Module: 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.

Inputs

	Type	Description	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
image	file	Nifti T1 volume to segment into tissue maps.	*.{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.	*.{nii,nii.gz}

Outputs

	Type	Description	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
wm_mask	file	Nifti WM mask volume.	*.{nii,nii.gz}
gm_mask	file	Nifti GM mask volume.	*.{nii,nii.gz}
csf_mask	file	Nifti CSF mask volume.	*.{nii,nii.gz}
wm_map	file	Nifti WM map volume.	*.{nii,nii.gz}
gm_map	file	Nifti GM map volume.	*.{nii,nii.gz}
csf_map	file	Nifti CSF map volume.	*.{nii,nii.gz}
versions	file	File containing software versions	versions.yml

Tools

	Description	Homepage	DOI
FSL	FSL Toolbox and Scilpy Toolbox	https://fsl.fmrib.ox.ac.uk/fsl/fslwiki
Scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.	https://github.com/scilus/scilpy.git

Keywords

Segmentation
T1
Tissues

Authors

@gagnonanthony