ENIGMA-OCD Protocols | Morphometry Pipeline (Slurm)

Welcome to our step-by-step tutorial on running the morphometry pipeline on slurm. 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 slurm servers: https://morphometry.readthedocs.io/en/latest/running_on_a_slurm_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. Navigate to the directory where the handler script will be executed (0:12) 2. Download the handler script (0:22) 3. Make the handler script executable (0:29) 4. Execute the handler script (0:39) 5. Enter the path to the directory where pipeline image will be built and the final image will be stored (0:50) 6. Enter the #SBATCH flags for the script that will be used to build the pipeline image and enter q at the end (0:59) 7. Enter whether the pipeline will be run as an array job (1:11) 8. Enter the #SBATCH flags for the script that will be used to run the pipeline image and enter q at the end (1:19) 9. Enter the absolute path to the directory with NIfTI files (1:37) 10. Enter the structure of the directory with NIfTI files (1:45) 11. Enter the absolute path to the directory with output from previous Freesurfer's recon-all runs (1:53) 12. Enter the number of threads to be used by the pipeline (2:03)