interfaces.elastix.registration

AnalyzeWarp

Link to code

Wraps the executable command transformix.

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 -threads 1 -out ./ -tp TransformParameters.0.txt'

Inputs:

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

[Optional]
num_threads: (an integer (int or long), nipype default value: 1)
        set the maximum number of threads of elastix
        argument: ``-threads %01d``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
moving_image: (an existing file name)
        input image to deform (not used)
        argument: ``-in %s``
points: (u'all', nipype default value: all)
        transform all points from the input-image, which effectively
        generates a deformation field.
        argument: ``-def %s``, position: 0
environ: (a dictionary with keys which are a newbytes or None or a
          newstr or None and with values which are a newbytes or None or a
          newstr or None, nipype default value: {})
        Environment variables
jac: (u'all', nipype default value: all)
        generate an image with the determinant of the spatial Jacobian
        argument: ``-jac %s``
jacmat: (u'all', nipype default value: all)
        generate an image with the spatial Jacobian matrix at each voxel
        argument: ``-jacmat %s``

Outputs:

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

ApplyWarp

Link to code

Wraps the executable 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 -threads 1 -out ./ -tp TransformParameters.0.txt'

Inputs:

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

[Optional]
num_threads: (an integer (int or long), nipype default value: 1)
        set the maximum number of threads of elastix
        argument: ``-threads %01d``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
environ: (a dictionary with keys which are a newbytes or None or a
          newstr or None and with values which are a newbytes or None or a
          newstr or None, nipype default value: {})
        Environment variables

Outputs:

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

PointsWarp

Link to code

Wraps the executable 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 -threads 1 -out ./ -def surf1.vtk -tp TransformParameters.0.txt'

Inputs:

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

[Optional]
num_threads: (an integer (int or long), nipype default value: 1)
        set the maximum number of threads of elastix
        argument: ``-threads %01d``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
environ: (a dictionary with keys which are a newbytes or None or a
          newstr or None and with values which are a newbytes or None or a
          newstr or None, nipype default value: {})
        Environment variables

Outputs:

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

Registration

Link to code

Wraps the executable 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 -threads 1 -out ./ -p elastix.txt'

Inputs:

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

[Optional]
num_threads: (an integer (int or long), nipype default value: 1)
        set the maximum number of threads of elastix
        argument: ``-threads %01d``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
moving_mask: (an existing file name)
        mask for moving image
        argument: ``-mMask %s``
fixed_mask: (an existing file name)
        mask for fixed image
        argument: ``-fMask %s``
environ: (a dictionary with keys which are a newbytes or None or a
          newstr or None and with values which are a newbytes or None or a
          newstr or None, nipype default value: {})
        Environment variables
initial_transform: (an existing file name)
        parameter file for initial transform
        argument: ``-t0 %s``

Outputs:

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