Preprocessing fMRI data

The steps here are required if you want to fully rerun the analysis. If you are not a SIMEXP member on Aliance Canada, you will need to clone fMRIPrep-slurm and modify paths accordingly. All scripts are under scripts/preprocessing. If you wish to use the produced metrics to generate the book, feel free to skip this section.

1. preprocessing/get_fmriprep.sh:

   We need to build the fMRIPrep singularity containers version 20.2.1 (fMRIPrep-slurm default) and 20.2.5. For details, please find the documentation on niprep. Alternatively, you can execute the script prepared get_fmriprep.sh. We recommend building the container in a tmux session. This will take a few hours! Run it before going home.

2. preprocessing/get_datasets.sh:

   While running Step 1 you can get the OpenNeuro datasets in parallel. Run the script in a tmux session. This will take an hour or so.

3. preprocessing/create_fmriprep_slurm_scripts.sh:

   After the containers are built and datasets downloaded, we generate the slurm files using fMRIPrep-slurm.

   Remember to check your script to make sure everything runs correctly. This will take the time of a coffee break.

4. Run fmriprep

   fMRIPrep-slurm will give you the exact commands you need to run. It should be something looking like this:

   find /scratch/${USER}/ds000228/UNIXTIME/.slurm/smriprep_sub-*.sh -type f | while read file; do sbatch "$file"; done
   

   This process will take up a day.