interfaces.elastix.registration¶
AnalyzeWarp¶
Wraps 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]
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 unicode string)
Additional parameters to the command
flag: %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', nipype default value: {})
Environment variables
jac: ('all', nipype default value: all)
generate an image with the determinant of the spatial Jacobian
flag: -jac %s
jacmat: ('all', nipype default value: all)
generate an image with the spatial Jacobian matrix at each voxel
flag: -jacmat %s
moving_image: (an existing file name)
input image to deform (not used)
flag: -in %s
num_threads: (an integer (int or long), nipype default value: 1)
set the maximum number of threads of elastix
flag: -threads %01d
points: ('all', nipype default value: all)
transform all points from the input-image, which effectively
generates a deformation field.
flag: -def %s, position: 0
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¶
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 -threads 1 -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 unicode string)
Additional parameters to the command
flag: %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', nipype default value: {})
Environment variables
num_threads: (an integer (int or long), nipype default value: 1)
set the maximum number of threads of elastix
flag: -threads %01d
Outputs:
warped_file: (a file name)
input moving image warped to fixed image
PointsWarp¶
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 -threads 1 -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 unicode string)
Additional parameters to the command
flag: %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', nipype default value: {})
Environment variables
num_threads: (an integer (int or long), nipype default value: 1)
set the maximum number of threads of elastix
flag: -threads %01d
Outputs:
warped_file: (a file name)
input points displaced in fixed image domain
Registration¶
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 -threads 1 -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 unicode string)
Additional parameters to the command
flag: %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', nipype default value: {})
Environment variables
fixed_mask: (an existing file name)
mask for fixed image
flag: -fMask %s
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), nipype default value: 1)
set the maximum number of threads of elastix
flag: -threads %01d
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