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.

Keywords : Registration, Brain imaging, MRI, Conversion

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Inputs

Input 1

Format : tuple val(meta), path(deform), path(affine), path(source), path(target), path(fs_license)

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

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Outputs

deform_transform

Format : tuple val(meta), path(*out_warp.{nii,nii.gz,mgz,m3z})

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*out_warp.{nii,nii.gz,mgz,m3z}	file	Deform transform. Default usage outputs ANTs (ITK) format .nii.gz	True	*out_warp.{nii,nii.gz,mgz,m3z}

affine_transform

Format : tuple val(meta), val(*out_affine.{txt,lta,mat,dat})

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*out_affine.{txt,lta,mat,dat}	map	Affine transform. Default usage outputs ANTs (ITK) format .txt	True	*out_affine.{txt,lta,mat,dat}

versions

Format : path(versions.yml)

	Type	Description	Mandatory	Pattern
versions.yml	file	File containing software versions	True	versions.yml

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Tools

	Description	DOI
Freesurfer	Open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images.	10.1016/j.neuroimage.2012.01.021

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Authors

• @anroy1

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Last updated : 2025-10-30