[{"content":" Project Overview # ","externalUrl":null,"permalink":"/research/harmonization/","section":"Research","summary":"Developing computational methods to remove scanner-specific biases and harmonize multi-site neuroimaging datasets.","title":"Data Harmonization","type":"research"},{"content":" Project Overview # Here you can dive into the specifics of your Image Registration work. Detail the algorithms you are developing and specific use cases for multi-modal brain mapping.\n","externalUrl":null,"permalink":"/research/registration/","section":"Research","summary":"Advanced algorithms for precise spatial alignment of brain images across different subjects and modalities.","title":"Image Registration","type":"research"},{"content":"The Brain Mapping and NeuroImaging Lab website has officially launched.\n","date":"8 April 2026","externalUrl":null,"permalink":"/news/website-launch/","section":"News","summary":"","title":"BMN Lab Website is Live","type":"news"},{"content":"Welcome to the BMN Lab. We develop advanced computational frameworks for Diffusion MRI and brain connectivity mapping.\n","date":"8 April 2026","externalUrl":null,"permalink":"/","section":"Brain Mapping and NeuroImaging Lab","summary":"","title":"Brain Mapping and NeuroImaging Lab","type":"page"},{"content":"Stay up to date with the latest happenings at the Brain Mapping and NeuroImaging Lab.\n","date":"8 April 2026","externalUrl":null,"permalink":"/news/","section":"News","summary":"","title":"News","type":"news"},{"content":"We are thrilled to welcome Dulaj Dasanayake and Sumonta Nandy Amit to the Brain Mapping and NeuroImaging Lab as our newest Ph.D. students. They will be contributing to our research in computational neuroimaging and brain connectivity.\n","date":"12 January 2026","externalUrl":null,"permalink":"/news/new-students-2026/","section":"News","summary":"","title":"Dulaj and Sumonta have joined the BMN Lab","type":"news"},{"content":"","externalUrl":null,"permalink":"/authors/","section":"Authors","summary":"","title":"Authors","type":"authors"},{"content":" Bramsh Qamar Chandio Assistant Professor \u0026 Director\n","externalUrl":null,"permalink":"/people/chandio/","section":"Meet the Team","summary":"","title":"Bramish Qamar Chandio","type":"people"},{"content":"","externalUrl":null,"permalink":"/categories/","section":"Categories","summary":"","title":"Categories","type":"categories"},{"content":" Dulaj Dasanayake Ph.D. Student\n","externalUrl":null,"permalink":"/people/dulaj/","section":"Meet the Team","summary":"","title":"Dulaj Dasanayake","type":"people"},{"content":" Principal Investigator # Bramsh Qamar Chandio Assistant Professor \u0026 Director\nGraduate Researchers # Dulaj Dasanayake Ph.D. Student\nSumonta Nandy Amit Ph.D. Student\n","externalUrl":null,"permalink":"/people/","section":"Meet the Team","summary":"","title":"Meet the Team","type":"people"},{"content":"View Full Profile on Google Scholar →\n2026 # 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). \u0026ldquo;Tractometry-Based Quantification of Along-Tract White-Matter Hemispheric Asymmetry in Alzheimer’s Disease.\u0026rdquo; bioRxiv. Scholar\nNabulsi, 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). \u0026ldquo;Along-Tract Microstructural Alterations Associated with Stimulant Misuse Localized using Diffusion MRI Tractometry.\u0026rdquo; bioRxiv. Scholar\n2025 # 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). \u0026ldquo;Microstructural mapping of neural pathways in Alzheimer\u0026rsquo;s disease using macrostructure-informed normative tractometry.\u0026rdquo; Alzheimer\u0026rsquo;s \u0026amp; Dementia, 21(1), e14371. Scholar\nKim, G. S., Chandio, B. Q., Benavidez, S. M., Thompson, P. M., \u0026amp; Lawrence, K. E. (2025). \u0026ldquo;White matter microstructural alterations in autism localized with bundle analytics.\u0026rdquo; 2025 IEEE 22nd international symposium on biomedical imaging (ISBI), 1–5. Scholar\nShuai, 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). \u0026ldquo;Deterministic versus probabilistic tractography: Impact on white matter bundle shape.\u0026rdquo; 2025 21st International Symposium on Biomedical Image Processing and Analysis (SIPAIM), 1–4. Scholar\nChandio, 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). \u0026ldquo;White Matter Tract Vulnerability to Amyloid Pathology on the Alzheimer’s Disease Continuum.\u0026rdquo; 2025 21st International Symposium on Biomedical Image Processing and Analysis (SIPAIM), 1–5. Scholar\nFeng, Y., Shuai, Y., Villalón-Reina, J. E., Chandio, B. Q., Thomopoulos, S. I., Nir, T. M., Jahanshad, N., \u0026amp; Thompson, P. M. (2025). \u0026ldquo;Streamline density normalization: A robust approach to mitigate bundle variability in multi-site diffusion mri.\u0026rdquo; International Workshop on Computational Diffusion MRI, 44–56. Scholar\nKim, G., Chandio, B., Benavidez, S., Thompson, P. M., \u0026amp; Lawrence, K. E. (2025). \u0026ldquo;Localized Mapping of White Matter Microstructural Alterations in Autism Using Advanced Tractometry.\u0026rdquo; INSAR 2025. Scholar\nChandio, B. Q., Schilling, K. G., \u0026amp; Villalón-Reina, J. E. (2025). \u0026ldquo;Methods and applications of diffusion MRI tractometry.\u0026rdquo; Frontiers in Neuroscience, 19, 1737026. Scholar\nChandio, B. Q., Villalón-Reina, J. E., Nir, T. M., Thomopoulos, S. I., Feng, Y., Benavidez, S., Jahanshad, N., Harezlak, J., Garyfallidis, E., \u0026amp; Thompson, P. M. (2025). \u0026ldquo;Amyloid, Tau, and APOE in Alzheimer’s Disease: Impact on White Matter Tracts.\u0026rdquo; Proceedings of the Pacific Symposium on Biocomputing, 30, 394–411. Scholar\nShuai, Y., Feng, Y., Villalon-Reina, J. E., Nir, T. M., Thomopoulos, S. I., Thompson, P. M., \u0026amp; Chandio, B. Q. (2025). \u0026ldquo;ASSESSING THE INFLUENCE OF TRACTOGRAPHY METHODS ON WHITE MATTER MICROSTRUCTURE AND TRACTOMETRY ANALYSIS IN ALZHEIMERS DISEASE.\u0026rdquo; bioRxiv, 2025–11. Scholar\nFeng, Y., Villalón-Reina, J. E., Gari, I. B., Alibrando, J. D., Nir, T. M., Jahanshad, N., Chandio, B. Q., \u0026amp; Thompson, P. M. (2025). \u0026ldquo;Evaluating Sample-Size Efficiency and Sensitivity of Tractometry in Alzheimer’s Disease.\u0026rdquo; bioRxiv, 2025–11. Scholar\nKim, G. S., Chandio, B. Q., Benavidez, S. M., Feng, Y., Thompson, P. M., \u0026amp; Lawrence, K. E. (2025). \u0026ldquo;Mapping along-tract commissural and association white matter microstructural differences in autistic children and young adults.\u0026rdquo; Cerebral Cortex, 35(11), bhaf291. Scholar\nSchilling, K. G., Villalon-Reina, J. E., \u0026amp; Chandio, B. Q. (2025). \u0026ldquo;Methods and Applications of Diffusion MRI Tractometry.\u0026rdquo; Frontiers Media SA. Scholar\nNabulsi, 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). \u0026ldquo;Along-Tract Mapping of White Matter Microstructural Abnormalities in Bipolar Disorder using Diffusion MRI.\u0026rdquo; 2025 21st International Symposium on Biomedical Image Processing and Analysis (SIPAIM), 1–5. Scholar\n2024 # Chandio, B. Q., Villalon-Reina, J. E., Nir, T. M., Thomopoulos, S. I., Feng, Y., Benavidez, S., Jahanshad, N., Harezlak, J., Garyfallidis, E., \u0026amp; Thompson, P. M. (2024). \u0026ldquo;Bundle analytics based data harmonization for multi-site diffusion mri tractometry.\u0026rdquo; 2024 46th annual international conference of the IEEE engineering in medicine and biology society (EMBC), 1–7. Scholar\nFeng, 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). \u0026ldquo;Deep normative tractometry for identifying joint white matter macro-and micro-structural abnormalities in Alzheimer’s disease.\u0026rdquo; 2024 46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 1–7. Scholar\nChandio, B. Q., Reina, J. E. V., Nir, T. M., Thomopoulos, S. I., Feng, Y., Benavidez, S. M., Jahanshad, N., Harezlak, J., Garyfallidis, E., \u0026amp; Thompson, P. M. (2024). \u0026ldquo;Harmonized Tractometry Visualizes Alzheimer’s Disease Effects on the Brain’s White Matter Tract Microstructure.\u0026rdquo; Alzheimer\u0026rsquo;s \u0026amp; Dementia, 20, e089548. Scholar\nFeng, Y., Villalón-Reina, J. E., Nir, T. M., Chandio, B. Q., Jahanshad, N., \u0026amp; Thompson, P. M. (2024). \u0026ldquo;BundleAGE: predicting white matter age using along-tract microstructural profiles from diffusion MRI.\u0026rdquo; 2024 20th International Symposium on Medical Information Processing and Analysis (SIPAIM), 1–4. Scholar\nNewlin, 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). \u0026ldquo;MICCAI-CDMRI 2023 QuantConn challenge findings on achieving robust quantitative connectivity through harmonized preprocessing of diffusion MRI.\u0026rdquo; ArXiv, arXiv–2411. Scholar\nNewlin, 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). \u0026ldquo;Introducing QuantConn: Overcoming Challenging Diffusion Acquisitions with Harmonization.\u0026rdquo; International Workshop on Computational Diffusion MRI, 164–174. Scholar\n2023 # Feng, Y., Chandio, B. Q., Chattopadhyay, T., Thomopoulos, S. I., Owens-Walton, C., Jahanshad, N., Garyfallidis, E., \u0026amp; Thompson, P. M. (2023). \u0026ldquo;Learning optimal white matter tract representations from tractography using a deep generative model for population analyses.\u0026rdquo; 18th International Symposium on Medical Information Processing and Analysis, 12567, 70–80. Scholar\nChandio, B. Q., Olivetti, E., Romero-Bascones, D., Harezlak, J., \u0026amp; Garyfallidis, E. (2023). \u0026ldquo;Bundlewarp, streamline-based nonlinear registration of white matter tracts.\u0026rdquo; bioRxiv. Scholar\nFeng, Y., Chandio, B. Q., Thomopoulos, S. I., Chattopadhyay, T., \u0026amp; Thompson, P. M. (2023). \u0026ldquo;Variational autoencoders for generating synthetic tractography-based bundle templates in a low-data setting.\u0026rdquo; 2023 45th Annual International Conference of the IEEE Engineering in Medicine \u0026amp; Biology Society (EMBC), 1–6. Scholar\nNabulsi, L., Chandio, B. Q., Dhinagar, N., Laltoo, E., McPhilemy, G., Martyn, F. M., Hallahan, B., McDonald, C., Thompson, P. M., \u0026amp; Cannon, D. M. (2023). \u0026ldquo;Along-tract statistical mapping of microstructural abnormalities in bipolar disorder: A pilot study.\u0026rdquo; 2023 45th Annual International Conference of the IEEE Engineering in Medicine \u0026amp; Biology Society (EMBC), 1–7. Scholar\nFeng, Y., Chandio, B. Q., Villalón-Reina, J. E., Thomopoulos, S. I., Joshi, H., Nair, G., Joshi, A. A., Venkatasubramanian, G., John, J. P., \u0026amp; Thompson, P. M. (2023). \u0026ldquo;BundleCleaner: unsupervised denoising and subsampling of diffusion MRI-derived tractography data.\u0026rdquo; International Workshop on Computational Diffusion MRI, 152–164. Scholar\nNabulsi, L., Chandio, B. Q., McPhilemy, G., Martyn, F. M., Roberts, G., Hallahan, B., Dannlowski, U., Kircher, T., Haarman, B., Mitchell, P., et al. (2023). \u0026ldquo;Multi-site statistical mapping of along-tract microstructural abnormalities in bipolar disorder with diffusion MRI Tractometry.\u0026rdquo; 2023 19th international symposium on medical information processing and analysis (SIPAIM), 1–5. Scholar\n2022 # Chandio, B. Q., Chattopadhyay, T., Owens-Walton, C., Reina, J. E. V., Nabulsi, L., Thomopoulos, S. I., Garyfallidis, E., \u0026amp; Thompson, P. M. (2022). \u0026ldquo;Fiberneat: Unsupervised white matter tract filtering.\u0026rdquo; 2022 44th annual international conference of the IEEE engineering in medicine \u0026amp; biology society (EMBC), 5055–5061. Scholar\nYang, 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). \u0026ldquo;Learning white matter subject-specific segmentation from structural MRI.\u0026rdquo; Medical physics, 49(4), 2502–2513. Scholar\nFeng, Y., Chandio, B. Q., Chattopadhyay, T., Thomopoulos, S. I., Owens-Walton, C., Garyfallidis, E., Jahanshad, N., \u0026amp; Thompson, P. M. (2022). \u0026ldquo;Learning Streamline Embeddings with Variational Autoencoder for Intersubject Bundle Comparison in Alzheimer’s Disease.\u0026rdquo; Alzheimer\u0026rsquo;s \u0026amp; Dementia, 18, e066204. Scholar\nChandio, B. Q., Owens-Walton, C., Villalon-Reina, J. E., Nabulsi, L., Thomopoulos, S. I., Guaje, J., Garyfallidis, E., \u0026amp; Thompson, P. M. (2022). \u0026ldquo;Microstructural changes in the white matter tracts of the brain due to mild cognitive impairment.\u0026rdquo; Alzheimer\u0026rsquo;s \u0026amp; Dementia, 18, e065339. Scholar\nFeng, Y., Chandio, B. Q., Chattopadhyay, T., Thomopoulos, S. I., Owens-Walton, C., Jahanshad, N., Garyfallidis, E., \u0026amp; Thompson, P. M. (2022). \u0026ldquo;Deep generative model for learning tractography streamline embeddings based on convolutional variational autoencoder.\u0026rdquo; International Society for Magnetic Resonance Imaging (ISMRM). Scholar\nRomero-Bascones, D., Ayala, U., Barrenechea, M., Chandio, B. Q., Fadnavis, S., Park, J. S., Koudoro, S., \u0026amp; Garyfallidis, E. (2022). \u0026ldquo;Bundleatlasing: unbiased population-specific atlasing of bundles in streamline space.\u0026rdquo; Proceedings of the Annual Meeting of the International Society for Magnetic Resonance in Medicine. Scholar\nChandio, B. Q. (2022). \u0026ldquo;Advancing white matter tractometry of the brain using diffusion MRI and machine learning.\u0026rdquo; Indiana University. Scholar\n2021 # 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). \u0026ldquo;Pandora: 4-D white matter bundle population-based atlases derived from diffusion MRI fiber tractography.\u0026rdquo; Neuroinformatics, 19(3), 447–460. Scholar\nSchilling, 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). \u0026ldquo;Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset?\u0026rdquo; NeuroImage, 243, 118502. Scholar\nKruper, 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). \u0026ldquo;Evaluating the reliability of human brain white matter tractometry.\u0026rdquo; Aperture neuro, 1(1), 10–52294. Scholar\nGau, 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). \u0026ldquo;Brainhack: Developing a culture of open, inclusive, community-driven neuroscience.\u0026rdquo; Neuron, 109(11), 1769–1775. Scholar\n2020 # Chandio, B. Q., Risacher, S. L., Pestilli, F., Bullock, D., Yeh, F., Koudoro, S., Rokem, A., Harezlak, J., \u0026amp; Garyfallidis, E. (2020). \u0026ldquo;Bundle analytics, a computational framework for investigating the shapes and profiles of brain pathways across populations.\u0026rdquo; Scientific reports, 10(1), 17149. Scholar\nChandio, B. Q., \u0026amp; Garyfallidis, E. (2020). \u0026ldquo;StND: Streamline-based Non-rigid partial-Deformation Tractography Registration.\u0026rdquo; Medical imaging meets NeurIPS. Scholar\nPreprints \u0026amp; Other Publications # Garyfallidis, E., Côté, M., Chandio, B. Q., Fadnavis, S., Guaje, J., Aggarwal, R., St-Onge, E., Juneja, K. S., Koudoro, S., \u0026amp; Reagan, D. \u0026ldquo;DIPY Horizon: fast, modular, unified and adaptive visualization.\u0026rdquo; Scholar\nChandio, B. Q., \u0026amp; Garyfallidis, E. \u0026ldquo;StND: Non-Rigid Partial Deformation Tractography Registration.\u0026rdquo; Scholar\nChandio, B. Q., Chattopadhyay, T., Owens-Walton, C., Reina, J. E. V., Nabulsi, L., Thomopoulos, S. I., Guaje, J., Garyfallidis, E., \u0026amp; Thompson, P. M. \u0026ldquo;Visualizing 4,230 White Matter Tracts at Once.\u0026rdquo; Scholar\nHansen, C., Yang, Q., Rheault, F., Qamar, B., Williams, O., Resnick, S., Garyfallidis, E., Anderson, A. W., Descoteaux, M., Landman, B. A., et al. \u0026ldquo;Learning white matter fingerprints from structural information.\u0026rdquo; Scholar\nYang, Q., Hansen, C., Rheault, F., Qamar, B., Williams, O., Resnick, S., Garyfallidis, E., Anderson, A. W., Descoteaux, M., Landman, B. A., et al. \u0026ldquo;Mapping white matter specificity captured by diffusion tractography through deep learning on structural MRI.\u0026rdquo; Scholar\nChandio, B. Q., Thomopoulos, S. I., Thompson, P. M., Harezlak, J., \u0026amp; Garyfallidis, E. \u0026ldquo;BUAN 2.0, streamlines as functions, nonlinear registration, and subdivision of bundles for advanced tractometry.\u0026rdquo; Scholar\n","externalUrl":null,"permalink":"/publications/","section":"Publications","summary":"","title":"Publications","type":"publications"},{"content":"The BMN Lab focuses on developing advanced computational tools to map the human brain\u0026rsquo;s structural and functional architecture.\nData Harmonization Developing computational methods to remove scanner-specific biases and harmonize multi-site neuroimaging datasets.\nLearn More → Image Registration Advanced algorithms for precise spatial alignment of brain images across different subjects and modalities.\nLearn More → ","externalUrl":null,"permalink":"/research/","section":"Research","summary":"","title":"Research","type":"research"},{"content":"","externalUrl":null,"permalink":"/series/","section":"Series","summary":"","title":"Series","type":"series"},{"content":" Sumonta Nandy Amit Ph.D. Student\n","externalUrl":null,"permalink":"/people/sumonta/","section":"Meet the Team","summary":"","title":"Sumonta Nandy Amit","type":"people"},{"content":"","externalUrl":null,"permalink":"/tags/","section":"Tags","summary":"","title":"Tags","type":"tags"}]