registration_antsapplytransforms

register image from transform

Keywords : MRI, registration, medical imaging

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Inputs

Input 1

Format : tuple val(meta), val(images), path(reference), val(transformations)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
images	list	Input images to transform onto reference.	True	*.{nii.nii.gz}
reference	file	Reference image for transformation.	True	*.{nii.nii.gz}
transformations	list	Transformation files (in the correct order).	True	*.{nii.gz,mat}

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Outputs

warped_image

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*.{nii,nii.gz}	file	Warped image(s).	True	*.{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.	False	*_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	Obligatory suffix to add to the output file name to prevent overwrite of input files. e.g. : the suffix warped will result in the name 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 input images. e.g. 2 for 2D images, 3 for 3D images.	3
image_type	integer	Type of the input image : - 0: scalar - 1: vector - 2: tensor - 3: time series - 4: multichannel - 5: five-dimensional	0	- 0 - 1 - 2 - 3 - 4 - 5
interpolation	string	Interpolation method to use for the transformation. Content in [...] is optional. Refer the the antsApplyTransforms documentation for more details.	Linear	- 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.	default	- 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.	0
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 : 2025-12-22