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()
- 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.