fc_gui.m

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

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 Functional Connectivity figure to show corresponding voxel's time-course and its freq amplitude
			theDataSetDir 	=pathname;
			theVoxelPosition=rest_sliceviewer('GetPosition', theViewer);
			theSamplePeriod =handles.Filter.SamplePeriod;
			theBandRange	=[handles.Filter.BandLow, handles.Filter.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)
	try
		Detrend(hObject,handles);
		msgbox('Remove the Linear Trend Over.',...
				'Detrend successfully' ,'help');
	catch
		rest_misc( 'DisplayLastException');
	end
	rest_waitbar;

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 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');
	









function btnROIVoxelWise_Callback(hObject, eventdata, handles)
	%msgbox( sprintf('There is two way to define a ROI:\n\n1. Define a ball with its central coordinate and radius. Such as defining a ROI ball which centered at (-2,-36,37) and had a radius 10, you could enter "(-2,-36,37), radius=10".\n\n2. Any other ROI that''s not a ball. This kind of ROI could be defined by MRIcro or other softwares and must be a ANALYZE hdr/img file. Then select this file as ROI definition like selecting a mask.'), ...
	%		'ROI Definition method' ,'help');
	try
		if ~iscell(handles.Cfg.ROIList),
			handles.Cfg.ROIList =rest_SetROI('Init', handles.Cfg.ROIList);		
		else
			if prod(size(handles.Cfg.ROIList)),
				handles.Cfg.ROIList =rest_SetROI('Init', handles.Cfg.ROIList{1});
			else
				handles.Cfg.ROIList =rest_SetROI('Init');
			end
		end
	catch
		rest_SetROI('Delete');
	end
	guidata(hObject, handles);
	UpdateDisplay(handles);
	

function btnROIRegionWise_Callback(hObject, eventdata, handles)
	if ~iscell(handles.Cfg.ROIList), handles.Cfg.ROIList={handles.Cfg.ROIList}; end
	handles.Cfg.ROIList=rest_ROIList_gui(handles.Cfg.ROIList);	 
	% if prod(size(handles.Cfg.ROIList)) && size(handles.Cfg.ROIList, 1)==1,
		% handles.Cfg.ROIList =handles.Cfg.ROIList{1};
	% end
	guidata(hObject, handles);
	UpdateDisplay(handles);


function btnComputeFC_Callback(hObject, eventdata, handles)
	if (size(handles.Cfg.DataDirs, 1)==0) %check legal parameter set first
		errordlg('No Data found! Please re-config'); 
		return;
	end
	if size(handles.Cfg.ROIList, 1) ==0,
		errordlg('No ROI Defined! Please define ROI first'); 
		return;
	end
	%Remove the blank ROI definition at the end before judging
	if iscell(handles.Cfg.ROIList) && all(isspace(handles.Cfg.ROIList{1})),
		handles.Cfg.ROIList(1)=[];
	end
	if iscell(handles.Cfg.ROIList) && size(handles.Cfg.ROIList,1)<2 ,
		errordlg('Only one ROI Defined for ROI-wise functional connectivity! Please define ROI first'); 
		return;
	end
	
    if (exist('fc.m','file')==2)
		%write log 20070830
		handles.Log.Filename =GetLogFilename(handles.Cfg.OutputDir, get(handles.edtPrefix, 'String'));
		Log2File(handles);
		handles.Performance =cputime; %Write down the Start time , 20070903
		%start computation
		theOldDir =pwd;
		theOldColor=get(hObject,'BackgroundColor');		
		set(hObject,'Enable','off', 'BackgroundColor', 'red');
		drawnow;
		try
			%%Remove the linear trend first, and create a new directory, then do filtering
			if strcmpi(handles.Filter.UseFilter, 'Yes') && strcmpi(handles.Detrend.BeforeFilter, 'Yes'),
				Detrend(hObject, handles);
				%20070614, Bug fix, Update the data structure manually
				handles =guidata(hObject);	% I have to read it again, because I changed it for further processing		
			end	
			
			%%Filter all the data and create a new directory, then compute the Functional Connectivity value, dawnsong 20070429
			%Band pass filter
			if strcmpi(handles.Filter.UseFilter, 'Yes')
				BandPass(hObject, handles);	
				%20070614, Bug fix, Update the data structure manually
				handles =guidata(hObject);	% I have to read it again, because I changed it	for further processing			
			end	
			
			%%Remove the linear trend after filtering, and create a new directory, then do ReHo
			if strcmpi(handles.Filter.UseFilter, 'Yes') && strcmpi(handles.Detrend.AfterFilter, 'Yes'),
				Detrend(hObject, handles);
				%20070614, Bug fix, Update the data structure manually
				handles =guidata(hObject);	% I have to read it again, because I changed it for further processing		
			end
			
			%compute the Functional Connectivity brain
			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}, ...
								'Functional connectivity Computing','Parent');
				end				
				fprintf('\nFunctional connectivity :"%s"\n', handles.Cfg.DataDirs{x, 1});				
				
				theOutputDir=get(handles.edtOutputDir, 'String');
				thePrefix =get(handles.edtPrefix, 'String');
				theDstFile=fullfile(theOutputDir,[thePrefix '_' ...
											GetDirName(handles.Cfg.DataDirs{x, 1}) ] );
											
		        ResultMaps =fc( handles.Cfg.DataDirs{x, 1}, ...
								handles.Cfg.MaskFile, ...
								handles.Cfg.ROIList, ...
								theDstFile, ...
								handles.Covariables);							
				
				%20070504, divide Functional Connectivity brain by the mean within the mask
				if strcmpi(handles.Cfg.WantFisherZMap, 'Yes')
					if ndims(ResultMaps)>2 && size(ResultMaps, 1)>1 ,
						%There are many correlation maps
						for y=1:size(ResultMaps, 1),
							theOrigFCMap =ResultMaps{y, 1};
							[pathstr, name, ext, versn] = fileparts(theOrigFCMap);
							theFisherZMap =[pathstr, filesep, 'z', name, ext, versn];
							theMaskFile =handles.Cfg.MaskFile;
							rest_Corr2FisherZ(theOrigFCMap, theFisherZMap, theMaskFile);
						end
					elseif size(ResultMaps, 1)==1,
						%There is only one correlation map
						theOrigFCMap =theDstFile;
						[pathstr, name, ext, versn] = fileparts(theOrigFCMap);
						theFisherZMap =[pathstr, filesep, 'z', name, ext, versn];
						theMaskFile =handles.Cfg.MaskFile;
						rest_Corr2FisherZ(theOrigFCMap, theFisherZMap, theMaskFile);
					elseif ndims(ResultMaps)==2,
						%Time series correlation matrix
						theOrigFCMap =theDstFile;
						[pathstr, name, ext, versn] = fileparts(theOrigFCMap);
						theFisherZMap =[pathstr, filesep, 'z', name, ext, versn];
						ResultMaps =0.5 * log((1 +ResultMaps)./(1- ResultMaps));
						save([theFisherZMap, '.txt'], 'ResultMaps', '-ASCII', '-DOUBLE','-TABS')
					end
				end
			end		
			handles.Performance =cputime -handles.Performance; %Write down the End time , 20070903
			LogPerformance(handles);		
		catch	
			rest_misc( 'DisplayLastException');			
			errordlg(sprintf('Exception occured: \n\n%s' , lasterr)); 
		end		
		cd(theOldDir);
		set(hObject,'Enable','on', 'BackgroundColor', theOldColor);
		drawnow;
		rest_waitbar;
    else
        errordlg('No fc.m ! Please re-install'); 
    end






	
function edtCovariableFile_Callback(hObject, eventdata, handles)
	handles.Covariables.ort_file =get(hObject, 'String');
	guidata(hObject,handles); 

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


function btnSelectCovariableFile_Callback(hObject, eventdata, handles)
	[filename, pathname] = uigetfile({'*.txt; *.1D', 'Covariables'' time course file (*.txt; *.1D)'; ...
												'*.txt','text file (*.txt)'; ...
												'*.1D', 'AFNI 1D file(*.1D)'}, ...
												'Pick Covariables'' time course file');
    if ~(filename==0),
        handles.Covariables.ort_file =[pathname filename];
        guidata(hObject,handles);    
    end    
    UpdateDisplay(handles);