Hoffman2:Software Tools: FMRIprep - Revision history

Hwang at 20:14, 25 February 2022

2022-02-25T20:14:24Z

← Older revision		Revision as of 20:14, 25 February 2022
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	[https://fmriprep.org/en/stable/ Official Website]		[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]		[https://fmriprep.org/en/stable/usage.html Fmriprep Command Line Usage]

2022-02-25T20:04:30Z

← Older revision		Revision as of 20:04, 25 February 2022
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	module load singularity		module load singularity
	singularity shell --userns /u/project/CCN/apps/fmriprep/rh7/20.2.1/fmriprep-20.2.5.sif		singularity shell --userns /u/project/CCN/apps/fmriprep/rh7/20.2.5/fmriprep-20.2.5.sif
	exit ##to stop container		exit ##to stop container

2021-12-09T02:26:56Z

← Older revision		Revision as of 02:26, 9 December 2021
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	module load singularity		module load singularity
	singularity shell --userns /u/project/CCN/apps/fmriprep/rh7/20.2.1/fmriprep-20.2.1.sif		singularity shell --userns /u/project/CCN/apps/fmriprep/rh7/20.2.1/fmriprep-20.2.5.sif
	exit ##to stop container		exit ##to stop container

2021-10-26T23:31:09Z

← Older revision		Revision as of 23:31, 26 October 2021
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	For more details, please check FMRIprep's [https://www.nipreps.org/apps/singularity/ \| official site ]		For more details, please check FMRIprep's [https://www.nipreps.org/apps/singularity/ \| official site ]

	* FMRIprep is no longer a module in ~~Hoffman~~, please use the container version		* FMRIprep is no longer a module in Hoffman2, please use the container version

	<!--		<!--

2021-10-26T23:19:37Z

← Older revision		Revision as of 23:19, 26 October 2021
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	Or use the following command to run it		Or use the following command to run it
	singularity run --cleanenv fmriprep.~~simg~~ path/to/data/dir path/to/output/dir \		singularity run --cleanenv fmriprep.sif path/to/data/dir path/to/output/dir \
	participant --participant-label label		participant --participant-label label

2021-10-26T23:18:21Z

← Older revision		Revision as of 23:18, 26 October 2021
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	singularity shell --userns /u/project/CCN/apps/fmriprep/rh7/20.2.1/fmriprep-20.2.1.sif		singularity shell --userns /u/project/CCN/apps/fmriprep/rh7/20.2.1/fmriprep-20.2.1.sif
	exit ##to stop container		exit ##to stop container

			Or use the following command to run it
			singularity run --cleanenv fmriprep.simg 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 Hoffman, please use the container version

	<!--		<!--

2021-10-26T23:14:53Z

← Older revision		Revision as of 23:14, 26 October 2021
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	exit ##to stop container		exit ##to stop container

			<!--
	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

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	Note:		Note:
	fmriprep version 20.1.1 has bug with multi echo scans.		fmriprep version 20.1.1 has bug with multi echo scans. -->

2021-08-11T23:36:31Z

← Older revision		Revision as of 23:36, 11 August 2021
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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
			The following command need to be run in a CentOS 7 node.

			module load singularity
			singularity shell --userns /u/project/CCN/apps/fmriprep/rh7/20.2.1/fmriprep-20.2.1.sif
			exit ##to stop container


	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

2021-04-01T22:42:32Z

← Older revision		Revision as of 22:42, 1 April 2021
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	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

	~~For~~ FMRIprep version 20.2.0rc0		FMRIprep version '''20.2.0rc0'''
	module load fsl/5.0.9		module load fsl/5.0.9
	module load python/3.7.0		module load python/3.7.0
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	~~(This example is for~~ FMRIprep version '''1.4.0''')		FMRIprep version '''1.4.0'''

	module load fsl/5.0.9		module load fsl/5.0.9
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	module av fmriprep		module av fmriprep

	~~To load FMRIprep module~~

	~~module load fmriprep/1.4.0~~

	To get fmriprep command line help, run command		To get fmriprep command line help, run command

2021-04-01T22:40:35Z

← Older revision		Revision as of 22:40, 1 April 2021
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	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

			For FMRIprep version 20.2.0rc0
			module load fsl/5.0.9
			module load python/3.7.0
			module load freesurfer/6.0.0
			module load ants/ants-2.2.0
			module load afni/19.0.15
			module load ica-aroma
			module load itksnap/3.6.0-RC1.QT4
			module load fmriprep/20.2.0rc0

			export PATH=/u/project/CCN/apps/c3d/c3d-1.0.0-Linux-x86_64/bin/:$PATH
			export NO_FSL_JOBS=true


	(This example is for FMRIprep version '''1.4.0''')		(This example is for FMRIprep version '''1.4.0''')

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	module load ica-aroma		module load ica-aroma
	module load itksnap/3.6.0-RC1.QT4		module load itksnap/3.6.0-RC1.QT4
			module load fmriprep/1.4.0

	export PATH=/u/project/CCN/apps/c3d/c3d-1.0.0-Linux-x86_64/bin/:$PATH		export PATH=/u/project/CCN/apps/c3d/c3d-1.0.0-Linux-x86_64/bin/:$PATH
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	(You should run FMRIprep with a interactive mode or a batch mode in Hoffman)		(You should run FMRIprep with a interactive mode or a batch mode in Hoffman)

	Note ~~on 7/16/2020~~:		Note:
	~~For the newest~~ version ~~fmriprep/~~20.1.1~~, python module version needs to be python/3.7~~.0		fmriprep version 20.1.1 has bug with multi echo scans.