Module: segmentation/fastsurfer
write your description here
Keywords : segmentation, fastsurfer, deepmi
| Type | Description | Mandatory | Pattern |
|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] | true | |
| 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 |
| Type | Description | Default | Choices |
|---|
| acq3T | boolean | Use this flag if the input T1w image was acquired at 3T. | False | |
| cerebnet | boolean | Use this flag to enable cerebellum sub-segmentation with CerebNet. | False | |
| hypvinn | boolean | Use this flag to enable hypothalamus sub-segmentation with HypVinn. | False | |
| seg_only | boolean | Use this flag to only run the segmentation part of FastSurfer. If false, will also run the surface reconstruction part (recon-surf). | True | |
| Description | DOI |
|---|
| Fastsurfer | The FastSurfer pipeline consists of two main parts for segmentation and surface reconstruction. | |
Authors
arnaudbore
Maintainers
arnaudbore
Last updated : 2025-07-15
