Freesurfer on ARC - Revision history

Dmitri: /* Freesurfer Apptainer Containers */

2026-03-02T18:51:07Z

Freesurfer Apptainer Containers

← Older revision		Revision as of 18:51, 2 March 2026
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	$ ls -l /global/software/freesurfer/containers/		$ ls -l /global/software/freesurfer/containers/

	-rwxr-xr-x 1 drozmano drozmano 4358946816 Oct 3 15:32 freesurfer-7.1.1.sif		-rwxr-xr-x 1 drozmano drozmano 4358946816 Oct 3 15:32 freesurfer-7.1.1.sif
	-rwxr-xr-x 1 drozmano drozmano 6402535424 Oct 3 15:31 freesurfer-7.3.2.sif		-rwxr-xr-x 1 drozmano drozmano 6402535424 Oct 3 15:31 freesurfer-7.3.2.sif
	-rwxr-xr-x 1 drozmano drozmano 9342550016 Oct 3 15:31 freesurfer-7.4.1.sif		-rwxr-xr-x 1 drozmano drozmano 9342550016 Oct 3 15:31 freesurfer-7.4.1.sif
			-rwxr-xr-x 1 drozmano drozmano 13807673344 Mar 2 11:47 freesurfer-8.1.0.sif
	</pre>		</pre>

Dmitri: /* Multiple Scans Reconstruction in Parallel with a Job Array */

2023-10-18T19:37:48Z

Multiple Scans Reconstruction in Parallel with a Job Array

← Older revision		Revision as of 19:37, 18 October 2023
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	If you want to know more about using array jobs on ARC you can also check this article:		If you want to know more about using array jobs on ARC you can also check this article:
	[[How to use array jobs in SLURM]].		[[How to use array jobs in SLURM]].

			= Links =

			[[ARC Software pages]]

	[[Category:Software]]		[[Category:Software]]
	[[Category:ARC]]		[[Category:ARC]]
	{{Navbox ARC}}		{{Navbox ARC}}

Dmitri at 19:23, 18 October 2023

2023-10-18T19:23:28Z

← Older revision		Revision as of 19:23, 18 October 2023
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	Freesurfer is a collection of neuroimaging software that can be used to process Magnetic Resonance Imaging files like DICOMs and NIFTIs. Detailed documentation can be found on the [https://surfer.nmr.mgh.harvard.edu/ Freesurfer website]. Most simple workflows that are scalable on ARC use recon-all to perform a reconstruction of the MRI image from the collection of slices. This is done by parallelizing over scans or subjects.		= Background =

			* Official site: https://surfer.nmr.mgh.harvard.edu/

			* Downloads: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

			* Wiki: https://surfer.nmr.mgh.harvard.edu/fswiki

			'''Freesurfer''' is a collection of neuroimaging software that can be used to process Magnetic Resonance Imaging files like DICOMs and NIFTIs. Detailed documentation can be found on the [https://surfer.nmr.mgh.harvard.edu/ Freesurfer website]. Most simple workflows that are scalable on ARC use recon-all to perform a reconstruction of the MRI image from the collection of slices. This is done by parallelizing over scans or subjects.

	= Freesurfer Apptainer Containers =		= Freesurfer Apptainer Containers =

	The more recent versions of Freesurfer installed on ARC have been built as Apptainer containers based off of the official public Freesurfer docker release: [https://hub.docker.com/r/freesurfer/freesurfer]		The more recent versions of '''Freesurfer''' installed on ARC have been built as Apptainer containers based off of the official public Freesurfer docker release: [https://hub.docker.com/r/freesurfer/freesurfer]

	Currently, on ARC there are containers for several versions of Freesurfer available.		Currently, on ARC there are containers for several versions of Freesurfer available.

Dmitri: /* Freesurfer Singularity Containers */

2023-10-03T22:59:27Z

Freesurfer Singularity Containers

← Older revision		Revision as of 22:59, 3 October 2023
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	Freesurfer is a collection of neuroimaging software that can be used to process Magnetic Resonance Imaging files like DICOMs and NIFTIs. Detailed documentation can be found on the [https://surfer.nmr.mgh.harvard.edu/ Freesurfer website]. Most simple workflows that are scalable on ARC use recon-all to perform a reconstruction of the MRI image from the collection of slices. This is done by parallelizing over scans or subjects.		Freesurfer is a collection of neuroimaging software that can be used to process Magnetic Resonance Imaging files like DICOMs and NIFTIs. Detailed documentation can be found on the [https://surfer.nmr.mgh.harvard.edu/ Freesurfer website]. Most simple workflows that are scalable on ARC use recon-all to perform a reconstruction of the MRI image from the collection of slices. This is done by parallelizing over scans or subjects.

	= Freesurfer ~~Singularity~~ Containers =		= Freesurfer Apptainer Containers =

	The more recent versions of Freesurfer installed on ARC have been built as ~~Singularity~~ containers based off of the official public Freesurfer docker release: [https://hub.docker.com/r/freesurfer/freesurfer]		The more recent versions of Freesurfer installed on ARC have been built as Apptainer containers based off of the official public Freesurfer docker release: [https://hub.docker.com/r/freesurfer/freesurfer]

	Currently, on ARC there are containers for several versions of Freesurfer available.		Currently, on ARC there are containers for several versions of Freesurfer available.

Dmitri: /* Single Scan Script */

2023-10-03T22:56:54Z

Single Scan Script

← Older revision		Revision as of 22:56, 3 October 2023
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	It makes sure that the container also mounts those file systems, in case you want to access / write files outside of your home directory.		It makes sure that the container also mounts those file systems, in case you want to access / write files outside of your home directory.

	The "/" character at the end of the command line allows to continue the command on the next line.		The "\" character at the end of the command line allows to continue the command on the next line.
	It is done for readability, when a command becomes too long.		It is done for readability, when a command becomes too long.

Dmitri: /* Single Scan Script */

2023-10-03T22:56:38Z

Single Scan Script

← Older revision		Revision as of 22:56, 3 October 2023
Line 125:		Line 125:

	The "/" character at the end of the command line allows to continue the command on the next line.		The "/" character at the end of the command line allows to continue the command on the next line.
	It is done for readability, when ~~the~~ command becomes too long.		It is done for readability, when a command becomes too long.

	!!! You '''have to replace the dummy file paths''' in this example with actual paths to the directories with your data. !!!		!!! You '''have to replace the dummy file paths''' in this example with actual paths to the directories with your data. !!!

Dmitri: /* Single Scan Script */

2023-10-03T22:56:12Z

Single Scan Script

← Older revision		Revision as of 22:56, 3 October 2023
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	Please note the <code>-B /scratch,/work,/bulk</code> option.		Please note the <code>-B /scratch,/work,/bulk</code> option.
	It makes sure that the container also mounts those file systems, in case you want to access / write files outside of your home directory.		It makes sure that the container also mounts those file systems, in case you want to access / write files outside of your home directory.

			The "/" character at the end of the command line allows to continue the command on the next line.
			It is done for readability, when the command becomes too long.

	!!! You '''have to replace the dummy file paths''' in this example with actual paths to the directories with your data. !!!		!!! You '''have to replace the dummy file paths''' in this example with actual paths to the directories with your data. !!!

Dmitri: /* Freesurfer Sample Script */

2023-10-03T22:54:04Z

Freesurfer Sample Script

← Older revision		Revision as of 22:54, 3 October 2023
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	Once you have a prompt inside the container you can run any non-graphical command that is part of freesurfer. We do not have instructions for running freeview yet.		Once you have a prompt inside the container you can run any non-graphical command that is part of freesurfer. We do not have instructions for running freeview yet.

	=~~Freesurfer Sample Script~~=		= Examples =

	As MRI reconstruction is memory intensive in general and highly serial for a single scan when using Freesurfer, we encourage users to submit jobs in a non-interactive mode.		As MRI reconstruction is memory intensive in general and highly serial for a single scan when using Freesurfer, we encourage users to submit jobs in a non-interactive mode.

Dmitri: /* Multiple Scans Reconstruction in Parallel with a Job Array */

2023-10-03T22:43:00Z

Multiple Scans Reconstruction in Parallel with a Job Array

← Older revision		Revision as of 22:43, 3 October 2023
Line 166:		Line 166:
	-all -sd ${output_dir}/		-all -sd ${output_dir}/
	</source>		</source>
			!!! You have to replace the dummy file paths in this example with actual paths to the directories with your data. !!!

			If you want to know more about using array jobs on ARC you can also check this article:
			[[How to use array jobs in SLURM]].

	[[Category:Software]]		[[Category:Software]]
	[[Category:ARC]]		[[Category:ARC]]
	{{Navbox ARC}}		{{Navbox ARC}}

Dmitri: /* Multiple Scans Reconstruction in Parallel with a Job Array */

2023-10-03T22:40:17Z

Multiple Scans Reconstruction in Parallel with a Job Array

← Older revision		Revision as of 22:40, 3 October 2023
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	<source lang="bash">		<source lang="bash">
	#!/bin/bash		#!/bin/bash
	~~#SBATCH --time=24:0:0~~
	#SBATCH --nodes=1		#SBATCH --nodes=1
	#SBATCH --ntasks-per-node=1		#SBATCH --ntasks-per-node=1
	#SBATCH --cpus-per-task=1		#SBATCH --cpus-per-task=1
	#SBATCH --mem=16G		#SBATCH --mem=16G
			#SBATCH --time=24:0:0
	#SBATCH --array=0-99		#SBATCH --array=0-99

	CONTAINER=/global/software/freesurfer/7.1.~~1/containers/freesurfer711~~.~~simg~~		CONTAINER=/global/software/freesurfer/containers/freesurfer-7.3.2.sif

	((i=SLURM_ARRAY_TASK_ID-1))		((i=SLURM_ARRAY_TASK_ID-1))
Line 161:		Line 161:

	#This is the actual processing command with task specific variables filled in		#This is the actual processing command with task specific variables filled in
	~~singularity~~ exec -B ~~$output_dir -B $subjects_dir~~ $CONTAINER recon-all -cw256 -subject ${subjects_dir}/${subject} -i ${subjects_dir}/${subject}/${dicom_file} -all -sd ${output_dir}/		apptainer exec -B /scratch,/work,/bulk $CONTAINER recon-all -cw256 \
			-subject ${subjects_dir}/${subject} \
			-i ${subjects_dir}/${subject}/${dicom_file} \
			-all -sd ${output_dir}/
	</source>		</source>