nipype.interfaces.dtitk.utils module¶
DTITK utility 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.
BinThresh¶
Bases: CommandLineDtitk
Wrapped executable:
BinaryThresholdImageFilter
.Binarizes an image.
Example
>>> from nipype.interfaces import dtitk >>> node = dtitk.BinThresh() >>> node.inputs.in_file = 'im1.nii' >>> node.inputs.lower_bound = 0 >>> node.inputs.upper_bound = 100 >>> node.inputs.inside_value = 1 >>> node.inputs.outside_value = 0 >>> node.cmdline 'BinaryThresholdImageFilter im1.nii im1_thrbin.nii 0 100 1 0' >>> node.run()
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Image to threshold/binarize. Maps to a command-line argument:
%s
(position: 0).inside_value (a float) – Value for voxels in binarization range. Maps to a command-line argument:
%g
(position: 4). (Nipype default value:1
)lower_bound (a float) – Lower bound of binarization range. Maps to a command-line argument:
%g
(position: 2). (Nipype default value:0.01
)outside_value (a float) – Value for voxelsoutside of binarization range. Maps to a command-line argument:
%g
(position: 5). (Nipype default value:0
)upper_bound (a float) – Upper bound of binarization range. Maps to a command-line argument:
%g
(position: 3). (Nipype default value:100
)- 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:
%s
(position: 1).- Outputs
out_file (a pathlike object or string representing an existing file)
BinThreshTask¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, BinThreshWrapped executable:
BinaryThresholdImageFilter
.
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Image to threshold/binarize. Maps to a command-line argument:
%s
(position: 0).inside_value (a float) – Value for voxels in binarization range. Maps to a command-line argument:
%g
(position: 4). (Nipype default value:1
)lower_bound (a float) – Lower bound of binarization range. Maps to a command-line argument:
%g
(position: 2). (Nipype default value:0.01
)outside_value (a float) – Value for voxelsoutside of binarization range. Maps to a command-line argument:
%g
(position: 5). (Nipype default value:0
)upper_bound (a float) – Upper bound of binarization range. Maps to a command-line argument:
%g
(position: 3). (Nipype default value:100
)- 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:
%s
(position: 1).- Outputs
out_file (a pathlike object or string representing an existing file)
SVAdjustVoxSp¶
Bases: CommandLineDtitk
Wrapped executable:
SVAdjustVoxelspace
.Adjusts the voxel space of a scalar volume.
Example
>>> from nipype.interfaces import dtitk >>> node = dtitk.SVAdjustVoxSp() >>> node.inputs.in_file = 'im1.nii' >>> node.inputs.target_file = 'im2.nii' >>> node.cmdline 'SVAdjustVoxelspace -in im1.nii -out im1_avs.nii -target im2.nii' >>> node.run()
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Scalar volume to modify. 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
.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:
{}
)origin (a tuple of the form: (a float, a float, a float)) – Xyz origin (superseded by target). Maps to a command-line argument:
-origin %g %g %g
. Mutually exclusive with inputs:target_file
.out_file (a pathlike object or string representing a file) – Output path. Maps to a command-line argument:
-out %s
.target_file (a pathlike object or string representing a file) – Target volume to match. Maps to a command-line argument:
-target %s
. Mutually exclusive with inputs:voxel_size
,origin
.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_file
.- Outputs
out_file (a pathlike object or string representing an existing file)
SVAdjustVoxSpTask¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, SVAdjustVoxSpWrapped executable:
SVAdjustVoxelspace
.
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Scalar volume to modify. 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
.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:
{}
)origin (a tuple of the form: (a float, a float, a float)) – Xyz origin (superseded by target). Maps to a command-line argument:
-origin %g %g %g
. Mutually exclusive with inputs:target_file
.out_file (a pathlike object or string representing a file) – Output path. Maps to a command-line argument:
-out %s
.target_file (a pathlike object or string representing a file) – Target volume to match. Maps to a command-line argument:
-target %s
. Mutually exclusive with inputs:voxel_size
,origin
.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_file
.- Outputs
out_file (a pathlike object or string representing an existing file)
SVResample¶
Bases: CommandLineDtitk
Wrapped executable:
SVResample
.Resamples a scalar volume.
Example
>>> from nipype.interfaces import dtitk >>> node = dtitk.SVResample() >>> node.inputs.in_file = 'im1.nii' >>> node.inputs.target_file = 'im2.nii' >>> node.cmdline 'SVResample -in im1.nii -out im1_resampled.nii -target im2.nii' >>> node.run()
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Image to resample. Maps to a command-line argument:
-in %s
.- Optional Inputs
align (‘center’ or ‘origin’) – How to align output volume to input volume. Maps to a command-line argument:
-align %s
.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.array_size (a tuple of the form: (an integer, an integer, an integer)) – Resampled array size. Maps to a command-line argument:
-size %d %d %d
. Mutually exclusive with inputs:target_file
.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:
{}
)origin (a tuple of the form: (a float, a float, a float)) – Xyz origin. Maps to a command-line argument:
-origin %g %g %g
. Mutually exclusive with inputs:target_file
.out_file (a pathlike object or string representing a file) – Output path. Maps to a command-line argument:
-out %s
.target_file (a pathlike object or string representing a file) – Specs read from the target volume. Maps to a command-line argument:
-target %s
. Mutually exclusive with inputs:array_size
,voxel_size
,origin
.voxel_size (a tuple of the form: (a float, a float, a float)) – Resampled voxel size. Maps to a command-line argument:
-vsize %g %g %g
. Mutually exclusive with inputs:target_file
.- Outputs
out_file (a pathlike object or string representing an existing file)
SVResampleTask¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, SVResampleWrapped executable:
SVResample
.
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Image to resample. Maps to a command-line argument:
-in %s
.- Optional Inputs
align (‘center’ or ‘origin’) – How to align output volume to input volume. Maps to a command-line argument:
-align %s
.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.array_size (a tuple of the form: (an integer, an integer, an integer)) – Resampled array size. Maps to a command-line argument:
-size %d %d %d
. Mutually exclusive with inputs:target_file
.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:
{}
)origin (a tuple of the form: (a float, a float, a float)) – Xyz origin. Maps to a command-line argument:
-origin %g %g %g
. Mutually exclusive with inputs:target_file
.out_file (a pathlike object or string representing a file) – Output path. Maps to a command-line argument:
-out %s
.target_file (a pathlike object or string representing a file) – Specs read from the target volume. Maps to a command-line argument:
-target %s
. Mutually exclusive with inputs:array_size
,voxel_size
,origin
.voxel_size (a tuple of the form: (a float, a float, a float)) – Resampled voxel size. Maps to a command-line argument:
-vsize %g %g %g
. Mutually exclusive with inputs:target_file
.- Outputs
out_file (a pathlike object or string representing an existing file)
TVAdjustOriginTask¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, TVAdjustVoxSpWrapped executable:
TVAdjustVoxelspace
.
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Tensor volume to modify. 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
.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:
{}
)origin (a tuple of the form: (a float, a float, a float)) – Xyz origin (superseded by target). Maps to a command-line argument:
-origin %g %g %g
. Mutually exclusive with inputs:target_file
.out_file (a pathlike object or string representing a file) – Output path. Maps to a command-line argument:
-out %s
.target_file (a pathlike object or string representing a file) – Target volume to match. Maps to a command-line argument:
-target %s
. Mutually exclusive with inputs:voxel_size
,origin
.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_file
.- Outputs
out_file (a pathlike object or string representing an existing file)
TVAdjustVoxSp¶
Bases: CommandLineDtitk
Wrapped executable:
TVAdjustVoxelspace
.Adjusts the voxel space of a tensor volume.
Example
>>> from nipype.interfaces import dtitk >>> node = dtitk.TVAdjustVoxSp() >>> node.inputs.in_file = 'im1.nii' >>> node.inputs.target_file = 'im2.nii' >>> node.cmdline 'TVAdjustVoxelspace -in im1.nii -out im1_avs.nii -target im2.nii' >>> node.run()
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Tensor volume to modify. 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
.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:
{}
)origin (a tuple of the form: (a float, a float, a float)) – Xyz origin (superseded by target). Maps to a command-line argument:
-origin %g %g %g
. Mutually exclusive with inputs:target_file
.out_file (a pathlike object or string representing a file) – Output path. Maps to a command-line argument:
-out %s
.target_file (a pathlike object or string representing a file) – Target volume to match. Maps to a command-line argument:
-target %s
. Mutually exclusive with inputs:voxel_size
,origin
.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_file
.- Outputs
out_file (a pathlike object or string representing an existing file)
TVAdjustVoxSpTask¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, TVAdjustVoxSpWrapped executable:
TVAdjustVoxelspace
.
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Tensor volume to modify. 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
.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:
{}
)origin (a tuple of the form: (a float, a float, a float)) – Xyz origin (superseded by target). Maps to a command-line argument:
-origin %g %g %g
. Mutually exclusive with inputs:target_file
.out_file (a pathlike object or string representing a file) – Output path. Maps to a command-line argument:
-out %s
.target_file (a pathlike object or string representing a file) – Target volume to match. Maps to a command-line argument:
-target %s
. Mutually exclusive with inputs:voxel_size
,origin
.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_file
.- Outputs
out_file (a pathlike object or string representing an existing file)
TVResample¶
Bases: CommandLineDtitk
Wrapped executable:
TVResample
.Resamples a tensor volume.
Example
>>> from nipype.interfaces import dtitk >>> node = dtitk.TVResample() >>> node.inputs.in_file = 'im1.nii' >>> node.inputs.target_file = 'im2.nii' >>> node.cmdline 'TVResample -in im1.nii -out im1_resampled.nii -target im2.nii' >>> node.run()
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Tensor volume to resample. Maps to a command-line argument:
-in %s
.- Optional Inputs
align (‘center’ or ‘origin’) – How to align output volume to input volume. Maps to a command-line argument:
-align %s
.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.array_size (a tuple of the form: (an integer, an integer, an integer)) – Resampled array size. Maps to a command-line argument:
-size %d %d %d
. Mutually exclusive with inputs:target_file
.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:
{}
)interpolation (‘LEI’ or ‘EI’) – Log Euclidean Euclidean Interpolation. Maps to a command-line argument:
-interp %s
.origin (a tuple of the form: (a float, a float, a float)) – Xyz origin. Maps to a command-line argument:
-origin %g %g %g
. Mutually exclusive with inputs:target_file
.out_file (a pathlike object or string representing a file) – Output path. Maps to a command-line argument:
-out %s
.target_file (a pathlike object or string representing a file) – Specs read from the target volume. Maps to a command-line argument:
-target %s
. Mutually exclusive with inputs:array_size
,voxel_size
,origin
.voxel_size (a tuple of the form: (a float, a float, a float)) – Resampled voxel size. Maps to a command-line argument:
-vsize %g %g %g
. Mutually exclusive with inputs:target_file
.- Outputs
out_file (a pathlike object or string representing an existing file)
TVResampleTask¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, TVResampleWrapped executable:
TVResample
.
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Tensor volume to resample. Maps to a command-line argument:
-in %s
.- Optional Inputs
align (‘center’ or ‘origin’) – How to align output volume to input volume. Maps to a command-line argument:
-align %s
.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.array_size (a tuple of the form: (an integer, an integer, an integer)) – Resampled array size. Maps to a command-line argument:
-size %d %d %d
. Mutually exclusive with inputs:target_file
.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:
{}
)interpolation (‘LEI’ or ‘EI’) – Log Euclidean Euclidean Interpolation. Maps to a command-line argument:
-interp %s
.origin (a tuple of the form: (a float, a float, a float)) – Xyz origin. Maps to a command-line argument:
-origin %g %g %g
. Mutually exclusive with inputs:target_file
.out_file (a pathlike object or string representing a file) – Output path. Maps to a command-line argument:
-out %s
.target_file (a pathlike object or string representing a file) – Specs read from the target volume. Maps to a command-line argument:
-target %s
. Mutually exclusive with inputs:array_size
,voxel_size
,origin
.voxel_size (a tuple of the form: (a float, a float, a float)) – Resampled voxel size. Maps to a command-line argument:
-vsize %g %g %g
. Mutually exclusive with inputs:target_file
.- Outputs
out_file (a pathlike object or string representing an existing file)
TVtool¶
Bases: CommandLineDtitk
Wrapped executable:
TVtool
.Calculates a tensor metric volume from a tensor volume.
Example
>>> from nipype.interfaces import dtitk >>> node = dtitk.TVtool() >>> node.inputs.in_file = 'im1.nii' >>> node.inputs.in_flag = 'fa' >>> node.cmdline 'TVtool -in im1.nii -fa -out im1_fa.nii' >>> node.run()
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Scalar volume to resample. 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
.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:
{}
)in_flag (‘fa’ or ‘tr’ or ‘ad’ or ‘rd’ or ‘pd’ or ‘rgb’) – Maps to a command-line argument:
-%s
.out_file (a pathlike object or string representing a file) – Maps to a command-line argument:
-out %s
.- Outputs
out_file (a pathlike object or string representing a file)
TVtoolTask¶
Bases:
nipype.interfaces.dtitk.base.DTITKRenameMixin
, TVtoolWrapped executable:
TVtool
.
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Scalar volume to resample. 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
.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:
{}
)in_flag (‘fa’ or ‘tr’ or ‘ad’ or ‘rd’ or ‘pd’ or ‘rgb’) – Maps to a command-line argument:
-%s
.out_file (a pathlike object or string representing a file) – Maps to a command-line argument:
-out %s
.- Outputs
out_file (a pathlike object or string representing a file)