Fmriprep on ARC: Difference between revisions
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= General = | = General = | ||
Project home: https://www.nipreps.org/ | |||
'''fMRIPrep''': fMRI PREProcessing workflows | |||
== On ARC == | |||
Currently we have two singularity containers: | |||
<pre> | |||
$ ls -l /global/software/fmriprep/containers/ | |||
-rwxr-xr-x 1 ian.percel ian.percel 4842659840 Jul 27 2021 fmriprep-20.2.3.simg | |||
-rwxr-xr-x 1 drozmano drozmano 3724558336 Sep 20 08:51 fmriprep-22.0.1.simg | |||
</pre> | |||
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 = | = Using on ARC = | ||
== Version 22.0.1 == | |||
<pre> | |||
$ 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 | |||
.... | |||
</pre> | |||
== Version 20.2.3 == | |||
<pre> | <pre> | ||
$ singularity run /global/software/fmriprep/containers/fmriprep-20.2.3.simg --help | $ singularity run /global/software/fmriprep/containers/fmriprep-20.2.3.simg --help | ||
| Line 12: | Line 47: | ||
.... | .... | ||
</pre> | </pre> | ||
= Links = | |||
[[ARC Software pages]] | |||
[[Category:Software]] | |||
[[Category:ARC]] | |||
{{Navbox ARC}} | |||
Latest revision as of 19:38, 18 October 2023
General
Project home: https://www.nipreps.org/
fMRIPrep: fMRI PREProcessing workflows
On ARC
Currently we have two singularity containers:
$ ls -l /global/software/fmriprep/containers/ -rwxr-xr-x 1 ian.percel ian.percel 4842659840 Jul 27 2021 fmriprep-20.2.3.simg -rwxr-xr-x 1 drozmano drozmano 3724558336 Sep 20 08:51 fmriprep-22.0.1.simg
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] ....