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Chandio BQ, Olivetti E, Romero-Bascones D, Harezlak J, Garyfallidis E. BundleWarp, streamline-based nonlinear registration of white matter tracts. bioRxiv 2023:2023.01.04.522802. [PMID: 36711974 PMCID: PMC9881938 DOI: 10.1101/2023.01.04.522802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nonlinear registration plays a central role in most neuroimage analysis methods and pipelines, such as in tractography-based individual and group-level analysis methods. However, nonlinear registration is a non-trivial task, especially when dealing with tractography data that digitally represent the underlying anatomy of the brain's white matter. Furthermore, such process often changes the structure of the data, causing artifacts that can suppress the underlying anatomical and structural details. In this paper, we introduce BundleWarp, a novel and robust streamline-based nonlinear registration method for the registration of white matter tracts. BundleWarp intelligently warps two bundles while preserving the bundles' crucial topological features. BundleWarp has two main steps. The first step involves the solution of an assignment problem that matches corresponding streamlines from the two bundles (iterLAP step). The second step introduces streamline-specific point-based deformations while keeping the topology of the bundle intact (mlCPD step). We provide comparisons against streamline-based linear registration and image-based nonlinear registration methods. BundleWarp quantitatively and qualitatively outperforms both, and we show that BundleWarp can deform and, at the same time, preserve important characteristics of the original anatomical shape of the bundles. Results are shown on 1,728 pairs of bundle registrations across 27 different bundle types. In addition, we present an application of BundleWarp for quantifying bundle shape differences using the generated deformation fields.
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Affiliation(s)
- Bramsh Qamar Chandio
- Department of Intelligent Systems Engineering, Indiana University Bloomington, USA
| | | | - David Romero-Bascones
- Biomedical Engineering Department, Faculty of Engineering (MU-ENG), Mondragon Unibertsitatea, Spain
- Moorfields Eye Hospital NHS Foundation Trust, UK
| | - Jaroslaw Harezlak
- Department of Epidemiology and Biostatistics, Indiana University Bloomington, USA
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Chandio BQ, Chattopadhyay T, Owens-Walton C, Reina JEV, Nabulsi L, Thomopoulos SI, Garyfallidis E, Thompson PM. FiberNeat: Unsupervised White Matter Tract Filtering. Annu Int Conf IEEE Eng Med Biol Soc 2022; 2022:5055-5061. [PMID: 36085780 DOI: 10.1109/embc48229.2022.9870877] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
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.
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Yang Q, Hansen CB, Cai LY, Rheault F, Lee HH, Bao S, Chandio BQ, Williams O, Resnick SM, Garyfallidis E, Anderson AW, Descoteaux M, Schilling KG, Landman BA. Learning white matter subject-specific segmentation from structural MRI. Med Phys 2022; 49:2502-2513. [PMID: 35090192 PMCID: PMC9053869 DOI: 10.1002/mp.15495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 12/20/2021] [Accepted: 01/10/2022] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Mapping brain white matter (WM) is essential for building an understanding of brain anatomy and function. Tractography-based methods derived from diffusion-weighted MRI (dMRI) are the principal tools for investigating WM. These procedures rely on time-consuming dMRI acquisitions that may not always be available, especially for legacy or time-constrained studies. To address this problem, we aim to generate WM tracts from structural magnetic resonance imaging (MRI) image by deep learning. METHODS Following recently proposed innovations in structural anatomical segmentation, we evaluate the feasibility of training multiply spatial localized convolution neural networks to learn context from fixed spatial patches from structural MRI on standard template. We focus on six widely used dMRI tractography algorithms (TractSeg, RecoBundles, XTRACT, Tracula, automated fiber quantification (AFQ), and AFQclipped) and train 125 U-Net models to learn these techniques from 3870 T1-weighted images from the Baltimore Longitudinal Study of Aging, the Human Connectome Project S1200 release, and scans acquired at Vanderbilt University. RESULTS The proposed framework identifies fiber bundles with high agreement against tractography-based pathways with a median Dice coefficient from 0.62 to 0.87 on a test cohort, achieving improved subject-specific accuracy when compared to population atlas-based methods. We demonstrate the generalizability of the proposed framework on three externally available datasets. CONCLUSIONS We show that patch-wise convolutional neural network can achieve robust bundle segmentation from T1w. We envision the use of this framework for visualizing the expected course of WM pathways when dMRI is not available.
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Affiliation(s)
- Qi Yang
- Department of Computer Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Colin B. Hansen
- Department of Computer Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Leon Y. Cai
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Francois Rheault
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Ho Hin Lee
- Department of Computer Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Shunxing Bao
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Bramsh Qamar Chandio
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, USA
| | - Owen Williams
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, Maryland, USA
| | - Susan M. Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, Maryland, USA
| | - Eleftherios Garyfallidis
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, USA,Program of Neuroscience, Indiana University, Bloomington, Indiana, USA
| | - Adam W. Anderson
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA,Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Maxime Descoteaux
- Sherbrooke Connectivity Imaging Laboratory (SCIL), Université de Sherbrooke, Sherbrooke, Canada
| | - Kurt G. Schilling
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Centre, Nashville, Tennessee, USA,Department of Radiology and Radiological Sciences, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Bennett A. Landman
- Department of Computer Science, Vanderbilt University, Nashville, Tennessee, USA,Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA,Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, Tennessee, USA,Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Centre, Nashville, Tennessee, USA,Department of Radiology and Radiological Sciences, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
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Chandio BQ. Editorial for "Unraveling the MRI-Based Microstructural Signatures Behind Primary Progressive and Relapsing-Remitting Multiple Sclerosis Phenotypes". J Magn Reson Imaging 2021; 55:164-165. [PMID: 34296789 DOI: 10.1002/jmri.27862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 07/15/2021] [Indexed: 11/11/2022] Open
Affiliation(s)
- Bramsh Qamar Chandio
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing and Engineering, Indiana University Bloomington, Bloomington, Indiana, USA
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Hansen CB, Yang Q, Lyu I, Rheault F, Kerley C, Chandio BQ, Fadnavis S, Williams O, Shafer AT, Resnick SM, Zald DH, Cutting LE, Taylor WD, Boyd B, Garyfallidis E, Anderson AW, Descoteaux M, Landman BA, Schilling KG. Pandora: 4-D White Matter Bundle Population-Based Atlases Derived from Diffusion MRI Fiber Tractography. Neuroinformatics 2021; 19:447-460. [PMID: 33196967 PMCID: PMC8124084 DOI: 10.1007/s12021-020-09497-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2020] [Indexed: 12/21/2022]
Abstract
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 automated state-of-the-art tractography techniques. This atlas is freely available and will be a useful resource for parcellation and segmentation.
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Affiliation(s)
- Colin B Hansen
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Qi Yang
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Ilwoo Lyu
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
- Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Francois Rheault
- Sherbrooke Connectivity Imaging Laboratory (SCIL), Université de Sherbrooke, Sherbrooke, Canada
| | - Cailey Kerley
- Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Bramsh Qamar Chandio
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Shreyas Fadnavis
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Owen Williams
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, MD, USA
| | - Andrea T Shafer
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, MD, USA
| | - Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, MD, USA
| | - David H Zald
- Center for Advanced Human Brain Imaging Research, Rutgers University, Piscataway, NJ, USA
| | - Laurie E Cutting
- Vanderbilt Kennedy Center, Vanderbilt University, Nashville, TN, USA
| | - Warren D Taylor
- Vanderbilt Kennedy Center, Vanderbilt University, Nashville, TN, USA
| | - Brian Boyd
- Vanderbilt Kennedy Center, Vanderbilt University, Nashville, TN, USA
| | - Eleftherios Garyfallidis
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
- Program of Neuroscience, Indiana University, Bloomington, IN, USA
| | - Adam W Anderson
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Maxime Descoteaux
- Sherbrooke Connectivity Imaging Laboratory (SCIL), Université de Sherbrooke, Sherbrooke, Canada
| | - Bennett A Landman
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
- Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Kurt G Schilling
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA.
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Chandio BQ, Risacher SL, Pestilli F, Bullock D, Yeh FC, Koudoro S, Rokem A, Harezlak J, Garyfallidis E. Bundle analytics, a computational framework for investigating the shapes and profiles of brain pathways across populations. Sci Rep 2020; 10:17149. [PMID: 33051471 PMCID: PMC7555507 DOI: 10.1038/s41598-020-74054-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/22/2020] [Indexed: 11/08/2022] Open
Abstract
Tractography has created new horizons for researchers to study brain connectivity in vivo. However, tractography is an advanced and challenging method that has not been used so far for medical data analysis at a large scale in comparison to other traditional brain imaging methods. This work allows tractography to be used for large scale and high-quality medical analytics. BUndle ANalytics (BUAN) is a fast, robust, and flexible computational framework for real-world tractometric studies. BUAN combines tractography and anatomical information to analyze the challenging datasets and identifies significant group differences in specific locations of the white matter bundles. Additionally, BUAN takes the shape of the bundles into consideration for the analysis. BUAN compares the shapes of the bundles using a metric called bundle adjacency which calculates shape similarity between two given bundles. BUAN builds networks of bundle shape similarities that can be paramount for automating quality control. BUAN is freely available in DIPY. Results are presented using publicly available Parkinson's Progression Markers Initiative data.
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Affiliation(s)
- Bramsh Qamar Chandio
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing and Engineering, Indiana University Bloomington, Bloomington, IN, USA.
| | | | - Franco Pestilli
- Department of Psychology, The University of Texas, Austin, TX, USA
| | - Daniel Bullock
- Department of Psychological and Brain Sciences, Indiana University Bloomington, Bloomington, IN, USA
| | - Fang-Cheng Yeh
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Serge Koudoro
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing and Engineering, Indiana University Bloomington, Bloomington, IN, USA
| | - Ariel Rokem
- Department of Psychology and eScience Institute, University of Washington, Washington, DC, USA
| | - Jaroslaw Harezlak
- School of Public Health, Indiana University Bloomington, Bloomington, IN, USA
| | - Eleftherios Garyfallidis
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing and Engineering, Indiana University Bloomington, Bloomington, IN, USA
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