nipype.interfaces.quickshear module

Quickshear is a simple geometric defacing algorithm.

Quickshear

Link to code

Bases: CommandLine

Wrapped executable: 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()  
Mandatory Inputs
  • in_file (a pathlike object or string representing an existing file) – Neuroimage to deface. Maps to a command-line argument: %s (position: 1).

  • mask_file (a pathlike object or string representing an existing file) – Brain mask. Maps to a command-line argument: %s (position: 2).

Optional Inputs
  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • buff (an integer) – Buffer size (in voxels) between shearing plane and the brain. Maps to a command-line argument: %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’) – Environment variables. (Nipype default value: {})

  • out_file (a pathlike object or string representing a file) – Defaced output image. Maps to a command-line argument: %s (position: 3).

Outputs

out_file (a pathlike object or string representing an existing file) – Defaced output image.