Hoffman2:Software Tools:FMRIprep: Difference between revisions
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The following command need to be run in a CentOS 7 node. | The following command need to be run in a CentOS 7 node. | ||
<!-- module load singularity | |||
singularity shell --userns /u/project/CCN/apps/fmriprep/rh7/20.2.1/fmriprep-20.2.1.sif | singularity shell --userns /u/project/CCN/apps/fmriprep/rh7/20.2.1/fmriprep-20.2.1.sif | ||
exit ##to stop container | exit ##to stop container | ||
Or as the instruction from FMRIPrep official site --> | |||
module load singularity | |||
singularity run --cleanenv /u/project/CCN/apps/fmriprep/rh7/20.2.1/fmriprep-20.2.1.sif \ | |||
path/to/data/dir path/to/output/dir \ | |||
participant --participant-label label | |||
From version '''23.1.3''', FMRIprep is provided through Apptainer | |||
module load apptainer/1.2.2 | |||
apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/23.1.3/23.1.3-fmriprep.sif \ | |||
path/to/data/dir path/to/output/dir \ | |||
participant --participant-label label | |||
For using FMRIprep module in Hoffman, the following modules are needed as well | <!--For using FMRIprep module in Hoffman, the following modules are needed as well | ||
FMRIprep version '''20.2.0rc0''' | FMRIprep version '''20.2.0rc0''' | ||
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Note: | Note: | ||
fmriprep version 20.1.1 has bug with multi echo scans. | fmriprep version 20.1.1 has bug with multi echo scans. --> | ||
Latest revision as of 18:19, 22 August 2023
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 run --cleanenv /u/project/CCN/apps/fmriprep/rh7/20.2.1/fmriprep-20.2.1.sif \ path/to/data/dir path/to/output/dir \ participant --participant-label label
From version 23.1.3, FMRIprep is provided through Apptainer
module load apptainer/1.2.2 apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/23.1.3/23.1.3-fmriprep.sif \ path/to/data/dir path/to/output/dir \ participant --participant-label label