Hoffman2:Software Tools: FMRIprep: Difference between revisions
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[https://fmriprep.org/en/stable/ Official Website] | [https://fmriprep.org/en/stable/ Official Website] | ||
[https://github.com/nipreps/fmriprep/blob/master/.versions.json Bug Report] | |||
[https://fmriprep.org/en/stable/usage.html Fmriprep Command Line Usage] | [https://fmriprep.org/en/stable/usage.html Fmriprep Command Line Usage] | ||
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module load singularity | module load singularity | ||
singularity shell --userns /u/project/CCN/apps/fmriprep/rh7/20.2. | singularity shell --userns /u/project/CCN/apps/fmriprep/rh7/20.2.5/fmriprep-20.2.5.sif | ||
exit ##to stop container | exit ##to stop container | ||
Or use the following command to run it | |||
singularity run --cleanenv fmriprep.sif path/to/data/dir path/to/output/dir \ | |||
participant --participant-label label | |||
For more details, please check FMRIprep's [https://www.nipreps.org/apps/singularity/ | official site ] | |||
* FMRIprep is no longer a module in Hoffman2, please use the container version | |||
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Latest revision as of 20:14, 25 February 2022
FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data
From version 20.2.1, FMRIprep is provided through Singularity The following command need to be run in a CentOS 7 node.
module load singularity singularity shell --userns /u/project/CCN/apps/fmriprep/rh7/20.2.5/fmriprep-20.2.5.sif exit ##to stop container
Or use the following command to run it
singularity run --cleanenv fmriprep.sif path/to/data/dir path/to/output/dir \ participant --participant-label label
For more details, please check FMRIprep's | official site
- FMRIprep is no longer a module in Hoffman2, please use the container version