nipype.interfaces.quickshear module¶
Quickshear is a simple geometric defacing algorithm.
Quickshear¶
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()
- in_filea pathlike object or string representing an existing file
Neuroimage to deface. Maps to a command-line argument:
%s
(position: 1).- mask_filea pathlike object or string representing an existing file
Brain mask. Maps to a command-line argument:
%s
(position: 2).
- argsa string
Additional parameters to the command. Maps to a command-line argument:
%s
.- buffan integer
Buffer size (in voxels) between shearing plane and the brain. Maps to a command-line argument:
%d
(position: 4).- environa 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_filea pathlike object or string representing a file
Defaced output image. Maps to a command-line argument:
%s
(position: 3).
- out_filea pathlike object or string representing an existing file
Defaced output image.