freesurferseg

Module: 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.

Inputs

	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.		*.mgz
wmparc	file	FreeSurfer WM parcellation output file.		*.mgz
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 file.	*.{nii,nii.gz}
gm_mask	file	Nifti GM mask file.	*.{nii,nii.gz}
csf_mask	file	Nifti CSF mask file.	*.{nii,nii.gz}
versions	file	File containing software versions	versions.yml

Tools

	Description	Homepage	DOI
Scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.	https://github.com/scilus/scilpy.git
MRtrix3	Toolbox for image processing, analysis and visualisation of dMRI.	https://mrtrix.readthedocs.io/en/latest/

Authors

@gagnonanthony