segmentation_fastseg

Perform Brain Tissues Segmentation using FSL fast on a T1 image. Optionally, a binary mask of lesion can be add to correct the white matter mask.

Keywords : Segmentation, T1, Tissues

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Inputs

Input 1

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', 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}

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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 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:'test', 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:'test', 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:'test', 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:'test', 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:'test', single_end:false ]	True
*map_csf.nii.gz	file	Nifti CSF map volume.	True	*map_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
FSL	FSL Toolbox	10.1016/j.neuroimage.2011.09.015
scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.

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Authors

• @gagnonanthony

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Last updated : 2025-10-30