Hoffman2:Software Tools: FMRIprep: Difference between revisions
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For using FMRIprep module, the following modules are needed as well | |||
FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data | |||
[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] | |||
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 [https://www.nipreps.org/apps/singularity/ | official site ] | |||
* FMRIprep is no longer a module in Hoffman2, please use the container version | |||
<!-- | |||
For using FMRIprep module in Hoffman, the following modules are needed as well | |||
FMRIprep version '''20.2.0rc0''' | |||
module load fsl/5.0.9 | |||
module load python/3.7.0 | |||
module load freesurfer/6.0.0 | |||
module load ants/ants-2.2.0 | |||
module load afni/19.0.15 | |||
module load ica-aroma | |||
module load itksnap/3.6.0-RC1.QT4 | |||
module load fmriprep/20.2.0rc0 | |||
export PATH=/u/project/CCN/apps/c3d/c3d-1.0.0-Linux-x86_64/bin/:$PATH | |||
export NO_FSL_JOBS=true | |||
FMRIprep version '''1.4.0''' | |||
module load fsl/5.0.9 | module load fsl/5.0.9 | ||
| Line 8: | Line 49: | ||
module load ica-aroma | module load ica-aroma | ||
module load itksnap/3.6.0-RC1.QT4 | module load itksnap/3.6.0-RC1.QT4 | ||
module load fmriprep/1.4.0 | |||
export PATH=/u/project/CCN/apps/c3d/c3d-1.0.0-Linux-x86_64/bin/:$PATH | |||
export NO_FSL_JOBS=true | |||
To find all FMRIprep version in Hoffman | |||
module av fmriprep | |||
To get fmriprep command line help, run command | |||
fmriprep -h | |||
(You should run FMRIprep with a interactive mode or a batch mode in Hoffman) | |||
Note: | |||
fmriprep version 20.1.1 has bug with multi echo scans. --> | |||
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