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@@ -80,7 +80,7 @@ catch |
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case '.csv'
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[Name, Position] = readCsv(filename);
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if all(isnan(Position))
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error('Anatomy not found: possibly patient implanted before 2009. Check implantation scheme!');
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warning('T1pre coordinates not found: possibly patient implanted before 2009.');
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end
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otherwise
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disp('ImaGIN> ERROR: Invalid input file type.');
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...
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@@ -109,9 +109,9 @@ end |
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% Set positions
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chNotFound = {};
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chMatchLog = {};
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for i0 = 1:size(t,1)
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chNotFound = {};
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chMatchLog = {};
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T = deblank(t(i0,:));
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% Clone file if requested in input
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if (nargin >= 1) && isfield(S, 'FileOut') && ~isempty(S.FileOut)
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...
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...
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@@ -133,10 +133,9 @@ for i0 = 1:size(t,1) |
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% Loop on all channels available in the file
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for i1 = 1:length(Sensors.label)
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sensLtmp = Sensors.label{i1};
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sensLtmp(ismember(double(sensLtmp),[',' ';' '-'])) ='';
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sensLtmp(ismember(double(sensLtmp),[',' ';' '-' '_'])) ='';
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Sensors.label{i1} = sensLtmp;
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iChanPos = findChannel(Sensors.label{i1}, Name, 'all_upper');
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iChanPos = findChannel(upper(Sensors.label{i1}), upper(Name), 'all_upper');
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% If the channel was already found in the list before: check the best option based on the case
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if ~isempty(iChanPos) && ~isempty(chMatchLog)
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iPrevious = find(strcmp(Name{iChanPos}, chMatchLog(:,2)));
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...
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...
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@@ -163,9 +162,11 @@ for i0 = 1:size(t,1) |
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% Copy channel name from input name file (ADDED BY FT 5-Oct-2018)
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chMatchLog{end+1,1} = Sensors.label{i1};
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chMatchLog{end,2} = Name{iChanPos};
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Sensors.label{i1} = strrep(Name{iChanPos},'-','');
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Sensors.label{i1} = Name{iChanPos};
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else
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disp(['ImaGIN> WARNING: ' Sensors.label{i1} ' not assigned']);
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disp(['ImaGIN> WARNING: ' Sensors.label{i1} ' not assigned']);
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Sensors.elecpos(i1,:) = NaN;
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Sensors.chanpos(i1,:) = NaN;
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chNotFound{end+1} = Sensors.label{i1};
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end
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end
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...
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...
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@@ -205,18 +206,16 @@ for i0 = 1:size(t,1) |
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end
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% Match file: Correspondance between SEEG-CSV-LENA conventions
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try
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if isfield(S, 'FileTxtOut') && ~isempty(S.FileTxtOut)
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try
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fid = fopen(S.FileTxtOut,'w');
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fprintf(fid,'SEEG,CSV\n');
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for i = 1:size(chMatchLog,1)
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fprintf(fid,'%s,%s\n', chMatchLog{i,1}, chMatchLog{i,2});
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end
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fclose(fid);
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catch
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disp('Log with matched channels names SEEG-CSV not saved.')
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if isfield(S, 'FileTxtOut') && ~isempty(S.FileTxtOut)
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try
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fid = fopen(S.FileTxtOut,'w');
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fprintf(fid,'SEEG,CSV\n');
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for i = 1:size(chMatchLog,1)
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fprintf(fid,'%s,%s\n', chMatchLog{i,1}, chMatchLog{i,2});
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end
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fclose(fid);
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catch
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disp('Log with matched channels names SEEG-CSV not saved.')
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end
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end
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...
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...
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@@ -226,7 +225,7 @@ for i0 = 1:size(t,1) |
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% Replace labels in D.channels
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for iChan = 1:length(SpmMat.D.channels)
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spmLtmp = SpmMat.D.channels(iChan).label;
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spmLtmp(ismember(double(spmLtmp),[',' ';' '-'])) ='';
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spmLtmp(ismember(double(spmLtmp),[',' ';' '-' '_'])) ='';
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SpmMat.D.channels(iChan).label = spmLtmp;
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iChanMatch = find(strcmpi(SpmMat.D.channels(iChan).label, chMatchLog(:,1)));
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...
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...
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@@ -311,20 +310,15 @@ for i0 = 1:size(t,1) |
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if (length(iChanMatch1) == 1) && (length(iChanMatch2) == 1)
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SpmMat.D.trials.events(iEvt).type = noteNameNew;
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end
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end
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try
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csv_struct.csv_labels = csv_all_electrodes(:,1);
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catch
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elec_labels = Name';
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elec_labels_no_primes = strrep(elec_labels,'p','''');
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csv_all_electrodes = [elec_labels elec_labels_no_primes];
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csv_struct.csv_labels = csv_all_electrodes(:,1);
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end
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if ~(exist('csv_all_electrodes','var') == 1)
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error('Could not match notes with channels found in the implantation file.')
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end
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csv_struct.csv_labels = csv_all_electrodes(:,1);
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SpmMat.D.other = csv_struct; % Add an extra field to the .mat so we have a listing of all channel labels in the csv.
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% Update existing .mat file
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save(SpmFile, '-struct', 'SpmMat');
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save(spm_eeg_load(SpmFile)); % SPM's save to create a valid SPM object
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clear csv_all_electrode csv_struct
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end
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end
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...
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...
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@@ -403,8 +397,6 @@ function iChanPos = findChannel(Label, List, caseType) |
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% Remove spaces
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Label(Label == ' ') = [];
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% Remove spaces
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List = strrep(List,'-','');
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% Switch case type
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switch (caseType)
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case 'no_change'
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...
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...
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