segmentation_freesurferseg

Performs Brain Tissues Segmentation using the FreeSurfer aparc and wmparc output files. Optionally, a binary mask of lesion can be add to correct the white matter mask.

Keywords : Segmentation, Tissues, FreeSurfer

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Inputs

Input 1

Format : tuple val(meta), path(aparc_aseg), path(wmparc), path(lesion)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
aparc_aseg	file	FreeSurfer cortical and subcortical parcellation output file.	True	*.mgz
wmparc	file	FreeSurfer WM parcellation output file.	True	*.mgz
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}

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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:'test', single_end:false ]	True
*__mask_wm.nii.gz	file	Nifti WM mask file.	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:'test', single_end:false ]	True
*__mask_gm.nii.gz	file	Nifti GM mask file.	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:'test', single_end:false ]	True
*__mask_csf.nii.gz	file	Nifti CSF mask file.	True	*__mask_csf.{nii,nii.gz}

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
scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.
MRtrix3	MRtrix3 is a software package for various types of diffusion imaging data, including diffusion-weighted, diffusion-tensor, and q-ball imaging.	10.1016/j.neuroimage.2019.116137

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Authors

• @gagnonanthony

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Last updated : 2025-10-30