pyAFQ provides a programmatic application programming interface (API) that can be used to integrate pyAFQ functionality into Python programs or into interactive analysis sessions (e.g., using Jupyter notebooks). Examples of using the API are provided in the examples documentation section.
In addition, pyAFQ provides a command-line interface (CLI). After installing the software, and organizing the data, run:
pointing the program to the location of a configuration file. This will run whole-brain tractography, segment the tracts, and extract tract-profiles for each tract, generating a CSV file under study/derivatives/afq/tract_profiles.csv that contains the tract profiles for all participants/tracts/statistics. The csv file has the same format as nodes.csv in AFQ Browser.