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()
Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – Moving scalar volume. Maps to a command-line argument: -in %s.

Optional Inputs:

  • args (a 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.

Outputs:

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()
Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – Moving tensor volume. Maps to a command-line argument: -in %s.

Optional Inputs:

  • args (a 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.

Outputs:

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()
Mandatory Inputs:

  • 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)

Optional Inputs:

  • args (a 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-FORMAT affine. Maps to a command-line argument: %s (position: 5).

Outputs:

  • 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.

Mandatory Inputs:

  • 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)

Optional Inputs:

  • args (a 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-FORMAT affine. Maps to a command-line argument: %s (position: 5).

Outputs:

  • 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()
Mandatory Inputs:

  • 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.

Optional Inputs:

  • args (a 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.

Outputs:

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.

Mandatory Inputs:

  • 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.

Optional Inputs:

  • args (a 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.

Outputs:

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()
Mandatory Inputs:

  • 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) – Number of iterations. Maps to a command-line argument: %d (position: 4). (Nipype default value: 6)

Optional Inputs:

  • args (a 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).

Outputs:

  • 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()
Mandatory Inputs:

  • 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.

Optional Inputs:

  • args (a 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, an integer, an integer)) – 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.

Outputs:

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()
Mandatory Inputs:

  • 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.

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • df (a 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, an integer, an integer)) – 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.

Outputs:

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.

Mandatory Inputs:

  • 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) – Number of iterations. Maps to a command-line argument: %d (position: 4). (Nipype default value: 6)

Optional Inputs:

  • args (a 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).

Outputs:

  • 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()
Mandatory Inputs:

  • 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)

Optional Inputs:

  • args (a 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-FORMAT affine. Maps to a command-line argument: %s (position: 5).

Outputs:

  • 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.

Mandatory Inputs:

  • 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)

Optional Inputs:

  • args (a 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-FORMAT affine. Maps to a command-line argument: %s (position: 5).

Outputs:

  • 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.

Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – Moving scalar volume. Maps to a command-line argument: -in %s.

Optional Inputs:

  • args (a 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.

Outputs:

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.

Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – Moving tensor volume. Maps to a command-line argument: -in %s.

Optional Inputs:

  • args (a 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.

Outputs:

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.

Mandatory Inputs:

  • 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.

Optional Inputs:

  • args (a 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, an integer, an integer)) – 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.

Outputs:

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.

Mandatory Inputs:

  • 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.

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • df (a 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, an integer, an integer)) – 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.

Outputs:

out_file (a pathlike object or string representing an existing file)