% This script runs through the list of patients for which muscle % degeneration values were calculated (i.e. already put in Database) % This script first creates a list of these patients and runs the script "muscleDegeneration" % This script outputs a table where the values for each muscle is given in this way: % Example for SS muscle: % muscle.caseID = caseID; % muscle.Stot %Stot: total area of the muscle fossa, manually delimited contours) % muscle.Satrophy % Sa: area of the atrophy (Stot - Sm) % muscle.Sinfiltration % Si: area of fat infiltration % muscle.Sosteochondroma % So: area of osteochondroma % muscle.Sdegeneration % Sm: area of the degenerated muscle, without atrophy, fat infiltration and osteochondroma % muscle.atrophy % ratio of muscle atrophy (area atrophy over total area of muscle fossa) % muscle.infiltration % ratio of fat infiltration in the muscle (area fat infiltration over total area of muscle fossa) % muscle.osteochondroma % ratio of osteochondroma in the muscle (area osteochondroma over total area of muscle fossa) % muscle.degeneration % the ratio of degeneration of the muscle % are saved. For more details, check the function "muscleDegeneration" % Important: Check location of your database!!! % created with MATLAB ver.: 9.2.0.556344 (R2017a) on Windows 7 % Author: K. Cosendey and Y. Boulanaache % Date: 16-Oct-2017 HUThresholdMuscle = 0; HUThresholdFat = 30; HUThresholdOsteochondroma = 166; listPatientNumber =[]; listPathologic = []; MatrixPCSA_SS = []; MatrixPCSA_IS = []; MatrixPCSA_SC = []; MatrixPCSA_TM = []; AveragePCSA_SS=0; AveragePCSA_IS=0; AveragePCSA_SC=0; AveragePCSA_TM=0; tabMuscle_SS=[]; tabMuscle_IS=[]; tabMuscle_SC=[]; tabMuscle_TM=[]; % mainFolder = dir('../../../../'); % %mainFolder = mainFolder(1).folder; %original % % XLSShoulderDatabaseLocation = [mainFolder '/methods/matlab/database/muscles/'];original % %XLSShoulderDatabaseLocation = pwd; % %output a column with only numbers in it % % CTDatabaseLocation = '../../../data'; % Location of the CT database XLSShoulderDatabaseLocation = '../../../data/Excel/'; % Location of the XLS ShoulderDatabase [~,~,raw] = xlsread([XLSShoulderDatabaseLocation '\ShoulderDataBase.xlsx'],2,'A:A'); A= raw; % outputs all values, numbers and text %Now read out SS degeneration to check if this patient had a calculated degeneration of muscle or not %If SS was calculated then the other muscles as well. [~,~,raw] = xlsread([XLSShoulderDatabaseLocation '\ShoulderDataBase.xlsx'],2,'CD:CD'); B = raw; %outputs all %make a 2-columns matrix that has caseID and corresponding muscle values %Now create a list which contains only patients that have muscle values. listCases = [A,B]; %for each non-number B value, we have corresponding value in column A. %Loop through i=1; while isnan(listCases{i,1}) == 0 if isnumeric(listCases{i,2})==1 listPathologic = [ listPathologic; listCases{i,1}(1)]; listPatientNumber=[ listPatientNumber; str2num(listCases{i,1}(2:end))]; end i=i+1; end listPatient = cell(size(listPathologic,1),1); listPatientCaseID = cell(size(listPathologic,1),1); for i=1:size(listPathologic,1) if listPatientNumber(i) < 100 if listPatientNumber(i)<10 listPatient{i,1} = [listPathologic(i) '00' num2str(listPatientNumber(i))]; else listPatient{i,1} = [listPathologic(i) '0' num2str(listPatientNumber(i))]; end else listPatient{i,1} = [listPathologic(i) num2str(listPatientNumber(i))]; end listPatientCaseID{i,1} = [listPathologic(i) num2str(listPatientNumber(i))]; end %FOR SUPRASPINATUS muscleName = 'SS'; for i=1:size(listPatient,1) caseID = listPatientCaseID{i,1}; caseID2 = listPatient{i,1}; %inputFile = [mainFolder 'data\' caseID2(1) '\' caseID2(2) '\' caseID2(3) '\' caseID '*']; inputFile = ['Y:\data\' caseID2(1) '\' caseID2(2) '\' caseID2(3) '\' caseID '*']; FindCaseCTFolder = dir(inputFile); CaseID_IPP = FindCaseCTFolder.name; % CaseCTFolder = [mainFolder 'data\' caseID2(1) '\' caseID2(2) '\' caseID2(3) '\' CaseID_IPP '\CT-' CaseID_IPP '-1']; CaseCTFolder = ['Y:\data\' caseID2(1) '\' caseID2(2) '\' caseID2(3) '\' CaseID_IPP '\CT-' CaseID_IPP '-1']; CaseMuscleFolder = [ CaseCTFolder '\muscles']; %Launch script "muscleDegeneration.m" muscle = muscleDegeneration (caseID, muscleName ,HUThresholdMuscle,HUThresholdFat,HUThresholdOsteochondroma, CaseMuscleFolder); CaseAmiraFolder = [CaseCTFolder '\amira']; muscle.pixel = infoPixel(CaseAmiraFolder); muscle.pixeldetail=muscle.pixel(1,1); muscle.totalarea=muscle.Stot*(muscle.pixeldetail*muscle.pixeldetail)*0.01; %multiply total area by number of pixels. Result in cm2 muscle.ratio=muscle.degeneration; %take the percentage degenerated muscle.degenerationarea=muscle.totalarea*muscle.ratio; %this is the degenerated area muscle.effectivePCSA=muscle.totalarea-muscle.degenerationarea; %the effective usable PCSA tabMuscle_SS=[tabMuscle_SS; muscle]; end %Because of ambiguity in pixelsize for some cases, chosen manually the pixel size tabMuscle_SS(1).totalarea=0.01*tabMuscle_SS(1).Stot*(0.244955)^2; %P2, , chose "new" for all tabMuscle_SS(3).totalarea=0.01*tabMuscle_SS(3).Stot*(0.310913)^2; %P6 % tabMuscle(30).totalarea=0.01*tabMuscle(30).Stot*()^2; %P64: no data! % tabMuscle(31).totalarea=0.01*tabMuscle(31).Stot*()^2; %P65: no data! % tabMuscle(32).totalarea=0.01*tabMuscle(32).Stot*()^2; %P68: no data! % tabMuscle(34).totalarea=0.01*tabMuscle(34).Stot*()^2; %P73: no data! % tabMuscle(35).totalarea=0.01*tabMuscle(35).Stot*()^2; %P75: no data! % tabMuscle(36).totalarea=0.01*tabMuscle(36).Stot*()^2; %P76: no data! % tabMuscle(38).totalarea=0.01*tabMuscle(38).Stot*()^2; %P78: no data! % tabMuscle(41).totalarea=0.01*tabMuscle(41).Stot*()^2; %P89: no data! % tabMuscle(42).totalarea=0.01*tabMuscle(42).Stot*()^2; %P90: no data! % tabMuscle(43).totalarea=0.01*tabMuscle(43).Stot*()^2; %P91: no data! % tabMuscle(44).totalarea=0.01*tabMuscle(44).Stot*()^2; %P92: no data! % tabMuscle(45).totalarea=0.01*tabMuscle(45).Stot*()^2; %P93: no data! tabMuscle_SS(46).totalarea=0.01*tabMuscle_SS(46).Stot*(0.277493)^2; %P103 tabMuscle_SS(47).totalarea=0.01*tabMuscle_SS(47).Stot*(0.290182)^2; %P105 tabMuscle_SS(48).totalarea=0.01*tabMuscle_SS(48).Stot*(0.31551)^2; %P107 tabMuscle_SS(61).totalarea=0.01*tabMuscle_SS(61).Stot*(0.271774)^2; %P145 tabMuscle_SS(69).totalarea=0.01*tabMuscle_SS(69).Stot*(0.28785)^2; %P163 tabMuscle_SS(73).totalarea=0.01*tabMuscle_SS(73).Stot*(0.334435)^2; %P170 tabMuscle_SS(75).totalarea=0.01*tabMuscle_SS(75).Stot*(0.230255)^2; %P173 tabMuscle_SS(78).totalarea=0.01*tabMuscle_SS(78).Stot*(0.280144)^2; %P176 tabMuscle_SS(83).totalarea=0.01*tabMuscle_SS(83).Stot*(0.155813)^2; %P188 for i=1:size(tabMuscle_SS) %update the degeneration information tabMuscle_SS(i).degenerationarea=tabMuscle_SS(i).totalarea*tabMuscle_SS(i).ratio; %this is the new degenerated area tabMuscle_SS(i).effectivePCSA=tabMuscle_SS(i).totalarea-tabMuscle_SS(i).degenerationarea; MatrixPCSA_SS=[MatrixPCSA_SS;tabMuscle_SS(i).totalarea,tabMuscle_SS(i).effectivePCSA,tabMuscle_SS(i).ratio]; end % %Update MatrixPCSA as well % MatrixPCSA(1,1)=tabMuscle(1).totalarea; % MatrixPCSA(3,1)=tabMuscle(3).totalarea; % % tabMuscle(30).totalarea=0.01*tabMuscle(30).Stot*()^2; %P64: no data! % % tabMuscle(31).totalarea=0.01*tabMuscle(31).Stot*()^2; %P65: no data! % % tabMuscle(32).totalarea=0.01*tabMuscle(32).Stot*()^2; %P68: no data! % % tabMuscle(34).totalarea=0.01*tabMuscle(34).Stot*()^2; %P73: no data! % % tabMuscle(35).totalarea=0.01*tabMuscle(35).Stot*()^2; %P75: no data! % % tabMuscle(36).totalarea=0.01*tabMuscle(36).Stot*()^2; %P76: no data! % % tabMuscle(38).totalarea=0.01*tabMuscle(38).Stot*()^2; %P78: no data! % % tabMuscle(41).totalarea=0.01*tabMuscle(41).Stot*()^2; %P89: no data! % % tabMuscle(42).totalarea=0.01*tabMuscle(42).Stot*()^2; %P90: no data! % % tabMuscle(43).totalarea=0.01*tabMuscle(43).Stot*()^2; %P91: no data! % % tabMuscle(44).totalarea=0.01*tabMuscle(44).Stot*()^2; %P92: no data! % % tabMuscle(45).totalarea=0.01*tabMuscle(45).Stot*()^2; %P93: no data! % MatrixPCSA(46,1)=tabMuscle(46).totalarea; % MatrixPCSA(47,1)=tabMuscle(47).totalarea; % MatrixPCSA(48,1)=tabMuscle(48).totalarea; % MatrixPCSA(61,1)=tabMuscle(61).totalarea; % MatrixPCSA(69,1)=tabMuscle(69).totalarea; % MatrixPCSA(73,1)=tabMuscle(73).totalarea; % MatrixPCSA(75,1)=tabMuscle(75).totalarea; % MatrixPCSA(78,1)=tabMuscle(78).totalarea; % MatrixPCSA(83,1)=tabMuscle(83).totalarea; AveragePCSA_SS = mean(MatrixPCSA_SS); %Result Oct2017: 5.62615579051498 StdDev_PCSA_SS = std (MatrixPCSA_SS); %Result Oct2017: 2.41206345030003 disp('end SS') %FOR Infraspinatus muscleName = 'IS'; for i=1:size(listPatient,1) caseID = listPatientCaseID{i,1}; caseID2 = listPatient{i,1}; %inputFile = [mainFolder 'data\' caseID2(1) '\' caseID2(2) '\' caseID2(3) '\' caseID '*']; inputFile = ['Y:\data\' caseID2(1) '\' caseID2(2) '\' caseID2(3) '\' caseID '*']; FindCaseCTFolder = dir(inputFile); CaseID_IPP = FindCaseCTFolder.name; % CaseCTFolder = [mainFolder 'data\' caseID2(1) '\' caseID2(2) '\' caseID2(3) '\' CaseID_IPP '\CT-' CaseID_IPP '-1']; CaseCTFolder = ['Y:\data\' caseID2(1) '\' caseID2(2) '\' caseID2(3) '\' CaseID_IPP '\CT-' CaseID_IPP '-1']; CaseMuscleFolder = [ CaseCTFolder '\muscles']; %Launch script "muscleDegeneration.m" muscle = muscleDegeneration (caseID, muscleName ,HUThresholdMuscle,HUThresholdFat,HUThresholdOsteochondroma, CaseMuscleFolder); CaseAmiraFolder = [CaseCTFolder '\amira']; muscle.pixel = infoPixel(CaseAmiraFolder); muscle.pixeldetail=muscle.pixel(1,1); muscle.totalarea=muscle.Stot*(muscle.pixeldetail*muscle.pixeldetail)*0.01; %multiply total area by number of pixels. Result in cm2 muscle.ratio=muscle.degeneration; %take the percentage degenerated muscle.degenerationarea=muscle.totalarea*muscle.ratio; %this is the degenerated area muscle.effectivePCSA=muscle.totalarea-muscle.degenerationarea; %the effective usable PCSA tabMuscle_IS=[tabMuscle_IS; muscle]; end %Because of ambiguity in pixelsize for some cases, chosen manually the pixel size tabMuscle_IS(1).totalarea=0.01*tabMuscle_IS(1).Stot*(0.244955)^2; %P2, , chose "new" for all tabMuscle_IS(3).totalarea=0.01*tabMuscle_IS(3).Stot*(0.310913)^2; %P6 % tabMuscle(30).totalarea=0.01*tabMuscle(30).Stot*()^2; %P64: no data! % tabMuscle(31).totalarea=0.01*tabMuscle(31).Stot*()^2; %P65: no data! % tabMuscle(32).totalarea=0.01*tabMuscle(32).Stot*()^2; %P68: no data! % tabMuscle(34).totalarea=0.01*tabMuscle(34).Stot*()^2; %P73: no data! % tabMuscle(35).totalarea=0.01*tabMuscle(35).Stot*()^2; %P75: no data! % tabMuscle(36).totalarea=0.01*tabMuscle(36).Stot*()^2; %P76: no data! % tabMuscle(38).totalarea=0.01*tabMuscle(38).Stot*()^2; %P78: no data! % tabMuscle(41).totalarea=0.01*tabMuscle(41).Stot*()^2; %P89: no data! % tabMuscle(42).totalarea=0.01*tabMuscle(42).Stot*()^2; %P90: no data! % tabMuscle(43).totalarea=0.01*tabMuscle(43).Stot*()^2; %P91: no data! % tabMuscle(44).totalarea=0.01*tabMuscle(44).Stot*()^2; %P92: no data! % tabMuscle(45).totalarea=0.01*tabMuscle(45).Stot*()^2; %P93: no data! tabMuscle_IS(46).totalarea=0.01*tabMuscle_IS(46).Stot*(0.277493)^2; %P103 tabMuscle_IS(47).totalarea=0.01*tabMuscle_IS(47).Stot*(0.290182)^2; %P105 tabMuscle_IS(48).totalarea=0.01*tabMuscle_IS(48).Stot*(0.31551)^2; %P107 tabMuscle_IS(61).totalarea=0.01*tabMuscle_IS(61).Stot*(0.271774)^2; %P145 tabMuscle_IS(69).totalarea=0.01*tabMuscle_IS(69).Stot*(0.28785)^2; %P163 tabMuscle_IS(73).totalarea=0.01*tabMuscle_IS(73).Stot*(0.334435)^2; %P170 tabMuscle_IS(75).totalarea=0.01*tabMuscle_IS(75).Stot*(0.230255)^2; %P173 tabMuscle_IS(78).totalarea=0.01*tabMuscle_IS(78).Stot*(0.280144)^2; %P176 tabMuscle_IS(83).totalarea=0.01*tabMuscle_IS(83).Stot*(0.155813)^2; %P188 for i=1:size(tabMuscle_IS) %update the degeneration information tabMuscle_IS(i).degenerationarea=tabMuscle_IS(i).totalarea*tabMuscle_IS(i).ratio; %this is the new degenerated area tabMuscle_IS(i).effectivePCSA=tabMuscle_IS(i).totalarea-tabMuscle_IS(i).degenerationarea; MatrixPCSA_IS=[MatrixPCSA_IS;tabMuscle_IS(i).totalarea,tabMuscle_IS(i).effectivePCSA,tabMuscle_IS(i).ratio]; end AveragePCSA_IS = mean(MatrixPCSA_IS); StdDev_PCSA_IS = std (MatrixPCSA_IS); disp('end IS') %FOR Subscapularis muscleName = 'SC'; for i=1:size(listPatient,1) caseID = listPatientCaseID{i,1}; caseID2 = listPatient{i,1}; %inputFile = [mainFolder 'data\' caseID2(1) '\' caseID2(2) '\' caseID2(3) '\' caseID '*']; inputFile = ['Y:\data\' caseID2(1) '\' caseID2(2) '\' caseID2(3) '\' caseID '*']; FindCaseCTFolder = dir(inputFile); CaseID_IPP = FindCaseCTFolder.name; % CaseCTFolder = [mainFolder 'data\' caseID2(1) '\' caseID2(2) '\' caseID2(3) '\' CaseID_IPP '\CT-' CaseID_IPP '-1']; CaseCTFolder = ['Y:\data\' caseID2(1) '\' caseID2(2) '\' caseID2(3) '\' CaseID_IPP '\CT-' CaseID_IPP '-1']; CaseMuscleFolder = [ CaseCTFolder '\muscles']; muscle = muscleDegeneration (caseID, muscleName ,HUThresholdMuscle,HUThresholdFat,HUThresholdOsteochondroma, CaseMuscleFolder); CaseAmiraFolder = [CaseCTFolder '\amira']; muscle.pixel = infoPixel(CaseAmiraFolder); muscle.pixeldetail=muscle.pixel(1,1); muscle.totalarea=muscle.Stot*(muscle.pixeldetail*muscle.pixeldetail)*0.01; %multiply total area by number of pixels. Result in cm2 muscle.ratio=muscle.degeneration; %take the percentage degenerated muscle.degenerationarea=muscle.totalarea*muscle.ratio; %this is the degenerated area muscle.effectivePCSA=muscle.totalarea-muscle.degenerationarea; %the effective usable PCSA tabMuscle_SC=[tabMuscle_SC; muscle]; end %Because of ambiguity in pixelsize for some cases, chosen manually the pixel size tabMuscle_SC(1).totalarea=0.01*tabMuscle_SC(1).Stot*(0.244955)^2; %P2, , chose "new" for all tabMuscle_SC(3).totalarea=0.01*tabMuscle_SC(3).Stot*(0.310913)^2; %P6 % tabMuscle(30).totalarea=0.01*tabMuscle(30).Stot*()^2; %P64: no data! % tabMuscle(31).totalarea=0.01*tabMuscle(31).Stot*()^2; %P65: no data! % tabMuscle(32).totalarea=0.01*tabMuscle(32).Stot*()^2; %P68: no data! % tabMuscle(34).totalarea=0.01*tabMuscle(34).Stot*()^2; %P73: no data! % tabMuscle(35).totalarea=0.01*tabMuscle(35).Stot*()^2; %P75: no data! % tabMuscle(36).totalarea=0.01*tabMuscle(36).Stot*()^2; %P76: no data! % tabMuscle(38).totalarea=0.01*tabMuscle(38).Stot*()^2; %P78: no data! % tabMuscle(41).totalarea=0.01*tabMuscle(41).Stot*()^2; %P89: no data! % tabMuscle(42).totalarea=0.01*tabMuscle(42).Stot*()^2; %P90: no data! % tabMuscle(43).totalarea=0.01*tabMuscle(43).Stot*()^2; %P91: no data! % tabMuscle(44).totalarea=0.01*tabMuscle(44).Stot*()^2; %P92: no data! % tabMuscle(45).totalarea=0.01*tabMuscle(45).Stot*()^2; %P93: no data! tabMuscle_SC(46).totalarea=0.01*tabMuscle_SC(46).Stot*(0.277493)^2; %P103 tabMuscle_SC(47).totalarea=0.01*tabMuscle_SC(47).Stot*(0.290182)^2; %P105 tabMuscle_SC(48).totalarea=0.01*tabMuscle_SC(48).Stot*(0.31551)^2; %P107 tabMuscle_SC(61).totalarea=0.01*tabMuscle_SC(61).Stot*(0.271774)^2; %P145 tabMuscle_SC(69).totalarea=0.01*tabMuscle_SC(69).Stot*(0.28785)^2; %P163 tabMuscle_SC(73).totalarea=0.01*tabMuscle_SC(73).Stot*(0.334435)^2; %P170 tabMuscle_SC(75).totalarea=0.01*tabMuscle_SC(75).Stot*(0.230255)^2; %P173 tabMuscle_SC(78).totalarea=0.01*tabMuscle_SC(78).Stot*(0.280144)^2; %P176 tabMuscle_SC(83).totalarea=0.01*tabMuscle_SC(83).Stot*(0.155813)^2; %P188 for i=1:size(tabMuscle_SC) %update the degeneration information tabMuscle_SC(i).degenerationarea=tabMuscle_SC(i).totalarea*tabMuscle_SC(i).ratio; %this is the new degenerated area tabMuscle_SC(i).effectivePCSA=tabMuscle_SC(i).totalarea-tabMuscle_SC(i).degenerationarea; MatrixPCSA_SC=[MatrixPCSA_SC;tabMuscle_SC(i).totalarea,tabMuscle_SC(i).effectivePCSA,tabMuscle_SC(i).ratio]; end AveragePCSA_SC = mean(MatrixPCSA_SC); StdDev_PCSA_SC = std (MatrixPCSA_SC); disp('end SC') %FOR Teres Minor muscleName = 'TM'; for i=1:size(listPatient,1) caseID = listPatientCaseID{i,1}; caseID2 = listPatient{i,1}; %inputFile = [mainFolder 'data\' caseID2(1) '\' caseID2(2) '\' caseID2(3) '\' caseID '*']; inputFile = ['Y:\data\' caseID2(1) '\' caseID2(2) '\' caseID2(3) '\' caseID '*']; FindCaseCTFolder = dir(inputFile); CaseID_IPP = FindCaseCTFolder.name; % CaseCTFolder = [mainFolder 'data\' caseID2(1) '\' caseID2(2) '\' caseID2(3) '\' CaseID_IPP '\CT-' CaseID_IPP '-1']; CaseCTFolder = ['Y:\data\' caseID2(1) '\' caseID2(2) '\' caseID2(3) '\' CaseID_IPP '\CT-' CaseID_IPP '-1']; CaseMuscleFolder = [ CaseCTFolder '\muscles']; muscle = muscleDegeneration (caseID, muscleName ,HUThresholdMuscle,HUThresholdFat,HUThresholdOsteochondroma, CaseMuscleFolder); CaseAmiraFolder = [CaseCTFolder '\amira']; muscle.pixel = infoPixel(CaseAmiraFolder); muscle.pixeldetail=muscle.pixel(1,1); muscle.totalarea=muscle.Stot*(muscle.pixeldetail*muscle.pixeldetail)*0.01; %multiply total area by number of pixels. Result in cm2 muscle.ratio=muscle.degeneration; %take the percentage degenerated muscle.degenerationarea=muscle.totalarea*muscle.ratio; %this is the degenerated area muscle.effectivePCSA=muscle.totalarea-muscle.degenerationarea; %the effective usable PCSA tabMuscle_TM=[tabMuscle_TM; muscle]; end %Because of ambiguity in pixelsize for some cases, chosen manually the pixel size tabMuscle_TM(1).totalarea=0.01*tabMuscle_TM(1).Stot*(0.244955)^2; %P2, , chose "new" for all tabMuscle_TM(3).totalarea=0.01*tabMuscle_TM(3).Stot*(0.310913)^2; %P6 % tabMuscle(30).totalarea=0.01*tabMuscle(30).Stot*()^2; %P64: no data! % tabMuscle(31).totalarea=0.01*tabMuscle(31).Stot*()^2; %P65: no data! % tabMuscle(32).totalarea=0.01*tabMuscle(32).Stot*()^2; %P68: no data! % tabMuscle(34).totalarea=0.01*tabMuscle(34).Stot*()^2; %P73: no data! % tabMuscle(35).totalarea=0.01*tabMuscle(35).Stot*()^2; %P75: no data! % tabMuscle(36).totalarea=0.01*tabMuscle(36).Stot*()^2; %P76: no data! % tabMuscle(38).totalarea=0.01*tabMuscle(38).Stot*()^2; %P78: no data! % tabMuscle(41).totalarea=0.01*tabMuscle(41).Stot*()^2; %P89: no data! % tabMuscle(42).totalarea=0.01*tabMuscle(42).Stot*()^2; %P90: no data! % tabMuscle(43).totalarea=0.01*tabMuscle(43).Stot*()^2; %P91: no data! % tabMuscle(44).totalarea=0.01*tabMuscle(44).Stot*()^2; %P92: no data! % tabMuscle(45).totalarea=0.01*tabMuscle(45).Stot*()^2; %P93: no data! tabMuscle_TM(46).totalarea=0.01*tabMuscle_TM(46).Stot*(0.277493)^2; %P103 tabMuscle_TM(47).totalarea=0.01*tabMuscle_TM(47).Stot*(0.290182)^2; %P105 tabMuscle_TM(48).totalarea=0.01*tabMuscle_TM(48).Stot*(0.31551)^2; %P107 tabMuscle_TM(61).totalarea=0.01*tabMuscle_TM(61).Stot*(0.271774)^2; %P145 tabMuscle_TM(69).totalarea=0.01*tabMuscle_TM(69).Stot*(0.28785)^2; %P163 tabMuscle_TM(73).totalarea=0.01*tabMuscle_TM(73).Stot*(0.334435)^2; %P170 tabMuscle_TM(75).totalarea=0.01*tabMuscle_TM(75).Stot*(0.230255)^2; %P173 tabMuscle_TM(78).totalarea=0.01*tabMuscle_TM(78).Stot*(0.280144)^2; %P176 tabMuscle_TM(83).totalarea=0.01*tabMuscle_TM(83).Stot*(0.155813)^2; %P188 for i=1:size(tabMuscle_TM) %update the degeneration information tabMuscle_TM(i).degenerationarea=tabMuscle_TM(i).totalarea*tabMuscle_TM(i).ratio; %this is the new degenerated area tabMuscle_TM(i).effectivePCSA=tabMuscle_TM(i).totalarea-tabMuscle_TM(i).degenerationarea; MatrixPCSA_TM=[MatrixPCSA_TM;tabMuscle_TM(i).totalarea,tabMuscle_TM(i).effectivePCSA,tabMuscle_TM(i).ratio]; end AveragePCSA_TM = mean(MatrixPCSA_TM); StdDev_PCSA_TM = std (MatrixPCSA_TM); disp('endTM') %Save data just in case save('D:\Data\FromdropboxOUtmemory\muscles\tabMuscle_SS.mat','tabMuscle_SS'); save('D:\Data\FromdropboxOUtmemory\muscles\tabMuscle_IS.mat','tabMuscle_IS'); save('D:\Data\FromdropboxOUtmemory\muscles\tabMuscle_SC.mat','tabMuscle_SC'); save('D:\Data\FromdropboxOUtmemory\muscles\tabMuscle_TM.mat','tabMuscle_TM'); save('D:\Data\FromdropboxOUtmemory\muscles\MatrixPCSA_SS.mat','MatrixPCSA_SS'); save('D:\Data\FromdropboxOUtmemory\muscles\MatrixPCSA_IS.mat','MatrixPCSA_IS'); save('D:\Data\FromdropboxOUtmemory\muscles\MatrixPCSA_SC.mat','MatrixPCSA_SC'); save('D:\Data\FromdropboxOUtmemory\muscles\MatrixPCSA_TM.mat','MatrixPCSA_TM');