interfaces.dtitk.utils¶
BinThreshTask¶
Wraps command BinaryThresholdImageFilter
Binarizes an image based on parameters
>>> import nipype.interfaces.dtitk as dtitk >>> node = dtitk.BinThreshTask() >>> node.inputs.in_file = 'diffusion.nii' >>> node.inputs.in_numbers = '0 100 1 0' >>> node.run()
Inputs:
[Mandatory]
[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
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
in_file: (a unicode string)
flag: %s, position: 0
in_numbers: (a unicode string)
LB UB inside_value outside_value
flag: %s, position: 2
out_file: (a unicode string)
flag: %s, position: 1
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (a file name)
SVAdjustVoxSpTask¶
Wraps command SVAdjustVoxelspace
Adjusts the voxel space of a scalar volume
>>> import nipype.interfaces.dtitk as dtitk >>> node = dtitk.SVAdjustVoxSpTask() >>> node.inputs.in_file = 'diffusion.nii.gz' >>> node.run()
Inputs:
[Mandatory]
in_file: (a unicode string)
image to resample
flag: -in %s, position: 0
[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
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
in_target: (a unicode string)
target volume
flag: -target %s, position: 2
in_voxsz: (a unicode string)
resampled voxel size
flag: -vsize %s, position: 3
origin: (a unicode string)
xyz voxel size
flag: -origin %s, position: 4
out_file: (a unicode string)
output path
flag: -out %s, position: 1
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (a file name)
SVResampleTask¶
Wraps command SVResample
Resamples a scalar volume
>>> import nipype.interfaces.dtitk as dtitk >>> node = dtitk.SVResampleTask() >>> node.inputs.in_file = 'diffusion.nii' >>> node.run()
Inputs:
[Mandatory]
in_file: (a unicode string)
image to resample
flag: -in %s, position: 0
[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
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
in_arraysz: (a unicode string)
resampled array size
flag: -size %s, position: 1
in_voxsz: (a unicode string)
resampled voxel size
flag: -vsize %s, position: 2
out_file: (a unicode string)
output path
flag: -out %s, position: 3
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (a file name)
TVAdjustOriginTask¶
Wraps command TVAdjustVoxelspace
Moves the origin of a tensor volume to zero
Example¶
>>> import nipype.interfaces.dtitk as dtitk
>>> node = dtitk.TVAdjustOriginTask()
>>> node.inputs.in_file = 'diffusion.nii'
>>> node.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
image to resample
flag: -in %s, position: 0
[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
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
origin: (a unicode string)
xyz voxel size
flag: -origin %s, position: 4
out_file: (a unicode string)
output path
flag: -out %s, position: 1
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (a unicode string)
TVAdjustVoxSpTask¶
Wraps command TVAdjustVoxelspace
Adjusts the voxel space of a tensor volume
Example¶
>>> import nipype.interfaces.dtitk as dtitk
>>> node = dtitk.TVAdjustVoxSpTask()
>>> node.inputs.in_file = 'diffusion.nii'
>>> node.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
image to resample
flag: -in %s, position: 0
[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
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
origin: (a unicode string)
xyz voxel size
flag: -origin %s, position: 4
out_file: (a unicode string)
output path
flag: -out %s, position: 1
target: (a unicode string)
target volume
flag: -target %s, position: 2
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
vsize: (a unicode string)
resampled voxel size
flag: -vsize %s, position: 3
Outputs:
out_file: (a unicode string)
TVResampleTask¶
Wraps command TVResample
Resamples a tensor volume
>>> import nipype.interfaces.dtitk as dtitk >>> node = dtitk.TVResampleTask() >>> node.inputs.in_file = 'diffusion.nii.gz' >>> node.run()
Inputs:
[Mandatory]
in_file: (a unicode string)
image to resample
flag: -in %s, position: 0
[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
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
in_arraysz: (a unicode string)
resampled array size
flag: -size %s, position: 1
in_voxsz: (a unicode string)
resampled voxel size
flag: -vsize %s, position: 2
out_file: (a unicode string)
output path
flag: -out %s, position: 3
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (a file name)
TVtoolTask¶
Wraps command TVtool
Calculates a tensor metric volume from a tensor volume
>>> import nipype.interfaces.dtitk as dtitk >>> node = dtitk.TVtoolTask() >>> node.inputs.in_file = 'diffusion.nii' >>> node.inputs.in_flag = 'fa' >>> node.run()
Inputs:
[Mandatory]
[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
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
in_file: (a unicode string)
image to resample
flag: -in %s, position: 0
in_flag: ('fa' or 'tr' or 'ad' or 'rd' or 'pd' or 'rgb')
flag: -%s, position: 1
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (a file name)