Diffusion ShoulderDB_ImportSegmentMeasureAnalyze (feat_muscle_subdivisions) Browse

R8218/dicominfoSCase.m
0fe4702f8808feat_muscle_subdivisions

dicominfoSCase.m
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			function outputArg = dicominfoSCase(varargin)
			%DICOMINFOSCASE Get info from dicom fields and save in csv, xls, mat, and SQL

			% This function should be started from /shoulder/methods/matlab/database
			% A logfile is written during execution in
			% /shoulder/methods/matlab/database/log/dicominfoSCase.log
			% If the function is called without arguments the csv file is overwritten,
			% otherwise it is updated. The same applies for xls, mat and SQL.

			% The fonction can be run from server (lbovenus) with
			% cd /home/shoulder/methods/matlab/database; matlab -nojvm -nodisplay -nosplash -r "dicominfoSCase;quit"
			% For 700 cases, it takes less than 60 seconds (when executed from server)

			% Progress can be be checked throuhth log file with following shell command
			% cd /home/shoulder/methods/matlab/database;tail -f log/dicominfoSCase.log

			% This funtion replaces
			% /home/shoulder/methods/matlab/database/CTinfoCT.m
			% which only works matlab R2015a on a Windows system

			% Syntax: outputArg = dicominfoSCase(varargin)
			%
			% Input:
			% varargin: can be nothing (all cases), 'N', 'P', or SCase(s)
			%
			% Output:
			% outputArg: 1 if ok and 0 otherwise
			%
			% Example: CTdicomInfo, CTdicominfo('P'), CTdicominfo('P315')
			% Other M-files required: listSCase
			% Subfunctions:
			% See also: measureSCase
			%
			% Author: Alexandre Terrier
			% EPFL-LBO
			% Creation date: 2018-07-01
			% Revision date: 2018-12-30
			%
			% TO DO:
			% When list of SCases as arguments it doesn't work properly because it
			% overwrites the CSV with only the listed SCased (by JSM 2019-02-13)
			% Re-check for double slash in paths
			% We should implement the ShoulderCase class
			% We should save data in SCase/matlab directory
			% We might add family name, given name (to check anonymity)
			% We should first read csv and then update
			% We should update MySQL
			% Check 'Index exceeds matrix dimensions' when 'using dicomdisp'
			% Structure SCaseDicom should match csv (and xlx aand sql) firld names
			% rather than dicom

			%% Open log file
			% Check if log dir exists in working directory
			logDir = 'log';
			if ~exist('log', 'dir') % If not create dir log
			mkdir('log')
			end
			logFile = [logDir '/dicominfoSCase.log'];
			logFileID = fopen(logFile, 'w');
			fprintf(logFileID, 'dicominfoSCase log file');
			fprintf(logFileID, '\nDate: ');
			fprintf(logFileID, datestr(datetime));

			%% Set the data directory from the configuration file config.txt
			configFile = 'config.txt';
			if ~exist(configFile, 'file')
			error([configFile, ' required']);
			end
			fileID = fopen(configFile,'r');
			dataDir = fscanf(fileID, '%s'); % Read config file without spaces
			fclose(fileID);
			k = strfind(dataDir, 'dataDir='); % Find definition of dataDir
			k = k + 8; % Remove 'dataDir='
			dataDir = dataDir(k:end); % Assume that config file ends with dataDir content
			% Check if dataDir exists
			if ~exist(dataDir, 'dir')
			fprintf(logFileID, ['Data directory not found, check ' configFile]);
			%error(['Data directory not found, check ' configFile]);

			% Select the \data directory
			try
			dataDir = uigetdir(pwd,"Please select the directory 'data or dataDev'");
			if ~exist(dataDir, 'dir')
			errordlg(sprintf("%s",...
			"Run 'dicominfoSCase.m' manually and select the data directory"),...
			"Error: data directory not found.")
			end
			catch mistake
			errordlg(sprintf("%s\n%s",...
			"Run 'dicominfoSCase.m' manually and select the data directory",...
			mistake.message),"Error: data directory not found.")
			end

			end
			% Location of the XLS ShoulderDatabase
			xlsDataDir = strcat(dataDir, '/Excel/xlsFromMatlab');

			%% Get list of SCases
			if nargin == 0 % dicominfoSCase called without argument
			SCaseList = listSCase(dataDir); % All SCases in data dir with valid dicom CT dir
			update = 0;
			elseif nargin == 1
			update = 1;
			inputArg = varargin{1};
			SCaseList = listSCase(dataDir,inputArg); % SCase related to inputArg ('N', 'P', or list)
			end

			%% Read dicom info
			tic; % Start stopwatch timer
			fprintf(logFileID, '\n\nRead dicom meta data\n'); % log file message

			% Struct below correponds to regular dicom field names, except SCase_ID
			SCaseDicom = struct(...
			'SCase_id' ,[],...
			'PatientID' ,[],...
			'PatientSex' ,[],...
			'PatientAge' ,[],...
			'PatientBirthDate' ,[],...
			'PatientSize' ,[],...
			'PatientWeight' ,[],...
			'PatientFamilyName' ,[],...
			'PatientGivenName' ,[],...
			'AcquisitionDate' ,[],...
			'ConvolutionKernel' ,[],...
			'PixelSpacing' ,[],...
			'SpacingBetweenSlices' ,[],...
			'SliceThickness' ,[],...
			'KVP' ,[],...
			'XrayTubeCurrent' ,[],...
			'InstitutionName' ,[],...
			'StudyDescription' ,[],...
			'SeriesDescription' ,[],... % Might describe shoulder side
			'Manufacturer' ,[],...
			'ManufacturerModelName' ,[],...
			'ProtocolName' ,[]...
			);

			% Loop over all SCases collected above
			for SCase_idx=1:1:numel(SCaseList)
			SCase_id = SCaseList(SCase_idx).id;
			dicomDir = [SCaseList(SCase_idx).dir '/dicom'];
			dicomFiles = dir([dicomDir, '/*.dcm']);

			% SCase_idx
			dicomFile1 = [dicomDir, '/', dicomFiles(10).name]; % seems better to check 10th than 1st !
			dicomInfoError = false;
			fprintf(logFileID, '\n');
			fprintf(logFileID, SCaseList(SCase_idx).id);
			fprintf(logFileID, ': ');
			% Try first with matlab function dicominfo
			try
			dicomInfo1 = dicominfo(dicomFile1, 'UseVRHeuristic', true);
			fprintf(logFileID, 'dicominfo ok');
			% If dicominfo didn't worked, try with matlab function dicomdisp
			catch ME
			dicomInfoError = true;
			fprintf(logFileID, '\n');
			fprintf(logFileID, 'dicominfo error --> using dicomdisp');
			fprintf(logFileID, ['\n' ME.message]);
			dicomdispStr = evalc('dicomdisp(dicomFile1)');
			end

			% If dicominfo didn't worked, continue with output of dicomdisp
			if dicomInfoError % get dicom info from dicomdisp()
			PatientID = extractAfter(dicomdispStr,'PatientID');
			PatientID = extractAfter(PatientID,'[');
			PatientID = extractBefore(PatientID,']');

			PatientSex = extractAfter(dicomdispStr,'PatientSex');
			PatientSex = extractAfter(PatientSex,'[');
			PatientSex = extractBefore(PatientSex,']');

			PatientAge = extractAfter(dicomdispStr,'PatientAge');
			PatientAge = extractAfter(PatientAge,'[');
			PatientAge = extractBefore(PatientAge,']');

			PatientBirthDate = extractAfter(dicomdispStr,'PatientBirthDate');
			PatientBirthDate = extractAfter(PatientBirthDate,'[');
			PatientBirthDate = extractBefore(PatientBirthDate,']');

			PatientSize = extractAfter(dicomdispStr,'PatientSize');
			PatientSize = extractAfter(PatientSize,'[');
			PatientSize = extractBefore(PatientSize,']');
			PatientSize = str2double(PatientSize);

			PatientWeight = extractAfter(dicomdispStr,'PatientWeight');
			PatientWeight = extractAfter(PatientWeight,'[');
			PatientWeight = extractBefore(PatientWeight,']');
			PatientWeight = str2double(PatientWeight);

			AcquisitionDate = extractAfter(dicomdispStr,'AcquisitionDate');
			AcquisitionDate = extractAfter(AcquisitionDate,'[');
			AcquisitionDate = extractBefore(AcquisitionDate,']');

			ConvolutionKernel = extractAfter(dicomdispStr,'ConvolutionKernel');
			ConvolutionKernel = extractAfter(ConvolutionKernel,'[');
			ConvolutionKernel = extractBefore(ConvolutionKernel,']');

			PixelSpacing = extractAfter(dicomdispStr,'PixelSpacing');
			PixelSpacing = extractAfter(PixelSpacing,'[');
			PixelSpacing = extractBefore(PixelSpacing,'\');

			SpacingBetweenSlices = extractAfter(dicomdispStr,'SpacingBetweenSlices');
			SpacingBetweenSlices = extractAfter(SpacingBetweenSlices,'[');
			SpacingBetweenSlices = extractBefore(SpacingBetweenSlices,']');
			SpacingBetweenSlices = str2double(SpacingBetweenSlices);

			SliceThickness = extractAfter(dicomdispStr,'SliceThickness');
			SliceThickness = extractAfter(SliceThickness,'[');
			SliceThickness = extractBefore(SliceThickness,']');
			SliceThickness = str2double(SliceThickness);

			KVP = extractAfter(dicomdispStr,'KVP');
			KVP = extractAfter(KVP,'[');
			KVP = extractBefore(KVP,']');
			KVP = str2double(KVP);

			XrayTubeCurrent = extractAfter(dicomdispStr,'XrayTubeCurrent');
			XrayTubeCurrent = extractAfter(XrayTubeCurrent,'[');
			XrayTubeCurrent = extractBefore(XrayTubeCurrent,']');
			XrayTubeCurrent = str2double(XrayTubeCurrent);

			InstitutionName = extractAfter(dicomdispStr,'InstitutionName');
			InstitutionName = extractAfter(InstitutionName,'[');
			InstitutionName = extractBefore(InstitutionName,']');

			Manufacturer = extractAfter(dicomdispStr,'Manufacturer');
			Manufacturer = extractAfter(Manufacturer,'[');
			Manufacturer = extractBefore(Manufacturer,']');

			ManufacturerModelName = extractAfter(dicomdispStr,'ManufacturerModelName');
			ManufacturerModelName = extractAfter(ManufacturerModelName,'[');
			ManufacturerModelName = extractBefore(ManufacturerModelName,']');

			ProtocolName = extractAfter(dicomdispStr,'ProtocolName');
			ProtocolName = extractAfter(ProtocolName,'[');
			ProtocolName = extractBefore(ProtocolName,']');

			SeriesDescription = extractAfter(dicomdispStr,'SeriesDescription');
			SeriesDescription = extractAfter(SeriesDescription,'[');
			SeriesDescription = extractBefore(SeriesDescription,']');

			else % dicomInfo exists
			if isfield(dicomInfo1,'PatientID')
			PatientID = dicomInfo1.PatientID;
			else
			PatientID = '';
			end
			if isfield(dicomInfo1,'PatientSex')
			PatientSex = dicomInfo1.PatientSex;
			else
			PatientSex = '';
			end
			if isfield(dicomInfo1,'PatientBirthDate')
			PatientBirthDate = dicomInfo1.PatientBirthDate;
			else
			PatientBirthDate = '';
			end
			if isfield(dicomInfo1,'PatientAge')
			PatientAge = dicomInfo1.PatientAge;
			else
			PatientAge = '';
			end
			if isfield(dicomInfo1,'PatientSize')
			PatientSize = dicomInfo1.PatientSize;
			else
			PatientSize = '';
			end
			if isfield(dicomInfo1,'PatientWeight')
			PatientWeight = dicomInfo1.PatientWeight;
			else
			PatientWeight='';
			end
			if isfield(dicomInfo1,'AcquisitionDate')
			AcquisitionDate = dicomInfo1.AcquisitionDate;
			else
			AcquisitionDate = '';
			end
			if isfield(dicomInfo1,'ConvolutionKernel')
			ConvolutionKernel = dicomInfo1.ConvolutionKernel;
			else
			ConvolutionKernel = '';
			end
			if isfield(dicomInfo1,'PixelSpacing')
			PixelSpacing = dicomInfo1.PixelSpacing(1);
			PixelSpacing = num2str(PixelSpacing);
			% PixelSpacing = [,PixelSpacing,]; % Commented because I (AT) don't
			% understand the effect
			else
			PixelSpacing='';
			end
			if isfield(dicomInfo1,'SpacingBetweenSlices')
			SpacingBetweenSlices = dicomInfo1.SpacingBetweenSlices;
			else % SpacingBetweenSlices estimated from 2 slices
			% fprintf(logFileID, '\n');
			fprintf(logFileID, ', SpacingBetweenSlices estimated from 2 slices');
			dicomFile2 = [dicomDir, '/', dicomFiles(11).name];
			dicomInfo2 = dicominfo(dicomFile2, 'UseVRHeuristic', true);
			ImagePositionPatient1 = dicomInfo1.ImagePositionPatient(3);
			ImagePositionPatient2 = dicomInfo2.ImagePositionPatient(3);
			posdDiff = abs(ImagePositionPatient2 - ImagePositionPatient1);
			InstanceNumber1 = dicomInfo1.InstanceNumber;
			InstanceNumber2 = dicomInfo2.InstanceNumber;
			InstanceNumberDiff = abs(InstanceNumber2 - InstanceNumber1);
			if InstanceNumberDiff == 0
			InstanceNumberDiff=1;
			end
			SpacingBetweenSlices = posdDiff/InstanceNumberDiff;
			end
			if isfield(dicomInfo1,'SliceThickness')
			SliceThickness = dicomInfo1.SliceThickness;
			else
			SliceThickness='';
			end
			if isfield(dicomInfo1,'KVP')
			KVP = dicomInfo1.KVP;
			else
			KVP= '';
			end
			if isfield(dicomInfo1,'XrayTubeCurrent')
			XrayTubeCurrent = dicomInfo1.XrayTubeCurrent;
			else
			XrayTubeCurrent = '';
			end
			if isfield(dicomInfo1,'InstitutionName')
			InstitutionName = dicomInfo1.InstitutionName;
			else
			InstitutionName = '';
			end
			if isfield(dicomInfo1,'Manufacturer')
			Manufacturer = dicomInfo1.Manufacturer;
			else
			Manufacturer ='';
			end
			if isfield(dicomInfo1,'ManufacturerModelName')
			ManufacturerModelName = dicomInfo1.ManufacturerModelName;
			else
			ManufacturerModelName = '';
			end
			if isfield(dicomInfo1,'ProtocolName')
			ProtocolName = dicomInfo1.ProtocolName;
			else
			ProtocolName = '';
			end
			if isfield(dicomInfo1,'SeriesDescription')
			SeriesDescription = dicomInfo1.SeriesDescription;
			else
			SeriesDescription = '';
			end
			% End of reading dimcom info
			end

			%% Format data
			PatientBirthDate = datetime(PatientBirthDate,'InputFormat','yyyyMMdd');
			PatientBirthDate = datestr(PatientBirthDate, 'yyyy-mm-dd');
			PatientAge = str2double(strtok(PatientAge,'Y'));
			PatientSize = round(100 * PatientSize);
			if PatientSize == 0
			PatientSize = '';
			end
			PatientWeight = round(PatientWeight);
			if PatientWeight == 0
			PatientWeight = '';
			end
			AcquisitionDate = datetime(AcquisitionDate,'InputFormat','yyyyMMdd');
			AcquisitionDate = datestr(AcquisitionDate, 'yyyy-mm-dd');

			PixelSpacing = str2double(PixelSpacing);
			PixelSpacing = round(PixelSpacing, 3);
			SpacingBetweenSlices = round(SpacingBetweenSlices, 3);
			SliceThickness = round(SliceThickness, 3);
			KVP = round(KVP);
			XrayTubeCurrent = round(XrayTubeCurrent);
			% Replace any ',' by ' ' to avoid problem in csv
			InstitutionName = strrep(InstitutionName,',',' ');
			Manufacturer = strrep(Manufacturer,',',' ');
			ManufacturerModelName = strrep(ManufacturerModelName,',',' ');
			ProtocolName = strrep(ProtocolName,',',' ');
			SeriesDescription = strrep(SeriesDescription,',',' ');

			%% Add data in SCaseDicom structure
			% This could be directly in SCase.CT object
			SCaseDicom(SCase_idx).id = SCase_id;
			SCaseDicom(SCase_idx).PatientID = PatientID;
			SCaseDicom(SCase_idx).PatientSex = PatientSex;
			SCaseDicom(SCase_idx).PatientBirthDate = PatientBirthDate;
			SCaseDicom(SCase_idx).PatientAge = PatientAge;
			SCaseDicom(SCase_idx).PatientSize = PatientSize;
			SCaseDicom(SCase_idx).PatientWeight = PatientWeight;
			SCaseDicom(SCase_idx).AcquisitionDate = AcquisitionDate;
			SCaseDicom(SCase_idx).ConvolutionKernel = ConvolutionKernel;
			SCaseDicom(SCase_idx).PixelSpacing = PixelSpacing;
			SCaseDicom(SCase_idx).SpacingBetweenSlices = SpacingBetweenSlices;
			SCaseDicom(SCase_idx).SliceThickness = SliceThickness;
			SCaseDicom(SCase_idx).KVP = KVP;
			SCaseDicom(SCase_idx).XrayTubeCurrent = XrayTubeCurrent;
			SCaseDicom(SCase_idx).InstitutionName = InstitutionName;
			SCaseDicom(SCase_idx).Manufacturer = Manufacturer;
			SCaseDicom(SCase_idx).ManufacturerModelName = ManufacturerModelName;
			SCaseDicom(SCase_idx).ProtocolName = ProtocolName;
			SCaseDicom(SCase_idx).SeriesDescription = SeriesDescription;
			end
			fprintf(logFileID, '\n\nElapsed time (s): %s', num2str(toc)); % stopwatch timer

			%% Write csv file
			% This might be a function. The input would be a filename and a structure
			% data

			dataHeader = [...
			'SCase_ID,' ...
			'patient_IPP,' ...
			'patient_gender,' ...
			'patient_birthDate,' ...
			'patient_age,' ...
			'patient_height,' ...
			'patient_weight,' ...
			'CT_date,' ...
			'CT_kernel,' ...
			'CT_pixelSize,' ...
			'CT_sliceSpacing,' ...
			'CT_sliceThickness,' ...
			'CT_tension,' ...
			'CT_current,' ...
			'CT_institution,' ...
			'CT_manufacturer,' ...
			'CT_model,' ...
			'CT_protocol,' ...
			'CT_SeriesDescription' ...
			];

			csvFilename = strcat(xlsDataDir, '/CTdicomInfo.csv');

			% If dicominfoSCase is called with argument, we have to update the csv.
			if update
			% Read the csv and put data in a structure like SCaseDicom
			% We should chech that file exists
			csvTable = readtable(csvFilename,'DatetimeType', 'text');
			% If 'DatetimeType' is specified as 'text', then the type for imported
			% date and time data depends on the value specified in the 'TextType'
			% parameter: If 'TextType' is 'char', then readtable returns dates as a
			% cell array of character vectors. If 'TextType' is 'string', then
			% readtable returns dates as an array of strings.

			% Set csv data in temporary SCaseDicomTmp structure
			SCaseDicom_csv = table2struct(csvTable);

			% Update the SCaseDicomTmp structure with new data
			for iSCaseDicom = 1:length(SCaseDicom) % loop on new SCase(s)
			iSCaseDicomTmp = strcmp({SCaseDicom_csv.SCase_ID}, SCaseDicom(iSCaseDicom).id); % 0/1 array
			iSCaseDicomTmp = find(iSCaseDicomTmp); % index with non-zero, correponding to SCaseID
			% We should test iSCaseDicomTmp => is overwriting the whole array
			% Must be changed by last SCase position +1

			SCaseDicom_csv(iSCaseDicomTmp).patient_IPP = SCaseDicom(iSCaseDicom).PatientID;
			SCaseDicom_csv(iSCaseDicomTmp).patient_gender = SCaseDicom(iSCaseDicom).PatientSex;
			SCaseDicom_csv(iSCaseDicomTmp).patient_birthDate = SCaseDicom(iSCaseDicom).PatientBirthDate;
			SCaseDicom_csv(iSCaseDicomTmp).patient_age = SCaseDicom(iSCaseDicom).PatientAge;
			SCaseDicom_csv(iSCaseDicomTmp).patient_height = SCaseDicom(iSCaseDicom).PatientSize;
			SCaseDicom_csv(iSCaseDicomTmp).patient_weight = SCaseDicom(iSCaseDicom).PatientWeight;
			SCaseDicom_csv(iSCaseDicomTmp).CT_date = SCaseDicom(iSCaseDicom).AcquisitionDate;
			SCaseDicom_csv(iSCaseDicomTmp).CT_kernel = SCaseDicom(iSCaseDicom).ConvolutionKernel;
			SCaseDicom_csv(iSCaseDicomTmp).CT_pixelSize = SCaseDicom(iSCaseDicom).PixelSpacing;
			SCaseDicom_csv(iSCaseDicomTmp).CT_sliceSpacing = SCaseDicom(iSCaseDicom).SpacingBetweenSlices;
			SCaseDicom_csv(iSCaseDicomTmp).CT_sliceThickness = SCaseDicom(iSCaseDicom).SliceThickness;
			SCaseDicom_csv(iSCaseDicomTmp).CT_tension = SCaseDicom(iSCaseDicom).KVP;
			SCaseDicom_csv(iSCaseDicomTmp).CT_current = SCaseDicom(iSCaseDicom).XrayTubeCurrent;
			SCaseDicom_csv(iSCaseDicomTmp).CT_institution = SCaseDicom(iSCaseDicom).InstitutionName;
			SCaseDicom_csv(iSCaseDicomTmp).CT_manufacturer = SCaseDicom(iSCaseDicom).Manufacturer;
			SCaseDicom_csv(iSCaseDicomTmp).CT_model = SCaseDicom(iSCaseDicom).ManufacturerModelName;
			SCaseDicom_csv(iSCaseDicomTmp).CT_protocol = SCaseDicom(iSCaseDicom).ProtocolName;
			SCaseDicom_csv(iSCaseDicomTmp).CT_SeriesDescription = SCaseDicom(iSCaseDicom).SeriesDescription;
			end

			% SCaseDicom must now be updated
			for iSCaseDicom = 1:length(SCaseDicom)
			SCaseDicom(iSCaseDicom).id = SCaseDicom_csv(iSCaseDicom).SCase_ID;
			SCaseDicom(iSCaseDicom).PatientID = SCaseDicom_csv(iSCaseDicom).patient_IPP;
			SCaseDicom(iSCaseDicom).PatientSex = SCaseDicom_csv(iSCaseDicom).patient_gender;
			SCaseDicom(iSCaseDicom).PatientBirthDate = SCaseDicom_csv(iSCaseDicom).patient_birthDate;
			SCaseDicom(iSCaseDicom).PatientAge = SCaseDicom_csv(iSCaseDicom).patient_age;
			SCaseDicom(iSCaseDicom).PatientSize = SCaseDicom_csv(iSCaseDicom).patient_height;
			SCaseDicom(iSCaseDicom).PatientWeight = SCaseDicom_csv(iSCaseDicom).patient_weight;
			SCaseDicom(iSCaseDicom).AcquisitionDate = SCaseDicom_csv(iSCaseDicom).CT_date;
			SCaseDicom(iSCaseDicom).ConvolutionKernel = SCaseDicom_csv(iSCaseDicom).CT_kernel;
			SCaseDicom(iSCaseDicom).PixelSpacing = SCaseDicom_csv(iSCaseDicom).CT_pixelSize;
			SCaseDicom(iSCaseDicom).SpacingBetweenSlices = SCaseDicom_csv(iSCaseDicom).CT_sliceSpacing;
			SCaseDicom(iSCaseDicom).SliceThickness = SCaseDicom_csv(iSCaseDicom).CT_sliceThickness;
			SCaseDicom(iSCaseDicom).KVP = SCaseDicom_csv(iSCaseDicom).CT_tension;
			SCaseDicom(iSCaseDicom).XrayTubeCurrent = SCaseDicom_csv(iSCaseDicom).CT_current;
			SCaseDicom(iSCaseDicom).InstitutionName = SCaseDicom_csv(iSCaseDicom).CT_institution;
			SCaseDicom(iSCaseDicom).Manufacturer = SCaseDicom_csv(iSCaseDicom).CT_manufacturer;
			SCaseDicom(iSCaseDicom).ManufacturerModelName = SCaseDicom_csv(iSCaseDicom).CT_model;
			SCaseDicom(iSCaseDicom).ProtocolName = SCaseDicom_csv(iSCaseDicom).CT_protocol;
			SCaseDicom(iSCaseDicom).SeriesDescription = SCaseDicom_csv(iSCaseDicom).CT_SeriesDescription;
			end

			end

			% Write csv file
			csvFileId = fopen(csvFilename, 'w');
			fprintf(csvFileId,dataHeader);
			for SCase_idx=1:1:numel(SCaseDicom) % Loop on all SCase provided by listSCase()
			fprintf(csvFileId,'\n%s,%s,%s,%s,%f,%f,%f,%s,%s,%f,%f,%f,%f,%f,%s,%s,%s,%s,%s',...
			SCaseDicom(SCase_idx).id,...
			SCaseDicom(SCase_idx).PatientID,...
			SCaseDicom(SCase_idx).PatientSex,...
			SCaseDicom(SCase_idx).PatientBirthDate,...
			SCaseDicom(SCase_idx).PatientAge,...
			SCaseDicom(SCase_idx).PatientSize,...
			SCaseDicom(SCase_idx).PatientWeight,...
			SCaseDicom(SCase_idx).AcquisitionDate,...
			SCaseDicom(SCase_idx).ConvolutionKernel,...
			SCaseDicom(SCase_idx).PixelSpacing,...
			SCaseDicom(SCase_idx).SpacingBetweenSlices,...
			SCaseDicom(SCase_idx).SliceThickness,...
			SCaseDicom(SCase_idx).KVP,...
			SCaseDicom(SCase_idx).XrayTubeCurrent,...
			SCaseDicom(SCase_idx).InstitutionName,...
			SCaseDicom(SCase_idx).Manufacturer,...
			SCaseDicom(SCase_idx).ManufacturerModelName,...
			SCaseDicom(SCase_idx).ProtocolName,...
			SCaseDicom(SCase_idx).SeriesDescription...
			);
			end
			fclose(csvFileId);

			fprintf(logFileID, sprintf('\n\n%s %s', 'Saved csv file: ', csvFilename));

			%% Write xls file (Windows only)
			[~,message] = csv2xlsSCase(csvFilename);
			fprintf(logFileID, message);

			%% Update MySQL
			% To be done
			%{
			addpath('XLS_MySQL_DB');
			MainExcel2SQL;
			%}

			%% Final log
			fprintf(logFileID, '\n\nSCases treated: %s', num2str(numel(SCaseDicom))); % Number of SCases treated
			fprintf(logFileID, '\nElapsed time (s): %s', num2str(toc)); % stopwatch timer
			fclose(logFileID); % Close log file

			outputArg = 1; % Might be extended
			end

R8218/dicominfoSCase.m0fe4702f8808feat_muscle_subdivisions

dicominfoSCase.mView Options

R8218/dicominfoSCase.m
0fe4702f8808feat_muscle_subdivisions

dicominfoSCase.m
View Options