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
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), path(transformation), val(input_type), val(output_type), path(reference), path(affine_source), path(fs_license)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| transformation | file | Input transformation to convert. | True | *.{nii,nii.gz,mgz,m3z,lta,txt,xfm,dat} |
| input_type | string | Type of input transformation : - affine : lta, fsl, mni, reg, niftyreg, itk, vox - deform : m3z, fsl, lps, itk, ras, vox | True | |
| output_type | string | Type of output transformation : - affine : lta, fsl, mni, reg, niftyreg, itk - deform : m3z, fsl, lps, itk, ras, vox | True | |
| reference | file | Reference volume used for registration. For affine transformations, it’s usually the target image, and for warp the moving (source) image. Validate with the tools you used to generate the transformation. | True | *.{nii,nii.gz} |
| affine_source | file | ONLY USED FOR CONVERSION OF AFFINES IN LTA FORMAT. Moving (source) Nifti volume used for registration. | False | *.{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 |
Outputs
Section titled “Outputs”transformation
Section titled “transformation”Format : tuple val(meta), path(*out_{affine,warp}.{nii,nii.gz,mgz,m3z,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,warp}.{nii,nii.gz,mgz,m3z,txt,lta,mat,dat} | file | Affine or warp converted to the desired format. | True | *out_{affine,warp}.{nii,nii.gz,mgz,m3z,txt,lta,mat,dat} |
versions
Section titled “versions”Format : path(versions.yml)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| versions.yml | file | File containing software versions | True | versions.yml |
Arguments (see process.ext)
Section titled “Arguments (see process.ext)”| Type | Description | Default | Choices | |
|---|---|---|---|---|
| invert | boolean | FOR AFFINE CONVERSION ONLY. Invert the transformation. | False | |
| conform | boolean | FOR AFFINE CONVERSION ONLY. Conform target geometry before conversion (see freesurfer documentation). | False | |
| output_space | string | FOR AFFINE CONVERSION ONLY. Reference space to convert to. Default is ras2ras. | ras2ras | - ras2ras - vox2vox - register_dat |
| downsample | boolean | FOR WARP CONVERSION ONLY. Downsample the input warp to 2mm isotropic resolution. | False |
| Description | DOI | |
|---|---|---|
| Freesurfer | Open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images. | 10.1016/j.neuroimage.2012.01.021 |
Authors
Section titled “Authors”Last updated : 2025-12-22