Requirements

  • At least one structural MR image that was processed with Freesurfer 6.0, 7.x, or FastSurfer 1.1 or later (including the surface pipeline).

  • A Python version >= 3.8 is required to run this script.

  • Required packages include (among others) the nibabel and skimage packages for the core functionality, plus the matplotlib, pandas, and transform3d packages for some optional functions and modules. See the requirements.txt file for a complete list. Use the following command to install these packages:

    ` bash pip install -r requirements.txt `

  • If installing the toolbox as a Python package or if using the Docker image, all required packages will be installed automatically, and manual installation as detailed above will not be necessary.

  • This software has been tested on Ubuntu 20.04 and Ubuntu 22.04.

  • A working FreeSurfer installation (version 6 or newer) is required for running the ‘shape’ module of this toolbox. Also, make sure that FreeSurfer is sourced (i.e., FREESURFER_HOME is set as an environment variable) before running an analysis.

Known issues

  • Aborted / restarted recon-all runs: the program will analyze recon-all logfiles, and may fail or return erroneous results if the logfile is appended by multiple restarts of recon-all runs. Ideally, the logfile should therefore consist of just a single, successful recon-all run.