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R8218/degenerationAll.m
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degenerationAll.m
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%% degenerationAll
%
% This script analyses the muscles data obtained by contouring SS, IS, SC, and
% TM. It returns an excel file (SpecificMusclesState_P###) for
% 'specific' argument. In case of 'new' or 'all' arguments, the script
% returns four DAT file (musclesState_SS, musclesState_IS, musclesState_SC,
% musclesState_TM). They are automatically connected to the Excel file
% "musclesStates". Don't forget to actualize the connections in Excel.
%
% Author: EPFL-LBO
% Date: 2016-09-05
%
%%
% Source is 'all' or 'specific' (for only one case, the subject is required as second argument)
% subject is the case ID: Case IDs for which you want to compute muscle degeneration.
% Case ID is a char in the form 'P###' or 'N###' (starts with "P" or "N" followed by 1 to 3 digits).
function [] = degenerationAll(source,subject)
clc
muscleName = cellstr(['SS';'IS';'SC';'TM']);
switch source
%% 'specific' Cases
case {'specific'}
Degen{1,1} = subject;
Degen{1,2} = 'Atrophy';
Degen{1,3} = 'Infiltration';
Degen{1,4} = 'Osteo';
Degen{1,5} = 'Degeneration';
for j=1:4
HUThresholdMuscle = -29;
HUThresholdOsteochondroma = 166.25;
close all
[~,~,~,~,~,Ra,Ri,Ro,Rd] = muscleDegeneration(subject, char(muscleName(j)),HUThresholdMuscle,HUThresholdOsteochondroma,'image');
Degen{j+1,1} = char(muscleName(j));
Degen{j+1,2} = cell2mat(Ra);
Degen{j+1,3} = cell2mat(Ri);
Degen{j+1,4} = cell2mat(Ro);
Degen{j+1,5} = cell2mat(Rd);
end
% Find the muscles folder to store output
CTDatabaseLocation = 'Z://data'; % Location of the CT database
listDirInCurrDir = dir([CTDatabaseLocation '/' subject(1) '/' subject(2) '/' subject(3)]);
listDirInCurrDir = listDirInCurrDir(3:end);
for i=1:length(listDirInCurrDir)
if ~isempty(regexp(listDirInCurrDir(i).name,['^[PN]\d{0,2}[' subject(4) '][-]\w*'], 'once'))
listDirInCaseFolder = dir([listDirInCurrDir(i).folder '\' listDirInCurrDir(i).name]);
listDirInCaseFolder = listDirInCaseFolder(3:end);
% In all CT folders in the current Case Folder, find CT #1
for j=1:length(listDirInCaseFolder)
if ~isempty(regexp(listDirInCaseFolder(j).name,'^[C][T][-][PN]\d{1,3}[-]\d*[-][1]', 'once'))
% If 'muscles' exists, save iput path
if exist([listDirInCaseFolder(j).folder '\' listDirInCaseFolder(j).name '\muscles'],'dir') == 7
inputPath = [listDirInCaseFolder(j).folder '\' listDirInCaseFolder(j).name '\muscles\'];
else
error(['Missing "muscles" directory for CaseID: ' subject]);
end
end
end
end
end
filename = [inputPath 'SpecificMusclesState_' subject '.xls'];
xlswrite(filename, Degen);
%% 'all' Cases
case {'all'}
l=1;
rootDir = '../../../../data/N';
for levelDir1 = 0:9
for levelDir2 = 0:9
curentDir = sprintf('%s/%d/%d/N*', rootDir, levelDir1, levelDir2);
folderInfo = dir(curentDir);
for i=1:1:numel(folderInfo)
sCases_normal{l,1} = folderInfo(i).name;
sCases_normal{l,2} = levelDir1;
sCases_normal{l,3} = levelDir2;
sCases_normal{l,4} = 'N';
l=l+1;
end
end
end
l=1;
rootDir = '../../../../data/P';
for levelDir1 = 0:9
for levelDir2 = 0:9
curentDir = sprintf('%s/%d/%d/P*', rootDir, levelDir1, levelDir2);
folderInfo = dir(curentDir);
for i=1:1:numel(folderInfo)
sCases_pathologic{l,1} = folderInfo(i).name;
sCases_pathologic{l,2} = levelDir1;
sCases_pathologic{l,3} = levelDir2;
sCases_pathologic{l,4} = 'P';
l=l+1;
end
end
end
sCases = [sCases_normal;sCases_pathologic];
for j=1:4
m=1;
HUThresholdMuscle = -29;
HUThresholdOsteochondroma = 166.25;
for i = 1:length(sCases)
patient = char(sCases(i,1));
location = char(sCases(i,4));
CTn = strtok(patient,'-');
CTn = strtok(CTn, location);
CTn = str2num(CTn);
CTn = sprintf('%s%03d',location,CTn);
if exist(sprintf('results/%s/%s', char(muscleName(j)),CTn),'dir') == 7
close all
clc
percentage = 100*i/length(sCases);
fprintf('%s %s, %3.0f%%\n', char(muscleName(j)), CTn, percentage);
[~,~,~,~,~,Ra(m),Ri(m),Ro(m),Rd(m)] = muscleDegeneration(CTn, char(muscleName(j)),HUThresholdMuscle,HUThresholdOsteochondroma,'image');
else
Ra(m) = cellstr(' ');
Ri(m) = cellstr(' ');
Ro(m) = cellstr(' ');
Rd(m) = cellstr(' ');
end
patientName{m} = strtok(patient,'-');
m=m+1;
end
if j==1
SS_results = [Ra(:) Ri(:) Ro(:) Rd(:)];
end
if j==2
IS_results = [Ra(:) Ri(:) Ro(:) Rd(:)];
end
if j==3
SC_results = [Ra(:) Ri(:) Ro(:) Rd(:)];
end
if j==4
TM_results = [Ra(:) Ri(:) Ro(:) Rd(:)];
end
end
result=[patientName, SS_results,IS_results, SC_results, TM_results];
xlswrite('muscles', result);
otherwise
disp('Unknown group name')
end
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