interfaces.dtitk.utils

BinThresh

Link to code

Wraps command 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() # doctest: +SKIP

Inputs:

[Mandatory]
in_file: (an existing file name)
        Image to threshold/binarize
        flag: %s, position: 0
inside_value: (a float, nipype default value: 1)
        value for voxels in binarization range
        flag: %g, position: 4
lower_bound: (a float, nipype default value: 0.01)
        lower bound of binarization range
        flag: %g, position: 2
outside_value: (a float, nipype default value: 0)
        value for voxelsoutside of binarization range
        flag: %g, position: 5
upper_bound: (a float, nipype default value: 100)
        upper bound of binarization range
        flag: %g, position: 3

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %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', nipype default value: {})
        Environment variables
out_file: (a file name)
        output path
        flag: %s, position: 1

Outputs:

out_file: (an existing file name)

BinThreshTask

Link to code

Wraps command BinaryThresholdImageFilter

Inputs:

[Mandatory]
in_file: (an existing file name)
        Image to threshold/binarize
        flag: %s, position: 0
inside_value: (a float, nipype default value: 1)
        value for voxels in binarization range
        flag: %g, position: 4
lower_bound: (a float, nipype default value: 0.01)
        lower bound of binarization range
        flag: %g, position: 2
outside_value: (a float, nipype default value: 0)
        value for voxelsoutside of binarization range
        flag: %g, position: 5
upper_bound: (a float, nipype default value: 100)
        upper bound of binarization range
        flag: %g, position: 3

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %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', nipype default value: {})
        Environment variables
out_file: (a file name)
        output path
        flag: %s, position: 1

Outputs:

out_file: (an existing file name)

SVAdjustVoxSp

Link to code

Wraps command SVAdjustVoxelspace

Adjusts the voxel space of a scalar volume

>>> 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() # doctest: +SKIP

Inputs:

[Mandatory]
in_file: (an existing file name)
        scalar volume to modify
        flag: -in %s

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %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', nipype default value: {})
        Environment variables
origin: (a tuple of the form: (a float, a float, a float))
        xyz origin (superseded by target)
        flag: -origin %g %g %g
        mutually_exclusive: target_file
out_file: (a file name)
        output path
        flag: -out %s
target_file: (a file name)
        target volume to match
        flag: -target %s
        mutually_exclusive: voxel_size, origin
voxel_size: (a tuple of the form: (a float, a float, a float))
        xyz voxel size (superseded by target)
        flag: -vsize %g %g %g
        mutually_exclusive: target_file

Outputs:

out_file: (an existing file name)

SVAdjustVoxSpTask

Link to code

Wraps command SVAdjustVoxelspace

Inputs:

[Mandatory]
in_file: (an existing file name)
        scalar volume to modify
        flag: -in %s

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %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', nipype default value: {})
        Environment variables
origin: (a tuple of the form: (a float, a float, a float))
        xyz origin (superseded by target)
        flag: -origin %g %g %g
        mutually_exclusive: target_file
out_file: (a file name)
        output path
        flag: -out %s
target_file: (a file name)
        target volume to match
        flag: -target %s
        mutually_exclusive: voxel_size, origin
voxel_size: (a tuple of the form: (a float, a float, a float))
        xyz voxel size (superseded by target)
        flag: -vsize %g %g %g
        mutually_exclusive: target_file

Outputs:

out_file: (an existing file name)

SVResample

Link to code

Wraps command SVResample

Resamples a scalar volume

>>> 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() # doctest: +SKIP

Inputs:

[Mandatory]
in_file: (an existing file name)
        image to resample
        flag: -in %s

[Optional]
align: ('center' or 'origin')
        how to align output volume to input volume
        flag: -align %s
args: (a unicode string)
        Additional parameters to the command
        flag: %s
array_size: (a tuple of the form: (an integer (int or long), an
         integer (int or long), an integer (int or long)))
        resampled array size
        flag: -size %d %d %d
        mutually_exclusive: 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', nipype default value: {})
        Environment variables
origin: (a tuple of the form: (a float, a float, a float))
        xyz origin
        flag: -origin %g %g %g
        mutually_exclusive: target_file
out_file: (a file name)
        output path
        flag: -out %s
target_file: (a file name)
        specs read from the target volume
        flag: -target %s
        mutually_exclusive: array_size, voxel_size, origin
voxel_size: (a tuple of the form: (a float, a float, a float))
        resampled voxel size
        flag: -vsize %g %g %g
        mutually_exclusive: target_file

Outputs:

out_file: (an existing file name)

SVResampleTask

Link to code

Wraps command SVResample

Inputs:

[Mandatory]
in_file: (an existing file name)
        image to resample
        flag: -in %s

[Optional]
align: ('center' or 'origin')
        how to align output volume to input volume
        flag: -align %s
args: (a unicode string)
        Additional parameters to the command
        flag: %s
array_size: (a tuple of the form: (an integer (int or long), an
         integer (int or long), an integer (int or long)))
        resampled array size
        flag: -size %d %d %d
        mutually_exclusive: 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', nipype default value: {})
        Environment variables
origin: (a tuple of the form: (a float, a float, a float))
        xyz origin
        flag: -origin %g %g %g
        mutually_exclusive: target_file
out_file: (a file name)
        output path
        flag: -out %s
target_file: (a file name)
        specs read from the target volume
        flag: -target %s
        mutually_exclusive: array_size, voxel_size, origin
voxel_size: (a tuple of the form: (a float, a float, a float))
        resampled voxel size
        flag: -vsize %g %g %g
        mutually_exclusive: target_file

Outputs:

out_file: (an existing file name)

TVAdjustOriginTask

Link to code

Wraps command TVAdjustVoxelspace

Inputs:

[Mandatory]
in_file: (an existing file name)
        tensor volume to modify
        flag: -in %s

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %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', nipype default value: {})
        Environment variables
origin: (a tuple of the form: (a float, a float, a float))
        xyz origin (superseded by target)
        flag: -origin %g %g %g
        mutually_exclusive: target_file
out_file: (a file name)
        output path
        flag: -out %s
target_file: (a file name)
        target volume to match
        flag: -target %s
        mutually_exclusive: voxel_size, origin
voxel_size: (a tuple of the form: (a float, a float, a float))
        xyz voxel size (superseded by target)
        flag: -vsize %g %g %g
        mutually_exclusive: target_file

Outputs:

out_file: (an existing file name)

TVAdjustVoxSp

Link to code

Wraps command 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() # doctest: +SKIP

Inputs:

[Mandatory]
in_file: (an existing file name)
        tensor volume to modify
        flag: -in %s

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %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', nipype default value: {})
        Environment variables
origin: (a tuple of the form: (a float, a float, a float))
        xyz origin (superseded by target)
        flag: -origin %g %g %g
        mutually_exclusive: target_file
out_file: (a file name)
        output path
        flag: -out %s
target_file: (a file name)
        target volume to match
        flag: -target %s
        mutually_exclusive: voxel_size, origin
voxel_size: (a tuple of the form: (a float, a float, a float))
        xyz voxel size (superseded by target)
        flag: -vsize %g %g %g
        mutually_exclusive: target_file

Outputs:

out_file: (an existing file name)

TVAdjustVoxSpTask

Link to code

Wraps command TVAdjustVoxelspace

Inputs:

[Mandatory]
in_file: (an existing file name)
        tensor volume to modify
        flag: -in %s

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %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', nipype default value: {})
        Environment variables
origin: (a tuple of the form: (a float, a float, a float))
        xyz origin (superseded by target)
        flag: -origin %g %g %g
        mutually_exclusive: target_file
out_file: (a file name)
        output path
        flag: -out %s
target_file: (a file name)
        target volume to match
        flag: -target %s
        mutually_exclusive: voxel_size, origin
voxel_size: (a tuple of the form: (a float, a float, a float))
        xyz voxel size (superseded by target)
        flag: -vsize %g %g %g
        mutually_exclusive: target_file

Outputs:

out_file: (an existing file name)

TVResample

Link to code

Wraps command TVResample

Resamples a tensor volume

>>> 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() # doctest: +SKIP

Inputs:

[Mandatory]
in_file: (an existing file name)
        tensor volume to resample
        flag: -in %s

[Optional]
align: ('center' or 'origin')
        how to align output volume to input volume
        flag: -align %s
args: (a unicode string)
        Additional parameters to the command
        flag: %s
array_size: (a tuple of the form: (an integer (int or long), an
         integer (int or long), an integer (int or long)))
        resampled array size
        flag: -size %d %d %d
        mutually_exclusive: 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', nipype default value: {})
        Environment variables
interpolation: ('LEI' or 'EI')
        Log Euclidean Euclidean Interpolation
        flag: -interp %s
origin: (a tuple of the form: (a float, a float, a float))
        xyz origin
        flag: -origin %g %g %g
        mutually_exclusive: target_file
out_file: (a file name)
        output path
        flag: -out %s
target_file: (a file name)
        specs read from the target volume
        flag: -target %s
        mutually_exclusive: array_size, voxel_size, origin
voxel_size: (a tuple of the form: (a float, a float, a float))
        resampled voxel size
        flag: -vsize %g %g %g
        mutually_exclusive: target_file

Outputs:

out_file: (an existing file name)

TVResampleTask

Link to code

Wraps command TVResample

Inputs:

[Mandatory]
in_file: (an existing file name)
        tensor volume to resample
        flag: -in %s

[Optional]
align: ('center' or 'origin')
        how to align output volume to input volume
        flag: -align %s
args: (a unicode string)
        Additional parameters to the command
        flag: %s
array_size: (a tuple of the form: (an integer (int or long), an
         integer (int or long), an integer (int or long)))
        resampled array size
        flag: -size %d %d %d
        mutually_exclusive: 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', nipype default value: {})
        Environment variables
interpolation: ('LEI' or 'EI')
        Log Euclidean Euclidean Interpolation
        flag: -interp %s
origin: (a tuple of the form: (a float, a float, a float))
        xyz origin
        flag: -origin %g %g %g
        mutually_exclusive: target_file
out_file: (a file name)
        output path
        flag: -out %s
target_file: (a file name)
        specs read from the target volume
        flag: -target %s
        mutually_exclusive: array_size, voxel_size, origin
voxel_size: (a tuple of the form: (a float, a float, a float))
        resampled voxel size
        flag: -vsize %g %g %g
        mutually_exclusive: target_file

Outputs:

out_file: (an existing file name)

TVtool

Link to code

Wraps command TVtool

Calculates a tensor metric volume from a tensor volume

>>> 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() # doctest: +SKIP

Inputs:

[Mandatory]
in_file: (an existing file name)
        scalar volume to resample
        flag: -in %s

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %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', nipype default value: {})
        Environment variables
in_flag: ('fa' or 'tr' or 'ad' or 'rd' or 'pd' or 'rgb')
        flag: -%s
out_file: (a file name)
        flag: -out %s

Outputs:

out_file: (a file name)

TVtoolTask

Link to code

Wraps command TVtool

Inputs:

[Mandatory]
in_file: (an existing file name)
        scalar volume to resample
        flag: -in %s

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %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', nipype default value: {})
        Environment variables
in_flag: ('fa' or 'tr' or 'ad' or 'rd' or 'pd' or 'rgb')
        flag: -%s
out_file: (a file name)
        flag: -out %s

Outputs:

out_file: (a file name)