3 dA @s`dZddlmZmZmZmZmZddlmZGdddeZ GdddeZ Gd d d eZ d S) z4Quickshear is a simple geometric defacing algorithm.)CommandLineInputSpec CommandLinetraits TraitedSpecFile)BibTeXc@sTeZdZeddddddZeddddddZed d d dd dd ZejddddZ dS)QuickshearInputSpecTrz%szneuroimage to deface)existspositionargstr mandatorydescrz brain mask)r r r rr z %s_defacedin_filezdefaced output image)Z name_templateZ name_sourcer r rZkeep_extensionz%dz/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/quickshear.pyr s&r c@seZdZedddZdS)QuickshearOutputSpecTzdefaced output image)r rN)rrrrrrrrrr"src@s.eZdZdZdZeZeZe ddgdgZ dS) Quicksheara 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 Z quicksheara@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}implementation)entrytagsN) rrr__doc__Z_cmdr Z input_specrZ output_specrZ _referencesrrrrr&s" rN) rbaserrrrrZ external.duerr rrrrrrs