interfaces.quickshear¶
Quickshear¶
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 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
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: ('stream' or 'allatonce' or 'file' or '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