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

Hoffman2:Software Tools:FMRIprep

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

Hoffman2:Singularity

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===

Hoffman2:Software Tools:FMRIprep

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

Scan Procedures

Melodie — Thu, 02 Apr 2026 15:46:34 GMT

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	*'''Participant Arrival:''' Please make sure that your study participants have a direct contact and that lab personnel will be available to take calls and/or respond promptly to texts/emails as the time of the scan approaches. Study participants should not wait inside of CCN unattended. If a participant arrives early and you are part of the research team, make sure someone is available to communicate with the person and direct them to wait on the bench right outside CCN. If you are in CCN and not part of the research team expecting this participant's arrival, it is up to you if you have the time to ask questions and help figure out who their research contact is. Regardless, still ask them to wait on the bench outside CCN.		*'''Participant Arrival:''' Please make sure that your study participants have a direct contact and that lab personnel will be available to take calls and/or respond promptly to texts/emails as the time of the scan approaches. Study participants should not wait inside of CCN unattended. If a participant arrives early and you are part of the research team, make sure someone is available to communicate with the person and direct them to wait on the bench right outside CCN. If you are in CCN and not part of the research team expecting this participant's arrival, it is up to you if you have the time to ask questions and help figure out who their research contact is. Regardless, still ask them to wait on the bench outside CCN.
	'''Pilot Program:''' NOTE: The pilot program is back! However, please still consider [https://ctsi.ucla.edu/funding-and-grant-support/funding-opportunities/ctsi-rfas/ctsi-core-voucher CTSI] for funding opportunities.* The Center will consider proposals by members of the UCLA community to access both the scanning and analysis core services for pilot studies without charge to the investigator. Priority will be given to junior investigators and to proposals for novel cognitive neuroscience projects that have a high likelihood of achieving extramural funding. To submit such a request, email the completed [https://drive.google.com/file/d/1rhfezXO3QP4pV5yjUnNmI8LNkjw7EqS9/view?usp=sharing application] to the CCN Managing Director. The proposal will be reviewed by the Executive Committee members and CCN personnel will contact you regarding the status of the submission. As stated in the application, if you need more space than provided for any item within <b>please use a Word document to submit your answers</b>.		'''Pilot Program:''' NOTE: The pilot program is back! However, please still consider [https://ctsi.ucla.edu/funding-and-grant-support/funding-opportunities/ctsi-rfas/ctsi-core-voucher CTSI] for funding opportunities.* The Center will consider proposals by members of the UCLA community to access both the scanning and analysis core services for pilot studies without charge to the investigator. Priority will be given to junior investigators and to proposals for novel cognitive neuroscience projects that have a high likelihood of achieving extramural funding. To submit such a request, email the completed [https://drive.google.com/file/d/1rhfezXO3QP4pV5yjUnNmI8LNkjw7EqS9/view?usp=sharing application] to the CCN Managing Director. The proposal will be reviewed by the Executive Committee members and CCN personnel will contact you regarding the status of the submission. As stated in the application, if you need more space than provided for any item within <b>please use a Word document to submit your answers</b>.
	*'''Protocol Testing:''' Each new protocol is granted off-hours time to test and refine the scanning protocol, at no charge. Development (and pilot) time is granted by CCN personnel and booked via SIStat.		*'''Protocol Testing:''' Each new protocol is granted off-hours time to test and refine the scanning protocol, at no charge. Development (and pilot) time is granted by CCN personnel and booked via SIStat. Please reach out to ccnsupport@g.ucla.edu for instructions on booking development time when your team is ready to test a protocol.
	*'''Scan Testing:''' Each new project is permitted two free scan sessions with a human phantom to ensure that the full setup is functional. The group is responsible for recruiting their own test participant, whose images cannot be used as publishable data, and who must still undergo safety screening despite not being included as a real study participant. All such scans must be booked with free Development/Practice time, assigned by CCN personnel.		*'''Scan Testing:''' Each new project is permitted two free scan sessions with a human phantom to ensure that the full setup is functional. The group is responsible for recruiting their own test participant, whose images cannot be used as publishable data, and who must still undergo safety screening despite not being included as a real study participant. All such scans must be booked with free Development/Practice time, assigned by CCN personnel.
	*'''Scan Time:''' All scans are expected to start and end promptly at the scheduled time. It is the investigators’ responsibility to communicate with the CCN staff and/or other investigators if these times cannot be met. Please note that CCN and/or other investigators may not be able to accommodate requests for change of scheduled time when these are communicated less than 24 hours prior to the appointment.		*'''Scan Time:''' All scans are expected to start and end promptly at the scheduled time. It is the investigators’ responsibility to communicate with the CCN staff and/or other investigators if these times cannot be met. Please note that CCN and/or other investigators may not be able to accommodate requests for change of scheduled time when these are communicated less than 24 hours prior to the appointment.

Current Designs Response Devices

Melodie — Tue, 31 Mar 2026 17:52:46 GMT

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	===Current Designs===		===Current Designs===
	*[https://www.curdes.com Product Site]		*[https://www.curdes.com Product Site]
	*CCN is currently outfitted with ~~three~~ MR safe response devices: [https://www.curdes.com/mainforp/responsedevices/hhsc-1x2-by.html 2 Button Box], [https://www.curdes.com/mainforp/responsedevices/hhsc-1x4-l.html 4 Button Box], and a [https://www.curdes.com/mainforp/responsedevices/hhsc-trk-2.html Track Ball]		*CCN is currently outfitted with four MR safe response devices: [https://www.curdes.com/mainforp/responsedevices/hhsc-1x2-by.html 2 Button Inline Box], [https://www.curdes.com/mainforp/responsedevices/hhsc-1x4-l.html 4 Button Inline Box], [https://www.curdes.com/mainforp/responsedevices/buttonboxes/hhsc-1x4-d.html 4 Button Diamond Box], and a [https://www.curdes.com/mainforp/responsedevices/hhsc-trk-2.html Track Ball]
	*CCN is also equipped with a USB 4 button practice device for use in the testing room outside of the scanner		*CCN is also equipped with a USB 4 button practice device for use in the testing room outside of the scanner
	**This device is '''NOT''' MR safe and should not enter the scanner room at any time		**This device is '''NOT''' MR safe and should not enter the scanner room at any time