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()  # 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 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
out_file: (a file name)
        defaced output image
        flag: %s, position: 3

Outputs:

out_file: (an existing file name)
        defaced output image

References:: BibTeX(‘@inproceedings{Schimke2011,address = {San Francisco},author = {Schimke, Nakeisha and Hale, John},booktitle = {Proceedings of the 2nd USENIX Conference on Health Security and Privacy},title = {{Quickshear Defacing for Neuroimages}},year = {2011},month = sep}’, key=’Schimke2011’)