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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