ENIGMA-OCD Protocols | Morphometry Pipeline (Desktop)

Welcome to our step-by-step video tutorial on running the morphometry pipeline on a desktop. This pipeline includes the preprocessing of T1-weighted MRI data with Freesurfer (https://surfer.nmr.mgh.harvard.edu/fswiki) and the computation of several morphometric statistics on cortical and subcortical regions. This pipeline has been developed by the ENIGMA-OCD. Important note: This video tutorial demonstrates a typical use case for executing the handler script, which automatically sets up and initiates the pipeline. The handler script is designed to manage various scenarios by presenting different prompts to the user. Therefore, during the execution of the handler script, you may come across a range of prompts and messages that differ slightly each time and from what is shown in the video tutorial. Useful links: - Detailed Tutorial for running the pipeline on desktop servers: https://morphometry.readthedocs.io/en/latest/running_on_a_desktop_server_ENIGMA_OCD.html - GitHub repository for access to our code and updates: https://github.com/csleo95/morphometry - ENIGMA-OCD homepage: https://enigma.ini.usc.edu/ongoing/enigma-ocd-working-group/ Video breakdown: 1. Go to the handler script link on GitHub (0:12) 2. Download the handler script (0:22) 3. Open terminal (0:30) 4. Navigate to the directory where the handler script was downloaded (0:41) 5. Make the handler script executable (0:52) 6. Execute the handler script (1:07) 7. Choose the container platform to be used (1:21) 8. Enter the absolute path to the directory with NIfTI files (1:35) 9. Enter the structure of the directory with NIfTI files (1:47) 10. Enter the absolute path to the directory with output from previous Freesurfer's recon-all runs (1:54) 11. Enter the number of threads to be used by the pipeline (2:06)