interfaces.ants.resampling¶
ApplyTransforms¶
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 = ['ants_Warp.nii.gz', 'trans.mat']
>>> 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 [ ants_Warp.nii.gz, 0 ] --transform [ trans.mat, 0 ]'
>>> 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 --input moving1.nii --interpolation BSpline[ 5 ] --output deformed_moving1.nii --reference-image fixed1.nii --transform [ ants_Warp.nii.gz, 0 ] --transform [ trans.mat, 0 ]'
Inputs:
[Mandatory]
input_image: (an existing file name)
image to apply transformation to (generally a coregistered
functional)
flag: --input %s
reference_image: (an existing file name)
reference image space that you wish to warp INTO
flag: --reference-image %s
transforms: (a list of items which are an existing file name)
transform files: will be applied in reverse order. For example, the
last specified transform will be applied first
flag: %s
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
default_value: (a float, nipype default value: 0.0)
flag: --default-value %g
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.
flag: --dimensionality %d
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
float: (a boolean)
Use float instead of double for computations.
flag: --float %d
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_type: (0 or 1 or 2 or 3)
Option specifying the input image type of scalar (default), vector,
tensor, or time series.
flag: --input-image-type %d
interpolation: ('Linear' or 'NearestNeighbor' or 'CosineWindowedSinc'
or 'WelchWindowedSinc' or 'HammingWindowedSinc' or
'LanczosWindowedSinc' or 'MultiLabel' or 'Gaussian' or 'BSpline',
nipype default value: Linear)
flag: %s
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), 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
flag: --output %s
print_out_composite_warp_file: (a boolean)
output a composite warp file instead of a transformed image
requires: output_image
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
output_image: (an existing file name)
Warped image
ApplyTransformsToPoints¶
Wraps command 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 ]'
Inputs:
[Mandatory]
input_file: (an existing file name)
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 spacerequired by
antsApplyTransformsToPoints try creating/drawing a simplelabel
volume with only one voxel set to 1 and all others set to 0.Write
down the voxel coordinates. Then use ImageMaths LabelStats to
findout what coordinates for this voxel antsApplyTransformsToPoints
isexpecting.
flag: --input %s
transforms: (a list of items which are an existing file name)
transforms that will be applied to the points
flag: %s
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
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.
flag: --dimensionality %d
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_transform_flags: (a list of items which are a boolean)
list indicating if a transform should be reversed
num_threads: (an integer (int or long), nipype default value: 1)
Number of ITK threads to use
output_file: (a string)
Name of the output CSV file
flag: --output %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
output_file: (an existing file name)
csv file with transformed coordinates
WarpImageMultiTransform¶
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)
flag: %s, position: 2
transformation_series: (a list of items which are an existing file
name)
transformation file(s) to be applied
flag: %s, position: -1
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
dimension: (3 or 2, nipype default value: 3)
image dimension (2 or 3)
flag: %d, position: 1
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 (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_threads: (an integer (int or long), 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
flag: %s, position: 3
mutually_exclusive: out_postfix
reference_image: (a file name)
reference image space that you wish to warp INTO
flag: -R %s
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
flag: --reslice-by-header
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `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)
flag: --tightest-bounding-box
mutually_exclusive: reference_image
use_bspline: (a boolean)
Use 3rd order B-Spline interpolation
flag: --use-BSpline
use_nearest: (a boolean)
Use nearest neighbor interpolation
flag: --use-NN
Outputs:
output_image: (an existing file name)
Warped image
WarpTimeSeriesImageMultiTransform¶
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)
flag: %s
transformation_series: (a list of items which are an existing file
name)
transformation file(s) to be applied
flag: %s
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
dimension: (4 or 3, nipype default value: 4)
image dimension (3 or 4)
flag: %d, position: 1
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 (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
num_threads: (an integer (int or long), 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)
flag: %s
reference_image: (a file name)
reference image space that you wish to warp INTO
flag: -R %s
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
flag: --reslice-by-header
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `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)
flag: --tightest-bounding-box
mutually_exclusive: reference_image
use_bspline: (a boolean)
Use 3rd order B-Spline interpolation
flag: --use-Bspline
use_nearest: (a boolean)
Use nearest neighbor interpolation
flag: --use-NN
Outputs:
output_image: (an existing file name)
Warped image