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R8218/ShoulderCase/@Muscles/newDegeneration.m
fd75f40ff87daterrier-plotUpdate

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newDegeneration.m
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function outputArg = newDegeneration(obj)
%METHOD1
%One needs to create two empty files in the current directory :
%data_degenerescence.mat (a table) and Didnotwork.mat (a
%string)
% This script calculates the degeneration of the 4 muscles
% of the rotator cuff : SS, SC, IS, TM. It is composed of four
% different steps :
% - Load CT images (DICOM files) in order to create a 3D matrix
% consituted with HU (Hounsfield unit) values
% - Create a slice of this 3D matrix along a patient-specific
% plane. Do image processing and set saving format usable by
% automatic segmentation code (Python's code from ARTORG team
% (UNIBE))
% - Execute automatic segmentation code on the new created
% images
% - Apply degeneration code (from Laboratoire de biom�canique
% orthop�dique (EPFL)) on new images with automatic
% segmentation and on image with manual segmentation (from CHUV
% radiologist). Save degeneration values under the "muscles"
% properties of each case in the LBO database
% Some "try-catch" are present in order to catch the errors
% while keeping running the script on the rest of the database.
% They are summarized underneath :
% (DicomReadVolume) : do not manage to load the dicoms
% Nothing : Automatic segmentation does not work (generally for TM)
% * : slice function does not work
% ** : does not want to crop image
% *** : black image, don't want to save png
% Main code starts here !
%% Load dicom
obj.createRotatorCuffSlices;
obj.segmentRotatorCuffMuscles;
obj.measureDegenerationFromSegmentationSet('auto');
end
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