interfaces.dtitk.utils¶
BinThresh¶
Wraps the executable 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: (a pathlike object or string representing an existing file)
Image to threshold/binarize
argument: ``%s``, position: 0
lower_bound: (a float, nipype default value: 0.01)
lower bound of binarization range
argument: ``%g``, position: 2
upper_bound: (a float, nipype default value: 100)
upper bound of binarization range
argument: ``%g``, position: 3
inside_value: (a float, nipype default value: 1)
value for voxels in binarization range
argument: ``%g``, position: 4
outside_value: (a float, nipype default value: 0)
value for voxelsoutside of binarization range
argument: ``%g``, position: 5
[Optional]
out_file: (a pathlike object or string representing a file)
output path
argument: ``%s``, position: 1
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a pathlike object or string representing an existing file)
BinThreshTask¶
Wraps the executable command BinaryThresholdImageFilter
.
Inputs:
[Mandatory]
in_file: (a pathlike object or string representing an existing file)
Image to threshold/binarize
argument: ``%s``, position: 0
lower_bound: (a float, nipype default value: 0.01)
lower bound of binarization range
argument: ``%g``, position: 2
upper_bound: (a float, nipype default value: 100)
upper bound of binarization range
argument: ``%g``, position: 3
inside_value: (a float, nipype default value: 1)
value for voxels in binarization range
argument: ``%g``, position: 4
outside_value: (a float, nipype default value: 0)
value for voxelsoutside of binarization range
argument: ``%g``, position: 5
[Optional]
out_file: (a pathlike object or string representing a file)
output path
argument: ``%s``, position: 1
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a pathlike object or string representing an existing file)
SVAdjustVoxSp¶
Wraps the executable 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: (a pathlike object or string representing an existing file)
scalar volume to modify
argument: ``-in %s``
[Optional]
out_file: (a pathlike object or string representing a file)
output path
argument: ``-out %s``
target_file: (a pathlike object or string representing a file)
target volume to match
argument: ``-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)
argument: ``-vsize %g %g %g``
mutually_exclusive: target_file
origin: (a tuple of the form: (a float, a float, a float))
xyz origin (superseded by target)
argument: ``-origin %g %g %g``
mutually_exclusive: target_file
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a pathlike object or string representing an existing file)
SVAdjustVoxSpTask¶
Wraps the executable command SVAdjustVoxelspace
.
Inputs:
[Mandatory]
in_file: (a pathlike object or string representing an existing file)
scalar volume to modify
argument: ``-in %s``
[Optional]
out_file: (a pathlike object or string representing a file)
output path
argument: ``-out %s``
target_file: (a pathlike object or string representing a file)
target volume to match
argument: ``-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)
argument: ``-vsize %g %g %g``
mutually_exclusive: target_file
origin: (a tuple of the form: (a float, a float, a float))
xyz origin (superseded by target)
argument: ``-origin %g %g %g``
mutually_exclusive: target_file
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a pathlike object or string representing an existing file)
SVResample¶
Wraps the executable 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: (a pathlike object or string representing an existing file)
image to resample
argument: ``-in %s``
[Optional]
out_file: (a pathlike object or string representing a file)
output path
argument: ``-out %s``
target_file: (a pathlike object or string representing a file)
specs read from the target volume
argument: ``-target %s``
mutually_exclusive: array_size, voxel_size, origin
align: ('center' or 'origin')
how to align output volume to input volume
argument: ``-align %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
argument: ``-size %d %d %d``
mutually_exclusive: target_file
voxel_size: (a tuple of the form: (a float, a float, a float))
resampled voxel size
argument: ``-vsize %g %g %g``
mutually_exclusive: target_file
origin: (a tuple of the form: (a float, a float, a float))
xyz origin
argument: ``-origin %g %g %g``
mutually_exclusive: target_file
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a pathlike object or string representing an existing file)
SVResampleTask¶
Wraps the executable command SVResample
.
Inputs:
[Mandatory]
in_file: (a pathlike object or string representing an existing file)
image to resample
argument: ``-in %s``
[Optional]
out_file: (a pathlike object or string representing a file)
output path
argument: ``-out %s``
target_file: (a pathlike object or string representing a file)
specs read from the target volume
argument: ``-target %s``
mutually_exclusive: array_size, voxel_size, origin
align: ('center' or 'origin')
how to align output volume to input volume
argument: ``-align %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
argument: ``-size %d %d %d``
mutually_exclusive: target_file
voxel_size: (a tuple of the form: (a float, a float, a float))
resampled voxel size
argument: ``-vsize %g %g %g``
mutually_exclusive: target_file
origin: (a tuple of the form: (a float, a float, a float))
xyz origin
argument: ``-origin %g %g %g``
mutually_exclusive: target_file
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a pathlike object or string representing an existing file)
TVAdjustOriginTask¶
Wraps the executable command TVAdjustVoxelspace
.
Inputs:
[Mandatory]
in_file: (a pathlike object or string representing an existing file)
tensor volume to modify
argument: ``-in %s``
[Optional]
out_file: (a pathlike object or string representing a file)
output path
argument: ``-out %s``
target_file: (a pathlike object or string representing a file)
target volume to match
argument: ``-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)
argument: ``-vsize %g %g %g``
mutually_exclusive: target_file
origin: (a tuple of the form: (a float, a float, a float))
xyz origin (superseded by target)
argument: ``-origin %g %g %g``
mutually_exclusive: target_file
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a pathlike object or string representing an existing file)
TVAdjustVoxSp¶
Wraps the executable 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: (a pathlike object or string representing an existing file)
tensor volume to modify
argument: ``-in %s``
[Optional]
out_file: (a pathlike object or string representing a file)
output path
argument: ``-out %s``
target_file: (a pathlike object or string representing a file)
target volume to match
argument: ``-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)
argument: ``-vsize %g %g %g``
mutually_exclusive: target_file
origin: (a tuple of the form: (a float, a float, a float))
xyz origin (superseded by target)
argument: ``-origin %g %g %g``
mutually_exclusive: target_file
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a pathlike object or string representing an existing file)
TVAdjustVoxSpTask¶
Wraps the executable command TVAdjustVoxelspace
.
Inputs:
[Mandatory]
in_file: (a pathlike object or string representing an existing file)
tensor volume to modify
argument: ``-in %s``
[Optional]
out_file: (a pathlike object or string representing a file)
output path
argument: ``-out %s``
target_file: (a pathlike object or string representing a file)
target volume to match
argument: ``-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)
argument: ``-vsize %g %g %g``
mutually_exclusive: target_file
origin: (a tuple of the form: (a float, a float, a float))
xyz origin (superseded by target)
argument: ``-origin %g %g %g``
mutually_exclusive: target_file
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a pathlike object or string representing an existing file)
TVResample¶
Wraps the executable 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: (a pathlike object or string representing an existing file)
tensor volume to resample
argument: ``-in %s``
[Optional]
out_file: (a pathlike object or string representing a file)
output path
argument: ``-out %s``
target_file: (a pathlike object or string representing a file)
specs read from the target volume
argument: ``-target %s``
mutually_exclusive: array_size, voxel_size, origin
align: ('center' or 'origin')
how to align output volume to input volume
argument: ``-align %s``
interpolation: ('LEI' or 'EI')
Log Euclidean Euclidean Interpolation
argument: ``-interp %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
argument: ``-size %d %d %d``
mutually_exclusive: target_file
voxel_size: (a tuple of the form: (a float, a float, a float))
resampled voxel size
argument: ``-vsize %g %g %g``
mutually_exclusive: target_file
origin: (a tuple of the form: (a float, a float, a float))
xyz origin
argument: ``-origin %g %g %g``
mutually_exclusive: target_file
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a pathlike object or string representing an existing file)
TVResampleTask¶
Wraps the executable command TVResample
.
Inputs:
[Mandatory]
in_file: (a pathlike object or string representing an existing file)
tensor volume to resample
argument: ``-in %s``
[Optional]
out_file: (a pathlike object or string representing a file)
output path
argument: ``-out %s``
target_file: (a pathlike object or string representing a file)
specs read from the target volume
argument: ``-target %s``
mutually_exclusive: array_size, voxel_size, origin
align: ('center' or 'origin')
how to align output volume to input volume
argument: ``-align %s``
interpolation: ('LEI' or 'EI')
Log Euclidean Euclidean Interpolation
argument: ``-interp %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
argument: ``-size %d %d %d``
mutually_exclusive: target_file
voxel_size: (a tuple of the form: (a float, a float, a float))
resampled voxel size
argument: ``-vsize %g %g %g``
mutually_exclusive: target_file
origin: (a tuple of the form: (a float, a float, a float))
xyz origin
argument: ``-origin %g %g %g``
mutually_exclusive: target_file
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a pathlike object or string representing an existing file)
TVtool¶
Wraps the executable 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: (a pathlike object or string representing an existing file)
scalar volume to resample
argument: ``-in %s``
[Optional]
in_flag: ('fa' or 'tr' or 'ad' or 'rd' or 'pd' or 'rgb')
argument: ``-%s``
out_file: (a pathlike object or string representing a file)
argument: ``-out %s``
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a pathlike object or string representing a file)
TVtoolTask¶
Wraps the executable command TVtool
.
Inputs:
[Mandatory]
in_file: (a pathlike object or string representing an existing file)
scalar volume to resample
argument: ``-in %s``
[Optional]
in_flag: ('fa' or 'tr' or 'ad' or 'rd' or 'pd' or 'rgb')
argument: ``-%s``
out_file: (a pathlike object or string representing a file)
argument: ``-out %s``
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a pathlike object or string representing a file)