Module: segmentation/fsreconall
Performs Freesurfer’s recon-all script to segment your anatomy (probably a T1) into labels, surfaces, and much more. See the full documentation here: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all.
| Type | Description | Mandatory | Pattern |
|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', 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:'test', single_end:false ] | |
| recon_all_out_folder | directory | Directory containing all recon-all outputs. | *.{nii,nii.gz} |
| versions | file | File containing software versions | versions.yml |
Authors
@EmmaRenauld
