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 voxelsoutside 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 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: %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 voxelsoutside 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 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: %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 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: {})

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 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: {})

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 unicode string

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

array_sizea tuple of the form: (an integer (int or long), an integer (int or long), an integer (int or long))

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 unicode string

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

array_sizea tuple of the form: (an integer (int or long), an integer (int or long), an integer (int or long))

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 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: {})

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 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: {})

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 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: {})

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 unicode string

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

array_sizea tuple of the form: (an integer (int or long), an integer (int or long), an integer (int or long))

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 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 unicode string

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

array_sizea tuple of the form: (an integer (int or long), an integer (int or long), an integer (int or long))

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 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 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: {})

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 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: {})

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