interfaces.dtitk.utils

BinThreshTask

Link to code

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

Link to code

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

Link to code

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

Link to code

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

Link to code

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

Link to code

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

Link to code

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)