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]
....

Links

ARC Software pages