registration
Subworkflow to perform registration between a moving and a fixed image (e.g. T1 -> DWI). It requires as input at least a moving (ch_image) and a reference (ch_ref) image to properly perform registration.
Output transformations curated for images for use with the REGISTRATION_ANTSAPPLYTRANSFORMS module are available under the names forward_image_transform and backward_image_transform. The same lists are also available for tractograms (forward_tractogram_transform and backward_tractogram_transform). However, to use the REGISTRATION_TRACTOGRAM module, you have to use the backward_affine and backward_warp channels provided by this subworkflow.
Registration suites:
- EasyReg (ML): params.run_easyreg = true
module: REGISTRATION_EASYREG
Run freesurfer EasyReg any-to-any modality registration.
NOTE: Outputs a combined warp field only, no affine transformations are available. CANNOT BE LINKED WITH THE BUNDLE_SEG SUBWORKFLOW.
- Synthmorph (ML): params.run_synthmorph = true
module: REGISTRATION_SYNTHMORPH
Run SynthMorph any-to-any modality registration. By default, the algorithm is configured to run a chain of affin+deformable transformations, making it suitable for use with most modules and subworkflows like BUNDLE_SEG.
NOTE: the output affine transformation file is in .lta format and needs to be converted to .mat to be used with ANTs using the REGISTRATION_CONVERT module.
- ANTs (SyN+SyN Quick): params.run_easyreg = false && params.run_synthmorph = false
module: REGISTRATION_ANTS or REGISTRATION_ANATTODWI
Run ANTs registration using antsRegistrationSyN.sh (quick version also available).
NOTE : Transformation to DWI space is available. To trigger it, supply a metric file (ch_metric) in DWI space (e.g. FA map) in addition to the moving (ch_image) and reference (ch_ref) images.
Keywords : Registration, Transformation, DWI, Anatomical
Components : registration/anattodwi, registration/ants, registration/convert, registration/easyreg, registration/synthmorph
Inputs
Section titled “Inputs”| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| ch_fixed_image | file | The input channel containing the fixed image files. If performing registration to DWI space, this is the reference image (e.g. b0 image). Structure: [ val(meta), path(fixed_image) ] | True | *.\{nii,nii.gz\} |
| ch_moving_image | file | Input channel containing the moving image files. If performing registration to DWI space, this is the anatomical image to be registered. Structure: [ val(meta), path(image) ] | True | *.\{nii,nii.gz\} |
| ch_metric | file | FOR USE WITH REGISTRATION TO DWI SPACE ONLY. The input channel containing the metric files, typically a FA map. Structure: [ val(meta), path(metric) ] | False | *.\{nii,nii.gz\} |
| ch_fixed_mask | file | FOR USE WITH ANTS SYN REGISTRATION ONLY. The input channel containing the mask file in fixed image space. Structure: [ val(meta), path(mask) ] | False | *.\{nii,nii.gz\} |
| ch_segmentation | file | FOR USE WITH SYNTHMORPH REGISTRATION ONLY. The input channel containing the SynthSeg v2 (non-robust) segmentation + parcellation in fixed image space (reference in Easyreg naming convention) image. | False | *.\{nii,nii.gz\} |
| ch_moving_segmentation | file | FOR USE WITH SYNTHMORPH REGISTRATION ONLY. The input channel containing the SynthSeg v2 (non-robust) segmentation + parcellation in moving image space (floating in Easyreg naming convention) image. | False | *.\{nii,nii.gz\} |
Outputs
Section titled “Outputs”| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| image_warped | file | Channel containing images warped in fixed space. Structure: [ val(meta), path(image) ] | True | *.\{nii,nii.gz\} |
| reference_warped | file | ONLY PROVIDED BY REGISTRATION_EASYREG. Channel containing the reference image warped in moving space. Structure: [ val(meta), path(image) ] | False | *.\{nii,nii.gz\} |
| forward_affine | file | Channel containing the affine transformation matrix to fixed space. Structure: [ val(meta), path(forward_affine) ] | False | *__forward*.\{lta,mat\} |
| forward_warp | file | Channel containing the deformation field to fixed space. Structure: [ val(meta), path(forward_warp) ] | False | *__forward*.\{nii,nii.gz\} |
| backward_warp | file | Channel containing the deformation field to moving space. Structure: [ val(meta), path(backward_warp) ] | False | *__backward*.\{nii,nii.gz\} |
| backward_affine | file | Channel containing the affine transformation matrix to moving space. Structure: [ val(meta), path(backward_affine) ] | False | *__backward*.\{lta,mat\} |
| forward_image_transform | list | Channel containing the transformation tuples to warp images to fixed space, in the correct order for REGISTRATION_ANTSAPPLYTRANSFORMS. Structure: [ val(meta), [ path(forward_warp), path(forward_affine) ] ]. | True | *__forward*.\{nii,nii.gz,mat,lta\} |
| backward_image_transform | list | Channel containing the transformation tuples to warp images to moving space, in the correct order for REGISTRATION_ANTSAPPLYTRANSFORMS. Structure: [ val(meta), [ path(backward_affine), path(backward_warp) ] ]. | True | *__backward*.\{nii,nii.gz,mat,lta\} |
| forward_tractogram_transform | list | Channel containing the transformation tuples to warp tractograms to fixed space, in the correct order for REGISTRATION_TRANSFORMTRACTOGRAM. Structure: [ val(meta), [ path(backward_warp), path(backward_affine) ] ]. | True | *__backward*.\{nii,nii.gz,mat,lta\} |
| backward_tractogram_transform | list | Channel containing the transformation tuples to warp tractograms to moving space, in the correct order for REGISTRATION_TRANSFORMTRACTOGRAM. Structure: [ val(meta), [ path(forward_warp), path(forward_affine) ] ]. | True | *__forward*.\{nii,nii.gz,mat,lta\} |
| segmentation | file | ONLY PROVIDED BY REGISTRATION_SYNTHMORPH. Channel containing the SynthSeg v2 (non-robust) segmentation + parcellation in moving space (floating in Easyreg naming convention). Structure: [ val(meta), path(segmentation) ] | False | *.\{nii,nii.gz\} |
| reference_segmentation | file | ONLY PROVIDED BY REGISTRATION_SYNTHMORPH. Channel containing the SynthSeg v2 (non-robust) segmentation + parcellation in fixed space (reference in Easyreg naming convention). Structure: [ val(meta), path(reference_segmentation) ] | False | *.\{nii,nii.gz\} |
| mqc | file | Channel containing the MultiQC report data for the registration. Structure: [ path(mqc) ] | False | *mqc.* |
| versions | file | File containing software versions used. Structure: [ path(versions.yml) ] | True | versions.yml |
Authors
Section titled “Authors”Last updated : 2026-02-12