Module: segmentation/fastsurfer

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Inputs

	Type	Description	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
anat	file	An anatomy (ex, .nii.gz).	*.{nii,nii.gz,mgz}
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 ]
fastsurferdirectory	file	Sorted BAM/CRAM/SAM file	*.{bam,cram,sam}
versions	file	File containing software versions	versions.yml

Tools

	Description	Homepage	DOI
Fastsurfer	The FastSurfer pipeline consists of two main parts for segmentation and surface reconstruction.	https://github.com/Deep-MI/FastSurfer

Keywords

segmentation
fastsurfer
deepmi

Authors

@arnaudbore

Maintainers

@arnaudbore