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R8218/muscles/MuscleInfoListPatient.m
00d767138ff5Bashardoust_SystCoord

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MuscleInfoListPatient.m
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% 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');
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