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2026
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  • Chandio, B. Q., Feng, Y., Gari, I. B., Alibrando, J. D., Thomopoulos, S. I., Villalón-Reina, J. E., Liou, K., Somu, S., Yoo, H., Nir, T. M., et al. (2026). “Tractometry-Based Quantification of Along-Tract White-Matter Hemispheric Asymmetry in Alzheimer’s Disease.” bioRxiv. Scholar

  • Nabulsi, L., Feng, Y., Chandio, B. Q., Villalon-Reina, J. E., Ba Gari, I., Alibrando, J. D., Nir, T. M., Juliano, A. C., Pancholi, D., Roundy, G. S., et al. (2026). “Along-Tract Microstructural Alterations Associated with Stimulant Misuse Localized using Diffusion MRI Tractometry.” bioRxiv. Scholar

2025
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  • Feng, Y., Chandio, B. Q., Villalon-Reina, J. E., Thomopoulos, S. I., Nir, T. M., Benavidez, S., Laltoo, E., Chattopadhyay, T., Joshi, H., Venkatasubramanian, G., et al. (2025). “Microstructural mapping of neural pathways in Alzheimer’s disease using macrostructure-informed normative tractometry.” Alzheimer’s & Dementia, 21(1), e14371. Scholar

  • Kim, G. S., Chandio, B. Q., Benavidez, S. M., Thompson, P. M., & Lawrence, K. E. (2025). “White matter microstructural alterations in autism localized with bundle analytics.” 2025 IEEE 22nd international symposium on biomedical imaging (ISBI), 1–5. Scholar

  • Shuai, Y., Chandio, B. Q., Feng, Y., Villalon-Reina, J. E., Nir, T. M., Ching, C. R., Gari, I. B., Thomopoulos, S. I., Alibrando, J. D., John, J. P., et al. (2025). “Deterministic versus probabilistic tractography: Impact on white matter bundle shape.” 2025 21st International Symposium on Biomedical Image Processing and Analysis (SIPAIM), 1–4. Scholar

  • Chandio, B. Q., Nir, T. M., Villalon-Reina, J. E., Thomopoulos, S. I., Feng, Y., Reid, R. I., Jack, C. R., Weiner, M. W., Garyfallidis, E., Jahanshad, N., et al. (2025). “White Matter Tract Vulnerability to Amyloid Pathology on the Alzheimer’s Disease Continuum.” 2025 21st International Symposium on Biomedical Image Processing and Analysis (SIPAIM), 1–5. Scholar

  • Feng, Y., Shuai, Y., Villalón-Reina, J. E., Chandio, B. Q., Thomopoulos, S. I., Nir, T. M., Jahanshad, N., & Thompson, P. M. (2025). “Streamline density normalization: A robust approach to mitigate bundle variability in multi-site diffusion mri.” International Workshop on Computational Diffusion MRI, 44–56. Scholar

  • Kim, G., Chandio, B., Benavidez, S., Thompson, P. M., & Lawrence, K. E. (2025). “Localized Mapping of White Matter Microstructural Alterations in Autism Using Advanced Tractometry.” INSAR 2025. Scholar

  • Chandio, B. Q., Schilling, K. G., & Villalón-Reina, J. E. (2025). “Methods and applications of diffusion MRI tractometry.” Frontiers in Neuroscience, 19, 1737026. Scholar

  • Chandio, B. Q., Villalón-Reina, J. E., Nir, T. M., Thomopoulos, S. I., Feng, Y., Benavidez, S., Jahanshad, N., Harezlak, J., Garyfallidis, E., & Thompson, P. M. (2025). “Amyloid, Tau, and APOE in Alzheimer’s Disease: Impact on White Matter Tracts.” Proceedings of the Pacific Symposium on Biocomputing, 30, 394–411. Scholar

  • Shuai, Y., Feng, Y., Villalon-Reina, J. E., Nir, T. M., Thomopoulos, S. I., Thompson, P. M., & Chandio, B. Q. (2025). “ASSESSING THE INFLUENCE OF TRACTOGRAPHY METHODS ON WHITE MATTER MICROSTRUCTURE AND TRACTOMETRY ANALYSIS IN ALZHEIMERS DISEASE.” bioRxiv, 2025–11. Scholar

  • Feng, Y., Villalón-Reina, J. E., Gari, I. B., Alibrando, J. D., Nir, T. M., Jahanshad, N., Chandio, B. Q., & Thompson, P. M. (2025). “Evaluating Sample-Size Efficiency and Sensitivity of Tractometry in Alzheimer’s Disease.” bioRxiv, 2025–11. Scholar

  • Kim, G. S., Chandio, B. Q., Benavidez, S. M., Feng, Y., Thompson, P. M., & Lawrence, K. E. (2025). “Mapping along-tract commissural and association white matter microstructural differences in autistic children and young adults.” Cerebral Cortex, 35(11), bhaf291. Scholar

  • Schilling, K. G., Villalon-Reina, J. E., & Chandio, B. Q. (2025). “Methods and Applications of Diffusion MRI Tractometry.” Frontiers Media SA. Scholar

  • Nabulsi, L., Chandio, B. Q., Kang, M. J., Im, Y., McPhilemy, G., Martyn, F. M., Roberts, G., Hallahan, B., Dannlowski, U., Borgers, T., et al. (2025). “Along-Tract Mapping of White Matter Microstructural Abnormalities in Bipolar Disorder using Diffusion MRI.” 2025 21st International Symposium on Biomedical Image Processing and Analysis (SIPAIM), 1–5. Scholar

2024
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  • Chandio, B. Q., Villalon-Reina, J. E., Nir, T. M., Thomopoulos, S. I., Feng, Y., Benavidez, S., Jahanshad, N., Harezlak, J., Garyfallidis, E., & Thompson, P. M. (2024). “Bundle analytics based data harmonization for multi-site diffusion mri tractometry.” 2024 46th annual international conference of the IEEE engineering in medicine and biology society (EMBC), 1–7. Scholar

  • Feng, Y., Chandio, B. Q., Villalon-Reina, J. E., Benavidez, S., Chattopadhyay, T., Chehrzadeh, S., Laltoo, E., Thomopoulos, S. I., Joshi, H., Venkatasubramanian, G., et al. (2024). “Deep normative tractometry for identifying joint white matter macro-and micro-structural abnormalities in Alzheimer’s disease.” 2024 46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 1–7. Scholar

  • Chandio, B. Q., Reina, J. E. V., Nir, T. M., Thomopoulos, S. I., Feng, Y., Benavidez, S. M., Jahanshad, N., Harezlak, J., Garyfallidis, E., & Thompson, P. M. (2024). “Harmonized Tractometry Visualizes Alzheimer’s Disease Effects on the Brain’s White Matter Tract Microstructure.” Alzheimer’s & Dementia, 20, e089548. Scholar

  • Feng, Y., Villalón-Reina, J. E., Nir, T. M., Chandio, B. Q., Jahanshad, N., & Thompson, P. M. (2024). “BundleAGE: predicting white matter age using along-tract microstructural profiles from diffusion MRI.” 2024 20th International Symposium on Medical Information Processing and Analysis (SIPAIM), 1–4. Scholar

  • Newlin, N. R., Schilling, K., Koudoro, S., Chandio, B. Q., Kanakaraj, P., Moyer, D., Kelly, C. E., Genc, S., Chen, J., Yang, J. Y., et al. (2024). “MICCAI-CDMRI 2023 QuantConn challenge findings on achieving robust quantitative connectivity through harmonized preprocessing of diffusion MRI.” ArXiv, arXiv–2411. Scholar

  • Newlin, N., Schilling, K., Koudoro, S., Chandio, B. Q., Kanakaraj, P., Moyer, D., Kelly, C. E., Genc, S., Yang, J. Y., Wu, Y., et al. (2024). “Introducing QuantConn: Overcoming Challenging Diffusion Acquisitions with Harmonization.” International Workshop on Computational Diffusion MRI, 164–174. Scholar

2023
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  • Feng, Y., Chandio, B. Q., Chattopadhyay, T., Thomopoulos, S. I., Owens-Walton, C., Jahanshad, N., Garyfallidis, E., & Thompson, P. M. (2023). “Learning optimal white matter tract representations from tractography using a deep generative model for population analyses.” 18th International Symposium on Medical Information Processing and Analysis, 12567, 70–80. Scholar

  • Chandio, B. Q., Olivetti, E., Romero-Bascones, D., Harezlak, J., & Garyfallidis, E. (2023). “Bundlewarp, streamline-based nonlinear registration of white matter tracts.” bioRxiv. Scholar

  • Feng, Y., Chandio, B. Q., Thomopoulos, S. I., Chattopadhyay, T., & Thompson, P. M. (2023). “Variational autoencoders for generating synthetic tractography-based bundle templates in a low-data setting.” 2023 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), 1–6. Scholar

  • Nabulsi, L., Chandio, B. Q., Dhinagar, N., Laltoo, E., McPhilemy, G., Martyn, F. M., Hallahan, B., McDonald, C., Thompson, P. M., & Cannon, D. M. (2023). “Along-tract statistical mapping of microstructural abnormalities in bipolar disorder: A pilot study.” 2023 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), 1–7. Scholar

  • Feng, Y., Chandio, B. Q., Villalón-Reina, J. E., Thomopoulos, S. I., Joshi, H., Nair, G., Joshi, A. A., Venkatasubramanian, G., John, J. P., & Thompson, P. M. (2023). “BundleCleaner: unsupervised denoising and subsampling of diffusion MRI-derived tractography data.” International Workshop on Computational Diffusion MRI, 152–164. Scholar

  • Nabulsi, L., Chandio, B. Q., McPhilemy, G., Martyn, F. M., Roberts, G., Hallahan, B., Dannlowski, U., Kircher, T., Haarman, B., Mitchell, P., et al. (2023). “Multi-site statistical mapping of along-tract microstructural abnormalities in bipolar disorder with diffusion MRI Tractometry.” 2023 19th international symposium on medical information processing and analysis (SIPAIM), 1–5. Scholar

2022
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  • Chandio, B. Q., Chattopadhyay, T., Owens-Walton, C., Reina, J. E. V., Nabulsi, L., Thomopoulos, S. I., Garyfallidis, E., & Thompson, P. M. (2022). “Fiberneat: Unsupervised white matter tract filtering.” 2022 44th annual international conference of the IEEE engineering in medicine & biology society (EMBC), 5055–5061. Scholar

  • Yang, Q., Hansen, C. B., Cai, L. Y., Rheault, F., Lee, H. H., Bao, S., Chandio, B. Q., Williams, O., Resnick, S. M., Garyfallidis, E., et al. (2022). “Learning white matter subject-specific segmentation from structural MRI.” Medical physics, 49(4), 2502–2513. Scholar

  • Feng, Y., Chandio, B. Q., Chattopadhyay, T., Thomopoulos, S. I., Owens-Walton, C., Garyfallidis, E., Jahanshad, N., & Thompson, P. M. (2022). “Learning Streamline Embeddings with Variational Autoencoder for Intersubject Bundle Comparison in Alzheimer’s Disease.” Alzheimer’s & Dementia, 18, e066204. Scholar

  • Chandio, B. Q., Owens-Walton, C., Villalon-Reina, J. E., Nabulsi, L., Thomopoulos, S. I., Guaje, J., Garyfallidis, E., & Thompson, P. M. (2022). “Microstructural changes in the white matter tracts of the brain due to mild cognitive impairment.” Alzheimer’s & Dementia, 18, e065339. Scholar

  • Feng, Y., Chandio, B. Q., Chattopadhyay, T., Thomopoulos, S. I., Owens-Walton, C., Jahanshad, N., Garyfallidis, E., & Thompson, P. M. (2022). “Deep generative model for learning tractography streamline embeddings based on convolutional variational autoencoder.” International Society for Magnetic Resonance Imaging (ISMRM). Scholar

  • Romero-Bascones, D., Ayala, U., Barrenechea, M., Chandio, B. Q., Fadnavis, S., Park, J. S., Koudoro, S., & Garyfallidis, E. (2022). “Bundleatlasing: unbiased population-specific atlasing of bundles in streamline space.” Proceedings of the Annual Meeting of the International Society for Magnetic Resonance in Medicine. Scholar

  • Chandio, B. Q. (2022). “Advancing white matter tractometry of the brain using diffusion MRI and machine learning.” Indiana University. Scholar

2021
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  • Hansen, C. B., Yang, Q., Lyu, I., Rheault, F., Kerley, C., Chandio, B. Q., Fadnavis, S., Williams, O., Shafer, A. T., Resnick, S. M., et al. (2021). “Pandora: 4-D white matter bundle population-based atlases derived from diffusion MRI fiber tractography.” Neuroinformatics, 19(3), 447–460. Scholar

  • Schilling, K. G., Rheault, F., Petit, L., Hansen, C. B., Nath, V., Yeh, F., Girard, G., Barakovic, M., Rafael-Patino, J., Yu, T., et al. (2021). “Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset?” NeuroImage, 243, 118502. Scholar

  • Kruper, J., Yeatman, J. D., Richie-Halford, A., Bloom, D., Grotheer, M., Caffarra, S., Kiar, G., Karipidis, I. I., Roy, E., Chandio, B. Q., et al. (2021). “Evaluating the reliability of human brain white matter tractometry.” Aperture neuro, 1(1), 10–52294. Scholar

  • Gau, R., Noble, S., Heuer, K., Bottenhorn, K. L., Bilgin, I. P., Yang, Y., Huntenburg, J. M., Bayer, J. M., Bethlehem, R. A., Rhoads, S. A., et al. (2021). “Brainhack: Developing a culture of open, inclusive, community-driven neuroscience.” Neuron, 109(11), 1769–1775. Scholar

2020
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  • Chandio, B. Q., Risacher, S. L., Pestilli, F., Bullock, D., Yeh, F., Koudoro, S., Rokem, A., Harezlak, J., & Garyfallidis, E. (2020). “Bundle analytics, a computational framework for investigating the shapes and profiles of brain pathways across populations.” Scientific reports, 10(1), 17149. Scholar

  • Chandio, B. Q., & Garyfallidis, E. (2020). “StND: Streamline-based Non-rigid partial-Deformation Tractography Registration.” Medical imaging meets NeurIPS. Scholar

Preprints & Other Publications
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  • Garyfallidis, E., Côté, M., Chandio, B. Q., Fadnavis, S., Guaje, J., Aggarwal, R., St-Onge, E., Juneja, K. S., Koudoro, S., & Reagan, D. “DIPY Horizon: fast, modular, unified and adaptive visualization.” Scholar

  • Chandio, B. Q., & Garyfallidis, E. “StND: Non-Rigid Partial Deformation Tractography Registration.” Scholar

  • Chandio, B. Q., Chattopadhyay, T., Owens-Walton, C., Reina, J. E. V., Nabulsi, L., Thomopoulos, S. I., Guaje, J., Garyfallidis, E., & Thompson, P. M. “Visualizing 4,230 White Matter Tracts at Once.” Scholar

  • Hansen, C., Yang, Q., Rheault, F., Qamar, B., Williams, O., Resnick, S., Garyfallidis, E., Anderson, A. W., Descoteaux, M., Landman, B. A., et al. “Learning white matter fingerprints from structural information.” Scholar

  • Yang, Q., Hansen, C., Rheault, F., Qamar, B., Williams, O., Resnick, S., Garyfallidis, E., Anderson, A. W., Descoteaux, M., Landman, B. A., et al. “Mapping white matter specificity captured by diffusion tractography through deep learning on structural MRI.” Scholar

  • Chandio, B. Q., Thomopoulos, S. I., Thompson, P. M., Harezlak, J., & Garyfallidis, E. “BUAN 2.0, streamlines as functions, nonlinear registration, and subdivision of bundles for advanced tractometry.” Scholar