interfaces.dtitk.registration¶
AffScalarVol¶
Wraps the executable command affineScalarVolume.
Applies affine transform to a scalar volume
Example¶
>>> from nipype.interfaces import dtitk
>>> node = dtitk.AffScalarVol()
>>> node.inputs.in_file = 'im1.nii'
>>> node.inputs.transform = 'im_affine.aff'
>>> node.cmdline
'affineScalarVolume -in im1.nii -interp 0 -out im1_affxfmd.nii -trans
im_affine.aff'
>>> node.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
moving scalar volume
argument: ``-in %s``
[Optional]
out_file: (a file name)
output filename
argument: ``-out %s``
transform: (an existing file name)
transform to apply: specify an input transformation file; parameters
input will be ignored
argument: ``-trans %s``
mutually_exclusive: target, translation, euler, deformation
interpolation: ('trilinear' or 'NN', nipype default value: trilinear)
trilinear or nearest neighbor interpolation
argument: ``-interp %s``
target: (an existing file name)
output volume specification read from the target volume if specified
argument: ``-target %s``
mutually_exclusive: transform
translation: (a tuple of the form: (a float, a float, a float))
translation (x,y,z) in mm
argument: ``-translation %g %g %g``
mutually_exclusive: transform
euler: (a tuple of the form: (a float, a float, a float))
(theta, phi, psi) in degrees
argument: ``-euler %g %g %g``
mutually_exclusive: transform
deformation: (a tuple of the form: (a float, a float, a float, a
float, a float, a float))
(xx,yy,zz,xy,yz,xz)
argument: ``-deformation %g %g %g %g %g %g``
mutually_exclusive: transform
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (an existing file name)
moved volume
AffSymTensor3DVol¶
Wraps the executable command affineSymTensor3DVolume.
Applies affine transform to a tensor volume
Example¶
>>> from nipype.interfaces import dtitk
>>> node = dtitk.AffSymTensor3DVol()
>>> node.inputs.in_file = 'im1.nii'
>>> node.inputs.transform = 'im_affine.aff'
>>> node.cmdline
'affineSymTensor3DVolume -in im1.nii -interp LEI -out im1_affxfmd.nii
-reorient PPD -trans im_affine.aff'
>>> node.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
moving tensor volume
argument: ``-in %s``
[Optional]
out_file: (a file name)
output filename
argument: ``-out %s``
transform: (an existing file name)
transform to apply: specify an input transformation file; parameters
input will be ignored
argument: ``-trans %s``
mutually_exclusive: target, translation, euler, deformation
interpolation: ('LEI' or 'EI', nipype default value: LEI)
Log Euclidean/Euclidean Interpolation
argument: ``-interp %s``
reorient: ('PPD' or 'NO' or 'FS', nipype default value: PPD)
Reorientation strategy: preservation of principal direction, no
reorientation, or finite strain
argument: ``-reorient %s``
target: (an existing file name)
output volume specification read from the target volume if specified
argument: ``-target %s``
mutually_exclusive: transform
translation: (a tuple of the form: (a float, a float, a float))
translation (x,y,z) in mm
argument: ``-translation %g %g %g``
mutually_exclusive: transform
euler: (a tuple of the form: (a float, a float, a float))
(theta, phi, psi) in degrees
argument: ``-euler %g %g %g``
mutually_exclusive: transform
deformation: (a tuple of the form: (a float, a float, a float, a
float, a float, a float))
(xx,yy,zz,xy,yz,xz)
argument: ``-deformation %g %g %g %g %g %g``
mutually_exclusive: transform
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (an existing file name)
Affine¶
Wraps the executable command dti_affine_reg.
Performs affine registration between two tensor volumes
Example¶
>>> from nipype.interfaces import dtitk
>>> node = dtitk.Affine()
>>> node.inputs.fixed_file = 'im1.nii'
>>> node.inputs.moving_file = 'im2.nii'
>>> node.inputs.similarity_metric = 'EDS'
>>> node.inputs.sampling_xyz = (4,4,4)
>>> node.inputs.ftol = 0.01
>>> node.inputs.initialize_xfm = 'im_affine.aff'
>>> node.cmdline
'dti_affine_reg im1.nii im2.nii EDS 4 4 4 0.01 im_affine.aff'
>>> node.run()
Inputs:
[Mandatory]
fixed_file: (an existing file name)
fixed tensor volume
argument: ``%s``, position: 0
moving_file: (an existing file name)
moving tensor volume
argument: ``%s``, position: 1
similarity_metric: ('EDS' or 'GDS' or 'DDS' or 'NMI', nipype default
value: EDS)
similarity metric
argument: ``%s``, position: 2
sampling_xyz: (a tuple of the form: (a value of class 'int', a value
of class 'int', a value of class 'int'), nipype default value: (4,
4, 4))
dist between samp points (mm) (x,y,z)
argument: ``%g %g %g``, position: 3
ftol: (a float, nipype default value: 0.01)
cost function tolerance
argument: ``%g``, position: 4
[Optional]
initialize_xfm: (an existing file name)
Initialize w/DTITK-FORMATaffine
argument: ``%s``, position: 5
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (an existing file name)
out_file_xfm: (an existing file name)
AffineTask¶
Wraps the executable command dti_affine_reg.
Inputs:
[Mandatory]
fixed_file: (an existing file name)
fixed tensor volume
argument: ``%s``, position: 0
moving_file: (an existing file name)
moving tensor volume
argument: ``%s``, position: 1
similarity_metric: ('EDS' or 'GDS' or 'DDS' or 'NMI', nipype default
value: EDS)
similarity metric
argument: ``%s``, position: 2
sampling_xyz: (a tuple of the form: (a value of class 'int', a value
of class 'int', a value of class 'int'), nipype default value: (4,
4, 4))
dist between samp points (mm) (x,y,z)
argument: ``%g %g %g``, position: 3
ftol: (a float, nipype default value: 0.01)
cost function tolerance
argument: ``%g``, position: 4
[Optional]
initialize_xfm: (an existing file name)
Initialize w/DTITK-FORMATaffine
argument: ``%s``, position: 5
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (an existing file name)
out_file_xfm: (an existing file name)
ComposeXfm¶
Wraps the executable command dfRightComposeAffine.
Combines diffeomorphic and affine transforms
Example¶
>>> from nipype.interfaces import dtitk
>>> node = dtitk.ComposeXfm()
>>> node.inputs.in_df = 'im_warp.df.nii'
>>> node.inputs.in_aff= 'im_affine.aff'
>>> node.cmdline
'dfRightComposeAffine -aff im_affine.aff -df im_warp.df.nii -out
im_warp_affdf.df.nii'
>>> node.run()
Inputs:
[Mandatory]
in_df: (an existing file name)
diffeomorphic warp file
argument: ``-df %s``
in_aff: (an existing file name)
affine transform file
argument: ``-aff %s``
[Optional]
out_file: (a file name)
output path
argument: ``-out %s``
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (an existing file name)
ComposeXfmTask¶
Wraps the executable command dfRightComposeAffine.
Inputs:
[Mandatory]
in_df: (an existing file name)
diffeomorphic warp file
argument: ``-df %s``
in_aff: (an existing file name)
affine transform file
argument: ``-aff %s``
[Optional]
out_file: (a file name)
output path
argument: ``-out %s``
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (an existing file name)
Diffeo¶
Wraps the executable command dti_diffeomorphic_reg.
Performs diffeomorphic registration between two tensor volumes
Example¶
>>> from nipype.interfaces import dtitk
>>> node = dtitk.Diffeo()
>>> node.inputs.fixed_file = 'im1.nii'
>>> node.inputs.moving_file = 'im2.nii'
>>> node.inputs.mask_file = 'mask.nii'
>>> node.inputs.legacy = 1
>>> node.inputs.n_iters = 6
>>> node.inputs.ftol = 0.002
>>> node.cmdline
'dti_diffeomorphic_reg im1.nii im2.nii mask.nii 1 6 0.002'
>>> node.run()
Inputs:
[Mandatory]
legacy: (1, nipype default value: 1)
legacy parameter; always set to 1
argument: ``%d``, position: 3
n_iters: (an integer (int or long), nipype default value: 6)
number of iterations
argument: ``%d``, position: 4
ftol: (a float, nipype default value: 0.002)
iteration for the optimization to stop
argument: ``%g``, position: 5
[Optional]
fixed_file: (an existing file name)
fixed tensor volume
argument: ``%s``, position: 0
moving_file: (an existing file name)
moving tensor volume
argument: ``%s``, position: 1
mask_file: (an existing file name)
mask
argument: ``%s``, position: 2
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (an existing file name)
out_file_xfm: (an existing file name)
DiffeoScalarVol¶
Wraps the executable command deformationScalarVolume.
Applies diffeomorphic transform to a scalar volume
Example¶
>>> from nipype.interfaces import dtitk
>>> node = dtitk.DiffeoScalarVol()
>>> node.inputs.in_file = 'im1.nii'
>>> node.inputs.transform = 'im_warp.df.nii'
>>> node.cmdline
'deformationScalarVolume -in im1.nii -interp 0 -out im1_diffeoxfmd.nii
-trans im_warp.df.nii'
>>> node.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
moving scalar volume
argument: ``-in %s``
transform: (an existing file name)
transform to apply
argument: ``-trans %s``
[Optional]
out_file: (a file name)
output filename
argument: ``-out %s``
target: (an existing file name)
output volume specification read from the target volume if specified
argument: ``-target %s``
mutually_exclusive: voxel_size
voxel_size: (a tuple of the form: (a float, a float, a float))
xyz voxel size (superseded by target)
argument: ``-vsize %g %g %g``
mutually_exclusive: target
flip: (a tuple of the form: (an integer (int or long), an integer
(int or long), an integer (int or long)))
argument: ``-flip %d %d %d``
resampling_type: ('backward' or 'forward')
use backward or forward resampling
argument: ``-type %s``
interpolation: ('trilinear' or 'NN', nipype default value: trilinear)
trilinear, or nearest neighbor
argument: ``-interp %s``
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (an existing file name)
moved volume
DiffeoSymTensor3DVol¶
Wraps the executable command deformationSymTensor3DVolume.
Applies diffeomorphic transform to a tensor volume
Example¶
>>> from nipype.interfaces import dtitk
>>> node = dtitk.DiffeoSymTensor3DVol()
>>> node.inputs.in_file = 'im1.nii'
>>> node.inputs.transform = 'im_warp.df.nii'
>>> node.cmdline
'deformationSymTensor3DVolume -df FD -in im1.nii -interp LEI -out
im1_diffeoxfmd.nii -reorient PPD -trans im_warp.df.nii'
>>> node.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
moving tensor volume
argument: ``-in %s``
transform: (an existing file name)
transform to apply
argument: ``-trans %s``
[Optional]
out_file: (a file name)
output filename
argument: ``-out %s``
df: (a unicode string, nipype default value: FD)
argument: ``-df %s``
interpolation: ('LEI' or 'EI', nipype default value: LEI)
Log Euclidean/Euclidean Interpolation
argument: ``-interp %s``
reorient: ('PPD' or 'FS', nipype default value: PPD)
Reorientation strategy: preservation of principal direction or
finite strain
argument: ``-reorient %s``
target: (an existing file name)
output volume specification read from the target volume if specified
argument: ``-target %s``
mutually_exclusive: voxel_size
voxel_size: (a tuple of the form: (a float, a float, a float))
xyz voxel size (superseded by target)
argument: ``-vsize %g %g %g``
mutually_exclusive: target
flip: (a tuple of the form: (an integer (int or long), an integer
(int or long), an integer (int or long)))
argument: ``-flip %d %d %d``
resampling_type: ('backward' or 'forward')
use backward or forward resampling
argument: ``-type %s``
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (an existing file name)
DiffeoTask¶
Wraps the executable command dti_diffeomorphic_reg.
Inputs:
[Mandatory]
legacy: (1, nipype default value: 1)
legacy parameter; always set to 1
argument: ``%d``, position: 3
n_iters: (an integer (int or long), nipype default value: 6)
number of iterations
argument: ``%d``, position: 4
ftol: (a float, nipype default value: 0.002)
iteration for the optimization to stop
argument: ``%g``, position: 5
[Optional]
fixed_file: (an existing file name)
fixed tensor volume
argument: ``%s``, position: 0
moving_file: (an existing file name)
moving tensor volume
argument: ``%s``, position: 1
mask_file: (an existing file name)
mask
argument: ``%s``, position: 2
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (an existing file name)
out_file_xfm: (an existing file name)
Rigid¶
Wraps the executable command dti_rigid_reg.
Performs rigid registration between two tensor volumes
Example¶
>>> from nipype.interfaces import dtitk
>>> node = dtitk.Rigid()
>>> node.inputs.fixed_file = 'im1.nii'
>>> node.inputs.moving_file = 'im2.nii'
>>> node.inputs.similarity_metric = 'EDS'
>>> node.inputs.sampling_xyz = (4,4,4)
>>> node.inputs.ftol = 0.01
>>> node.cmdline
'dti_rigid_reg im1.nii im2.nii EDS 4 4 4 0.01'
>>> node.run()
Inputs:
[Mandatory]
fixed_file: (an existing file name)
fixed tensor volume
argument: ``%s``, position: 0
moving_file: (an existing file name)
moving tensor volume
argument: ``%s``, position: 1
similarity_metric: ('EDS' or 'GDS' or 'DDS' or 'NMI', nipype default
value: EDS)
similarity metric
argument: ``%s``, position: 2
sampling_xyz: (a tuple of the form: (a value of class 'int', a value
of class 'int', a value of class 'int'), nipype default value: (4,
4, 4))
dist between samp points (mm) (x,y,z)
argument: ``%g %g %g``, position: 3
ftol: (a float, nipype default value: 0.01)
cost function tolerance
argument: ``%g``, position: 4
[Optional]
initialize_xfm: (an existing file name)
Initialize w/DTITK-FORMATaffine
argument: ``%s``, position: 5
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (an existing file name)
out_file_xfm: (an existing file name)
RigidTask¶
Wraps the executable command dti_rigid_reg.
Inputs:
[Mandatory]
fixed_file: (an existing file name)
fixed tensor volume
argument: ``%s``, position: 0
moving_file: (an existing file name)
moving tensor volume
argument: ``%s``, position: 1
similarity_metric: ('EDS' or 'GDS' or 'DDS' or 'NMI', nipype default
value: EDS)
similarity metric
argument: ``%s``, position: 2
sampling_xyz: (a tuple of the form: (a value of class 'int', a value
of class 'int', a value of class 'int'), nipype default value: (4,
4, 4))
dist between samp points (mm) (x,y,z)
argument: ``%g %g %g``, position: 3
ftol: (a float, nipype default value: 0.01)
cost function tolerance
argument: ``%g``, position: 4
[Optional]
initialize_xfm: (an existing file name)
Initialize w/DTITK-FORMATaffine
argument: ``%s``, position: 5
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (an existing file name)
out_file_xfm: (an existing file name)
affScalarVolTask¶
Wraps the executable command affineScalarVolume.
Inputs:
[Mandatory]
in_file: (an existing file name)
moving scalar volume
argument: ``-in %s``
[Optional]
out_file: (a file name)
output filename
argument: ``-out %s``
transform: (an existing file name)
transform to apply: specify an input transformation file; parameters
input will be ignored
argument: ``-trans %s``
mutually_exclusive: target, translation, euler, deformation
interpolation: ('trilinear' or 'NN', nipype default value: trilinear)
trilinear or nearest neighbor interpolation
argument: ``-interp %s``
target: (an existing file name)
output volume specification read from the target volume if specified
argument: ``-target %s``
mutually_exclusive: transform
translation: (a tuple of the form: (a float, a float, a float))
translation (x,y,z) in mm
argument: ``-translation %g %g %g``
mutually_exclusive: transform
euler: (a tuple of the form: (a float, a float, a float))
(theta, phi, psi) in degrees
argument: ``-euler %g %g %g``
mutually_exclusive: transform
deformation: (a tuple of the form: (a float, a float, a float, a
float, a float, a float))
(xx,yy,zz,xy,yz,xz)
argument: ``-deformation %g %g %g %g %g %g``
mutually_exclusive: transform
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (an existing file name)
moved volume
affSymTensor3DVolTask¶
Wraps the executable command affineSymTensor3DVolume.
Inputs:
[Mandatory]
in_file: (an existing file name)
moving tensor volume
argument: ``-in %s``
[Optional]
out_file: (a file name)
output filename
argument: ``-out %s``
transform: (an existing file name)
transform to apply: specify an input transformation file; parameters
input will be ignored
argument: ``-trans %s``
mutually_exclusive: target, translation, euler, deformation
interpolation: ('LEI' or 'EI', nipype default value: LEI)
Log Euclidean/Euclidean Interpolation
argument: ``-interp %s``
reorient: ('PPD' or 'NO' or 'FS', nipype default value: PPD)
Reorientation strategy: preservation of principal direction, no
reorientation, or finite strain
argument: ``-reorient %s``
target: (an existing file name)
output volume specification read from the target volume if specified
argument: ``-target %s``
mutually_exclusive: transform
translation: (a tuple of the form: (a float, a float, a float))
translation (x,y,z) in mm
argument: ``-translation %g %g %g``
mutually_exclusive: transform
euler: (a tuple of the form: (a float, a float, a float))
(theta, phi, psi) in degrees
argument: ``-euler %g %g %g``
mutually_exclusive: transform
deformation: (a tuple of the form: (a float, a float, a float, a
float, a float, a float))
(xx,yy,zz,xy,yz,xz)
argument: ``-deformation %g %g %g %g %g %g``
mutually_exclusive: transform
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (an existing file name)
diffeoScalarVolTask¶
Wraps the executable command deformationScalarVolume.
Inputs:
[Mandatory]
in_file: (an existing file name)
moving scalar volume
argument: ``-in %s``
transform: (an existing file name)
transform to apply
argument: ``-trans %s``
[Optional]
out_file: (a file name)
output filename
argument: ``-out %s``
target: (an existing file name)
output volume specification read from the target volume if specified
argument: ``-target %s``
mutually_exclusive: voxel_size
voxel_size: (a tuple of the form: (a float, a float, a float))
xyz voxel size (superseded by target)
argument: ``-vsize %g %g %g``
mutually_exclusive: target
flip: (a tuple of the form: (an integer (int or long), an integer
(int or long), an integer (int or long)))
argument: ``-flip %d %d %d``
resampling_type: ('backward' or 'forward')
use backward or forward resampling
argument: ``-type %s``
interpolation: ('trilinear' or 'NN', nipype default value: trilinear)
trilinear, or nearest neighbor
argument: ``-interp %s``
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (an existing file name)
moved volume
diffeoSymTensor3DVolTask¶
Wraps the executable command deformationSymTensor3DVolume.
Inputs:
[Mandatory]
in_file: (an existing file name)
moving tensor volume
argument: ``-in %s``
transform: (an existing file name)
transform to apply
argument: ``-trans %s``
[Optional]
out_file: (a file name)
output filename
argument: ``-out %s``
df: (a unicode string, nipype default value: FD)
argument: ``-df %s``
interpolation: ('LEI' or 'EI', nipype default value: LEI)
Log Euclidean/Euclidean Interpolation
argument: ``-interp %s``
reorient: ('PPD' or 'FS', nipype default value: PPD)
Reorientation strategy: preservation of principal direction or
finite strain
argument: ``-reorient %s``
target: (an existing file name)
output volume specification read from the target volume if specified
argument: ``-target %s``
mutually_exclusive: voxel_size
voxel_size: (a tuple of the form: (a float, a float, a float))
xyz voxel size (superseded by target)
argument: ``-vsize %g %g %g``
mutually_exclusive: target
flip: (a tuple of the form: (an integer (int or long), an integer
(int or long), an integer (int or long)))
argument: ``-flip %d %d %d``
resampling_type: ('backward' or 'forward')
use backward or forward resampling
argument: ``-type %s``
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (an existing file name)