fc_gui.m

While resting-state fMRI is drawing more and more attention, there has not been a software for its d

	set(handles.txtTR,	...		
		'Style', 'text', ...
		'Units', 'pixels', ...
		'Position', [230 530 40 16], ...
		'String', 'TR: (s)');
		
	% --- PUSHBUTTONS -------------------------------------
	set(handles.btnSelectOutputDir,	...		
		'Style', 'pushbutton', ...
		'Units', 'pixels', ...
		'Position', [396 107 30 25], ...
		'FontSize', 18, ...
		'String', '...');

	set(handles.btnSelectDataDir,	...		
		'Style', 'pushbutton', ...
		'Units', 'pixels', ...
		'Position', [396 372 30 25], ...
		'FontSize', 18, ...
		'String', '...', ...
		'CData', zeros(1,0));

	set(handles.btnSelectMask,	...		
		'Style', 'pushbutton', ...
		'Units', 'pixels', ...
		'Position', [396 275 30 25], ...
		'FontSize', 18, ...
		'String', '...', ...
		'Enable', 'off', ...
		'CData', zeros(1,0));

	set(handles.btnComputeFC,	...		
		'Style', 'pushbutton', ...
		'Units', 'pixels', ...
		'Position', [320 186 107 33], ...
		'FontSize', 12, ...
		'FontWeight', 'bold', ...
		'String', 'Do all');

		
	set(handles.btnDetrend , ...
		'Style', 'pushbutton', ...
		'Units', 'pixels', ...
		'Position', [337 593 90 25], ...
		'FontSize', 10, ...
		'String', 'Detrend');
	set(handles.btnBandPass , ...
		'Style', 'pushbutton', ...
		'Units', 'pixels', ...
		'Position', [337 530 90 25], ...
		'FontSize', 10, ...
		'String', 'Filter');
	
		
	set(handles.btnROIVoxelWise , ...
		'Style', 'pushbutton', ...
		'Units', 'pixels', ...
		'Position', [5 315 85 25], ...%'FontSize', 10, ...		
		'ForegroundColor', 'red', ...	
		'TooltipString', 'Functional Connectivity with whole brain', ...
		'String', 'Voxel wise');
	set(handles.btnROIRegionWise , ...
		'Style', 'pushbutton', ...
		'Units', 'pixels', ...
		'Position', [5 275 85 25], ... 		%'FontSize', 18, ... 
		'ForegroundColor', 'red', ...				
		'TooltipString', 'Functional Connectivity between defined regions', ...
		'String', 'ROI wise');	
		
	set(handles.btnCovariable,	...		%'Style', 'pushbutton', ...		
		'Style', 'text', ...	%20071103
		'Units', 'pixels', ...
		'Position', [5 234 85 25], ...
		'FontSize', 10, ...  %'FontWeight', 'bold', ...		
		'ForegroundColor', 'blue', ...
		'Visible', 'on', ...
		'String', 'Covariables:');
		
	set(handles.btnSelectCovariableFile , ...
		'Style', 'pushbutton', ...
		'Units', 'pixels', ...
		'Position', [396 234 30 25], ...
		'FontSize', 18, ...
		'ForegroundColor', 'blue', ...
		'String', '...');	
		
		
	set(handles.btnHelp,	...
		'Style', 'pushbutton', ...
		'Units', 'pixels', ...
		'Position', [10 10 90 33], ...
		'FontSize', 10, ...
		'String', 'Help');	
	set(handles.btnFisherZ,	...
		'Style', 'pushbutton', ...
		'Units', 'pixels', ...
		'Position', [110 10 90 33], ...
		'FontSize', 10, ...
		'String', 'Fisher Z');
	set(handles.btnSliceViewer,	...
		'Style', 'pushbutton', ...
		'Units', 'pixels', ...
		'Position', [210 10 90 33], ...
		'FontSize', 10, ...
		'String', 'Slice Viewer');	
	set(handles.btnWaveGraph,	...
		'Style', 'pushbutton', ...
		'Units', 'pixels', ...
		'Position', [314 10 110 33], ...
		'FontSize', 10, ...
		'String', 'Power Spectrum');
		
		
	% --- RADIO BUTTONS -------------------------------------
	set(handles.rbtnDefaultMask,	...		
		'Style', 'radiobutton', ...
		'Units', 'pixels', ...
		'Position', [110 335 158 16], ...
		'String', 'Default mask');

	set(handles.rbtnUserMask,	...		
		'Style', 'radiobutton', ...
		'Units', 'pixels', ...
		'Position', [110 305 148 16], ...
		'String', 'User''s defined mask');

	set(handles.rbtnNullMask,	...		
		'Style', 'radiobutton', ...
		'Units', 'pixels', ...
		'Position', [277 335 82 16], ...
		'String', 'No mask');

	% --- CHECKBOXES -------------------------------------
	set(handles.ckboxFilter,	...		
		'Style', 'checkbox', ...
		'Units', 'pixels', ...
		'Position', [14 530 80 22], ...
		'String', 'Band (Hz)');

	set(handles.ckboxFisherZ,	...		
		'Style', 'checkbox', ...
		'Units', 'pixels', ...
		'Position', [12 82 430 19], ...
		'String', 'Fisher Z-score transformation within the mask (zPrefix_DirectoryName.{hdr/img})');

	set(handles.ckboxRetrend,	...		
		'Style', 'checkbox', ...
		'Units', 'pixels', ...
		'Position', [366 530 60 22], ...
		'Enable', 'Off', ...
		'String', 'Retrend');

	set(handles.ckboxRemoveTrendBefore, ...
		'Style', 'checkbox', ...
		'Units', 'pixels', ...
		'Position', [13 595 160 21],...
		'String', 'detrend');
	set(handles.ckboxRemoveTrendAfter, ...
		'Style', 'checkbox', ...
		'Units', 'pixels', ...
		'Position', [171 595 140 21],...
		'Visible', 'off', ...
		'String', 'detrend AFTER Filter');	
		
	% --- EDIT TEXTS -------------------------------------
	set(handles.edtOutputDir,	...		
		'Style', 'edit', ...
		'Units', 'pixels', ...
		'Position', [94 109 300 23], ...
		'BackgroundColor', [1 1 1], ...
		'String', 'Edit Text');

	set(handles.edtDataDirectory,	...		
		'Style', 'edit', ...
		'Units', 'pixels', ...
		'Position', [94 373 300 22], ...
		'BackgroundColor', [1 1 1], ...
		'String', '');

	set(handles.edtMaskfile,	...		
		'Style', 'edit', ...
		'Units', 'pixels', ...
		'Position', [94 275 300 23], ...
		'BackgroundColor', [1 1 1], ...
		'String', 'Default', ...
		'Enable', 'off');

	set(handles.edtPrefix,	...		
		'Style', 'edit', ...
		'Units', 'pixels', ...
		'Position', [94 142 115 22], ...
		'BackgroundColor', [1 1 1], ...
		'String', 'FCMap');

	set(handles.edtBandLow,	...		
		'Style', 'edit', ...
		'Units', 'pixels', ...
		'Position', [94 531 50 22], ...
		'BackgroundColor', [1 1 1], ...
		'String', '0.01', ...
		'Enable', 'off');

	set(handles.edtBandHigh,	...		
		'Style', 'edit', ...
		'Units', 'pixels', ...
		'Position', [171 531 50 22], ...
		'BackgroundColor', [1 1 1], ...
		'String', '0.08', ...
		'Enable', 'off');

	set(handles.edtSamplePeriod,	...		
		'Style', 'edit', ...
		'Units', 'pixels', ...
		'Position', [276 531 50 22], ...
		'BackgroundColor', [1 1 1], ...
		'String', '2', ...
		'Enable', 'off');

	
	set(handles.edtCovariableFile,	...		
		'Style', 'edit', ...
		'Units', 'pixels', ...
		'Position', [94 235 300 23], ...
		'BackgroundColor', [1 1 1], ...
		'String', '', ...
		'ForegroundColor', 'blue', ...
		'Enable', 'on');
		
	% --- LISTBOXES -------------------------------------
	set(handles.listDataDirs,	...		
		'Style', 'listbox', ...
		'Units', 'pixels', ...
		'Position', [14 400 413 108], ...
		'BackgroundColor', [1 1 1], ...
		'String', '');

	%20071103, Add context menu to Input Data Directories to add、delete、export、import……
	handles.hContextMenu =uicontextmenu;
	set(handles.listDataDirs, 'UIContextMenu', handles.hContextMenu);	
	uimenu(handles.hContextMenu, 'Label', 'Add a directory', 'Callback', get(handles.btnSelectDataDir, 'Callback'));	
	uimenu(handles.hContextMenu, 'Label', 'Remove selected directory', 'Callback', 'fc_gui(''DeleteSelectedDataDir'',gcbo,[], guidata(gcbo))');
	uimenu(handles.hContextMenu, 'Label', 'Add recursively all sub-folders of a directory', 'Callback', 'fc_gui(''RecursiveAddDataDir'',gcbo,[], guidata(gcbo))');
	uimenu(handles.hContextMenu, 'Label', '=============================');	
	uimenu(handles.hContextMenu, 'Label', 'Clear all data directories', 'Callback', 'fc_gui(''ClearDataDirectories'',gcbo,[], guidata(gcbo))');
	
	
	% Save handles structure	
	guidata(hObject,handles);

%% Log options to a log file for further investigation, 20070507 before Computing
function Log2File(handles)
	constLineSep= '-------------------------------------------------------------------------------';
	[theVer, theRelease] =rest_misc( 'GetRestVersion');
	theMsgVersion = sprintf('REST Version:%s, Release %s\r\n%s\r\n', theVer, theRelease, constLineSep);	
	theMsgHead = sprintf('Functional Connectivity computation log %s\r\n%s\r\n', rest_misc( 'GetDateTimeStr'), constLineSep);
	theMsg =sprintf('%s\r\n%s\r\n\r\n%s', theMsgVersion, theMsgHead, constLineSep);
	theMsg =sprintf('%s\r\nRemove Linear Trend options:\r\n%s\r\n\r\n%s',theMsg,...
					LogRemoveLinearTrend(handles), constLineSep);
	theMsg =sprintf('%s\r\nIdeal Band Pass filter options:\r\n%s\r\n\r\n%s',theMsg,...
					LogBandPassFilter(handles), constLineSep);
	theMsg =sprintf('%s\r\nFunctional Connectivity input parameters:\r\n%s\r\n\r\n%s', theMsg, ...
					LogInputParameters(handles), constLineSep);
	theMsg =sprintf('%s\r\nFunctional Connectivity output parameters:\r\n%s\r\n\r\n%s', theMsg, ...
					LogOutputParameters(handles), constLineSep);
	
	fid = fopen(handles.Log.Filename,'w');
	if fid~=-1
		fprintf(fid,'%s',theMsg);
		fclose(fid);
	else
		errordlg(sprintf('Error to open log file:\n\n%s', handles.Log.Filename));
	end
	
%Log the total elapsed time by once "Do all"
function LogPerformance(handles)	
	theMsg =sprintf('\r\n\r\nTotal elapsed time for Functional Connectivity Computing: %g  seconds\r\n',handles.Performance);
	fid = fopen(handles.Log.Filename,'r+');
	fseek(fid, 0, 'eof');
	if fid~=-1
		fprintf(fid,'%s',theMsg);
		fclose(fid);
	else
		errordlg(sprintf('Error to open log file:\n\n%s', handles.Log.Filename));
	end
	
	
function ResultLogString=LogRemoveLinearTrend(handles)
	ResultLogString ='';
	ResultLogString =sprintf('%s\tremove linear trend BEFORE filter: %s\r\n',ResultLogString, handles.Detrend.BeforeFilter);
	%ResultLogString =sprintf('%s\tremove linear trend AFTER filter: %s\r\n',ResultLogString, handles.Detrend.AfterFilter);
	
function ResultLogString=LogBandPassFilter(handles)
	ResultLogString ='';
	ResultLogString =sprintf('%s\tUse Filter: %s\r\n',ResultLogString, handles.Filter.UseFilter);
	ResultLogString =sprintf('%s\tBand Low: %g\r\n', ResultLogString, handles.Filter.BandLow);
	ResultLogString =sprintf('%s\tBand High: %g\r\n',ResultLogString, handles.Filter.BandHigh);
	ResultLogString =sprintf('%s\tSample Period(i.e. TR): %g\r\n',ResultLogString, handles.Filter.SamplePeriod);
	
function ResultLogString=LogInputParameters(handles)
	ResultLogString ='';
	constLineSep= '-------------------------------------------------------------------------------';
	theDataDirString= '';
	theDataDirCells =get(handles.listDataDirs, 'string');
	for x=1:length(theDataDirCells)
		theDataDirString =sprintf('%s\r\n\t%s', theDataDirString, theDataDirCells{x});
	end
	theDirType ='';
	if strcmpi(handles.Detrend.BeforeFilter, 'Yes')
		theDirType =sprintf(' %s after Detrend processing', theDirType);
	end
	if strcmpi(handles.Detrend.BeforeFilter, 'Yes') && ...
		strcmpi(handles.Filter.UseFilter, 'Yes'),
		theDirType =sprintf(' %s and ', theDirType);
	end
	if strcmpi(handles.Filter.UseFilter, 'Yes')
		theDirType =sprintf(' %s after Filter processing', theDirType);
	end
	ResultLogString =sprintf('%s\tInput Data Directories( %s): \r\n\t%s%s\r\n\t%s\r\n',ResultLogString,...
							theDirType, ...
							constLineSep, ...
							theDataDirString, ...
							constLineSep);
	ResultLogString =sprintf('%s\tMask file: %s\r\n', ResultLogString, handles.Cfg.MaskFile);	
		
	%Functional Connectivity
	ResultLogString =sprintf('%s\n\n\tFunctional Connectivity Parameters\r\n', ResultLogString);	
	%ROI Definition log
	if iscell(handles.Cfg.ROIList),
		for x=1:size(handles.Cfg.ROIList, 1),
			ResultLogString =sprintf('%s\tROI Definition: \n\t\t%s\r\n', ResultLogString, handles.Cfg.ROIList{x});	
		end
	else
		ResultLogString =sprintf('%s\tROI Definition: \n\t\t%s\r\n', ResultLogString, handles.Cfg.ROIList);	
	end
	%Covariable log
	ResultLogString =sprintf('%s\tCovariables Definition File: \n\t\t%s\r\n', ResultLogString, handles.Covariables.ort_file);	
	ResultLogString =sprintf('%s\tCovariables Polort (Polynomial Orthogonal Degree): \n\t\t%d\r\n', ResultLogString, handles.Covariables.polort);	
		
function ResultLogString=LogOutputParameters(handles)
	ResultLogString ='';
	ResultLogString =sprintf('%s\tPrefix to the Data directories: %s\r\n',ResultLogString, get(handles.edtPrefix, 'String'));
	ResultLogString =sprintf('%s\tOutput Data Directories: %s\r\n',ResultLogString, handles.Cfg.OutputDir);
	ResultLogString =sprintf('%s\tWant Fisher Z-score map transformation: %s \r\n',ResultLogString, handles.Cfg.WantFisherZMap);
	

%compose the log filename