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/config.toml

pointing the program to the location of a configuration file (see
:doc:`configuration file specification </reference/config>` for an
explanation of this file). 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.