Hoffman2:Software Tools: FMRIprep: Difference between revisions

Latest revision as of 20:14, 25 February 2022

FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data

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

@@ Line 3: / Line 3: @@
 [https://fmriprep.org/en/stable/ Official Website]
+[https://github.com/nipreps/fmriprep/blob/master/.versions.json Bug Report]
 [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
@@ Line 47: / Line 65: @@
 Note:
-fmriprep version 20.1.1 has bug with multi echo scans.
+fmriprep version 20.1.1 has bug with multi echo scans. -->