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# interfaces.quickshear

## Quickshear

Link to code

Wraps command quickshear

Quickshear is a simple geometric defacing algorithm

Given an anatomical image and a reasonable brainmask, Quickshear estimates a shearing plane with the brain mask on one side and the face on the other, zeroing out the face side.

    >>> from nipype.interfaces.quickshear import Quickshear
    >>> qs = Quickshear(in_file='T1.nii', mask_file='brain_mask.nii')
    >>> qs.cmdline
    'quickshear T1.nii brain_mask.nii T1_defaced.nii'

In the absence of a precomputed mask, a simple pipeline can be generated with any tool that generates brain masks:

    >>> from nipype.pipeline import engine as pe
    >>> from nipype.interfaces import utility as niu
    >>> from nipype.interfaces.fsl import BET
    >>> deface_wf = pe.Workflow('deface_wf')
    >>> inputnode = pe.Node(niu.IdentityInterface(['in_file']),
    ...                     name='inputnode')
    >>> outputnode = pe.Node(niu.IdentityInterface(['out_file']),
    ...                      name='outputnode')
    >>> bet = pe.Node(BET(mask=True), name='bet')
    >>> quickshear = pe.Node(Quickshear(), name='quickshear')
    >>> deface_wf.connect([
    ...     (inputnode, bet, [('in_file', 'in_file')]),
    ...     (inputnode, quickshear, [('in_file', 'in_file')]),
    ...     (bet, quickshear, [('mask_file', 'mask_file')]),
    ...     (quickshear, outputnode, [('out_file', 'out_file')]),
    ...     ])
    >>> inputnode.inputs.in_file = 'T1.nii'
    >>> res = deface_wf.run()

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            neuroimage to deface
            flag: %s, position: 1
    mask_file: (an existing file name)
            brain mask
            flag: %s, position: 2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    buff: (an integer (int or long))
            buffer size (in voxels) between shearing plane and the brain
            flag: %d, position: 4
    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
    out_file: (a file name)
            defaced output image
            flag: %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: (an existing file name)
            defaced output image

References:: None