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# interfaces.ants.resampling

## ApplyTransforms

Link to code

Wraps command 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.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 = ['trans.mat', 'ants_Warp.nii.gz']
    >>> at.inputs.invert_transform_flags = [False, False]
    >>> at.cmdline
    'antsApplyTransforms --default-value 0 --dimensionality 3 --input moving1.nii --interpolation Linear --output deformed_moving1.nii --reference-image fixed1.nii --transform [trans.mat,0] --transform [ants_Warp.nii.gz,0]'

Inputs:

    [Mandatory]
    input_image: (an existing file name)
            image to apply transformation to (generally a coregistered
            functional)
    reference_image: (an existing file name)
            reference image space that you wish to warp INTO
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    transforms: (a list of items which are an existing file name)

    [Optional]
    args: (a string)
            Additional parameters to the command
    default_value: (a float, nipype default value: 0.0)
    dimension: (2 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.
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    input_image: (an existing file name)
            image to apply transformation to (generally a coregistered
            functional)
    input_image_type: (0 or 1 or 2 or 3)
            Option specifying the input image type of scalar (default), vector,
            tensor, or time series.
    interpolation: ('Linear' or 'NearestNeighbor' or 'CosineWindowedSinc'
             or 'WelchWindowedSinc' or 'HammingWindowedSinc' or
             'LanczosWindowedSinc' or 'MultiLabel' or 'Gaussian' or 'BSpline',
             nipype default value: Linear)
    invert_transform_flags: (a list of items which are a boolean)
    num_threads: (an integer, nipype default value: -1)
            Number of ITK threads to use
    out_postfix: (a string, nipype default value: _trans)
            Postfix that is appended to all output files (default = _trans)
    output_image: (a string)
            output file name
    print_out_composite_warp_file: (0 or 1)
            requires: output_image
    reference_image: (an existing file name)
            reference image space that you wish to warp INTO
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    transforms: (a list of items which are an existing file name)

Outputs:

    output_image: (an existing file name)
            Warped image

## WarpImageMultiTransform

Link to code

Wraps command 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]
    >>> 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'

Inputs:

    [Mandatory]
    input_image: (a file name)
            image to apply transformation to (generally a coregistered
            functional)
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    transformation_series: (an existing file name)
            transformation file(s) to be applied

    [Optional]
    args: (a string)
            Additional parameters to the command
    dimension: (3 or 2, nipype default value: 3)
            image dimension (2 or 3)
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    input_image: (a file name)
            image to apply transformation to (generally a coregistered
            functional)
    invert_affine: (a list of items which are an integer)
            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_threads: (an integer, nipype default value: -1)
            Number of ITK threads to use
    out_postfix: (a file name, nipype default value: _wimt)
            Postfix that is prepended to all output files (default = _wimt)
            mutually_exclusive: output_image
    output_image: (a file name)
            name of the output warped image
            mutually_exclusive: out_postfix
    reference_image: (a file name)
            reference image space that you wish to warp INTO
            mutually_exclusive: tightest_box
    reslice_by_header: (a boolean)
            Uses orientation matrix and origin encoded in reference image file
            header. Not typically used with additional transforms
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    tightest_box: (a boolean)
            computes tightest bounding box (overrided by reference_image if
            given)
            mutually_exclusive: reference_image
    transformation_series: (an existing file name)
            transformation file(s) to be applied
    use_bspline: (a boolean)
            Use 3rd order B-Spline interpolation
    use_nearest: (a boolean)
            Use nearest neighbor interpolation

Outputs:

    output_image: (an existing file name)
            Warped image

## WarpTimeSeriesImageMultiTransform

Link to code

Wraps command 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'

Inputs:

    [Mandatory]
    input_image: (a file name)
            image to apply transformation to (generally a coregistered
            functional)
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    transformation_series: (an existing file name)
            transformation file(s) to be applied

    [Optional]
    args: (a string)
            Additional parameters to the command
    dimension: (4 or 3, nipype default value: 4)
            image dimension (3 or 4)
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    input_image: (a file name)
            image to apply transformation to (generally a coregistered
            functional)
    invert_affine: (a list of items which are an integer)
            List of Affine transformations to invert. E.g.: [1,4,5] inverts the
            1st, 4th, and 5th Affines found in transformation_series
    num_threads: (an integer, nipype default value: -1)
            Number of ITK threads to use
    out_postfix: (a string, nipype default value: _wtsimt)
            Postfix that is prepended to all output files (default = _wtsimt)
    reference_image: (a file name)
            reference image space that you wish to warp INTO
            mutually_exclusive: tightest_box
    reslice_by_header: (a boolean)
            Uses orientation matrix and origin encoded in reference image file
            header. Not typically used with additional transforms
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    tightest_box: (a boolean)
            computes tightest bounding box (overrided by reference_image if
            given)
            mutually_exclusive: reference_image
    transformation_series: (an existing file name)
            transformation file(s) to be applied
    use_bspline: (a boolean)
            Use 3rd order B-Spline interpolation
    use_nearest: (a boolean)
            Use nearest neighbor interpolation

Outputs:

    output_image: (an existing file name)
            Warped image