segmentation_fsreconall

Performs Freesurfer’s recon-all script to segment your anatomy (probably a T1) into labels, surfaces, and much more. See the full documentation here: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all.

Keywords : neural network, Artificial intelligence, machine learning, Segmentation, Tissues

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Inputs

Input 1

Format : tuple val(meta), path(anat), path(fs_license)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
anat	file	An anatomy (ex, .nii.gz).	True	*.{nii,nii.gz,mgz}
fs_license	file	The path to your FreeSurfer license. To get one, go to https://surfer.nmr.mgh.harvard.edu/registration.html. Optional. If you have already set your license as prescribed by Freesurfer (copied to a .license file in your $FREESURFER_HOME), this is not required.	True	*.txt

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Outputs

recon_all_out_folder

Format : tuple val(meta), path(*__recon_all)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__recon_all	directory	Directory containing all recon-all outputs.	True	*__recon_all

versions

Format : path(versions.yml)

	Type	Description	Mandatory	Pattern
versions.yml	file	File containing software versions	True	versions.yml

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Arguments (see process.ext)

	Type	Description	Default	Choices
single_thread	boolean	If true, the command will be run in single-threaded mode. By default, the command will use multiple threads based on the number of CPUs allocated to the task.	False

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Tools

	Description	DOI
Freesurfer	Open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images.	10.1016/j.neuroimage.2012.01.021

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Authors

• @EmmaRenauld

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Last updated : 2026-04-22