Automated Fiber Quantification

Tractography based on diffusion weighted MRI (dMRI) is used to find the major white matter fascicles (tracts) in the living human brain. The health of these tracts is an important factor underlying many cognitive and neurological disorders.

Tissue properties may vary systematically along each tract: different populations of axons enter and exit the tract, and disease can strike at local positions within the tract. Because of this, quantifying and understanding diffusion measures along each fiber tract (the tract profile) may reveal new insights into white matter development, function, and disease that are not obvious from mean measures of that tract ([Yeatman2012]).

pyAFQ is a software package focused on automated delineation of the major fiber tracts in individual human brains, and quantification of the tissue properties within the tracts. To learn more about the software please refer to the Table of Contents.

Tractometry

AFQ Tractometry Pipeline

Tractography

Registration

Segmentation

Cleaning

Profiling

Visualization

Citing our work

If you use this software in your work, please consider citing the papers that describe the method [Yeatman2012], the specific implementation [Kruper2021], as well as the underlying modeling and tractography implementations in DIPY [Garyfallidis2014]. If you use the RecoBundles method, please also cite the original paper describing that method [Garyfallidis2018].

Yeatman2012(1,2)

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

Kruper2021
  1. 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

Garyfallidis2014

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

Garyfallidis2018

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.