alff_gui.m

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

		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 alff.m ! Please re-install'); 
    end



function edtMaskfile_Callback(hObject, eventdata, handles)
	theMaskfile =get(hObject, 'String');
	if rest_misc('GetMatlabVersion')>=7.3,
		theMaskfile =strtrim(theMaskfile);
	end
	if exist(theMaskfile, 'file')
		handles.Cfg.MaskFile =theMaskfile;
		guidata(hObject, handles);
	else
		errordlg(sprintf('The mask file "%s" does not exist!\n Please re-check it.', theMaskfile));
	end

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


function btnSelectMask_Callback(hObject, eventdata, handles)
	[filename, pathname] = uigetfile({'*.img;*.mat', 'All Mask files (*.img; *.mat)'; ...
												'*.mat','MAT masks (*.mat)'; ...
												'*.img', 'ANALYZE masks(*.img)'}, ...
												'Pick a user''s  mask');
    if ~(filename==0)
        handles.Cfg.MaskFile =[pathname filename];
        guidata(hObject,handles);
    elseif ~( exist(handles.Cfg.MaskFile, 'file')==2)
        set(handles.rbtnDefaultMask, 'Value',[1]);        
        set(handles.rbtnUserMask, 'Value',[0]); 
		set(handles.edtMaskfile, 'Enable','off');
		set(handles.btnSelectMask, 'Enable','off');			
		handles.Cfg.MaskFile ='Default';
		guidata(hObject, handles);        
    end    
    UpdateDisplay(handles);


	
	

function rbtnDefaultMask_Callback(hObject, eventdata, handles)
	set(handles.edtMaskfile, 'Enable','off', 'String','Use Default Mask');
	set(handles.btnSelectMask, 'Enable','off');	
	drawnow;
    handles.Cfg.MaskFile ='Default';
	guidata(hObject, handles);
    set(handles.rbtnDefaultMask,'Value',1);
	set(handles.rbtnNullMask,'Value',0);
	set(handles.rbtnUserMask,'Value',0);

function rbtnUserMask_Callback(hObject, eventdata, handles)
	set(handles.edtMaskfile,'Enable','on', 'String',handles.Cfg.MaskFile);
	set(handles.btnSelectMask, 'Enable','on');
	set(handles.rbtnDefaultMask,'Value',0);
	set(handles.rbtnNullMask,'Value',0);
	set(handles.rbtnUserMask,'Value',1);
    drawnow;
	
function rbtnNullMask_Callback(hObject, eventdata, handles)
	set(handles.edtMaskfile, 'Enable','off', 'String','Don''t use any Mask');
	set(handles.btnSelectMask, 'Enable','off');
	drawnow;
	handles.Cfg.MaskFile ='';
	guidata(hObject, handles);
    set(handles.rbtnDefaultMask,'Value',0);
	set(handles.rbtnNullMask,'Value',1);
	set(handles.rbtnUserMask,'Value',0);



	

function listDataDirs_Callback(hObject, eventdata, handles)
	theIndex =get(hObject, 'Value');
	if isempty(theIndex) || theIndex<1,
        msgbox(sprintf('Nothing added.\n\nYou must add some diretories containing only paired {hdr/img} files first'), ...
					'REST' ,'help');
		return;
    end	
	
	if strcmp(get(handles.figAlffMain, 'SelectionType'), 'open') %when double click 
	    msgbox(sprintf('%s \t\nhas\t %d\t volumes\n\nTotal: %d Data Directories' , ... 
					handles.Cfg.DataDirs{theIndex, 1} , ...
	                handles.Cfg.DataDirs{theIndex, 2} , ...
					size(handles.Cfg.DataDirs,1)), ...
					'Volume count in selected dir' ,'help');
	end

function listDataDirs_KeyPressFcn(hObject, eventdata, handles)
	%Delete the selected item when 'Del' is pressed
    key =get(handles.figAlffMain, 'currentkey');
    if seqmatch({key},{'delete', 'backspace'})
       DeleteSelectedDataDir(hObject, eventdata,handles);
    end   
	
function DeleteSelectedDataDir(hObject, eventdata, handles)	
	theIndex =get(handles.listDataDirs, 'Value');
	if prod(size(handles.Cfg.DataDirs))==0 ...
		|| size(handles.Cfg.DataDirs, 1)==0 ...
		|| theIndex>size(handles.Cfg.DataDirs, 1),
		return;
	end
	theDir     =handles.Cfg.DataDirs{theIndex, 1};
	theVolumnCount=handles.Cfg.DataDirs{theIndex, 2};
	tmpMsg=sprintf('Delete\n\n "%s" \nVolumn Count :%d ?', theDir, theVolumnCount);
	if strcmp(questdlg(tmpMsg, 'Delete confirmation'), 'Yes')
		if theIndex>1,
			set(handles.listDataDirs, 'Value', theIndex-1);
		end
		handles.Cfg.DataDirs(theIndex, :)=[];
		if size(handles.Cfg.DataDirs, 1)==0
			handles.Cfg.DataDirs={};
		end	
		guidata(hObject, handles);
		UpdateDisplay(handles);
	end  

function ClearDataDirectories(hObject, eventdata, handles)	
	if prod(size(handles.Cfg.DataDirs))==0 ...
		|| size(handles.Cfg.DataDirs, 1)==0,
		return;
	end
	tmpMsg=sprintf('Attention!\n\n\nDelete all data directories?');
	if strcmpi(questdlg(tmpMsg, 'Clear confirmation'), 'Yes'),		
		handles.Cfg.DataDirs(:)=[];
		if prod(size(handles.Cfg.DataDirs))==0,
			handles.Cfg.DataDirs={};
		end	
		guidata(hObject, handles);
		UpdateDisplay(handles);
	end		
	
function listDataDirs_CreateFcn(hObject, eventdata, handles)
	if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
	    set(hObject,'BackgroundColor','white');
	end

	
function edtPrefix_Callback(hObject, eventdata, handles)
%nothing need to do, because I get the prefix when I need. Look at line 229 "thePrefix =get(handles.edtPrefix, 'String');"

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


	
	
function edtOutputDir_Callback(hObject, eventdata, handles)
	theDir =get(hObject, 'String');	
	SetOutputDir(hObject,handles, theDir);

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


function btnSelectOutputDir_Callback(hObject, eventdata, handles)
	theDir =handles.Cfg.OutputDir;
	theDir =uigetdir(theDir, 'Please select the data directory to compute alff map: ');
	if ~isequal(theDir, 0)
		SetOutputDir(hObject,handles, theDir);	
	end	
	
function SetOutputDir(hObject, handles, ADir)
	if 7==exist(ADir,'dir')
		handles.Cfg.OutputDir =ADir;
		guidata(hObject, handles);
	    UpdateDisplay(handles);
	end

function Result=GetDirName(ADir)
	if isempty(ADir), Result=ADir; return; end
	theDir =ADir;
	if strcmp(theDir(end),filesep)==1
		theDir=theDir(1:end-1);
	end	
	[tmp,Result]=fileparts(theDir);

	
function ckboxFilter_Callback(hObject, eventdata, handles)
	if get(hObject,'Value')
		handles.Filter.UseFilter ='Yes';
	else	
		handles.Filter.UseFilter ='No';
	end	
	guidata(hObject, handles);
	UpdateDisplay(handles);

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

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


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

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



function ckboxRetrend_Callback(hObject, eventdata, handles)
	if get(hObject,'Value')
		handles.Filter.Retrend ='Yes';
	else	
		handles.Filter.Retrend ='No';
	end	
	guidata(hObject, handles);
	UpdateDisplay(handles);

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

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

	
function ckboxDivideMean_Callback(hObject, eventdata, handles)
	if get(hObject,'Value')
		handles.Cfg.WantMeanAlffMap ='Yes';
	else	
		handles.Cfg.WantMeanAlffMap ='No';
	end
	guidata(hObject, handles);
	UpdateDisplay(handles);
	
function btnDivideMean_Callback(hObject, eventdata, handles)
	theOldColor=get(hObject,'BackgroundColor');		
	set(hObject,'Enable','off', 'BackgroundColor', 'red');
	drawnow;
	try
		[filename, pathname] = uigetfile({'*.img', 'alff files (*.img)'}, ...
													'Pick one alff map');
	    if (filename~=0)% not canceled
			if strcmpi(filename(end-3:end), '.img')%revise filename to remove extension		
				filename = filename(1:end-4);
			end
			if ~strcmpi(pathname(end), filesep)%revise filename to remove extension		
				pathname = [pathname filesep];
			end
			theOrigAlffMap =[pathname filename];
			theMeanAlffMap =[pathname 'm' filename];
			theMaskFile =handles.Cfg.MaskFile;
			rest_DivideMeanWithinMask(theOrigAlffMap, theMeanAlffMap, theMaskFile);
			msgbox(sprintf('Alff brain "%s.{hdr/img}" \ndivide its mean within mask successfully.\t\n\nSave to "%s.{hdr/img}"\n' , ... 
					theOrigAlffMap, theMeanAlffMap), ...				
					'Divide mean within mask successfully' ,'help');
	    end    
	catch
		rest_misc( 'DisplayLastException');
	end
	set(hObject,'Enable','on', 'BackgroundColor', theOldColor);
	drawnow;
	
function btnBandPass_Callback(hObject, eventdata, handles)
	theOldColor=get(hObject,'BackgroundColor');		
	set(hObject,'Enable','off', 'BackgroundColor', 'red');
	drawnow;
	try
	    %Band pass filter
		if strcmpi(handles.Filter.UseFilter, 'Yes')
			BandPass(hObject, handles);
			msgbox('Ideal Band Pass filter Over.',...
					'Filter successfully' ,'help');
		else
			errordlg(sprintf('You didn''t select option "Band Pass". \n\nPlease slect first.'));
		end
		UpdateDisplay(handles);	
	catch
		rest_misc( 'DisplayLastException');
	end
	rest_waitbar;
	set(hObject,'Enable','on', 'BackgroundColor', theOldColor);
	drawnow;

function InitFrames(hObject,handles)
	offsetY =83; %dawnsong, 20070504, add for the divide by the mask mean, the Y of Edit "OutPut Diectory"
	% for Matlab 6.5 compatible, draw a panel
	uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY+152 433 1]);
	uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY+202 433 1]);
	uicontrol(handles.figAlffMain, 'Style','Frame','Position',[90 offsetY+291 343 1]);
	uicontrol(handles.figAlffMain, 'Style','Frame','Position',[90 offsetY+202 1 90]);	
	uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY+152 1 280]);	
	uicontrol(handles.figAlffMain, 'Style','Frame','Position',[435 offsetY+152 1 280]);	
	uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY+432 433 1]);	
	uicontrol(handles.figAlffMain,'Style','Text','Position',[152 offsetY+430 100 14],...
		'String','Input Parameters');	
	uicontrol(handles.figAlffMain,'Style','Text','Position',[208 offsetY+288 40 14],...
		'String','Mask');	
	
	uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY+94 433 1]);	
	uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY-8 433 1]);	
	uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY-8 1 102]);	
	uicontrol(handles.figAlffMain, 'Style','Frame','Position',[435 offsetY-8 1 102]);	
	uicontrol(handles.figAlffMain,'Style','Text','Position',[152 offsetY+88 160 14],...
		'String','Output Parameters (ALFF map)');
		
	uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY+450 433 1]);	
	uicontrol(handles.figAlffMain, 'Style','Frame','Position',[435 offsetY+450 1 50]);	
	uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY+450 1 50]);	
	uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY+500 433 1]);	
	uicontrol(handles.figAlffMain,'Style','Text','Position',[142 offsetY+495 180 14],...
		'String','Option: Ideal Band Pass Filter');
	
	uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY+515 433 1]);	
	uicontrol(handles.figAlffMain, 'Style','Frame','Position',[435 offsetY+515 1 50]);