📋 Setup and run group-level processing

✅ Log on to HPC OOD

Dataset

You will be working with the same CAM003_bids_data.zip (226 MB) you used for the MRIQC participant-level processing in a previous lesson. The dataset should be in your groups or xdisk directory, and you should have named it mri_practice.

✅ Navigate to the mri_practice directory and note the path to this directory (Use pwd to display the path), as you'll need it for the export MRIS statement modification.

Script

In the preceding practice, you copied two mriqc scripts to your bin directory. Now you will edit the second script so you can run group-level processing.

✅ Open your copy of runmriqc_group_dev.sh in the OOD editor. You are going to make the same modifications you did with runmriqc_dev.sh, so feel free to open that one and double-check yourself:

✅ Modify the account, e.g., change --account=dkp to your own account name, e.g., --account=akielar.

✅ Modify #SBATCH --mail-user=dkp@arizona.edu to use your email address instead of mine.

✅ Modify the export MRIS statement to point to your mri_practice directory.

✅ Save your modified script.

In the terminal

✅ Type elgato to switch to that machine.

🟢 QA & MRIQC 4: Pr: Group-level