interfaces.elastix.registration

AnalyzeWarp

Link to code

Wraps command transformix -def all -jac all -jacmat all

Use transformix to get details from the input transform (generate the corresponding deformation field, generate the determinant of the Jacobian map or the Jacobian map itself)

Example

>>> from nipype.interfaces.elastix import AnalyzeWarp
>>> reg = AnalyzeWarp()
>>> reg.inputs.transform_file = 'TransformParameters.0.txt'  
>>> reg.cmdline  
'transformix -def all -jac all -jacmat all -out ./ -tp TransformParameters.0.txt'

Inputs:

[Mandatory]
output_path: (an existing directory name, nipype default value: ./)
        output directory
        flag: -out %s
transform_file: (an existing file name)
        transform-parameter file, only 1
        flag: -tp %s

[Optional]
args: (a string)
        Additional parameters to the command
        flag: %s
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
num_threads: (an integer (int or long))
        set the maximum number of threads of elastix
        flag: -threads %01d
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:

disp_field: (a file name)
        displacements field
jacdet_map: (a file name)
        det(Jacobian) map
jacmat_map: (a file name)
        Jacobian matrix map

ApplyWarp

Link to code

Wraps command transformix

Use transformix to apply a transform on an input image. The transform is specified in the transform-parameter file.

Example

>>> from nipype.interfaces.elastix import ApplyWarp
>>> reg = ApplyWarp()
>>> reg.inputs.moving_image = 'moving1.nii'  
>>> reg.inputs.transform_file = 'TransformParameters.0.txt'  
>>> reg.cmdline  
'transformix -in moving1.nii -out ./ -tp TransformParameters.0.txt'

Inputs:

[Mandatory]
moving_image: (an existing file name)
        input image to deform
        flag: -in %s
output_path: (an existing directory name, nipype default value: ./)
        output directory
        flag: -out %s
transform_file: (an existing file name)
        transform-parameter file, only 1
        flag: -tp %s

[Optional]
args: (a string)
        Additional parameters to the command
        flag: %s
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
num_threads: (an integer (int or long))
        set the maximum number of threads of elastix
        flag: -threads %01d
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:

warped_file: (a file name)
        input moving image warped to fixed image

PointsWarp

Link to code

Wraps command transformix

Use transformix to apply a transform on an input point set. The transform is specified in the transform-parameter file.

Example

>>> from nipype.interfaces.elastix import PointsWarp
>>> reg = PointsWarp()
>>> reg.inputs.points_file = 'surf1.vtk'  
>>> reg.inputs.transform_file = 'TransformParameters.0.txt'  
>>> reg.cmdline  
'transformix -out ./ -def surf1.vtk -tp TransformParameters.0.txt'

Inputs:

[Mandatory]
output_path: (an existing directory name, nipype default value: ./)
        output directory
        flag: -out %s
points_file: (an existing file name)
        input points (accepts .vtk triangular meshes).
        flag: -def %s
transform_file: (an existing file name)
        transform-parameter file, only 1
        flag: -tp %s

[Optional]
args: (a string)
        Additional parameters to the command
        flag: %s
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
num_threads: (an integer (int or long))
        set the maximum number of threads of elastix
        flag: -threads %01d
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:

warped_file: (a file name)
        input points displaced in fixed image domain

Registration

Link to code

Wraps command elastix

Elastix nonlinear registration interface

Example

>>> from nipype.interfaces.elastix import Registration
>>> reg = Registration()
>>> reg.inputs.fixed_image = 'fixed1.nii'  
>>> reg.inputs.moving_image = 'moving1.nii'  
>>> reg.inputs.parameters = ['elastix.txt']  
>>> reg.cmdline  
'elastix -f fixed1.nii -m moving1.nii -out ./ -p elastix.txt'

Inputs:

[Mandatory]
fixed_image: (an existing file name)
        fixed image
        flag: -f %s
moving_image: (an existing file name)
        moving image
        flag: -m %s
output_path: (an existing directory name, nipype default value: ./)
        output directory
        flag: -out %s
parameters: (a list of items which are an existing file name)
        parameter file, elastix handles 1 or more -p
        flag: -p %s...

[Optional]
args: (a string)
        Additional parameters to the command
        flag: %s
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
fixed_mask: (an existing file name)
        mask for fixed image
        flag: -fMask %s
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
initial_transform: (an existing file name)
        parameter file for initial transform
        flag: -t0 %s
moving_mask: (an existing file name)
        mask for moving image
        flag: -mMask %s
num_threads: (an integer (int or long))
        set the maximum number of threads of elastix
        flag: -threads %01d
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:

transform: (a list of items which are an existing file name)
        output transform
warped_file: (a file name)
        input moving image warped to fixed image
warped_files: (a list of items which are a file name)
        input moving image warped to fixed image at each level
warped_files_flags: (a list of items which are a boolean)
        flag indicating if warped image was generated