Hoffman2:Software Tools:FMRIprep: Difference between revisions

Latest revision as of 18:28, 8 April 2026

FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data

FMRIprep is provided through Apptainer

module load apptainer
apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/25.1.3/fmriprep-25.1.3.sif \
-w PATH/TO/WORKSPACE \
--output-spaces SPACE_NAME \
--fs-license-file /u/project/CCN/apps/freesurfer/rh7/7.2.0/.license \
PATH/TO/DATA/DIR PATH/TO/OUTPUT/DIR \
participant --participant-label label

Note: By default, fmriprep uses "MNI152NLin2009cAsym" space if no SPACE_NAME specified with --output-spaces option

@@ Line 6: / Line 6: @@
 [https://fmriprep.org/en/stable/usage.html Fmriprep Command Line Usage]
-From version '''20.2.1''', FMRIprep is provided through Singularity
+FMRIprep is provided through Apptainer
-The following command need to be run in a CentOS 7 node.
-  module load singularity
+  module load apptainer
-  singularity shell --userns /u/project/CCN/apps/fmriprep/rh7/20.2.1/fmriprep-20.2.1.sif
+  apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/25.1.3/fmriprep-25.1.3.sif \
-  exit ##to stop container
+ -w PATH/TO/WORKSPACE \
+ --output-spaces SPACE_NAME \
+ --fs-license-file /u/project/CCN/apps/freesurfer/rh7/7.2.0/.license \
+ PATH/TO/DATA/DIR PATH/TO/OUTPUT/DIR \
+  participant --participant-label label
-Or as the instruction from FMRIPrep official site
- module load singularity
- singularity run --cleanenv /u/project/CCN/apps/fmriprep/rh7/20.2.1/fmriprep-20.2.1.sif \
- path/to/data/dir path/to/output/dir \
-    participant --participant-label label
+* Note: By default, fmriprep uses "MNI152NLin2009cAsym" space if no SPACE_NAME specified with --output-spaces option
 <!--For using FMRIprep module in Hoffman, the following modules are needed as well

Hoffman2:Software Tools:FMRIprep: Difference between revisions

Latest revision as of 18:28, 8 April 2026

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