Fmriprep on ARC: Difference between revisions
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Project home: https://www.nipreps.org/ | Project home: https://www.nipreps.org/ | ||
DockerHub: https://hub.docker.com/r/nipreps/fmriprep | |||
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== On ARC == | == On ARC == | ||
Currently we have | Currently we have the following Apptainer containers: | ||
<pre> | <pre> | ||
$ ls -l /global/software/fmriprep/containers/ | $ ls -l /global/software/fmriprep/containers/ | ||
-rwxr-xr-x 1 | -rwxr-xr-x 1 drozmano drozmano 4842659840 Jul 27 2021 fmriprep-20.2.3.simg | ||
-rwxr-xr-x 1 drozmano | -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 | |||
</pre> | </pre> | ||
The containers were converted from their Docker versions using the command: | The containers were converted from their Docker versions using the command: | ||
apptainer build mfreprep-25.2.4.sif docker://nipreps/fmriprep:25.2.4 | |||
The discussion and instructions are here: | The discussion and instructions are here: | ||
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= Using on ARC = | = Using on ARC = | ||
== Version 25.2.4 == | |||
<pre> | |||
$ apptainer run -B/work,/bulk /global/software/fmriprep/containers/fmriprep-25.2.4.sif --version | |||
fMRIPrep v25.2.4 | |||
$ apptainer run -B/work,/bulk /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 | |||
.... | |||
</pre> | |||
== Version 22.0.1 == | == Version 22.0.1 == | ||
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[[ARC Software pages]] | [[ARC Software pages]] | ||
[[Category:Software]] | |||
[[Category:ARC]] | |||
{{Navbox ARC}} | |||
Latest revision as of 16:30, 9 March 2026
General
Project home: https://www.nipreps.org/
DockerHub: https://hub.docker.com/r/nipreps/fmriprep
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:
apptainer build mfreprep-25.2.4.sif docker://nipreps/fmriprep:25.2.4
The discussion and instructions are here: https://www.nipreps.org/apps/singularity/
Using on ARC
Version 25.2.4
$ apptainer run -B/work,/bulk /global/software/fmriprep/containers/fmriprep-25.2.4.sif --version
fMRIPrep v25.2.4
$ apptainer run -B/work,/bulk /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] ....