Center for Cognitive Neuroscience - Recent changes [en]

Hoffman2:FSL

Hwang — Tue, 05 May 2026 18:15:48 GMT

Known Issue in Hoffman

@@ Line 180: / Line 180: @@
   # now run eddy_cuda9.1 or bedpostx_gpu
 ==External Links==
 * Official FSL website http://www.fmrib.ox.ac.uk/fsl/

FAQs

Melodie — Mon, 04 May 2026 23:15:56 GMT

How do I transfer my scanning protocols from the BMC scanner to the CCN scanner?

← Older revision		Revision as of 23:15, 4 May 2026
Line 85:		Line 85:

	===How do I transfer my scanning protocols from the BMC scanner to the CCN scanner?===		===How do I transfer my scanning protocols from the BMC scanner to the CCN scanner?===
	*Please export a copy of the .exar1 files of the scanning protocol from BMC scanner computer and email the .exar1 to CCN Technical Staff, who can import the protocol. Alternately, you can also copy the DICOM data of a subject directly from the BMC scanner computer (or from a server) onto a CD, which can be converted in the exam interface. Please contact CCN lab manager with requests and files for transferring protocols. Note: CCN scanner computer does support data/protocols stored on flash drives, but drives must be virus scanned every time before being connected to the host machine. ~~Sophos~~ anti-virus is available on the CCN iMac next to the scan computer.		*Please export a copy of the .exar1 files of the scanning protocol from BMC scanner computer and email the .exar1 to CCN Technical Staff, who can import the protocol. Alternately, you can also copy the DICOM data of a subject directly from the BMC scanner computer (or from a server) onto a CD, which can be converted in the exam interface. Please contact CCN lab manager with requests and files for transferring protocols. Note: CCN scanner computer does support data/protocols stored on flash drives, but drives must be virus scanned every time before being connected to the host machine. Malwarebytes anti-virus is available on the CCN iMac next to the scan computer.

	===Can People Visit CCN for Teaching, Filming, or Other Purposes?===		===Can People Visit CCN for Teaching, Filming, or Other Purposes?===

Testing

Melodie — Mon, 04 May 2026 23:15:26 GMT

How do I transfer my scanning protocols from the BMC scanner to the CCN scanner?

← Older revision		Revision as of 23:15, 4 May 2026
Line 49:		Line 49:

	===How do I transfer my scanning protocols from the BMC scanner to the CCN scanner?===		===How do I transfer my scanning protocols from the BMC scanner to the CCN scanner?===
	*Please export a copy of the .exar1 files of the scanning protocol from BMC scanner computer and email the .exar1 to CCN Technical Staff, who can import the protocol. Alternately, you can also copy the DICOM data of a subject directly from the BMC scanner computer (or from a server) onto a CD, which can be converted in the exam interface. Please contact CCN lab manager with requests and files for transferring protocols. Note: CCN scanner computer does support data/protocols stored on flash drives, but drives must be virus scanned every time before being connected to the host machine. ~~Sophos~~ anti-virus is available on the CCN iMac next to the scan computer.		*Please export a copy of the .exar1 files of the scanning protocol from BMC scanner computer and email the .exar1 to CCN Technical Staff, who can import the protocol. Alternately, you can also copy the DICOM data of a subject directly from the BMC scanner computer (or from a server) onto a CD, which can be converted in the exam interface. Please contact CCN lab manager with requests and files for transferring protocols. Note: CCN scanner computer does support data/protocols stored on flash drives, but drives must be virus scanned every time before being connected to the host machine. Malwarebytes anti-virus is available on the CCN iMac next to the scan computer.

	===Can People Visit CCN for Teaching, Filming, or Other Purposes?===		===Can People Visit CCN for Teaching, Filming, or Other Purposes?===

Staglin MR Suite

Melodie — Wed, 15 Apr 2026 17:56:10 GMT

Incidental Findings

← Older revision		Revision as of 17:56, 15 April 2026
(One intermediate revision by the same user not shown)
Line 30:		Line 30:
	A neuroradiologist is on CCN retainer for reviewing potential incidental findings. <b>To be clear, you may only submit images for incidental finding review if you have this explicitly described in your approved IRB protocol.</b> As a reminder, CCN is not a clinical facility, and other than our collaborating neuroradiologist, no CCN faculty or staff are medically trained.		A neuroradiologist is on CCN retainer for reviewing potential incidental findings. <b>To be clear, you may only submit images for incidental finding review if you have this explicitly described in your approved IRB protocol.</b> As a reminder, CCN is not a clinical facility, and other than our collaborating neuroradiologist, no CCN faculty or staff are medically trained.
	For sample language, please refer to the [https://ohrpp.research.ucla.edu/consent-templates/ OHRPP's Consent, Assent, and Screening Templates], in particular the section of the [https://ucla.app.box.com/v/FR-05f01-Biomed-ICF-Stand-Lang Biomedical Research Consent Form Standards and Sample Language document] addressing clinically relevant results.		For sample language, please refer to the [https://ohrpp.research.ucla.edu/consent-templates/ OHRPP's Consent, Assent, and Screening Templates], in particular the section of the [https://ucla.app.box.com/v/FR-05f01-Biomed-ICF-Stand-Lang Biomedical Research Consent Form Standards and Sample Language document] addressing clinically relevant results.

			See the [https://www.ccn.ucla.edu/wiki/index.php/Incidental_Finding_Report_Tool Incidental Finding Report Tool page] for instructions on submitting a report for review.

	===Common forms===		===Common forms===

Hoffman2:Software Tools

Hwang — Wed, 08 Apr 2026 18:45:49 GMT

FMRIprep

← Older revision		Revision as of 18:45, 8 April 2026
(One intermediate revision by the same user not shown)
Line 328:		Line 328:
	! 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

← Older revision		Revision as of 18:28, 8 April 2026
(One intermediate revision by the same user not shown)
Line 10:		Line 10:
	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

← Older revision		Revision as of 18:19, 8 April 2026
(2 intermediate revisions by the same user not shown)
Line 3:		Line 3:

	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

← Older revision		Revision as of 18:16, 8 April 2026
(7 intermediate revisions by the same user not shown)
Line 6:		Line 6:
	[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