nipype.interfaces.ants.utils module¶
ANTS Apply Transforms interface
AffineInitializer¶
Bases: ANTSCommand
Wrapped executable:
antsAffineInitializer.Initialize an affine transform (as in antsBrainExtraction.sh)
>>> from nipype.interfaces.ants import AffineInitializer >>> init = AffineInitializer() >>> init.inputs.fixed_image = 'fixed1.nii' >>> init.inputs.moving_image = 'moving1.nii' >>> init.cmdline 'antsAffineInitializer 3 fixed1.nii moving1.nii transform.mat 15.000000 0.100000 0 10'
- Mandatory Inputs
fixed_image (a pathlike object or string representing an existing file) – Reference image. Maps to a command-line argument:
%s(position: 1).moving_image (a pathlike object or string representing an existing file) – Moving image. Maps to a command-line argument:
%s(position: 2).- Optional Inputs
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.dimension (3 or 2) – Dimension. Maps to a command-line argument:
%s(position: 0). (Nipype default value:3)environ (a 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:
{})local_search (an integer) – determines if a local optimization is run at each search point for the set number of iterations. Maps to a command-line argument:
%d(position: 7). (Nipype default value:10)num_threads (an integer) – Number of ITK threads to use. (Nipype default value:
1)out_file (a pathlike object or string representing a file) – Output transform file. Maps to a command-line argument:
%s(position: 3). (Nipype default value:transform.mat)principal_axes (a boolean) – Whether the rotation is searched around an initial principal axis alignment. Maps to a command-line argument:
%d(position: 6). (Nipype default value:False)radian_fraction (0.0 <= a floating point number <= 1.0) – Search this arc +/- principal axes. Maps to a command-line argument:
%f(position: 5). (Nipype default value:0.1)search_factor (a float) – Increments (degrees) for affine search. Maps to a command-line argument:
%f(position: 4). (Nipype default value:15.0)- Outputs
out_file (a pathlike object or string representing a file) – Output transform file.
AverageAffineTransform¶
Bases: ANTSCommand
Wrapped executable:
AverageAffineTransform.Examples
>>> from nipype.interfaces.ants import AverageAffineTransform >>> avg = AverageAffineTransform() >>> avg.inputs.dimension = 3 >>> avg.inputs.transforms = ['trans.mat', 'func_to_struct.mat'] >>> avg.inputs.output_affine_transform = 'MYtemplatewarp.mat' >>> avg.cmdline 'AverageAffineTransform 3 MYtemplatewarp.mat trans.mat func_to_struct.mat'
- Mandatory Inputs
dimension (3 or 2) – Image dimension (2 or 3). Maps to a command-line argument:
%d(position: 0).output_affine_transform (a pathlike object or string representing a file) – Outputfname.txt: the name of the resulting transform. Maps to a command-line argument:
%s(position: 1).transforms (a list of items which are a pathlike object or string representing an existing file) – Transforms to average. Maps to a command-line argument:
%s(position: 3).- Optional Inputs
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})num_threads (an integer) – Number of ITK threads to use. (Nipype default value:
1)- Outputs
affine_transform (a pathlike object or string representing an existing file) – Average transform file.
AverageImages¶
Bases: ANTSCommand
Wrapped executable:
AverageImages.Examples
>>> from nipype.interfaces.ants import AverageImages >>> avg = AverageImages() >>> avg.inputs.dimension = 3 >>> avg.inputs.output_average_image = "average.nii.gz" >>> avg.inputs.normalize = True >>> avg.inputs.images = ['rc1s1.nii', 'rc1s1.nii'] >>> avg.cmdline 'AverageImages 3 average.nii.gz 1 rc1s1.nii rc1s1.nii'
- Mandatory Inputs
dimension (3 or 2) – Image dimension (2 or 3). Maps to a command-line argument:
%d(position: 0).images (a list of items which are a pathlike object or string representing an existing file) – Image to apply transformation to (generally a coregistered functional). Maps to a command-line argument:
%s(position: 3).normalize (a boolean) – Normalize: if true, the 2nd image is divided by its mean. This will select the largest image to average into. Maps to a command-line argument:
%d(position: 2).- Optional Inputs
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})num_threads (an integer) – Number of ITK threads to use. (Nipype default value:
1)output_average_image (a pathlike object or string representing a file) – The name of the resulting image. Maps to a command-line argument:
%s(position: 1). (Nipype default value:average.nii)- Outputs
output_average_image (a pathlike object or string representing an existing file) – Average image file.
ComposeMultiTransform¶
Bases: ANTSCommand
Wrapped executable:
ComposeMultiTransform.Take a set of transformations and convert them to a single transformation matrix/warpfield.
Examples
>>> from nipype.interfaces.ants import ComposeMultiTransform >>> compose_transform = ComposeMultiTransform() >>> compose_transform.inputs.dimension = 3 >>> compose_transform.inputs.transforms = ['struct_to_template.mat', 'func_to_struct.mat'] >>> compose_transform.cmdline 'ComposeMultiTransform 3 struct_to_template_composed.mat struct_to_template.mat func_to_struct.mat'
- Mandatory Inputs
transforms (a list of items which are a pathlike object or string representing an existing file) – Transforms to average. Maps to a command-line argument:
%s(position: 3).- Optional Inputs
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.dimension (3 or 2) – Image dimension (2 or 3). Maps to a command-line argument:
%d(position: 0). (Nipype default value:3)environ (a 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:
{})num_threads (an integer) – Number of ITK threads to use. (Nipype default value:
1)output_transform (a pathlike object or string representing a file) – The name of the resulting transform. Maps to a command-line argument:
%s(position: 1).reference_image (a pathlike object or string representing a file) – Reference image (only necessary when output is warpfield). Maps to a command-line argument:
%s(position: 2).- Outputs
output_transform (a pathlike object or string representing an existing file) – Composed transform file.
CreateJacobianDeterminantImage¶
Bases: ANTSCommand
Wrapped executable:
CreateJacobianDeterminantImage.Examples
>>> from nipype.interfaces.ants import CreateJacobianDeterminantImage >>> jacobian = CreateJacobianDeterminantImage() >>> jacobian.inputs.imageDimension = 3 >>> jacobian.inputs.deformationField = 'ants_Warp.nii.gz' >>> jacobian.inputs.outputImage = 'out_name.nii.gz' >>> jacobian.cmdline 'CreateJacobianDeterminantImage 3 ants_Warp.nii.gz out_name.nii.gz'
- Mandatory Inputs
deformationField (a pathlike object or string representing an existing file) – Deformation transformation file. Maps to a command-line argument:
%s(position: 1).imageDimension (3 or 2) – Image dimension (2 or 3). Maps to a command-line argument:
%d(position: 0).outputImage (a pathlike object or string representing a file) – Output filename. Maps to a command-line argument:
%s(position: 2).- Optional Inputs
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.doLogJacobian (0 or 1) – Return the log jacobian. Maps to a command-line argument:
%d(position: 3).environ (a 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:
{})num_threads (an integer) – Number of ITK threads to use. (Nipype default value:
1)useGeometric (0 or 1) – Return the geometric jacobian. Maps to a command-line argument:
%d(position: 4).- Outputs
jacobian_image (a pathlike object or string representing an existing file) – Jacobian image.
LabelGeometry¶
Bases: ANTSCommand
Wrapped executable:
LabelGeometryMeasures.Extracts geometry measures using a label file and an optional image file
Examples
>>> from nipype.interfaces.ants import LabelGeometry >>> label_extract = LabelGeometry() >>> label_extract.inputs.dimension = 3 >>> label_extract.inputs.label_image = 'atlas.nii.gz' >>> label_extract.cmdline 'LabelGeometryMeasures 3 atlas.nii.gz [] atlas.csv'>>> label_extract.inputs.intensity_image = 'ants_Warp.nii.gz' >>> label_extract.cmdline 'LabelGeometryMeasures 3 atlas.nii.gz ants_Warp.nii.gz atlas.csv'
- Mandatory Inputs
intensity_image (a pathlike object or string representing an existing file) – Intensity image to extract values from. This is an optional input. Maps to a command-line argument:
%s(position: 2). (Nipype default value:[])label_image (a pathlike object or string representing a file) – Label image to use for extracting geometry measures. Maps to a command-line argument:
%s(position: 1).- Optional Inputs
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.dimension (3 or 2) – Image dimension (2 or 3). Maps to a command-line argument:
%d(position: 0). (Nipype default value:3)environ (a 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:
{})num_threads (an integer) – Number of ITK threads to use. (Nipype default value:
1)output_file (a string) – Name of output file. Maps to a command-line argument:
%s(position: 3).- Outputs
output_file (a pathlike object or string representing an existing file) – CSV file of geometry measures.
MultiplyImages¶
Bases: ANTSCommand
Wrapped executable:
MultiplyImages.Examples
>>> from nipype.interfaces.ants import MultiplyImages >>> test = MultiplyImages() >>> test.inputs.dimension = 3 >>> test.inputs.first_input = 'moving2.nii' >>> test.inputs.second_input = 0.25 >>> test.inputs.output_product_image = "out.nii" >>> test.cmdline 'MultiplyImages 3 moving2.nii 0.25 out.nii'
- Mandatory Inputs
dimension (3 or 2) – Image dimension (2 or 3). Maps to a command-line argument:
%d(position: 0).first_input (a pathlike object or string representing an existing file) – Image 1. Maps to a command-line argument:
%s(position: 1).output_product_image (a pathlike object or string representing a file) – Outputfname.nii.gz: the name of the resulting image. Maps to a command-line argument:
%s(position: 3).second_input (a pathlike object or string representing an existing file or a float) – Image 2 or multiplication weight. Maps to a command-line argument:
%s(position: 2).- Optional Inputs
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})num_threads (an integer) – Number of ITK threads to use. (Nipype default value:
1)- Outputs
output_product_image (a pathlike object or string representing an existing file) – Average image file.