Module: registration/convert

Freesurfer transform conversion tool. Default usage is aim at receiving freesurfer format and converting to ANTs (ITK). See lta_convert —help and mri_warp_convert —help for options.

Inputs

	Type	Description	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
deform	file	Deform transform to convert. Default usage expects Freesurfer .mgz format from mri_synthmorph	*.{nii,nii.gz,mgz,m3z}
affine	file	Affine transform to convert. Default usage expects Freesurfer .lta format from mri_synthmorph	*.{lta,txt,xfm,dat}
source	file	Moving Nifti volume used for registration. Defines source image geometry	*.{nii,nii.gz}
target	file	Fixed Nifti volume used for registration. Defines target image geometry. (optional)	*.{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:'test', single_end:false ]
deform_transform	file	Deform transform. Default usage outputs ANTs (ITK) format .nii.gz	*.{nii,nii.gz,mgz,m3z}
affine_transform	file	Affine transform. Default usage outputs ANTs (ITK) format .txt	*.{txt,lta,mat,dat}
versions	file	File containing software versions	versions.yml

Tools

	Description	Homepage	DOI
Freesurfer	Freesurfer lta_convert (affine conversion) and mri_warp_convert (deform) tools for transform conversion	https://surfer.nmr.mgh.harvard.edu/

Keywords

Registration
Brain imaging
MRI
Conversion

Authors

@anroy1