Hoffman2:Software Tools: FMRIprep: Difference between revisions

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For using FMRIprep, please load the following pre-requisite modules as well


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://github.com/nipreps/fmriprep/blob/master/.versions.json Bug Report]
module load ica-aroma
 
module load itksnap/3.6.0-RC1.QT4
[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 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. -->

Latest revision as of 20:14, 25 February 2022

FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data

Official Website

Bug Report

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 | official site

  • FMRIprep is no longer a module in Hoffman2, please use the container version