Fmriprep on ARC
General
Project home: https://www.nipreps.org/
fMRIPrep: fMRI PREProcessing workflows
On ARC
Currently we have the following Apptainer containers:
$ ls -l /global/software/fmriprep/containers/ -rwxr-xr-x 1 drozmano drozmano 4842659840 Jul 27 2021 fmriprep-20.2.3.simg -rwxr-xr-x 1 drozmano drozmano 3724558336 Sep 20 2022 fmriprep-22.0.1.simg -rwxr-xr-x 1 drozmano drozmano 2413367296 Mar 9 10:18 fmriprep-25.2.4.sif
The containers were converted from their Docker versions using the command:
singularity build /my_images/fmriprep-22.0.1.simg docker://nipreps/fmriprep:22.0.1
The discussion and instructions are here: https://www.nipreps.org/apps/singularity/
Using on ARC
Version 25.2.4
$ apptainer run /global/software/fmriprep/containers/fmriprep-25.2.4.sif --help
usage: fmriprep [-h] [--skip_bids_validation] [--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [--session-label SESSION_LABEL [SESSION_LABEL ...]]
[-t TASK_ID] [--echo-idx ECHO_IDX] [--subject-anatomical-reference {first-lex,unbiased,sessionwise}] [--bids-filter-file FILE]
....
fMRIPrep: fMRI PREProcessing workflows v25.2.4
positional arguments:
bids_dir The root folder of a BIDS valid dataset (sub-XXXXX folders should be found at the top level in this folder).
output_dir The output path for the outcomes of preprocessing and visual reports
....
Version 22.0.1
$ singularity run /global/software/fmriprep/containers/fmriprep-20.2.3.simg --help usage: fmriprep [-h] [--version] [--skip_bids_validation] .... fMRIPrep: fMRI PREProcessing workflows v22.0.1 positional arguments: bids_dir the root folder of a BIDS valid dataset (sub-XXXXX ....
Version 20.2.3
$ singularity run /global/software/fmriprep/containers/fmriprep-20.2.3.simg --help You are using fMRIPrep-20.2.3, and a newer version of fMRIPrep is available: 21.0.2. Please check out our documentation about how and when to upgrade: https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading usage: fmriprep [-h] [--version] [--skip_bids_validation] ....