nipype.interfaces.dtitk.registration module

DTITK registration interfaces

DTI-TK developed by Gary Hui Zhang, gary.zhang@ucl.ac.uk For additional help, visit http://dti-tk.sf.net

The high-dimensional tensor-based DTI registration algorithm

Zhang, H., Avants, B.B, Yushkevich, P.A., Woo, J.H., Wang, S., McCluskey, L.H.,
Elman, L.B., Melhem, E.R., Gee, J.C., High-dimensional spatial normalization of diffusion tensor images improves the detection of white matter differences in amyotrophic lateral sclerosis, IEEE Transactions on Medical Imaging, 26(11):1585-1597, November 2007. PMID: 18041273.

The original piecewise-affine tensor-based DTI registration algorithm at the core of DTI-TK

Zhang, H., Yushkevich, P.A., Alexander, D.C., Gee, J.C., Deformable
registration of diffusion tensor MR images with explicit orientation optimization, Medical Image Analysis, 10(5):764-785, October 2006. PMID: 16899392.

AffScalarVol

Link to code

Bases: CommandLineDtitk

Wrapped executable: 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() # doctest: +SKIP
in_file : a pathlike object or string representing an existing file
Moving scalar volume. Maps to a command-line argument: -in %s.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
deformation : a tuple of the form: (a float, a float, a float, a float, a float, a float)
(xx,yy,zz,xy,yz,xz). Maps to a command-line argument: -deformation %g %g %g %g %g %g. Mutually exclusive with inputs: transform.
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: {})
euler : a tuple of the form: (a float, a float, a float)
(theta, phi, psi) in degrees. Maps to a command-line argument: -euler %g %g %g. Mutually exclusive with inputs: transform.
interpolation : ‘trilinear’ or ‘NN’
Trilinear or nearest neighbor interpolation. Maps to a command-line argument: -interp %s. (Nipype default value: trilinear)
out_file : a pathlike object or string representing a file
Output filename. Maps to a command-line argument: -out %s.
target : a pathlike object or string representing an existing file
Output volume specification read from the target volume if specified. Maps to a command-line argument: -target %s. Mutually exclusive with inputs: transform.
transform : a pathlike object or string representing an existing file
Transform to apply: specify an input transformation file; parameters input will be ignored. Maps to a command-line argument: -trans %s. Mutually exclusive with inputs: target, translation, euler, deformation.
translation : a tuple of the form: (a float, a float, a float)
Translation (x,y,z) in mm. Maps to a command-line argument: -translation %g %g %g. Mutually exclusive with inputs: transform.
out_file : a pathlike object or string representing an existing file
Moved volume.

AffSymTensor3DVol

Link to code

Bases: CommandLineDtitk

Wrapped executable: 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() # doctest: +SKIP
in_file : a pathlike object or string representing an existing file
Moving tensor volume. Maps to a command-line argument: -in %s.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
deformation : a tuple of the form: (a float, a float, a float, a float, a float, a float)
(xx,yy,zz,xy,yz,xz). Maps to a command-line argument: -deformation %g %g %g %g %g %g. Mutually exclusive with inputs: transform.
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: {})
euler : a tuple of the form: (a float, a float, a float)
(theta, phi, psi) in degrees. Maps to a command-line argument: -euler %g %g %g. Mutually exclusive with inputs: transform.
interpolation : ‘LEI’ or ‘EI’
Log Euclidean/Euclidean Interpolation. Maps to a command-line argument: -interp %s. (Nipype default value: LEI)
out_file : a pathlike object or string representing a file
Output filename. Maps to a command-line argument: -out %s.
reorient : ‘PPD’ or ‘NO’ or ‘FS’
Reorientation strategy: preservation of principal direction, no reorientation, or finite strain. Maps to a command-line argument: -reorient %s. (Nipype default value: PPD)
target : a pathlike object or string representing an existing file
Output volume specification read from the target volume if specified. Maps to a command-line argument: -target %s. Mutually exclusive with inputs: transform.
transform : a pathlike object or string representing an existing file
Transform to apply: specify an input transformation file; parameters input will be ignored. Maps to a command-line argument: -trans %s. Mutually exclusive with inputs: target, translation, euler, deformation.
translation : a tuple of the form: (a float, a float, a float)
Translation (x,y,z) in mm. Maps to a command-line argument: -translation %g %g %g. Mutually exclusive with inputs: transform.

out_file : a pathlike object or string representing an existing file

Affine

Link to code

Bases: Rigid

Wrapped executable: 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() # doctest: +SKIP
fixed_file : a pathlike object or string representing an existing file
Fixed tensor volume. Maps to a command-line argument: %s (position: 0).
ftol : a float
Cost function tolerance. Maps to a command-line argument: %g (position: 4). (Nipype default value: 0.01)
moving_file : a pathlike object or string representing an existing file
Moving tensor volume. Maps to a command-line argument: %s (position: 1).
sampling_xyz : a tuple of the form: (a value of class ‘int’, a value of class ‘int’, a value of class ‘int’)
Dist between samp points (mm) (x,y,z). Maps to a command-line argument: %g %g %g (position: 3). (Nipype default value: (4, 4, 4))
similarity_metric : ‘EDS’ or ‘GDS’ or ‘DDS’ or ‘NMI’
Similarity metric. Maps to a command-line argument: %s (position: 2). (Nipype default value: EDS)
args : a unicode 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: {})
initialize_xfm : a pathlike object or string representing an existing file
Initialize w/DTITK-FORMATaffine. Maps to a command-line argument: %s (position: 5).

out_file : a pathlike object or string representing an existing file out_file_xfm : a pathlike object or string representing an existing file

AffineTask

Link to code

Bases: nipype.interfaces.dtitk.base.DTITKRenameMixin, Affine

Wrapped executable: dti_affine_reg.

fixed_file : a pathlike object or string representing an existing file
Fixed tensor volume. Maps to a command-line argument: %s (position: 0).
ftol : a float
Cost function tolerance. Maps to a command-line argument: %g (position: 4). (Nipype default value: 0.01)
moving_file : a pathlike object or string representing an existing file
Moving tensor volume. Maps to a command-line argument: %s (position: 1).
sampling_xyz : a tuple of the form: (a value of class ‘int’, a value of class ‘int’, a value of class ‘int’)
Dist between samp points (mm) (x,y,z). Maps to a command-line argument: %g %g %g (position: 3). (Nipype default value: (4, 4, 4))
similarity_metric : ‘EDS’ or ‘GDS’ or ‘DDS’ or ‘NMI’
Similarity metric. Maps to a command-line argument: %s (position: 2). (Nipype default value: EDS)
args : a unicode 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: {})
initialize_xfm : a pathlike object or string representing an existing file
Initialize w/DTITK-FORMATaffine. Maps to a command-line argument: %s (position: 5).

out_file : a pathlike object or string representing an existing file out_file_xfm : a pathlike object or string representing an existing file

ComposeXfm

Link to code

Bases: CommandLineDtitk

Wrapped executable: 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() # doctest: +SKIP
in_aff : a pathlike object or string representing an existing file
Affine transform file. Maps to a command-line argument: -aff %s.
in_df : a pathlike object or string representing an existing file
Diffeomorphic warp file. Maps to a command-line argument: -df %s.
args : a unicode 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: {})
out_file : a pathlike object or string representing a file
Output path. Maps to a command-line argument: -out %s.

out_file : a pathlike object or string representing an existing file

ComposeXfmTask

Link to code

Bases: nipype.interfaces.dtitk.base.DTITKRenameMixin, ComposeXfm

Wrapped executable: dfRightComposeAffine.

in_aff : a pathlike object or string representing an existing file
Affine transform file. Maps to a command-line argument: -aff %s.
in_df : a pathlike object or string representing an existing file
Diffeomorphic warp file. Maps to a command-line argument: -df %s.
args : a unicode 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: {})
out_file : a pathlike object or string representing a file
Output path. Maps to a command-line argument: -out %s.

out_file : a pathlike object or string representing an existing file

Diffeo

Link to code

Bases: CommandLineDtitk

Wrapped executable: 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() # doctest: +SKIP
ftol : a float
Iteration for the optimization to stop. Maps to a command-line argument: %g (position: 5). (Nipype default value: 0.002)
legacy : 1
Legacy parameter; always set to 1. Maps to a command-line argument: %d (position: 3). (Nipype default value: 1)
n_iters : an integer (int or long)
Number of iterations. Maps to a command-line argument: %d (position: 4). (Nipype default value: 6)
args : a unicode 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: {})
fixed_file : a pathlike object or string representing an existing file
Fixed tensor volume. Maps to a command-line argument: %s (position: 0).
mask_file : a pathlike object or string representing an existing file
Mask. Maps to a command-line argument: %s (position: 2).
moving_file : a pathlike object or string representing an existing file
Moving tensor volume. Maps to a command-line argument: %s (position: 1).

out_file : a pathlike object or string representing an existing file out_file_xfm : a pathlike object or string representing an existing file

DiffeoScalarVol

Link to code

Bases: CommandLineDtitk

Wrapped executable: 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() # doctest: +SKIP
in_file : a pathlike object or string representing an existing file
Moving scalar volume. Maps to a command-line argument: -in %s.
transform : a pathlike object or string representing an existing file
Transform to apply. Maps to a command-line argument: -trans %s.
args : a unicode 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: {})
flip : a tuple of the form: (an integer (int or long), an integer (int or long), an integer (int or long))
Maps to a command-line argument: -flip %d %d %d.
interpolation : ‘trilinear’ or ‘NN’
Trilinear, or nearest neighbor. Maps to a command-line argument: -interp %s. (Nipype default value: trilinear)
out_file : a pathlike object or string representing a file
Output filename. Maps to a command-line argument: -out %s.
resampling_type : ‘backward’ or ‘forward’
Use backward or forward resampling. Maps to a command-line argument: -type %s.
target : a pathlike object or string representing an existing file
Output volume specification read from the target volume if specified. Maps to a command-line argument: -target %s. Mutually exclusive with inputs: voxel_size.
voxel_size : a tuple of the form: (a float, a float, a float)
Xyz voxel size (superseded by target). Maps to a command-line argument: -vsize %g %g %g. Mutually exclusive with inputs: target.
out_file : a pathlike object or string representing an existing file
Moved volume.

DiffeoSymTensor3DVol

Link to code

Bases: CommandLineDtitk

Wrapped executable: 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() # doctest: +SKIP
in_file : a pathlike object or string representing an existing file
Moving tensor volume. Maps to a command-line argument: -in %s.
transform : a pathlike object or string representing an existing file
Transform to apply. Maps to a command-line argument: -trans %s.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
df : a unicode string
Maps to a command-line argument: -df %s. (Nipype default value: FD)
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: {})
flip : a tuple of the form: (an integer (int or long), an integer (int or long), an integer (int or long))
Maps to a command-line argument: -flip %d %d %d.
interpolation : ‘LEI’ or ‘EI’
Log Euclidean/Euclidean Interpolation. Maps to a command-line argument: -interp %s. (Nipype default value: LEI)
out_file : a pathlike object or string representing a file
Output filename. Maps to a command-line argument: -out %s.
reorient : ‘PPD’ or ‘FS’
Reorientation strategy: preservation of principal direction or finite strain. Maps to a command-line argument: -reorient %s. (Nipype default value: PPD)
resampling_type : ‘backward’ or ‘forward’
Use backward or forward resampling. Maps to a command-line argument: -type %s.
target : a pathlike object or string representing an existing file
Output volume specification read from the target volume if specified. Maps to a command-line argument: -target %s. Mutually exclusive with inputs: voxel_size.
voxel_size : a tuple of the form: (a float, a float, a float)
Xyz voxel size (superseded by target). Maps to a command-line argument: -vsize %g %g %g. Mutually exclusive with inputs: target.

out_file : a pathlike object or string representing an existing file

DiffeoTask

Link to code

Bases: nipype.interfaces.dtitk.base.DTITKRenameMixin, Diffeo

Wrapped executable: dti_diffeomorphic_reg.

ftol : a float
Iteration for the optimization to stop. Maps to a command-line argument: %g (position: 5). (Nipype default value: 0.002)
legacy : 1
Legacy parameter; always set to 1. Maps to a command-line argument: %d (position: 3). (Nipype default value: 1)
n_iters : an integer (int or long)
Number of iterations. Maps to a command-line argument: %d (position: 4). (Nipype default value: 6)
args : a unicode 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: {})
fixed_file : a pathlike object or string representing an existing file
Fixed tensor volume. Maps to a command-line argument: %s (position: 0).
mask_file : a pathlike object or string representing an existing file
Mask. Maps to a command-line argument: %s (position: 2).
moving_file : a pathlike object or string representing an existing file
Moving tensor volume. Maps to a command-line argument: %s (position: 1).

out_file : a pathlike object or string representing an existing file out_file_xfm : a pathlike object or string representing an existing file

Rigid

Link to code

Bases: CommandLineDtitk

Wrapped executable: 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() # doctest: +SKIP
fixed_file : a pathlike object or string representing an existing file
Fixed tensor volume. Maps to a command-line argument: %s (position: 0).
ftol : a float
Cost function tolerance. Maps to a command-line argument: %g (position: 4). (Nipype default value: 0.01)
moving_file : a pathlike object or string representing an existing file
Moving tensor volume. Maps to a command-line argument: %s (position: 1).
sampling_xyz : a tuple of the form: (a value of class ‘int’, a value of class ‘int’, a value of class ‘int’)
Dist between samp points (mm) (x,y,z). Maps to a command-line argument: %g %g %g (position: 3). (Nipype default value: (4, 4, 4))
similarity_metric : ‘EDS’ or ‘GDS’ or ‘DDS’ or ‘NMI’
Similarity metric. Maps to a command-line argument: %s (position: 2). (Nipype default value: EDS)
args : a unicode 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: {})
initialize_xfm : a pathlike object or string representing an existing file
Initialize w/DTITK-FORMATaffine. Maps to a command-line argument: %s (position: 5).

out_file : a pathlike object or string representing an existing file out_file_xfm : a pathlike object or string representing an existing file

RigidTask

Link to code

Bases: nipype.interfaces.dtitk.base.DTITKRenameMixin, Rigid

Wrapped executable: dti_rigid_reg.

fixed_file : a pathlike object or string representing an existing file
Fixed tensor volume. Maps to a command-line argument: %s (position: 0).
ftol : a float
Cost function tolerance. Maps to a command-line argument: %g (position: 4). (Nipype default value: 0.01)
moving_file : a pathlike object or string representing an existing file
Moving tensor volume. Maps to a command-line argument: %s (position: 1).
sampling_xyz : a tuple of the form: (a value of class ‘int’, a value of class ‘int’, a value of class ‘int’)
Dist between samp points (mm) (x,y,z). Maps to a command-line argument: %g %g %g (position: 3). (Nipype default value: (4, 4, 4))
similarity_metric : ‘EDS’ or ‘GDS’ or ‘DDS’ or ‘NMI’
Similarity metric. Maps to a command-line argument: %s (position: 2). (Nipype default value: EDS)
args : a unicode 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: {})
initialize_xfm : a pathlike object or string representing an existing file
Initialize w/DTITK-FORMATaffine. Maps to a command-line argument: %s (position: 5).

out_file : a pathlike object or string representing an existing file out_file_xfm : a pathlike object or string representing an existing file

affScalarVolTask

Link to code

Bases: nipype.interfaces.dtitk.base.DTITKRenameMixin, AffScalarVol

Wrapped executable: affineScalarVolume.

in_file : a pathlike object or string representing an existing file
Moving scalar volume. Maps to a command-line argument: -in %s.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
deformation : a tuple of the form: (a float, a float, a float, a float, a float, a float)
(xx,yy,zz,xy,yz,xz). Maps to a command-line argument: -deformation %g %g %g %g %g %g. Mutually exclusive with inputs: transform.
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: {})
euler : a tuple of the form: (a float, a float, a float)
(theta, phi, psi) in degrees. Maps to a command-line argument: -euler %g %g %g. Mutually exclusive with inputs: transform.
interpolation : ‘trilinear’ or ‘NN’
Trilinear or nearest neighbor interpolation. Maps to a command-line argument: -interp %s. (Nipype default value: trilinear)
out_file : a pathlike object or string representing a file
Output filename. Maps to a command-line argument: -out %s.
target : a pathlike object or string representing an existing file
Output volume specification read from the target volume if specified. Maps to a command-line argument: -target %s. Mutually exclusive with inputs: transform.
transform : a pathlike object or string representing an existing file
Transform to apply: specify an input transformation file; parameters input will be ignored. Maps to a command-line argument: -trans %s. Mutually exclusive with inputs: target, translation, euler, deformation.
translation : a tuple of the form: (a float, a float, a float)
Translation (x,y,z) in mm. Maps to a command-line argument: -translation %g %g %g. Mutually exclusive with inputs: transform.
out_file : a pathlike object or string representing an existing file
Moved volume.

affSymTensor3DVolTask

Link to code

Bases: nipype.interfaces.dtitk.base.DTITKRenameMixin, AffSymTensor3DVol

Wrapped executable: affineSymTensor3DVolume.

in_file : a pathlike object or string representing an existing file
Moving tensor volume. Maps to a command-line argument: -in %s.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
deformation : a tuple of the form: (a float, a float, a float, a float, a float, a float)
(xx,yy,zz,xy,yz,xz). Maps to a command-line argument: -deformation %g %g %g %g %g %g. Mutually exclusive with inputs: transform.
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: {})
euler : a tuple of the form: (a float, a float, a float)
(theta, phi, psi) in degrees. Maps to a command-line argument: -euler %g %g %g. Mutually exclusive with inputs: transform.
interpolation : ‘LEI’ or ‘EI’
Log Euclidean/Euclidean Interpolation. Maps to a command-line argument: -interp %s. (Nipype default value: LEI)
out_file : a pathlike object or string representing a file
Output filename. Maps to a command-line argument: -out %s.
reorient : ‘PPD’ or ‘NO’ or ‘FS’
Reorientation strategy: preservation of principal direction, no reorientation, or finite strain. Maps to a command-line argument: -reorient %s. (Nipype default value: PPD)
target : a pathlike object or string representing an existing file
Output volume specification read from the target volume if specified. Maps to a command-line argument: -target %s. Mutually exclusive with inputs: transform.
transform : a pathlike object or string representing an existing file
Transform to apply: specify an input transformation file; parameters input will be ignored. Maps to a command-line argument: -trans %s. Mutually exclusive with inputs: target, translation, euler, deformation.
translation : a tuple of the form: (a float, a float, a float)
Translation (x,y,z) in mm. Maps to a command-line argument: -translation %g %g %g. Mutually exclusive with inputs: transform.

out_file : a pathlike object or string representing an existing file

diffeoScalarVolTask

Link to code

Bases: nipype.interfaces.dtitk.base.DTITKRenameMixin, DiffeoScalarVol

Wrapped executable: deformationScalarVolume.

in_file : a pathlike object or string representing an existing file
Moving scalar volume. Maps to a command-line argument: -in %s.
transform : a pathlike object or string representing an existing file
Transform to apply. Maps to a command-line argument: -trans %s.
args : a unicode 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: {})
flip : a tuple of the form: (an integer (int or long), an integer (int or long), an integer (int or long))
Maps to a command-line argument: -flip %d %d %d.
interpolation : ‘trilinear’ or ‘NN’
Trilinear, or nearest neighbor. Maps to a command-line argument: -interp %s. (Nipype default value: trilinear)
out_file : a pathlike object or string representing a file
Output filename. Maps to a command-line argument: -out %s.
resampling_type : ‘backward’ or ‘forward’
Use backward or forward resampling. Maps to a command-line argument: -type %s.
target : a pathlike object or string representing an existing file
Output volume specification read from the target volume if specified. Maps to a command-line argument: -target %s. Mutually exclusive with inputs: voxel_size.
voxel_size : a tuple of the form: (a float, a float, a float)
Xyz voxel size (superseded by target). Maps to a command-line argument: -vsize %g %g %g. Mutually exclusive with inputs: target.
out_file : a pathlike object or string representing an existing file
Moved volume.

diffeoSymTensor3DVolTask

Link to code

Bases: nipype.interfaces.dtitk.base.DTITKRenameMixin, DiffeoSymTensor3DVol

Wrapped executable: deformationSymTensor3DVolume.

in_file : a pathlike object or string representing an existing file
Moving tensor volume. Maps to a command-line argument: -in %s.
transform : a pathlike object or string representing an existing file
Transform to apply. Maps to a command-line argument: -trans %s.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
df : a unicode string
Maps to a command-line argument: -df %s. (Nipype default value: FD)
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: {})
flip : a tuple of the form: (an integer (int or long), an integer (int or long), an integer (int or long))
Maps to a command-line argument: -flip %d %d %d.
interpolation : ‘LEI’ or ‘EI’
Log Euclidean/Euclidean Interpolation. Maps to a command-line argument: -interp %s. (Nipype default value: LEI)
out_file : a pathlike object or string representing a file
Output filename. Maps to a command-line argument: -out %s.
reorient : ‘PPD’ or ‘FS’
Reorientation strategy: preservation of principal direction or finite strain. Maps to a command-line argument: -reorient %s. (Nipype default value: PPD)
resampling_type : ‘backward’ or ‘forward’
Use backward or forward resampling. Maps to a command-line argument: -type %s.
target : a pathlike object or string representing an existing file
Output volume specification read from the target volume if specified. Maps to a command-line argument: -target %s. Mutually exclusive with inputs: voxel_size.
voxel_size : a tuple of the form: (a float, a float, a float)
Xyz voxel size (superseded by target). Maps to a command-line argument: -vsize %g %g %g. Mutually exclusive with inputs: target.

out_file : a pathlike object or string representing an existing file