segmentation_synthseg

Perform Brain Tissues Segmentation using Freesurfer synthseg on a T1 image. Optionally, a binary mask of lesion can be add to correct the white matter mask. Note that tests using synthseg are non-reproductible.

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

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Inputs

Input 1

Format : tuple val(meta), path(image), path(lesion), path(fs_license)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
image	file	Nifti T1 volume to segment into tissue maps.	True	*.{nii,nii.gz}
lesion	file	Nifti lesion volume to correct the white matter with a lesion mask. The lesion mask must be a binary mask.	True	*.{nii,nii.gz}
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

wm_mask

Format : tuple val(meta), path(*__mask_wm.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
*__mask_wm.nii.gz	file	Nifti WM mask volume.	True	*__mask_wm.{nii,nii.gz}

gm_mask

Format : tuple val(meta), path(*__mask_gm.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
*__mask_gm.nii.gz	file	Nifti GM mask volume.	True	*__mask_gm.{nii,nii.gz}

csf_mask

Format : tuple val(meta), path(*__mask_csf.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
*__mask_csf.nii.gz	file	Nifti CSF mask volume.	True	*__mask_csf.{nii,nii.gz}

wm_map

Format : tuple val(meta), path(*__map_wm.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
*__map_wm.nii.gz	file	Nifti WM map volume.	True	*__map_wm.{nii,nii.gz}

gm_map

Format : tuple val(meta), path(*__map_gm.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
*__map_gm.nii.gz	file	Nifti GM map volume.	True	*__map_gm.{nii,nii.gz}

csf_map

Format : tuple val(meta), path(*__map_csf.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
*__map_csf.nii.gz	file	Nifti CSF map volume.	True	*__map_csf.{nii,nii.gz}

seg

Format : tuple val(meta), path(*__seg.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
*__seg.nii.gz	file	(optional) Nifti cortical segmentation volume.	True	*__seg.{nii,nii.gz}

aparc_aseg

Format : tuple val(meta), path(*__aparc_aseg.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
*__aparc_aseg.nii.gz	file	(optional) Nifti cortical parcellation volume and segmentation.	True	*__aparc_aseg.{nii,nii.gz}

resample

Format : tuple val(meta), path(*__resampled_image.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
*__resampled_image.nii.gz	file	(optional) in order to return segmentations at 1mm resolution, the input images are internally resampled (except if they already are at 1mm). Use this optional flag to save the resampled images. This must be the same type as —i.	True	*__resampled_image.{nii,nii.gz}

volume

Format : tuple val(meta), path(*__volume.csv)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
*__volume.csv	file	(optional) Output CSV file with volumes for all structures and subjects.	True	*__volume.csv

qc_score

Format : tuple val(meta), path(*__qc_score.csv)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
*__qc_score.csv	file	(optional) Output CSV file with qc scores for all subjects.	True	*__qc_score.csv

versions

Format : path(versions.yml)

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

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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

• @anroy1

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Last updated : 2025-10-30