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 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 configuration file specification 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.

2. The second is to write a program that uses pyAFQ as a software library. Detailed tutorials for this are provided in the next documentation section:

• Tutorials: getting started with the pyAFQ Python library