Hoffman2:Software Tools: FMRIprep: Difference between revisions
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(Created page with "For using FMRIprep, please load the following pre-requisite modules as well module load fsl/5.0.9 module load python/3.7.2 module load freesurfer/6.0.0 module load ants/ants-...") |
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module load fsl/5.0.9 | FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data | ||
module load python/3.7.2 | |||
module load freesurfer/6.0.0 | [https://fmriprep.org/en/stable/ Official Website] | ||
module load ants/ants-2.2.0 | |||
module load afni/19.0.15 | [https://fmriprep.org/en/stable/usage.html Fmriprep Command Line Usage] | ||
module load ica-aroma | |||
module load itksnap/3.6.0-RC1.QT4 | 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/:$PATH | |||
export NO_FSL_JOBS=true | |||
To find all FMRIprep version in Hoffman | |||
module av fmriprep | |||
To load FMRIprep module | |||
module load fmriprep/1.4.0 | |||
To get fmriprep command line help, run command | |||
fmriprep -h | |||
(You should run FMRIprep with a interactive mode or a batch mode in Hoffman) | |||
Note on 7/16/2020: | |||
For the newest version fmriprep/20.1.1, python module version needs to be python/3.7.0 | |||
Revision as of 21:52, 15 July 2020
FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data
For using FMRIprep module in Hoffman, the following modules are needed as well (This example is for FMRIprep version 1.4.0)
module load fsl/5.0.9 module load python/3.7.2 module load freesurfer/6.0.0 module load ants/ants-2.2.0 module load afni/19.0.15 module load ica-aroma module load itksnap/3.6.0-RC1.QT4 export PATH=/u/project/CCN/apps/c3d/c3d-1.0.0-Linux-x86_64/bin/:$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