ds005256 - fMRIPrep derivatives

This is a BIDS Derivatives dataset resulting from running fMRIPrep on ds005256.

Methods

fMRIPrep documentation can be found on https://fmriprep.readthedocs.io/.

A containerized version of fMRIPrep is stored in code/containers/fmriprep_25_1_4.sif. This container was built using

apptainer build code/containers/fmriprep_25_1_4.sif docker://nipreps/fmriprep:25.1.4

Products were generated with the Slurm script code/run. That script uses Slurm arrays to process participants in parallel (one participant per job). Slurm logs (combined stdout and stderr) are stored in logs/$SLURM_ARRAY_TASK_ID.log. Running all participants would entail setting the array argument during the call to sbatch.

sbatch --array=0-116 code/run

Derivatives were saved in the dataset with git/git-annex using code/save. For example, to save sub-0133, run the following.

# NOTE: the argument (116) is the SLURM_ARRAY_TASK_ID, not the participant_label
./code/save 116

Defacing

To acheive the highest quality derivatives possible, these derivatives were generated on the raw (that is, not defaced) structural scans (sha: 86007170141050f875acfd6daf802d93bd9a7dac). This processing was committed to branch main-w-faces. After all participants were added, a new branch was created, main-w-faces-defacing, and the defaced images were committed to there (see code/remove_faces). The main branch contains references to only defaced files.

Environment

$ apptainer --version
apptainer version 1.2.2-2.el8

Caveats

At the time of writing, most fMRIPrep products are not covered by BIDS, and so most of this dataset is covered by a .bidsignore.