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¶
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¶
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¶
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-FORMATaffine. 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¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, AffineWrapped 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-FORMATaffine. 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¶
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¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, ComposeXfmWrapped 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¶
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¶
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¶
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¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, DiffeoWrapped 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¶
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-FORMATaffine. 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¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, RigidWrapped 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-FORMATaffine. 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¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, AffScalarVolWrapped 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¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, AffSymTensor3DVolWrapped 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¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, DiffeoScalarVolWrapped 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¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, DiffeoSymTensor3DVolWrapped 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)