Module: 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.

Inputs

	Type	Description	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', 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}
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.	*.txt

Outputs

	Type	Description	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', 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}
seg	file	(optional) Nifti cortical segmentation volume.	*.{nii,nii.gz}
aparc_aseg	file	(optional) Nifti cortical parcellation volume and segmentation.	*.{nii,nii.gz}
resample	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.	*.{nii,nii.gz}
volume	file	(optional) Output CSV file with volumes for all structures and subjects.	*.csv
qc_score	file	(optional) Output CSV file with qc scores for all subjects.	*.csv
versions	file	File containing software versions	versions.yml

Tools

	Description	Homepage	DOI
Freesurfer	An open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images.	https://surfer.nmr.mgh.harvard.edu/

Keywords

Segmentation
Freesurfer
Tissues
Synthetic
AI
CNN

Authors

@anroy1

Maintainers

@anroy1