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 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]
....

Links

ARC Software pages