry.

neuroscience↗

bioRxiv2020

Pandora: 4-D white matter bundle population-based atlasesderived from diffusion MRI fiber tractography

Brain atlases have proven to be valuable neuroscience tools for localizing regions of interest and performing statistical inferences on populations. Although many human brain atlases exist, most do not contain information about white matter structures, often neglecting them completely or labelling all white matter as a single homogenous substrate. While few white matter atlases do exist based on diffusion MRI fiber tractography, they are often limited to descriptions of white matter as spatially separate "regions" rather than as white matter "bundles" or fascicles, which are well-known to overlap throughout the brain. Additional limitations include small sample sizes, few white matter pathways, and the use of outdated diffusion models and techniques. Here, we present a new population-based collection of white matter atlases represented in both volumetric and surface coordinates in a standard space. These atlases are based on 2443 subjects, and include 216 white matter bundles derived from 6 different state-of-the-art tractography techniques. This atlas is freely available and will be a useful resource for parcellation and segmentation.

neuroscience↗