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# 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 newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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: (u'stream' or u'allatonce' or u'file' or u'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 newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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: (u'stream' or u'allatonce' or u'file' or u'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 newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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: (u'stream' or u'allatonce' or u'file' or u'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 newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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: (u'stream' or u'allatonce' or u'file' or u'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 newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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: (u'stream' or u'allatonce' or u'file' or u'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 newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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: (u'stream' or u'allatonce' or u'file' or u'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 newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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: (u'stream' or u'allatonce' or u'file' or u'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 newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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: (u'stream' or u'allatonce' or u'file' or u'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