alff_gui.m

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

%% Log options to a log file for further investigation, 20070507
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('ALFF 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\nALFF input parameters:\r\n%s\r\n\r\n%s', theMsg, ...
					LogInputParameters(handles), constLineSep);
	theMsg =sprintf('%s\r\nALFF Band Config:\r\n%s\r\n\r\n%s',theMsg,...
					LogALFFParameters(handles), constLineSep);
	theMsg =sprintf('%s\r\nALFF 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
	
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=LogALFFParameters(handles)
	ResultLogString ='';	
	ResultLogString =sprintf('%s\tBand Low: %g\r\n', ResultLogString, handles.ALFF.BandLow);
	ResultLogString =sprintf('%s\tBand High: %g\r\n',ResultLogString, handles.ALFF.BandHigh);
	ResultLogString =sprintf('%s\tSample Period(i.e. TR): %g\r\n',ResultLogString, handles.ALFF.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);	
		
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 mean ReHo map computation: %s \r\n',ResultLogString, handles.Cfg.WantMeanAlffMap);
	

%Log the total elapsed time by once "Do all"
function LogPerformance(handles)	
	theMsg =sprintf('\r\n\r\nTotal elapsed time for ALFF 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

	
%compose the log filename	
function ResultLogFileName=GetLogFilename(ALogDirectory, APrefix)
	if isempty(ALogDirectory)
		[pathstr, name, ext, versn] = fileparts(mfilename('fullpath'));	
		ALogDirectory =pathstr;
	end
	if ~strcmp(ALogDirectory(end), filesep)
		ALogDirectory =[ALogDirectory filesep];
	end
	ResultLogFileName=sprintf('%s%s_%s.log', ...
		ALogDirectory, ...
		APrefix, ...
		rest_misc( 'GetDateTimeStr'));
		

function btnSliceViewer_Callback(hObject, eventdata, handles)
	%Display a brain image like MRIcro
	theOldColor=get(hObject,'BackgroundColor');		
	set(hObject,'Enable','off', 'BackgroundColor', 'red');
	drawnow;
	try
		rest_sliceviewer;
		% [filename, pathname] = uigetfile({'*.img', 'ANALYZE files (*.img)'}, ...
														% 'Pick one brain map');
		% if any(filename~=0) && ischar(filename) && length(filename)>4 ,	% not canceled and legal			
			% if ~strcmpi(pathname(end), filesep)%revise pathname to remove extension		
				% pathname = [pathname filesep];
			% end
			% theBrainMap =[pathname filename];
			% rest_sliceviewer('ShowImage', theBrainMap);
		% end
	catch
		rest_misc( 'DisplayLastException');
	end	
	set(hObject,'Enable','on', 'BackgroundColor', theOldColor);
	drawnow;



function btnWaveGraph_Callback(hObject, eventdata, handles)
	%Display a brain image like MRIcro, and show specific voxel's time course and its freq domain's fluctuation
	theOldColor=get(hObject,'BackgroundColor');		
	set(hObject,'Enable','off', 'BackgroundColor', 'red');
	drawnow;
	try
		[filename, pathname] = uigetfile({'*.img', 'ANALYZE files (*.img)'}, ...
														'Pick one functional EPI brain map in the dataset''s directory');
		if any(filename~=0) && ischar(filename),	% not canceled and legal			
			if ~strcmpi(pathname(end), filesep)%revise pathname to remove extension		
				pathname = [pathname filesep];
			end
			theBrainMap 	=[pathname filename];			
			theViewer =rest_sliceviewer('ShowImage', theBrainMap);
			
			%Set the ALFF figure to show corresponding voxel's time-course and its freq amplitude
			theDataSetDir 	=pathname;
			theVoxelPosition=rest_sliceviewer('GetPosition', theViewer);
			theSamplePeriod =handles.ALFF.SamplePeriod;
			theBandRange	=[handles.ALFF.BandLow, handles.ALFF.BandHigh];						
			rest_powerspectrum('ShowFluctuation', theDataSetDir, theVoxelPosition, ...
							theSamplePeriod, theBandRange);
							
			%Update the Callback
			theCallback 	='';
			cmdDataSetDir	=sprintf('theDataSetDir= ''%s'';', theDataSetDir);
			cmdBrainMap 	=sprintf('theVoxelPosition=rest_sliceviewer(''GetPosition'', %g);', theViewer);
			cmdSamplePeriod =sprintf('theSamplePeriod= %g;', theSamplePeriod);
			cmdBandRange	=sprintf('theBandRange= [%g, %g];', theBandRange(1), theBandRange(2));
			cmdUpdateWaveGraph	='rest_powerspectrum(''ShowFluctuation'', theDataSetDir, theVoxelPosition, theSamplePeriod, theBandRange);';
			theCallback	=sprintf('%s\n%s\n%s\n%s\n%s\n',cmdDataSetDir, ...
								cmdBrainMap, cmdSamplePeriod, cmdBandRange, ...
								cmdUpdateWaveGraph);
			cmdClearVar ='clear theDataSetDir theVoxelPosition theSamplePeriod theBandRange;';
			rest_sliceviewer('UpdateCallback', theViewer, [theCallback cmdClearVar], 'ALFF Analysis');
			
			% Update some Message
			theMsg =sprintf('TR( s): %g\nBand( Hz): %g~%g', ...
							theSamplePeriod, theBandRange(1), theBandRange(2) );
			rest_sliceviewer('SetMessage', theViewer, theMsg);
		end
	catch
		rest_misc( 'DisplayLastException');
	end	
	set(hObject,'Enable','on', 'BackgroundColor', theOldColor);
	drawnow;
	rest_waitbar;


function ckboxRemoveTrendBefore_Callback(hObject, eventdata, handles)
	if get(hObject,'Value')
		handles.Detrend.BeforeFilter ='Yes';
	else	
		handles.Detrend.BeforeFilter ='No';
	end	
	guidata(hObject, handles);
	UpdateDisplay(handles);

function ckboxRemoveTrendAfter_Callback(hObject, eventdata, handles)
	if get(hObject,'Value')
		handles.Detrend.AfterFilter ='Yes';
	else	
		handles.Detrend.AfterFilter ='No';
	end	
	guidata(hObject, handles);
	UpdateDisplay(handles);

function btnDetrend_Callback(hObject, eventdata, handles)
	theOldColor=get(hObject,'BackgroundColor');		
	set(hObject,'Enable','off', 'BackgroundColor', 'red');
	drawnow;
	try
		Detrend(hObject,handles);
		msgbox('Remove the Linear Trend Over.',...
				'Detrend successfully' ,'help');
	catch
		rest_misc( 'DisplayLastException');
	end
	rest_waitbar;
	set(hObject,'Enable','on', 'BackgroundColor', theOldColor);
	drawnow;
	
function Detrend(hObject,handles)
	for x=1:size(handles.Cfg.DataDirs, 1)	
		%Update display
		set(handles.listDataDirs, 'Value', x);
		drawnow;
		if size(handles.Cfg.DataDirs, 1)>1,
			rest_waitbar((x-1)/size(handles.Cfg.DataDirs, 1)+0.01, ...
					handles.Cfg.DataDirs{x, 1}, ...
					'Removing the Linear Trend','Parent');
		end		
		rest_detrend(handles.Cfg.DataDirs{x, 1}, '_detrend');
		
		%Revise the data directories
		handles.Cfg.DataDirs{x, 1}=[handles.Cfg.DataDirs{x, 1} , '_detrend'];
		guidata(hObject, handles);	% Save Dir names
	end	
	UpdateDisplay(handles);
	


function edtAlffBandLow_Callback(hObject, eventdata, handles)
	handles.ALFF.BandLow =str2double(get(hObject,'String'));
	guidata(hObject, handles);

function edtAlffBandLow_CreateFcn(hObject, eventdata, handles)
	if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
	    set(hObject,'BackgroundColor','white');
	end


function edtAlffBandHigh_Callback(hObject, eventdata, handles)
	handles.ALFF.BandHigh =str2double(get(hObject,'String'));
	guidata(hObject, handles);

function edtAlffBandHigh_CreateFcn(hObject, eventdata, handles)
	if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
	    set(hObject,'BackgroundColor','white');
	end


function edtAlffSamplePeriod_Callback(hObject, eventdata, handles)
	handles.ALFF.SamplePeriod =str2double(get(hObject,'String'));
	guidata(hObject, handles);

function edtAlffSamplePeriod_CreateFcn(hObject, eventdata, handles)
	if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
	    set(hObject,'BackgroundColor','white');
	end




function btnAlffBandDetail_Callback(hObject, eventdata, handles)
%Compute the ALFF Band detailed message and show it
	sampleLength =inputdlg('Please input sample length: (i.e. the total number of time points)', ...
							'ALFF Band Detailed Message');
	sampleLength 	=str2num(sampleLength{1});
	sampleFreq 	 	=1/handles.ALFF.SamplePeriod;
	paddedLength	=rest_nextpow2_one35(sampleLength);
	freqPrecision	=sampleFreq /paddedLength;
	BandLowIdx		=handles.ALFF.BandLow * paddedLength * handles.ALFF.SamplePeriod;
	rBandLowIdx		=round(BandLowIdx);
	rBandLow		=rBandLowIdx /paddedLength /handles.ALFF.SamplePeriod;
	BandHighIdx		=handles.ALFF.BandHigh * paddedLength * handles.ALFF.SamplePeriod;
	rBandHighIdx	=round(BandHighIdx);
	rBandHigh		=rBandHighIdx /paddedLength /handles.ALFF.SamplePeriod;
	
	theWantBandInfo  =sprintf('%gHz --> Index=%g,    %gHz --> Index=%g', ...
						handles.ALFF.BandLow, BandLowIdx, ...
						handles.ALFF.BandHigh, BandHighIdx);
	theRealBandInfo  =sprintf('%gHz --> Index=%g,    %gHz --> Index=%g', ...
						rBandLow, rBandLowIdx, ...
						rBandHigh, rBandHighIdx);
	if rBandLowIdx==ceil(BandLowIdx)
		rBandLowIdx =floor(BandLowIdx);		
	else
		rBandLowIdx =ceil(BandLowIdx);
	end
	rBandLow		=rBandLowIdx /paddedLength /handles.ALFF.SamplePeriod;
	if rBandHighIdx==ceil(BandHighIdx)
		rBandHighIdx =floor(BandHighIdx);		
	else
		rBandHighIdx =ceil(BandHighIdx);
	end
	rBandHigh		=rBandHighIdx /paddedLength /handles.ALFF.SamplePeriod;	
	theAnother2Point =sprintf('%gHz --> Index=%g,    %gHz --> Index=%g', ...
						rBandLow, rBandLowIdx, ...
						rBandHigh, rBandHighIdx);

	msgbox( sprintf('The Band you want to use is:\n%s\n\nAdopted ALFF Band is:\n%s\n\n\nAnother 2 points'' Infomation:\n%s\n\nYou can view full information in "Power Spectrum"', theWantBandInfo, theRealBandInfo, theAnother2Point), ...
			'Calculated Band Range Hint' ,'help');
			
function BandPass(hObject, handles)
	for x=1:size(handles.Cfg.DataDirs, 1)	
		%Update display
		set(handles.listDataDirs, 'Value', x);
		drawnow;
		if size(handles.Cfg.DataDirs, 1)>1,
			rest_waitbar((x-1)/size(handles.Cfg.DataDirs, 1)+0.01, ...
					handles.Cfg.DataDirs{x, 1}, ...
					'Band Pass filter','Parent');
		end
				
		rest_bandpass(handles.Cfg.DataDirs{x, 1}, ...
					  handles.Filter.SamplePeriod, ...								  
					  handles.Filter.BandHigh, ...
					  handles.Filter.BandLow, ...
					  handles.Filter.Retrend, ...
					  handles.Cfg.MaskFile);
		%build the postfix for filtering
		thePostfix ='_filtered';					
		%Revise the data directories
		handles.Cfg.DataDirs{x, 1}=[handles.Cfg.DataDirs{x, 1} , thePostfix];
		guidata(hObject, handles);	% Save Dir names
	end
	UpdateDisplay(handles);

function btnHelp_Callback(hObject, eventdata, handles)
	web('http://resting-fmri.sourceforge.net');
	%web (sprintf('%s/man/English/ALFF/index.html', rest_misc( 'WhereIsREST')), '-helpbrowser');