Automated Fiber Quantification in Python (pyAFQ)#

pyAFQ is an open-source software tool for the analysis of brain white matter in diffusion MRI measurements. It implements a complete and automated data processing pipeline for tractometry, from raw DTI data to white matter tract identification , as well as quantification of tissue properties along the length of the major long-range brain white matter connections.


Tractography is concerned with the visualization and mapping of white matter tracts in the brain, while tractometry involves the quantitative analysis of the structural properties of these tracts. Both techniques are valuable in understanding the brain’s connectivity and can provide insights into various neurological conditions and cognitive processes. More information can be found in the Explanations page.

How To

User’s guide to pyAFQ. This guide assumes you know the basics and walks through more commonly used examples.


Beginner’s guide to pyAFQ. This guide introduces pyAFQ’S basic concepts and walks through fundamentals of using the software.


For more experienced users. This guide contains in depth explanations on how to use pyAFQ methods. It includes how to create detailed visualizations and analyses.

API Reference

The API Reference contains technical descriptions of methods and objects used in pyAFQ. It also contains descriptions of how methods work and parameters used for each method.


Work on this software is supported through grant 1RF1MH121868-01 from the National Institutes for Mental Health / The BRAIN Initiative and by a grant from the Gordon & Betty Moore Foundation, and from the Alfred P. Sloan Foundation to the University of Washington eScience Institute, by a CRCNS grant (NIH R01EB027585) to Eleftherios Garyfallidis and to Ariel Rokem , and by NSF grant 1551330 to Jason Yeatman.