registration_synthregistration
Perform registration using SynthMorph from Freesurfer. Outputs transforms in Freesurfer format .lta for affine and .nii.gz (synthmorph also supports .mgz) for deform, both in RAS orientation. Conversion to other formats is done using lta_convert and mri_warp_convert respectively, which support a wide range of conversion formats and orientations, such as ANTs ans FSL. To convert the output of this module, use the registration/convert module successively to it. Note that tests using synthmorph are non-reproductible.
Keywords : Registration, Brain imaging, MRI, Synthetic, AI, CNN
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), path(moving), path(fixed)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| moving | file | Nifti volume moving for registration | True | *.{nii,nii.gz} |
| fixed | file | Nifti volume fixed for registration | True | *.{nii,nii.gz} |
Outputs
Section titled “Outputs”warped_image
Section titled “warped_image”Format : tuple val(meta), path(*__output_warped.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *__output_warped.nii.gz | file | Warped image | True | *__output_warped.nii.gz |
Format : tuple val(meta), val(*__deform_warp.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *__deform_warp.nii.gz | list | Nifti volume containing warp field from moving to fixed | True | *__deform_warp.nii.gz |
affine
Section titled “affine”Format : tuple val(meta), val(*__affine_warp.lta)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *__affine_warp.lta | list | Affine transformation from moving to fixed | True | *__affine_warp.lta |
versions
Section titled “versions”Format : path(versions.yml)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| versions.yml | file | File containing software versions | True | versions.yml |
| 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 : 2025-10-30