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()
- in_filea pathlike object or string representing an existing file
Moving scalar volume. Maps to a command-line argument:
-in %s
.
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- deformationa 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
.- environa 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:
{}
)- eulera 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_filea pathlike object or string representing a file
Output filename. Maps to a command-line argument:
-out %s
.- targeta 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
.- transforma 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
.- translationa 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_filea 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()
- in_filea pathlike object or string representing an existing file
Moving tensor volume. Maps to a command-line argument:
-in %s
.
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- deformationa 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
.- environa 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:
{}
)- eulera 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_filea 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
)- targeta 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
.- transforma 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
.- translationa 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¶
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()
- fixed_filea pathlike object or string representing an existing file
Fixed tensor volume. Maps to a command-line argument:
%s
(position: 0).- ftola float
Cost function tolerance. Maps to a command-line argument:
%g
(position: 4). (Nipype default value:0.01
)- moving_filea pathlike object or string representing an existing file
Moving tensor volume. Maps to a command-line argument:
%s
(position: 1).- sampling_xyza 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
)
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- environa 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_xfma 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¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, AffineWrapped executable:
dti_affine_reg
.
- fixed_filea pathlike object or string representing an existing file
Fixed tensor volume. Maps to a command-line argument:
%s
(position: 0).- ftola float
Cost function tolerance. Maps to a command-line argument:
%g
(position: 4). (Nipype default value:0.01
)- moving_filea pathlike object or string representing an existing file
Moving tensor volume. Maps to a command-line argument:
%s
(position: 1).- sampling_xyza 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
)
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- environa 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_xfma 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¶
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()
- in_affa pathlike object or string representing an existing file
Affine transform file. Maps to a command-line argument:
-aff %s
.- in_dfa pathlike object or string representing an existing file
Diffeomorphic warp file. Maps to a command-line argument:
-df %s
.
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- environa 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_filea 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¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, ComposeXfmWrapped executable:
dfRightComposeAffine
.
- in_affa pathlike object or string representing an existing file
Affine transform file. Maps to a command-line argument:
-aff %s
.- in_dfa pathlike object or string representing an existing file
Diffeomorphic warp file. Maps to a command-line argument:
-df %s
.
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- environa 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_filea 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¶
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()
- ftola float
Iteration for the optimization to stop. Maps to a command-line argument:
%g
(position: 5). (Nipype default value:0.002
)- legacy1
Legacy parameter; always set to 1. Maps to a command-line argument:
%d
(position: 3). (Nipype default value:1
)- n_itersan integer (int or long)
Number of iterations. Maps to a command-line argument:
%d
(position: 4). (Nipype default value:6
)
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- environa 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_filea pathlike object or string representing an existing file
Fixed tensor volume. Maps to a command-line argument:
%s
(position: 0).- mask_filea pathlike object or string representing an existing file
Mask. Maps to a command-line argument:
%s
(position: 2).- moving_filea 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¶
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()
- in_filea pathlike object or string representing an existing file
Moving scalar volume. Maps to a command-line argument:
-in %s
.- transforma pathlike object or string representing an existing file
Transform to apply. Maps to a command-line argument:
-trans %s
.
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- environa 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:
{}
)- flipa 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_filea 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
.- targeta 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_sizea 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_filea 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()
- in_filea pathlike object or string representing an existing file
Moving tensor volume. Maps to a command-line argument:
-in %s
.- transforma pathlike object or string representing an existing file
Transform to apply. Maps to a command-line argument:
-trans %s
.
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- dfa unicode string
Maps to a command-line argument:
-df %s
. (Nipype default value:FD
)- environa 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:
{}
)- flipa 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_filea 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
.- targeta 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_sizea 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¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, DiffeoWrapped executable:
dti_diffeomorphic_reg
.
- ftola float
Iteration for the optimization to stop. Maps to a command-line argument:
%g
(position: 5). (Nipype default value:0.002
)- legacy1
Legacy parameter; always set to 1. Maps to a command-line argument:
%d
(position: 3). (Nipype default value:1
)- n_itersan integer (int or long)
Number of iterations. Maps to a command-line argument:
%d
(position: 4). (Nipype default value:6
)
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- environa 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_filea pathlike object or string representing an existing file
Fixed tensor volume. Maps to a command-line argument:
%s
(position: 0).- mask_filea pathlike object or string representing an existing file
Mask. Maps to a command-line argument:
%s
(position: 2).- moving_filea 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¶
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()
- fixed_filea pathlike object or string representing an existing file
Fixed tensor volume. Maps to a command-line argument:
%s
(position: 0).- ftola float
Cost function tolerance. Maps to a command-line argument:
%g
(position: 4). (Nipype default value:0.01
)- moving_filea pathlike object or string representing an existing file
Moving tensor volume. Maps to a command-line argument:
%s
(position: 1).- sampling_xyza 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
)
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- environa 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_xfma 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¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, RigidWrapped executable:
dti_rigid_reg
.
- fixed_filea pathlike object or string representing an existing file
Fixed tensor volume. Maps to a command-line argument:
%s
(position: 0).- ftola float
Cost function tolerance. Maps to a command-line argument:
%g
(position: 4). (Nipype default value:0.01
)- moving_filea pathlike object or string representing an existing file
Moving tensor volume. Maps to a command-line argument:
%s
(position: 1).- sampling_xyza 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
)
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- environa 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_xfma 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¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, AffScalarVolWrapped executable:
affineScalarVolume
.
- in_filea pathlike object or string representing an existing file
Moving scalar volume. Maps to a command-line argument:
-in %s
.
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- deformationa 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
.- environa 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:
{}
)- eulera 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_filea pathlike object or string representing a file
Output filename. Maps to a command-line argument:
-out %s
.- targeta 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
.- transforma 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
.- translationa 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_filea pathlike object or string representing an existing file
Moved volume.
affSymTensor3DVolTask¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, AffSymTensor3DVolWrapped executable:
affineSymTensor3DVolume
.
- in_filea pathlike object or string representing an existing file
Moving tensor volume. Maps to a command-line argument:
-in %s
.
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- deformationa 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
.- environa 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:
{}
)- eulera 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_filea 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
)- targeta 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
.- transforma 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
.- translationa 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¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, DiffeoScalarVolWrapped executable:
deformationScalarVolume
.
- in_filea pathlike object or string representing an existing file
Moving scalar volume. Maps to a command-line argument:
-in %s
.- transforma pathlike object or string representing an existing file
Transform to apply. Maps to a command-line argument:
-trans %s
.
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- environa 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:
{}
)- flipa 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_filea 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
.- targeta 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_sizea 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_filea pathlike object or string representing an existing file
Moved volume.
diffeoSymTensor3DVolTask¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, DiffeoSymTensor3DVolWrapped executable:
deformationSymTensor3DVolume
.
- in_filea pathlike object or string representing an existing file
Moving tensor volume. Maps to a command-line argument:
-in %s
.- transforma pathlike object or string representing an existing file
Transform to apply. Maps to a command-line argument:
-trans %s
.
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- dfa unicode string
Maps to a command-line argument:
-df %s
. (Nipype default value:FD
)- environa 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:
{}
)- flipa 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_filea 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
.- targeta 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_sizea 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