Apptainer Example

This video, describes an apptainer command to run fmriprep. It would normally be a single line, but I split it up for display.

In black is a typical call to run apptainer, the bind mounts for the input and output directories and the path to the container itself (It assumes the data is under the present working directory).
In red I list the typical BIDS arguments: input, output, analysis level (participant) and the label of the participant to process (Note there is no group option for fmriprep).
In blue I provide paths to the Freesurfer license file and the work directory.
- 6) --fs-license-file indicates the location of the FreeSurfer license. Because this is apptainer, it mounts your home directory by default so you do not need to explicitly bind-mount the FreeSurfer license.
- 7) ${PWD}/fmriprep_work designates a work directory to hold intermediate results.
In green are selected fmriprep-specific flags and arguments detailing the processing steps I want run.
- 8) --stop-on-first-crash stops running the job if it crashes
- 9) --ignore slice-timing refrains from running slice-timing correction.
- 10) --cifti-output generates Human-Connectome-Project compliant CIFTI files for surface-based analyses.
- 11) --output-spaces takes a space-delimited list of standard and subject-specific templates to register the bold data. fsnative instructs fMRIPrep to sample the original BOLD data onto FreeSurfer’s reconstructed surfaces for this individual. MNI152NLin6Asym:res-2 is the preferred output space for CONN.
At the very bottom of the slide, in purple, I list optional flags I sometimes find useful:
- 12) --fs-no-reconall prevents FreeSurfer from running. This means fmriprep is much faster, but the results are not as good. This is nice for testing scripts or new versions of fMRIprep.
- 13) --skip-bids-validation can be helpful if something in your directory is preventing the run (like non-compliant ASL files that don't affect fmriprep anyhow).

fmriprep 2: Setup