Center for Cognitive Neuroscience - Recent changes [en]

Hoffman2:Software Tools

Hwang — Wed, 08 Apr 2026 18:45:49 GMT

FMRIprep

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	! class="ccn-table-header"\| Install Date		! class="ccn-table-header"\| Install Date
	! class="ccn-table-header"\| Notes		! class="ccn-table-header"\| Notes
			\|- class="ccn-table-odd"
			\| 25.1.3 \|\|2025.07.27 \|\| In Apptainer
			\|- class="ccn-table-even"
			\| 24.1.1 \|\|2024.11.01 \|\| In Apptainer
			\|- class="ccn-table-odd"
			\| 23.2.0 \|\|2024.03.12 \|\| In Apptainer
	\|- class="ccn-table-even" style="background-color:#E5FFCC;"		\|- class="ccn-table-even" style="background-color:#E5FFCC;"
	\| 23.1.3 \|\|2023.08.22 \|\| Use Apptainer module		\| 23.1.3 \|\|2023.08.22 \|\| Use Apptainer module

Hwang — Wed, 08 Apr 2026 18:28:55 GMT

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	module load apptainer		module load apptainer
	apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/25.1.3/fmriprep-25.1.3.sif \		apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/25.1.3/fmriprep-25.1.3.sif \
	-w ~~path~~/to/~~workspace~~ \		-w PATH/TO/WORKSPACE \
			--output-spaces SPACE_NAME \
	--fs-license-file /u/project/CCN/apps/freesurfer/rh7/7.2.0/.license \		--fs-license-file /u/project/CCN/apps/freesurfer/rh7/7.2.0/.license \
	~~path~~/to/~~data~~/~~dir path~~/to/~~output~~/~~dir~~ \		PATH/TO/DATA/DIR PATH/TO/OUTPUT/DIR \
	participant --participant-label label		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		<!--For using FMRIprep module in Hoffman, the following modules are needed as well

Hwang — Wed, 08 Apr 2026 18:19:45 GMT

Singularity

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	Singularity is a type of container technology. It is provided in Hoffman2 currently.		Singularity is a type of container technology. It is provided in Hoffman2 currently.

			* Note: Singularity's newer versions are under its new name "Apptainer". It's recommended to use Apptainer instead of Singularity.
			Just need to replace all the "singularity" with "apptainer" in the following command and it should work the same way.

	===How to use Singularity===		===How to use Singularity===

Hwang — Wed, 08 Apr 2026 18:16:11 GMT

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	[https://fmriprep.org/en/stable/usage.html Fmriprep Command Line Usage]		[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 \
			--fs-license-file /u/project/CCN/apps/freesurfer/rh7/7.2.0/.license \
	~~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~~

	~~From version '''23.1.3''', FMRIprep is provided through Apptainer~~

	~~module load apptainer/1.2.2~~
	~~apptainer run~~ -~~-cleanenv~~ /u/project/CCN/apps/~~fmriprep~~/rh7/23.1.3/23.~~1.3-fmriprep.sif~~ \
	path/to/data/dir path/to/output/dir \		path/to/data/dir path/to/output/dir \
	participant --participant-label label		participant --participant-label label