Hoffman2:Software Tools: FMRIprep: Difference between revisions
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FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data | FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data | ||
[https://fmriprep.org/en/stable/ Official Website] | |||
[https://fmriprep.org/en/stable/usage.html Fmriprep Command Line Usage] | |||
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 | ||
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export PATH=/u/project/CCN/apps/c3d/c3d-1.0.0-Linux-x86_64/bin/:$PATH | export PATH=/u/project/CCN/apps/c3d/c3d-1.0.0-Linux-x86_64/bin/:$PATH | ||
export NO_FSL_JOBS=true | export NO_FSL_JOBS=true | ||
To find all FMRIprep version in Hoffman | |||
module av fmriprep | |||
To load FMRIprep module | To load FMRIprep module |
Revision as of 21:52, 15 July 2020
FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data
For using FMRIprep module in Hoffman, the following modules are needed as well (This example is for FMRIprep version 1.4.0)
module load fsl/5.0.9 module load python/3.7.2 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 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 load FMRIprep module
module load fmriprep/1.4.0
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 on 7/16/2020: For the newest version fmriprep/20.1.1, python module version needs to be python/3.7.0