Home · Quickstart · User Guide and Examples · Interfaces Index · Developers · About · Nipy

# 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

Link to code

> 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()

> in_filea pathlike object or string representing an existing file

>   Image to threshold/binarize. Maps to a command-line argument: `%s` (position: 0).

> inside_valuea float

>   Value for voxels in binarization range. Maps to a command-line argument: `%g` (position: 4). (Nipype default value: `1`)

> lower_bounda float

>   Lower bound of binarization range. Maps to a command-line argument: `%g` (position: 2). (Nipype default value: `0.01`)

> outside_valuea float

>   Value for voxels outside of binarization range. Maps to a command-line argument: `%g` (position: 5). (Nipype default value: `0`)

> upper_bounda float

>   Upper bound of binarization range. Maps to a command-line argument: `%g` (position: 3). (Nipype default value: `100`)

> argsa 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: `%s` (position: 1).

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

## BinThreshTask

Link to code

> Bases: `nipype.interfaces.dtitk.base.DTITKRenameMixin`, BinThresh

> Wrapped executable: `BinaryThresholdImageFilter`.

> in_filea pathlike object or string representing an existing file

>   Image to threshold/binarize. Maps to a command-line argument: `%s` (position: 0).

> inside_valuea float

>   Value for voxels in binarization range. Maps to a command-line argument: `%g` (position: 4). (Nipype default value: `1`)

> lower_bounda float

>   Lower bound of binarization range. Maps to a command-line argument: `%g` (position: 2). (Nipype default value: `0.01`)

> outside_valuea float

>   Value for voxels outside of binarization range. Maps to a command-line argument: `%g` (position: 5). (Nipype default value: `0`)

> upper_bounda float

>   Upper bound of binarization range. Maps to a command-line argument: `%g` (position: 3). (Nipype default value: `100`)

> argsa 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: `%s` (position: 1).

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

## SVAdjustVoxSp

Link to code

> 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()

> in_filea pathlike object or string representing an existing file

>   Scalar volume to modify. Maps to a command-line argument: `-in %s`.

> argsa 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: `{}`)

> origina 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_filea pathlike object or string representing a file

>   Output path. Maps to a command-line argument: `-out %s`.

> target_filea 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_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_file`.

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

## SVAdjustVoxSpTask

Link to code

> Bases: `nipype.interfaces.dtitk.base.DTITKRenameMixin`, SVAdjustVoxSp

> Wrapped executable: `SVAdjustVoxelspace`.

> in_filea pathlike object or string representing an existing file

>   Scalar volume to modify. Maps to a command-line argument: `-in %s`.

> argsa 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: `{}`)

> origina 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_filea pathlike object or string representing a file

>   Output path. Maps to a command-line argument: `-out %s`.

> target_filea 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_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_file`.

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

## SVResample

Link to code

> 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()

> in_filea pathlike object or string representing an existing file

>   Image to resample. Maps to a command-line argument: `-in %s`.

> align‘center’ or ‘origin’

>   How to align output volume to input volume. Maps to a command-line argument: `-align %s`.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> array_sizea 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`.

> 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: `{}`)

> origina 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_filea pathlike object or string representing a file

>   Output path. Maps to a command-line argument: `-out %s`.

> target_filea 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_sizea 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`.

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

## SVResampleTask

Link to code

> Bases: `nipype.interfaces.dtitk.base.DTITKRenameMixin`, SVResample

> Wrapped executable: `SVResample`.

> in_filea pathlike object or string representing an existing file

>   Image to resample. Maps to a command-line argument: `-in %s`.

> align‘center’ or ‘origin’

>   How to align output volume to input volume. Maps to a command-line argument: `-align %s`.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> array_sizea 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`.

> 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: `{}`)

> origina 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_filea pathlike object or string representing a file

>   Output path. Maps to a command-line argument: `-out %s`.

> target_filea 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_sizea 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`.

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

## TVAdjustOriginTask

Link to code

> Bases: `nipype.interfaces.dtitk.base.DTITKRenameMixin`, TVAdjustVoxSp

> Wrapped executable: `TVAdjustVoxelspace`.

> in_filea pathlike object or string representing an existing file

>   Tensor volume to modify. Maps to a command-line argument: `-in %s`.

> argsa 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: `{}`)

> origina 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_filea pathlike object or string representing a file

>   Output path. Maps to a command-line argument: `-out %s`.

> target_filea 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_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_file`.

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

## TVAdjustVoxSp

Link to code

> 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()

> in_filea pathlike object or string representing an existing file

>   Tensor volume to modify. Maps to a command-line argument: `-in %s`.

> argsa 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: `{}`)

> origina 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_filea pathlike object or string representing a file

>   Output path. Maps to a command-line argument: `-out %s`.

> target_filea 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_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_file`.

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

## TVAdjustVoxSpTask

Link to code

> Bases: `nipype.interfaces.dtitk.base.DTITKRenameMixin`, TVAdjustVoxSp

> Wrapped executable: `TVAdjustVoxelspace`.

> in_filea pathlike object or string representing an existing file

>   Tensor volume to modify. Maps to a command-line argument: `-in %s`.

> argsa 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: `{}`)

> origina 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_filea pathlike object or string representing a file

>   Output path. Maps to a command-line argument: `-out %s`.

> target_filea 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_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_file`.

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

## TVResample

Link to code

> 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()

> in_filea pathlike object or string representing an existing file

>   Tensor volume to resample. Maps to a command-line argument: `-in %s`.

> align‘center’ or ‘origin’

>   How to align output volume to input volume. Maps to a command-line argument: `-align %s`.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> array_sizea 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`.

> 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: `{}`)

> interpolation‘LEI’ or ‘EI’

>   Log Euclidean Interpolation. Maps to a command-line argument: `-interp %s`.

> origina 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_filea pathlike object or string representing a file

>   Output path. Maps to a command-line argument: `-out %s`.

> target_filea 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_sizea 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`.

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

## TVResampleTask

Link to code

> Bases: `nipype.interfaces.dtitk.base.DTITKRenameMixin`, TVResample

> Wrapped executable: `TVResample`.

> in_filea pathlike object or string representing an existing file

>   Tensor volume to resample. Maps to a command-line argument: `-in %s`.

> align‘center’ or ‘origin’

>   How to align output volume to input volume. Maps to a command-line argument: `-align %s`.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> array_sizea 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`.

> 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: `{}`)

> interpolation‘LEI’ or ‘EI’

>   Log Euclidean Interpolation. Maps to a command-line argument: `-interp %s`.

> origina 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_filea pathlike object or string representing a file

>   Output path. Maps to a command-line argument: `-out %s`.

> target_filea 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_sizea 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`.

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

## TVtool

Link to code

> 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()

> in_filea pathlike object or string representing an existing file

>   Scalar volume to resample. Maps to a command-line argument: `-in %s`.

> argsa 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: `{}`)

> in_flag‘fa’ or ‘tr’ or ‘ad’ or ‘rd’ or ‘pd’ or ‘rgb’

>   Maps to a command-line argument: `-%s`.

> out_filea pathlike object or string representing a file

>   Maps to a command-line argument: `-out %s`.

> out_file : a pathlike object or string representing a file

## TVtoolTask

Link to code

> Bases: `nipype.interfaces.dtitk.base.DTITKRenameMixin`, TVtool

> Wrapped executable: `TVtool`.

> in_filea pathlike object or string representing an existing file

>   Scalar volume to resample. Maps to a command-line argument: `-in %s`.

> argsa 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: `{}`)

> in_flag‘fa’ or ‘tr’ or ‘ad’ or ‘rd’ or ‘pd’ or ‘rgb’

>   Maps to a command-line argument: `-%s`.

> out_filea pathlike object or string representing a file

>   Maps to a command-line argument: `-out %s`.

> out_file : a pathlike object or string representing a file