registration_antsapplytransforms

register image from transform

Keywords : MRI, registration, medical imaging

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Inputs

Input 1

Format : tuple val(meta), path(image), path(reference), path(warp), path(affine)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
image	file	Input image to register	True	*.{nii.nii.gz}
reference	file	Reference image for registration	True	*.{nii.nii.gz}
warp	file	Warp transformation file to warp image or trk.	True	*.{nii,nii.gz}
affine	file	Affine or rigig transformation file to warp image or trk (*mat). If a rigid or affine transformation needs to be inverted before being applied, use antsApplyTransforms with the -o Linear[inversedTransform,1], as this module does not handles it.	True	*.mat

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Outputs

warped_image

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	Warped image.	True	*__warped.{nii.nii.gz}

mqc

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*_registration_antsapplytransforms_mqc.gif	file	.gif file containing quality control image for the registration process. Made for use in MultiQC report.	True	*_registration_antsapplytransforms_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
prefix	string	Prefix to add to the output file name. e.g. warped_ will result in warped_image.nii.gz.	${meta.id}
suffix	string	Suffix to add to the output file name. e.g. _warped will result in image_warped.nii.gz.	__warped
suffix_qc	string	Suffix to add to the quality control image file name. e.g. qc will result in *qc_registration_antsapplytransforms_mqc.gif.
dimensionality	number	Dimensionality of the input image. e.g. 2 for 2D images, 3 for 3D images.
image_type	integer	Type of the input image.		- 0 (scalar) - 1 (vector) - 2 (tensor) - 3 (time series) - 4 (multichannel) - 5 (five-dimensional)
interpolation	string	Interpolation method to use for the transformation. Content in [...] is optional. Refer the the antsApplyTransforms documentation for more details.		- Linear - NearestNeighbor - MultiLabel[<sigma=imageSpacing>,<alpha=4.0>] - Gaussian[<sigma=imageSpacing>,<alpha=1.0>] - BSpline[<order=3>] - CosineWindowedSinc - WelchWindowedSinc - HammingWindowedSinc - LanczosWindowedSinc - GenericLabel[<interpolator=Linear>]
output_dtype	string	Output data type for the warped image.		- char - uchar - float - double - short - int - default
default_val	number	Default value to use for the input image. It specifies the voxel value when the input point maps outside the output domain.
run_qc	boolean	Whether to run quality control for the registration process. e.g. true to generate a quality control image, false to skip it.	False

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Tools

	Description	DOI
ANTs	perform registration using transform as input

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Authors

• @scilus

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Last updated : 2025-10-30