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# nipype.interfaces.ants.resampling module

ANTS Apply Transforms interface

## ApplyTransforms

Link to code

> Bases: ANTSCommand

> Wrapped executable: `antsApplyTransforms`.

> ApplyTransforms, applied to an input image, transforms it according to a reference image and a transform (or a set of transforms).

> Examples

>     >>> from nipype.interfaces.ants import ApplyTransforms
>     >>> at = ApplyTransforms()
>     >>> at.inputs.input_image = 'moving1.nii'
>     >>> at.inputs.reference_image = 'fixed1.nii'
>     >>> at.inputs.transforms = 'identity'
>     >>> at.cmdline
>     'antsApplyTransforms --default-value 0 --float 0 --input moving1.nii --interpolation Linear --output moving1_trans.nii --reference-image fixed1.nii --transform identity'

>     >>> at = ApplyTransforms()
>     >>> at.inputs.dimension = 3
>     >>> at.inputs.input_image = 'moving1.nii'
>     >>> at.inputs.reference_image = 'fixed1.nii'
>     >>> at.inputs.output_image = 'deformed_moving1.nii'
>     >>> at.inputs.interpolation = 'Linear'
>     >>> at.inputs.default_value = 0
>     >>> at.inputs.transforms = ['ants_Warp.nii.gz', 'trans.mat']
>     >>> at.inputs.invert_transform_flags = [False, True]
>     >>> at.cmdline
>     'antsApplyTransforms --default-value 0 --dimensionality 3 --float 0 --input moving1.nii --interpolation Linear --output deformed_moving1.nii --reference-image fixed1.nii --transform ants_Warp.nii.gz --transform [ trans.mat, 1 ]'

>     >>> at1 = ApplyTransforms()
>     >>> at1.inputs.dimension = 3
>     >>> at1.inputs.input_image = 'moving1.nii'
>     >>> at1.inputs.reference_image = 'fixed1.nii'
>     >>> at1.inputs.output_image = 'deformed_moving1.nii'
>     >>> at1.inputs.interpolation = 'BSpline'
>     >>> at1.inputs.interpolation_parameters = (5,)
>     >>> at1.inputs.default_value = 0
>     >>> at1.inputs.transforms = ['ants_Warp.nii.gz', 'trans.mat']
>     >>> at1.inputs.invert_transform_flags = [False, False]
>     >>> at1.cmdline
>     'antsApplyTransforms --default-value 0 --dimensionality 3 --float 0 --input moving1.nii --interpolation BSpline[ 5 ] --output deformed_moving1.nii --reference-image fixed1.nii --transform ants_Warp.nii.gz --transform trans.mat'

> Identity transforms may be used as part of a chain:

>     >>> at2 = ApplyTransforms()
>     >>> at2.inputs.dimension = 3
>     >>> at2.inputs.input_image = 'moving1.nii'
>     >>> at2.inputs.reference_image = 'fixed1.nii'
>     >>> at2.inputs.output_image = 'deformed_moving1.nii'
>     >>> at2.inputs.interpolation = 'BSpline'
>     >>> at2.inputs.interpolation_parameters = (5,)
>     >>> at2.inputs.default_value = 0
>     >>> at2.inputs.transforms = ['identity', 'ants_Warp.nii.gz', 'trans.mat']
>     >>> at2.cmdline
>     'antsApplyTransforms --default-value 0 --dimensionality 3 --float 0 --input moving1.nii --interpolation BSpline[ 5 ] --output deformed_moving1.nii --reference-image fixed1.nii --transform identity --transform ants_Warp.nii.gz --transform trans.mat'

> input_imagea pathlike object or string representing an existing file

>   Image to apply transformation to (generally a coregistered functional). Maps to a command-line argument: `--input %s`.

> reference_imagea pathlike object or string representing an existing file

>   Reference image space that you wish to warp INTO. Maps to a command-line argument: `--reference-image %s`.

> transformsa list of items which are a pathlike object or string representing an existing file or ‘identity’

>   Transform files: will be applied in reverse order. For example, the last specified transform will be applied first. Maps to a command-line argument: `%s`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> default_valuea float

>   Maps to a command-line argument: `--default-value %g`. (Nipype default value: `0.0`)

> dimension2 or 3 or 4

>   This option forces the image to be treated as a specified-dimensional image. If not specified, antsWarp tries to infer the dimensionality from the input image. Maps to a command-line argument: `--dimensionality %d`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> floata boolean

>   Use float instead of double for computations. Maps to a command-line argument: `--float %d`. (Nipype default value: `False`)

> input_image_type0 or 1 or 2 or 3

>   Option specifying the input image type of scalar (default), vector, tensor, or time series. Maps to a command-line argument: `--input-image-type %d`.

> interpolation‘Linear’ or ‘NearestNeighbor’ or ‘CosineWindowedSinc’ or ‘WelchWindowedSinc’ or ‘HammingWindowedSinc’ or ‘LanczosWindowedSinc’ or ‘MultiLabel’ or ‘Gaussian’ or ‘BSpline’

>   Maps to a command-line argument: `%s`. (Nipype default value: `Linear`)

> interpolation_parameters : a tuple of the form: (an integer (int or long)) or a tuple of the form: (a float, a float) invert_transform_flags : a list of items which are a boolean num_threads : an integer (int or long)

> > Number of ITK threads to use. (Nipype default value: `1`)

> out_postfixa unicode string

>   Postfix that is appended to all output files (default = _trans). (Nipype default value: `_trans`)

> output_imagea unicode string

>   Output file name. Maps to a command-line argument: `--output %s`.

> print_out_composite_warp_filea boolean

>   Output a composite warp file instead of a transformed image. Requires inputs: `output_image`.

> output_imagea pathlike object or string representing an existing file

>   Warped image.

## ApplyTransformsToPoints

Link to code

> Bases: ANTSCommand

> Wrapped executable: `antsApplyTransformsToPoints`.

> ApplyTransformsToPoints, applied to an CSV file, transforms coordinates using provided transform (or a set of transforms).

> Examples

>     >>> from nipype.interfaces.ants import ApplyTransforms
>     >>> at = ApplyTransformsToPoints()
>     >>> at.inputs.dimension = 3
>     >>> at.inputs.input_file = 'moving.csv'
>     >>> at.inputs.transforms = ['trans.mat', 'ants_Warp.nii.gz']
>     >>> at.inputs.invert_transform_flags = [False, False]
>     >>> at.cmdline
>     'antsApplyTransformsToPoints --dimensionality 3 --input moving.csv --output moving_transformed.csv --transform [ trans.mat, 0 ] --transform [ ants_Warp.nii.gz, 0 ]'

> input_filea pathlike object or string representing an existing file

>   Currently, the only input supported is a csv file with columns including x,y (2D), x,y,z (3D) or x,y,z,t,label (4D) column headers. The points should be defined in physical space. If in doubt how to convert coordinates from your files to the space required by antsApplyTransformsToPoints try creating/drawing a simple label volume with only one voxel set to 1 and all others set to 0. Write down the voxel coordinates. Then use ImageMaths LabelStats to find out what coordinates for this voxel antsApplyTransformsToPoints is expecting. Maps to a command-line argument: `--input %s`.

> transformsa list of items which are a pathlike object or string representing an existing file

>   Transforms that will be applied to the points. Maps to a command-line argument: `%s`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> dimension2 or 3 or 4

>   This option forces the image to be treated as a specified-dimensional image. If not specified, antsWarp tries to infer the dimensionality from the input image. Maps to a command-line argument: `--dimensionality %d`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> invert_transform_flagsa list of items which are a boolean

>   List indicating if a transform should be reversed.

> num_threadsan integer (int or long)

>   Number of ITK threads to use. (Nipype default value: `1`)

> output_filea unicode string

>   Name of the output CSV file. Maps to a command-line argument: `--output %s`.

> output_filea pathlike object or string representing an existing file

>   Csv file with transformed coordinates.

## WarpImageMultiTransform

Link to code

> Bases: ANTSCommand

> Wrapped executable: `WarpImageMultiTransform`.

> Warps an image from one space to another

> Examples

>     >>> from nipype.interfaces.ants import WarpImageMultiTransform
>     >>> wimt = WarpImageMultiTransform()
>     >>> wimt.inputs.input_image = 'structural.nii'
>     >>> wimt.inputs.reference_image = 'ants_deformed.nii.gz'
>     >>> wimt.inputs.transformation_series = ['ants_Warp.nii.gz','ants_Affine.txt']
>     >>> wimt.cmdline
>     'WarpImageMultiTransform 3 structural.nii structural_wimt.nii -R ants_deformed.nii.gz ants_Warp.nii.gz ants_Affine.txt'

>     >>> wimt = WarpImageMultiTransform()
>     >>> wimt.inputs.input_image = 'diffusion_weighted.nii'
>     >>> wimt.inputs.reference_image = 'functional.nii'
>     >>> wimt.inputs.transformation_series = ['func2anat_coreg_Affine.txt','func2anat_InverseWarp.nii.gz',     'dwi2anat_Warp.nii.gz','dwi2anat_coreg_Affine.txt']
>     >>> wimt.inputs.invert_affine = [1]  # this will invert the 1st Affine file: 'func2anat_coreg_Affine.txt'
>     >>> wimt.cmdline
>     'WarpImageMultiTransform 3 diffusion_weighted.nii diffusion_weighted_wimt.nii -R functional.nii -i func2anat_coreg_Affine.txt func2anat_InverseWarp.nii.gz dwi2anat_Warp.nii.gz dwi2anat_coreg_Affine.txt'

> input_imagea pathlike object or string representing a file

>   Image to apply transformation to (generally a coregistered functional). Maps to a command-line argument: `%s` (position: 2).

> transformation_seriesa list of items which are a pathlike object or string representing an existing file

>   Transformation file(s) to be applied. Maps to a command-line argument: `%s` (position: -1).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> dimension3 or 2

>   Image dimension (2 or 3). Maps to a command-line argument: `%d` (position: 1). (Nipype default value: `3`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> invert_affinea list of items which are an integer (int or long)

>   List of Affine transformations to invert.E.g.: [1,4,5] inverts the 1st, 4th, and 5th Affines found in transformation_series. Note that indexing starts with 1 and does not include warp fields. Affine transformations are distinguished from warp fields by the word “affine” included in their filenames.

> num_threadsan integer (int or long)

>   Number of ITK threads to use. (Nipype default value: `1`)

> out_postfixa pathlike object or string representing a file

>   Postfix that is prepended to all output files (default = _wimt). Mutually exclusive with inputs: `output_image`. (Nipype default value: `_wimt`)

> output_imagea pathlike object or string representing a file

>   Name of the output warped image. Maps to a command-line argument: `%s` (position: 3). Mutually exclusive with inputs: `out_postfix`.

> reference_imagea pathlike object or string representing a file

>   Reference image space that you wish to warp INTO. Maps to a command-line argument: `-R %s`. Mutually exclusive with inputs: `tightest_box`.

> reslice_by_headera boolean

>   Uses orientation matrix and origin encoded in reference image file header. Not typically used with additional transforms. Maps to a command-line argument: `--reslice-by-header`.

> tightest_boxa boolean

>   Computes tightest bounding box (overrided by reference_image if given). Maps to a command-line argument: `--tightest-bounding-box`. Mutually exclusive with inputs: `reference_image`.

> use_bsplinea boolean

>   Use 3rd order B-Spline interpolation. Maps to a command-line argument: `--use-BSpline`.

> use_nearesta boolean

>   Use nearest neighbor interpolation. Maps to a command-line argument: `--use-NN`.

> output_imagea pathlike object or string representing an existing file

>   Warped image.

## WarpTimeSeriesImageMultiTransform

Link to code

> Bases: ANTSCommand

> Wrapped executable: `WarpTimeSeriesImageMultiTransform`.

> Warps a time-series from one space to another

> Examples

>     >>> from nipype.interfaces.ants import WarpTimeSeriesImageMultiTransform
>     >>> wtsimt = WarpTimeSeriesImageMultiTransform()
>     >>> wtsimt.inputs.input_image = 'resting.nii'
>     >>> wtsimt.inputs.reference_image = 'ants_deformed.nii.gz'
>     >>> wtsimt.inputs.transformation_series = ['ants_Warp.nii.gz','ants_Affine.txt']
>     >>> wtsimt.cmdline
>     'WarpTimeSeriesImageMultiTransform 4 resting.nii resting_wtsimt.nii -R ants_deformed.nii.gz ants_Warp.nii.gz ants_Affine.txt'

>     >>> wtsimt = WarpTimeSeriesImageMultiTransform()
>     >>> wtsimt.inputs.input_image = 'resting.nii'
>     >>> wtsimt.inputs.reference_image = 'ants_deformed.nii.gz'
>     >>> wtsimt.inputs.transformation_series = ['ants_Warp.nii.gz','ants_Affine.txt']
>     >>> wtsimt.inputs.invert_affine = [1] # # this will invert the 1st Affine file: ants_Affine.txt
>     >>> wtsimt.cmdline
>     'WarpTimeSeriesImageMultiTransform 4 resting.nii resting_wtsimt.nii -R ants_deformed.nii.gz ants_Warp.nii.gz -i ants_Affine.txt'

> input_imagea pathlike object or string representing a file

>   Image to apply transformation to (generally a coregistered functional). Maps to a command-line argument: `%s`.

> transformation_seriesa list of items which are a pathlike object or string representing an existing file

>   Transformation file(s) to be applied. Maps to a command-line argument: `%s`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> dimension4 or 3

>   Image dimension (3 or 4). Maps to a command-line argument: `%d` (position: 1). (Nipype default value: `4`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> invert_affinea list of items which are an integer (int or long)

>   List of Affine transformations to invert.E.g.: [1,4,5] inverts the 1st, 4th, and 5th Affines found in transformation_series. Note that indexing starts with 1 and does not include warp fields. Affine transformations are distinguished from warp fields by the word “affine” included in their filenames.

> num_threadsan integer (int or long)

>   Number of ITK threads to use. (Nipype default value: `1`)

> out_postfixa unicode string

>   Postfix that is prepended to all output files (default = _wtsimt). Maps to a command-line argument: `%s`. (Nipype default value: `_wtsimt`)

> reference_imagea pathlike object or string representing a file

>   Reference image space that you wish to warp INTO. Maps to a command-line argument: `-R %s`. Mutually exclusive with inputs: `tightest_box`.

> reslice_by_headera boolean

>   Uses orientation matrix and origin encoded in reference image file header. Not typically used with additional transforms. Maps to a command-line argument: `--reslice-by-header`.

> tightest_boxa boolean

>   Computes tightest bounding box (overrided by reference_image if given). Maps to a command-line argument: `--tightest-bounding-box`. Mutually exclusive with inputs: `reference_image`.

> use_bsplinea boolean

>   Use 3rd order B-Spline interpolation. Maps to a command-line argument: `--use-Bspline`.

> use_nearesta boolean

>   Use nearest neighbor interpolation. Maps to a command-line argument: `--use-NN`.

> output_imagea pathlike object or string representing an existing file

>   Warped image.