.. AUTO-GENERATED FILE -- DO NOT EDIT!

interfaces.quickshear
=====================


.. _nipype.interfaces.quickshear.Quickshear:


.. index:: Quickshear

Quickshear
----------

`Link to code <file:///build/nipype-fj7ofr/nipype-1.0.0+git69-gdb2670326/nipype/interfaces/quickshear.py#L47>`__

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()  # doctest: +SKIP

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
