interfaces.dtitk.registration

AffineTask

Link to code

Wraps command dti_affine_reg

Performs affine registration between two tensor volumes

>>> import nipype.interfaces.dtitk as dtitk
>>> node = dtitk.AffineTask()
>>> node.inputs.fixed_file = 'diffusion.nii.gz'
>>> node.inputs.moving_file = 'diffusion2.nii.gz'
>>> node.inputs.similarity_metric = 'EDS'
>>> node.inputs.samplingX = 4
>>> node.inputs.samplingY = 4
>>> node.inputs.samplingZ = 4
>>> node.inputs.ftol = 0.01
>>> node.inputs.useInTrans = 1
>>> node.run() 

Inputs:

[Mandatory]
fixed_file: (a unicode string)
        fixed diffusion tensor image
        flag: %s, position: 0
ftol: (a float)
        cost function tolerance
        flag: %s, position: 6
moving_file: (a unicode string)
        diffusion tensor image path
        flag: %s, position: 1
samplingX: (a float)
        dist between samp points (mm)
        flag: %s, position: 3
samplingY: (a float)
        dist between samp points (mm)
        flag: %s, position: 4
samplingZ: (a float)
        dist between samp points (mm)
        flag: %s, position: 5
similarity_metric: ('EDS' or 'GDS' or 'DDS' or 'NMI')
        similarity metric
        flag: %s, position: 2

[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
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
useInTrans: (a float)
        to initialize with existing xfm set as 1
        flag: %s, position: 7

Outputs:

out_file: (a file name)
out_file_xfm: (a file name)

ComposeXfmTask

Link to code

Wraps command dfRightComposeAffine

Combines diffeomorphic and affine transforms

>>> import nipype.interfaces.dtitk as dtitk
>>> node = dtitk.ComposeXfmTask()
>>> node.inputs.in_df = 'ants_Warp.nii.gz'
>>> node.inputs.in_aff= 'ants_Affine.txt'
>>> 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_aff: (a unicode string)
        affine file.aff
        flag: -aff %s, position: 0
in_df: (a unicode string)
        diffeomorphic file.df.nii.gz
        flag: -df %s, position: 1
out_file: (a unicode string)
        output_path
        flag: -out %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

Outputs:

out_file: (a file name)
        cheese

DiffeoTask

Link to code

Wraps command dti_diffeomorphic_reg

Performs diffeomorphic registration between two tensor volumes

>>> import nipype.interfaces.dtitk as dtitk
>>> node = dtitk.DiffeoTask()
>>> node.inputs.fixed_file = 'diffusion.nii.gz'
>>> node.inputs.moving_file = 'diffusion2.nii.gz'
>>> node.inputs.mask = 'mask.nii.gz'
>>> node.inputs.legacy = 1
>>> node.inputs.n_iters = 6
>>> node.inputs.ftol = 0.002
>>> node.run() 

Inputs:

[Mandatory]
ftol: (a float)
        iteration for the optimization to stop
        flag: %s, position: 5
legacy: (a float)
        legacy parameter; always set to 1
        flag: %s, position: 3
n_iters: (a float)
        number of iterations
        flag: %s, position: 4

[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
fixed_file: (a unicode string)
        fixed diffusion tensor image
        flag: %s, position: 0
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
mask: (a unicode string)
        mask
        flag: %s, position: 2
moving_file: (a unicode string)
        moving diffusion tensor image
        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)
out_file_xfm: (a file name)

RigidTask

Link to code

Wraps command dti_rigid_reg

Performs rigid registration between two tensor volumes

>>> import nipype.interfaces.dtitk as dtitk
>>> node = dtitk.RigidTask()
>>> node.inputs.fixed_file = 'diffusion.nii.gz'
>>> node.inputs.moving_file = 'diffusion2.nii.gz'
>>> node.inputs.similarity_metric = 'EDS'
>>> node.inputs.samplingX = 4
>>> node.inputs.samplingY = 4
>>> node.inputs.samplingZ = 4
>>> node.inputs.ftol = 0.01
>>> node.inputs.useInTrans = 1
>>> node.run() 

Inputs:

[Mandatory]
fixed_file: (a unicode string)
        fixed diffusion tensor image
        flag: %s, position: 0
ftol: (a float)
        cost function tolerance
        flag: %s, position: 6
moving_file: (a unicode string)
        diffusion tensor image path
        flag: %s, position: 1
samplingX: (a float)
        dist between samp points (mm)
        flag: %s, position: 3
samplingY: (a float)
        dist between samp points (mm)
        flag: %s, position: 4
samplingZ: (a float)
        dist between samp points (mm)
        flag: %s, position: 5
similarity_metric: ('EDS' or 'GDS' or 'DDS' or 'NMI')
        similarity metric
        flag: %s, position: 2

[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
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
useInTrans: (a float)
        to initialize with existing xfm set as 1
        flag: %s, position: 7

Outputs:

out_file: (a file name)
out_file_xfm: (a file name)

affScalarVolTask

Link to code

Wraps command affineScalarVolume

Applies affine transform to a scalar volume

>>> import nipype.interfaces.dtitk as dtitk
>>> node = dtitk.affScalarVolTask()
>>> node.inputs.in_volume = 'fa.nii.gz'
>>> node.inputs.in_xfm = 'ants_Affine.txt'
>>> 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_target: (a unicode string)
        flag: -target %s, position: 2
in_volume: (a unicode string)
        moving volume
        flag: -in %s, position: 0
in_xfm: (a unicode string)
        transform to apply
        flag: -trans %s, position: 1
out_file: (a unicode string)
        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)
        moved volume

affSymTensor3DVolTask

Link to code

Wraps command affineSymTensor3DVolume

Applies affine transform to a tensor volume

>>> import nipype.interfaces.dtitk as dtitk
>>> node = dtitk.affSymTensor3DVolTask()
>>> node.inputs.in_tensor = 'diffusion.nii'
>>> node.inputs.in_xfm = 'ants_Affine.txt'
>>> 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_target: (a unicode string)
        flag: -target %s, position: 2
in_tensor: (a unicode string)
        moving tensor
        flag: -in %s, position: 0
in_xfm: (a unicode string)
        transform to apply
        flag: -trans %s, position: 1
out_file: (a unicode string)
        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)
        cheese

diffeoScalarVolTask

Link to code

Wraps command deformationScalarVolume

Applies diffeomorphic transform to a scalar volume

>>> import nipype.interfaces.dtitk as dtitk
>>> node = dtitk.diffeoScalarVolTask()
>>> node.inputs.in_volume = 'fa.nii.gz'
>>> node.inputs.in_xfm = 'ants_Warp.nii.gz'
>>> 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_flip: (a unicode string)
        flag: -flip %s, position: 5
in_interp: (a unicode string)
        0 trilin, 1 NN
        flag: -interp %s, position: 7
in_target: (a unicode string)
        flag: -target %s, position: 3
in_type: (a unicode string)
        flag: -type %s, position: 6
in_volume: (a unicode string)
        moving volume
        flag: -in %s, position: 0
in_vsize: (a unicode string)
        flag: -vsize %s, position: 4
in_xfm: (a unicode string)
        transform to apply
        flag: -trans %s, position: 2
out_file: (a unicode string)
        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)
        moved volume

diffeoSymTensor3DVolTask

Link to code

Wraps command deformationSymTensor3DVolume

Applies diffeomorphic transform to a tensor volume

>>> import nipype.interfaces.dtitk as dtitk
>>> node = dtitk.diffeoSymTensor3DVolTask()
>>> node.inputs.in_tensor = 'diffusion.nii'
>>> node.inputs.in_xfm = 'ants_Warp.nii.gz'
>>> 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_target: (a unicode string)
        flag: -target %s, position: 2
in_tensor: (a unicode string)
        moving tensor
        flag: -in %s, position: 0
in_xfm: (a unicode string)
        transform to apply
        flag: -trans %s, position: 1
out_file: (a unicode string)
        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)
        cheese