registration_ants

Image registration with antsRegistrationSyN or antsRegistrationSyNQuick.

Defaults: 3D images and 3-stage registration (rigid + affine + deformable)

Main features: (1) Supports multiple transformation types (see transform argument). (2) Supports initial transformations (see initial_transform argument) via a closure, e.g. { [$fixedimage,$movingimage,0] }. (3) Automatic creation of backward (inverse) transformations matrices. (4) Curated combined output transformations for REGISTRATION_ANTSAPPLYTRANSFORMS and REGISTRATION_TRANSFORMTRACTOGRAM processes : forward_image_transform, forward_tractogram_transform, and their backward versions. (5) Quality control (QC) image generation for MultiQC reports.

Keywords : nifti, registration, antsRegistrationSyN, antsRegistrationSyNQuick

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Inputs

Input 1

Format : tuple val(meta), path(fixed_image), path(moving_image), path(mask)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
fixed_image	file	Fixed image(s) or source image(s) or reference image(s)	True	*.{nii,nii.gz}
moving_image	file	Moving image(s) or target image(s)	True	*.{nii,nii.gz}
mask	file	Mask(s) for the fixed image space	False	*.{nii,nii.gz}

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Outputs

image_warped

Format : tuple val(meta), path(*_warped.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*_warped.nii.gz	file	Nifti volume after registration.	True	*_warped.nii.gz

forward_affine

Format : tuple val(meta), path(*_forward1_affine.mat)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*_forward1_affine.mat	file	Affine transformation from moving to fixed	False	*_forward1_affine.mat

forward_warp

Format : tuple val(meta), path(*_forward0_warp.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*_forward0_warp.nii.gz	file	Nifti volume containing warp field from moving to fixed	False	*_forward0_warp.nii.gz

backward_warp

Format : tuple val(meta), path(*_backward1_warp.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*_backward1_warp.nii.gz	file	Nifti volume containing warp field from fixed to moving	False	*_backward1_warp.nii.gz

backward_affine

Format : tuple val(meta), path(*_backward0_affine.mat)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*_backward0_affine.mat	file	Affine transformation from fixed to moving	False	*_backward0_affine.mat

forward_image_transform

Format : tuple val(meta), val(*_forward*.{nii.gz,mat})

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
_forward.{nii.gz,mat}	list	Tuple, Transformation files to warp images in fixed space, in the correct order for REGISTRATION_TRANSFORMTRACTOGRAM : [ meta, [ forward_warp, forward_affine ] ].	True	*_forward*.{nii.gz,mat}

backward_image_transform

Format : tuple val(meta), val(*_backward*.{nii.gz,mat})

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
_backward.{nii.gz,mat}	list	Tuple, transformation files to warp images in moving space, in the correct order for REGISTRATION_TRANSFORMTRACTOGRAM : [ meta, [ backward_affine, backward_warp ] ].	True	*_backward*.{nii.gz,mat}

forward_tractogram_transform

Format : tuple val(meta), val(*_backward*.{nii.gz,mat})

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
_backward.{nii.gz,mat}	list	Tuple, transformation files to warp tractograms into fixed space, in the correct order for REGISTRATION_TRANSFORMTRACTOGRAM : [ meta, [ backward_affine, backward_warp ] ].	True	*_backward*.{nii.gz,mat}

backward_tractogram_transform

Format : tuple val(meta), val(*_forward*.{nii.gz,mat})

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
_forward.{nii.gz,mat}	list	Tuple, transformation files to warp tractograms into moving space, in the correct order for REGISTRATION_TRANSFORMTRACTOGRAM : [ meta, [ forward_affine, forward_warp ] ].	True	*_forward*.{nii.gz,mat}

mqc

Format : tuple val(meta), path(*_registration_ants_mqc.gif)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*_registration_ants_mqc.gif	file	.gif file containing quality control image for the registration process. Made for use in MultiQC report.	False	*_registration_ants_mqc.gif

versions

Format : path(versions.yml)

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

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Arguments (see process.ext)

	Type	Description	Default	Choices
quick	boolean	Use antsRegistrationSyNQuick instead of antsRegistrationSyN.	False
repro_mode	boolean	Run in reproducibility mode (single threaded).	False
histogram_matching	boolean	Perform histogram matching between images before registration.	False
transform	string	Type of transformation to perform : - t : translation (1 stage) - r : rigid (1 stage) - a : rigid + affine (2 stages) - s : rigid + affine + deformable syn (3 stages) - sr : rigid + deformable syn (2 stages) - so : deformable syn only (1 stage) - b : rigid + affine + deformable b-spline syn (3 stages) - br : rigid + deformable b-spline syn (2 stages) - bo : deformable b-spline syn only (1 stage)	s	- t - r - a - s - sr - so - b - br - bo
initial_transform	string	Algorithmic initialization by geometric center, intensities, or origin.		- geometric center - intensities - origin
dimension	int	Number of spatial dimensions of the images	3
gradient_step	float	Gradient step size for the optimization of SyN and B-spline SyN.	0.1
histogram_bins	int	Number of histogram bins when using the Mutual Information metric with SyN and B-spline SyN.	32
spline_distance	float	Distance between control points for B-spline SyN.	26
run_qc	boolean	Run quality control (QC) to generate a MultiQC report.	False
suffix_qc	string	Suffix for the QC image file.
precision	string	Precision of the output image.	float	- float - double
collapse_output	boolean	Collapse output transformations into a single file.	False
random_seed	int	Random seed for reproducibility.	1234

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Tools

	Description	DOI
ANTs	Advanced Normalization Tools.	10.1038/s41598-021-87564-6
ImageMagick	ImageMagick is a software suite to create, edit, compose, or convert bitmap images.
MRtrix3	MRtrix3 is a software package for processing diffusion MRI data.	10.1016/j.neuroimage.2019.116137
Scilpy	Scilpy is a Python library for processing diffusion MRI data.

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Authors

• @ThoumyreStanislas
• @AlexVCaron

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Last updated : 2025-12-22