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.