.. AUTO-GENERATED FILE -- DO NOT EDIT!

interfaces.ants.utils
=====================


.. _nipype.interfaces.ants.utils.ApplyTransforms:


.. index:: ApplyTransforms

ApplyTransforms
---------------

Code: http://github.com/nipy/nipype/blob/master/nipype/interfaces/ants/utils.py#L38

Wraps command **antsApplyTransforms**

antsApplyTransforms, 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
>>> atms = ApplyTransforms()
>>> atms.inputs.input_image = 'structural.nii'
>>> atms.inputs.reference_image = 'ants_deformed.nii.gz'
>>> atms.inputs.transformation_files = ['ants_Warp.nii.gz','ants_Affine.txt']
>>> atms.cmdline
'antsApplyTransforms --dimensionality 3 --input structural.nii --output structural_trans.nii --reference-image ants_deformed.nii.gz --transform ants_Warp.nii.gz --transform ants_Affine.txt'

Inputs::

        [Mandatory]
        input_image: (a file name)
                image to apply transformation to (generally a coregistered functional)
        transformation_files: (an existing file name)
                transformation file(s) to be applied

        [Optional]
        args: (a string)
                Additional parameters to the command
        default_value: (a float)
                Default voxel value to be used with input images only. Specifies the voxel value when
                the input point maps outside the output domain
        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
        interpolation: (a string)
                Use nearest neighbor interpolation
        invert_transforms: (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
        output_image: (a string)
                output file name
        reference_image: (a file name)
                reference image space that you wish to warp INTO

Outputs::

        output_image: (an existing file name)
                Warped image

.. _nipype.interfaces.ants.utils.WarpImageMultiTransform:


.. index:: WarpImageMultiTransform

WarpImageMultiTransform
-----------------------

Code: http://github.com/nipy/nipype/blob/master/nipype/interfaces/ants/utils.py#L123

Wraps command **WarpImageMultiTransform**

Warps an image from one space to another

Examples
~~~~~~~~

>>> from nipype.interfaces.ants import WarpImageMultiTransform
>>> wimt = WarpImageMultiTransform()
>>> wimt.inputs.moving_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'


>>> from nipype.interfaces.ants import WarpImageMultiTransform
>>> wimt = WarpImageMultiTransform()
>>> wimt.inputs.moving_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]
        moving_image: (a file name)
                image to apply transformation to (generally a coregistered functional)
        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
        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: _wimt)
                Postfix that is prepended to all output files (default = _wimt)
        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
        tightest_box: (a boolean)
                computes tightest bounding box (overrided by reference_image if given)
                mutually_exclusive: reference_image
        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

.. _nipype.interfaces.ants.utils.WarpTimeSeriesImageMultiTransform:


.. index:: WarpTimeSeriesImageMultiTransform

WarpTimeSeriesImageMultiTransform
---------------------------------

Code: http://github.com/nipy/nipype/blob/master/nipype/interfaces/ants/utils.py#L216

Wraps command **WarpTimeSeriesImageMultiTransform**

Warps a time-series from one space to another

Examples
~~~~~~~~

>>> from nipype.interfaces.ants import WarpTimeSeriesImageMultiTransform
>>> wtsimt = WarpTimeSeriesImageMultiTransform()
>>> wtsimt.inputs.moving_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'

>>> from nipype.interfaces.ants import WarpTimeSeriesImageMultiTransform
>>> wtsimt = WarpTimeSeriesImageMultiTransform()
>>> wtsimt.inputs.moving_image = 'resting.nii'
>>> wtsimt.inputs.reference_image = 'diffusion_weighted.nii'
>>> wtsimt.inputs.transformation_series = ['dwi2anat_coreg_Affine.txt','dwi2anat_InverseWarp.nii.gz','resting2anat_Warp.nii.gz','resting2anat_coreg_Affine.txt']
>>> wtsimt.inputs.invert_affine = [1]
>>> wtsimt.cmdline
'WarpTimeSeriesImageMultiTransform 4 resting.nii resting_wtsimt.nii -R diffusion_weighted.nii -i dwi2anat_coreg_Affine.txt dwi2anat_InverseWarp.nii.gz resting2anat_Warp.nii.gz resting2anat_coreg_Affine.txt'

Inputs::

        [Mandatory]
        moving_image: (a file name)
                image to apply transformation to (generally a coregistered functional)
        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
        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
        tightest_box: (a boolean)
                computes tightest bounding box (overrided by reference_image if given)
                mutually_exclusive: reference_image
        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
