alff_gui.m

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

function varargout = alff_gui(varargin)
%ALFF GUI by Xiaowei Song
%-----------------------------------------------------------
%	Copyright(c) 2007~2010
%	State Key Laboratory of Cognitive Neuroscience and Learning in Beijing Normal University
%	Written by Xiao-Wei Song 
%	http://resting-fmri.sourceforge.net
% $mail     =[e-mail]
% $Version =1.0;
% $Date =20070421;
%-----------------------------------------------------------
% 	<a href="[e-mail]">Mail to Author</a>: Xiaowei Song
%	Version=1.1;
%	Release=20070903;
% Last Modified by GUIDE v2.5 31-May-2007 17:32:29

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @alff_gui_OpeningFcn, ...
                   'gui_OutputFcn',  @alff_gui_OutputFcn, ...
                   'gui_LayoutFcn',  [] , ...
                   'gui_Callback',   []);
if nargin && ischar(varargin{1})
    gui_State.gui_Callback = str2func(varargin{1});
end

if nargout
    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
    gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT


% --- Executes just before alff_gui is made visible.
function alff_gui_OpeningFcn(hObject, eventdata, handles, varargin)
	%Matlab -Linux compatible, Initialize controls' default properties, dawnsong , 20070507
	InitControlProperties(hObject, handles);
	%Matlab -v6 compatible, create some frames instead of panels
	InitFrames(hObject,handles);
		
    [pathstr, name, ext, versn] = fileparts(mfilename('fullpath'));	
	%the {hdr/img} directories to be processed , count of volumns(i.e. time series' point number) corresponding to the dir		
    handles.Cfg.DataDirs ={}; %{[pathstr '\SampleData'], 10} ;	
    handles.Cfg.MaskFile = 'Default';                 %the  user defined mask file    	
	handles.Cfg.OutputDir =pwd;			    % pwd is the default dir for alff map result
	handles.Cfg.WantMeanAlffMap ='Yes';		%Calcute the mean alff map default
	handles.Filter.BandLow  =0.01;			%Config about Band pass filter, dawnsong 20070429
	handles.Filter.BandHigh =0.08;
	handles.Filter.UseFilter   	='No';
	handles.Filter.Retrend		='Yes';		% by default, always re-trend after linear filtering after removing linear trend	20070614, bug fixes
	handles.Filter.SamplePeriod=2;			%by default, set TR=2s
	handles.Detrend.BeforeFilter ='No';% ZangYF, 20070530 decide
	handles.Detrend.AfterFilter  ='No';% ZangYF, 20070530 decide
	handles.ALFF.BandLow =0.01;				% Band Info for ALFF computing
	handles.ALFF.BandHigh =0.08;			% Band Info for ALFF computing
	handles.ALFF.SamplePeriod =2;			% Band Info for ALFF computing
	handles.Log.SelfPath =pathstr;			% 20070507, dawnsong, just for writing log to file for further investigation
	handles.Log.Filename =GetLogFilename('','');
	%Performance record, use elapsed time to describe it, 20070507
	handles.Performance =0;				
	
    guidata(hObject, handles);
    UpdateDisplay(handles);
	movegui(handles.figAlffMain, 'center');
	set(handles.figAlffMain,'Name','Amplitude of Low Frequency Fluctuation');
	
    % Choose default command line output for alff_gui
    handles.output = hObject;	    
    guidata(hObject, handles);% Update handles structure

	% UIWAIT makes alff_gui wait for user response (see UIRESUME)
	% uiwait(handles.figAlffMain);

% --- Outputs from this function are returned to the command line.
function varargout = alff_gui_OutputFcn(hObject, eventdata, handles) 
	% Get default command line output from handles structure
	varargout{1} = handles.output;




function edtDataDirectory_Callback(hObject, eventdata, handles)
	theDir =get(hObject, 'String');    
	SetDataDir(hObject, theDir,handles);

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


function btnSelectDataDir_Callback(hObject, eventdata, handles)
	if size(handles.Cfg.DataDirs, 1)>0
		theDir =handles.Cfg.DataDirs{1,1};
	else
		theDir =pwd;
	end
    theDir =uigetdir(theDir, 'Please select the data directory to compute alff map: ');
	if ischar(theDir),
		SetDataDir(hObject, theDir,handles);	
	end	

function RecursiveAddDataDir(hObject, eventdata, handles)
	if prod(size(handles.Cfg.DataDirs))>0 && size(handles.Cfg.DataDirs, 1)>0,
		theDir =handles.Cfg.DataDirs{1,1};
	else
		theDir =pwd;
	end
	theDir =uigetdir(theDir, 'Please select the parent data directory of many sub-folders containing EPI data to compute ALFF map: ');
	if ischar(theDir),%Make the warning dlg off! 20071201
		setappdata(0, 'ALFF_DoingRecursiveDir', 1);
		theOldColor =get(handles.listDataDirs, 'BackgroundColor');
		set(handles.listDataDirs, 'BackgroundColor', [ 0.7373    0.9804    0.4784]);
		try			
			rest_RecursiveDir(theDir, 'alff_gui(''SetDataDir'',gcbo, ''%s'', guidata(gcbo) )');
		catch
			rest_misc( 'DisplayLastException');
		end	
		set(handles.listDataDirs, 'BackgroundColor', theOldColor);
		rmappdata(0, 'ALFF_DoingRecursiveDir');
	end	
	
function SetDataDir(hObject, ADir, handles)
	if ~ischar(ADir), return; end	
	theOldWarnings =warning('off', 'all');
    % if (~isequal(ADir , 0)) &&( (size(handles.Cfg.DataDirs, 1)==0)||(0==seqmatch({ADir} ,handles.Cfg.DataDirs( : , 1) ) ) )
	if rest_misc('GetMatlabVersion')>=7.3,
		ADir =strtrim(ADir);
	end	
	if (~isequal(ADir , 0)) &&( (size(handles.Cfg.DataDirs, 1)==0)||(0==length(strmatch(ADir,handles.Cfg.DataDirs( : , 1),'exact' ) ) ))
        handles.Cfg.DataDirs =[ {ADir , 0}; handles.Cfg.DataDirs];%update the dir    
		theVolumnCount =CheckDataDir(handles.Cfg.DataDirs{1,1} );	
		if (theVolumnCount<=0),
			if isappdata(0, 'ALFF_DoingRecursiveDir') && getappdata(0, 'ALFF_DoingRecursiveDir'), 
			else
				fprintf('There is no data or non-data files in this directory:\n%s\nPlease re-select\n\n', ADir);
				errordlg( sprintf('There is no data or non-data files in this directory:\n\n%s\n\nPlease re-select', handles.Cfg.DataDirs{1,1} )); 
			end
			handles.Cfg.DataDirs(1,:)=[];
			if size(handles.Cfg.DataDirs, 1)==0
				handles.Cfg.DataDirs=[];
			end	%handles.Cfg.DataDirs = handles.Cfg.DataDirs( 2:end, :);%update the dir        
		else
			handles.Cfg.DataDirs{1,2} =theVolumnCount;
		end	
	
        guidata(hObject, handles);
        UpdateDisplay(handles);
    end
	warning(theOldWarnings);
	
%% Update All the uiControls' display on the GUI
function UpdateDisplay(handles)
	if size(handles.Cfg.DataDirs,1)>0	
		theOldIndex =get(handles.listDataDirs, 'Value');
		%set(handles.listDataDirs, 'String',  handles.Cfg.DataDirs(: ,1) , 'Value', 1);	
		set(handles.listDataDirs, 'String',  GetInputDirDisplayList(handles) , 'Value', 1);
		theCount =size(handles.Cfg.DataDirs,1);
		if (theOldIndex>0) && (theOldIndex<= theCount)
			set(handles.listDataDirs, 'Value', theOldIndex);
		end
		set(handles.edtDataDirectory,'String', handles.Cfg.DataDirs{1,1});
		theResultFilename=get(handles.edtPrefix, 'String');
		theResultFilename=[theResultFilename '_' GetDirName(handles.Cfg.DataDirs{1,1})];
		set(handles.txtResultFilename, 'String', [theResultFilename  '.{hdr/img}']);
	else
		set(handles.listDataDirs, 'String', '' , 'Value', 0);
		set(handles.txtResultFilename, 'String', 'Result: Prefix_DirectoryName.{hdr/img}');
	end
	% set(handles.pnlParametersInput,'Title', ...			%show the first dir's Volumn count in the panel's title	
		 % ['Input Parameters (Volumn count= '...
		  % num2str( cell2mat(handles.Cfg.DataDirs(1,2)) )...
		  % ' in 'handles.Cfg.DataDirs(1,1) ' )']);
	set(handles.edtOutputDir ,'String', handles.Cfg.OutputDir);	
    if isequal(handles.Cfg.MaskFile, '')
        set(handles.edtMaskfile, 'String', 'Don''t use any Mask');
    else
        set(handles.edtMaskfile, 'String', handles.Cfg.MaskFile);    
    end
	%Set detrend dawnsong 20070820
	if strcmpi(handles.Detrend.BeforeFilter, 'Yes')
		%Update filter and detrend button's state according to Option: detrend/Filter 20070820
		set(handles.btnDetrend, 'Enable', 'on');
	else
		%Update filter and detrend button's state according to Option: detrend/Filter 20070820
		set(handles.btnDetrend, 'Enable', 'off');
	end
	%Set filter, dawnsong 20070430
	if strcmpi(handles.Filter.UseFilter, 'Yes')
		set(handles.ckboxFilter, 'Value', 1);		
		set(handles.ckboxRetrend, 'Enable', 'on');		
		set(handles.edtBandLow, 'Enable', 'on', 'String', num2str(handles.Filter.BandLow));
		set(handles.edtBandHigh, 'Enable', 'on', 'String', num2str(handles.Filter.BandHigh));
		set(handles.edtSamplePeriod, 'Enable', 'on', 'String', num2str(handles.Filter.SamplePeriod));
		%Update filter and detrend button's state according to Option: detrend/Filter 20070820
		set(handles.btnBandPass, 'Enable', 'on');	
	else
		set(handles.ckboxFilter, 'Value', 0);		
		set(handles.ckboxRetrend,'Enable', 'off');
		set(handles.edtBandLow, 'Enable', 'off', 'String', num2str(handles.Filter.BandLow));
		set(handles.edtBandHigh, 'Enable', 'off', 'String', num2str(handles.Filter.BandHigh));
		set(handles.edtSamplePeriod, 'Enable', 'off', 'String', num2str(handles.Filter.SamplePeriod));		
		%Update filter and detrend button's state according to Option: detrend/Filter 20070820
		set(handles.btnBandPass, 'Enable', 'off');	
	end
	
	%Set mean calculation, dawnsong 20070504	
	set(handles.ckboxDivideMean, 'Value', strcmpi(handles.Cfg.WantMeanAlffMap, 'Yes'));		
	
	% Set detrend option
	set(handles.ckboxRemoveTrendBefore, 'Value', strcmpi(handles.Detrend.BeforeFilter, 'Yes'));
	set(handles.ckboxRemoveTrendAfter, 'Value', strcmpi(handles.Detrend.AfterFilter, 'Yes'));	
	
	
%% check the Data dir to make sure that there are only {hdr,img}
function Result=GetInputDirDisplayList(handles)
	Result ={};
	for x=size(handles.Cfg.DataDirs, 1):-1:1
		Result =[{sprintf('%d# %s',handles.Cfg.DataDirs{x, 2},handles.Cfg.DataDirs{x, 1})} ;Result];
	end

% in this dir
function [nVolumn]=CheckDataDir(ADataDir)
    theFilenames = dir(ADataDir);
	theHdrFiles=dir(fullfile(ADataDir,'*.hdr'));
	theImgFiles=dir(fullfile(ADataDir,'*.img'));
	% if (length(theFilenames)-length(theHdrFiles)-length(theImgFiles))>2
		% nVolumn =-1;
		% errordlg(sprintf(['There should not be any file other than *.{hdr,img} .' ...
					% 'Please re-examin the DataDir\n\n%s '] ...
					% , ADataDir)); 
		% return;
	% end
	if ~length(theHdrFiles)==length(theImgFiles)
		nVolumn =-1;
		fprintf('%s, *.{hdr,img} should be pairwise. Please re-examin them.\n', ADataDir);
		errordlg('*.{hdr,img} should be pairwise. Please re-examin them.'); 
		return;
	end		
    count = 3; nVolumn = 0;		
	for count = 3:size(struct2cell(theFilenames),2)				
		if	(length(theFilenames(count).name)>4) && ...
			strcmpi(theFilenames(count).name(end-3:end) , '.hdr') 
			if strcmpi(theFilenames(count).name(1:end-4) ...                %hdr
					        , theFilenames(count+1).name(1:end-4) )     %img
				nVolumn = nVolumn + 1;  
			else
				%error('*.{hdr,img} should be pairwise. Please re-examin them.'); 
				nVolumn =-1;
				fprintf('%s, *.{hdr,img} should be pairwise. Please re-examin them.\n', ADataDir);
				errordlg('*.{hdr,img} should be pairwise. Please re-examin them.'); 
				break;
			end
		end			
	end
 	

	
function btnComputeAlff_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 (exist('alff.m','file')==2)
		%write log 20070507
		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 change it for further processing		
			end	
			
			%%Filter all the data and create a new directory, then compute the alff 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 change 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 change it for further processing		
			end
			
			%compute the alff 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}, ...
								'ALFF Computing','Parent');
				end				
				fprintf('\nALFF :"%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}) ] );
											
		        alff(   handles.Cfg.DataDirs{x, 1}, ...
						handles.ALFF.SamplePeriod, ...	
						handles.ALFF.BandHigh, ...
						handles.ALFF.BandLow, ...		                
		                handles.Cfg.MaskFile, ...
						theDstFile);							
				
				%20070504, divide alff brain by the mean within the mask
				if strcmpi(handles.Cfg.WantMeanAlffMap, 'Yes')
					theOrigAlffMap =theDstFile;				
					theMeanAlffMap =fullfile(theOutputDir,['m' thePrefix '_' ...
												GetDirName(handles.Cfg.DataDirs{x, 1}) ] );
					theMaskFile =handles.Cfg.MaskFile;
					rest_DivideMeanWithinMask(theOrigAlffMap, theMeanAlffMap, theMaskFile);
				end
			end		
			handles.Performance =cputime -handles.Performance; %Write down the End time , 20070903
			LogPerformance(handles);