This is a repository with detailed tutorials and tools to help imaging researchers more easily visualize their work.
pyAFQ tutorial contains tutorials on the tractography software pyAFQ, developed by the Yeatman Lab at Stanford.
basics.ipynb follows a basic tutorial of how to use the GroupAFQ object and the possible outputs. Slides from the tutorial are available here
Citations:Jason D Yeatman, Robert F Dougherty, Nathaniel J Myall, Brian A Wandell, Heidi M Feldman. Tract profiles of white matter properties: automating fiber-tract quantification. PloS One, 7: e49790. https://doi.org/10.1371/journal.pone.0049790
Kruper, J. D. Yeatman, A. Richie-Halford, D. Bloom, M. Grotheer, S. Caffarra, G. Kiar, I. I. Karipidis, E. Roy, B. Q. Chandio, E. Garyfallidis, and A. Rokem. Evaluating the reliability of human brain white matter tractometry. Aperture, in press, 2021. doi: https://doi.org/10.1101/2021.02.24.432740
Garyfallidis E, Brett M, Amirbekian B, Rokem A, van der Walt S, Descoteaux M, Nimmo-Smith I and Dipy Contributors (2014) Dipy, a library for the analysis of diffusion MRI data. Front. Neuroinform. 8:8. doi: https://doi.org/10.3389/fninf.2014.00008
Garyfallidis E, Côté MA, Rheault F, Sidhu J, Hau J, Petit L, Fortin D, Cunanne S, Descoteaux M. Recognition of white matter bundles using local and global streamline-based registration and clustering. Neuroimage. 2018 170:283-295. https://doi.org/10.1016/j.neuroimage.2017.07.015.