Hoffman2:Software Tools: FMRIprep: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 8: | Line 8: | ||
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''' | |||
module load fsl/5.0.9 | module load fsl/5.0.9 | ||
module load python/3.7.0 | module load python/3.7.0 | ||
| Line 22: | Line 22: | ||
FMRIprep version '''1.4.0''' | |||
module load fsl/5.0.9 | module load fsl/5.0.9 | ||
| Line 39: | Line 39: | ||
module av fmriprep | module av fmriprep | ||
To get fmriprep command line help, run command | To get fmriprep command line help, run command | ||
Revision as of 22:42, 1 April 2021
FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data
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/:$PATH export NO_FSL_JOBS=true
FMRIprep version 1.4.0
module load fsl/5.0.9 module load python/3.7.2 module load freesurfer/6.0.0 module load ants/ants-2.2.0 module load afni/19.0.15 module load ica-aroma module load itksnap/3.6.0-RC1.QT4 module load fmriprep/1.4.0 export PATH=/u/project/CCN/apps/c3d/c3d-1.0.0-Linux-x86_64/bin/:$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.