Getting started with pyAFQ

First, install the software following these instructions.

Next, organize your preprocessed diffusion data according to the BIDS standard.

Then, you are ready to run pyAFQ in one of the following ways:

1. The first is to write a program that uses pyAFQ as a software library. Detailed tutorials for this are provided in the link at the bottom of the page.

1. The second is as a program run in the command line. After installing the software and organizing the data, run: pyAFQ /path/to/dwi /path/to/t1 /path/to/output_folder, (see The pyAFQ CLI). This will run whole-brain tractography, segment the tracts, and extract tract-profiles for each tract, generating a CSV file under that contains the tract profiles for all participants/tracts/statistics.

• Tutorials: Getting started
  • Getting started with pyAFQ - GroupAFQ
  • Getting started with pyAFQ - ParticipantAFQ
  • Re-running pyAFQ
  • Exporting pyAFQ Results
  • Visualizing AFQ derivatives
  • How pyAFQ uses BIDS
  • Plotting Default Regions of Interest (ROIs) to Understand the Tracts