DPARSF_rest_sliceviewer.m
22f22bf83060master

DPARSF_rest_sliceviewer.m
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			function [varargout]=DPARSF_rest_sliceviewer(AOperation, varargin)
			% Show a brain's slice. "DPARSF_rest_sliceviewer" can be opened more than one instance like MRIcro, and supports multi-slice, overlay and so on. by Xiao-Wei Song
			%Usage: hFig =DPARSF_rest_sliceviewer('ShowImage', AFilename, CallBack);
			% DPARSF_rest_sliceviewer('Delete', AFigHandle);
			%Detailed usage is the code file "DPARSF_rest_sliceviewer.m"
			%------------------------------------------------------------------------------------------------------------------------------
			% Copyright(c) 2007~2010
			% State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University
			% Written by Xiao-Wei Song
			% http://www.restfmri.net
			% Mail to Authors: <a href="Dawnwei.Song@gmail.com">SONG Xiao-Wei</a>; <a href="ycg.yan@gmail.com">YAN Chao-Gan</a>; <a href="dongzy08@gmail.com">DONG Zhang-Ye</a>
			% Version=1.4;
			% Release=20100420;
			% Modified by SONG Xiao-Wei 20071101: change Position
			% Modified by YAN Chao-Gan 080808: also support NIFTI (.img/.hdr) images.
			% Modified by YAN Chao-Gan 080903: also support NIFTI (.nii) images.
			% Modified by YAN Chao-Gan 090101: added "save image as" function; change the display mode of transverse multislices as similar to AFNI; fixed the bug of cluster size threshold.
			% Modified by YAN Chao-Gan 090401: added "Correction Thresholds by AlphaSim" (under Misc menu); Fixed the bug of 'Set Overlay's Color bar' in Matlab R2007a or latter version which caused by the revision of imresize funtion in Matlab R2007a.
			% Modified by YAN Chao-Gan 090601: added color bar similar as AFNI.
			% Modified by YAN Chao-Gan and DONG Zhang-Ye 090808: make the Cluster Connectivity Criterion could be chosen among 6 voxels (surface), 18 voxels (edge) or 26 voxels (corner) according to rmm value.
			% Modified by YAN Chao-Gan, DONG Zhang-Ye and ZHU Wei-Xuan 091105: added P<->T, P<->F, P<->Z, P<->R; reading df from SPM statistical images; only+; save thrd; cluster report functions; fixed the bugs of color, montage and resize.
			% Modified by YAN Chao-Gan and DONG Zhang-Ye 100201: Added False Discovery Rate (FDR) Correction.
			% Modified by DONG Zhang-Ye and YAN Chao-Gan 100420: Fixed a bug in displaying overlay with different bounding box from those of underlay.
			% Modified by YAN Chao-Gan 090919: For DPARSF's special use, printing normalize pictures.
			% Modified by YAN Chao-Gan 100420: updated for DPARSF's special use, printing normalize pictures.
			%------------------------------------------------------------------------------------------------------------------------------

			if nargin<1, %No param Launch, 20070918
			%help(mfilename); %YAN Chao-Gan 090919
			if nargout>=1,
			varargout{1}=DPARSF_rest_sliceviewer('ShowImage',''); %by Default, I show a black brain image
			else
			DPARSF_rest_sliceviewer('ShowImage',''); %by Default, I show a black brain image
			end
			return;
			end

			%Initializitation
			global DPARSF_rest_sliceviewer_Cfg; %YAN Chao-Gan, 090919. %persistent REST_SliceViewer_Cfg; % run-time persistent config
			%if isempty(DPARSF_rest_sliceviewer_Cfg), disp('ko'); end
			if ~mislocked(mfilename),mlock; end
			%For further Debug, 20070915, to make sure the Config variable exist
			% if isempty(DPARSF_rest_sliceviewer_Cfg),
			% DPARSF_rest_sliceviewer_Cfg =getappdata(0, 'DPARSF_rest_sliceviewer_Cfg');
			% else
			% setappdata(0, 'DPARSF_rest_sliceviewer_Cfg', DPARSF_rest_sliceviewer_Cfg);
			% end

			try
			switch upper(AOperation),
			case 'SHOWIMAGE', %ShowImage
			if nargin==2,
			%DPARSF_rest_sliceviewer('ShowImage', theBrainMap); %reho_gui.m 989
			AFilename =varargin{1};
			ACallback ='';
			elseif nargin==3,
			%DPARSF_rest_sliceviewer('ShowImage', theBrainMap, [theCallback cmdClearVar], 'Power Spectrum');%reho_gui.m 1010
			AFilename =varargin{1};
			ACallback =varargin{2};
			else
			error(sprintf('Usage: hFig =DPARSF_rest_sliceviewer(''ShowImage'', AFilename); \n\t hFig =DPARSF_rest_sliceviewer(''ShowImage'', AFilename, ACallback);'));
			end

			%Let current handle of the figure be a GUID for the current SliceViewer
			% theFig =ExistDisplayFigure(DPARSF_rest_sliceviewer_Cfg, AFilename);
			% isExistFig =rest_misc( 'ForceCheckExistFigure' , theFig); %Force check whether the figure exist
			% if ~isExistFig
			%the specific image didn't exist, so I create one
			DPARSF_rest_sliceviewer_Cfg.Config(1+GetDisplayCount(DPARSF_rest_sliceviewer_Cfg)) =InitControls(AFilename, ACallback);
			%To Force display following the end of this if-clause
			theFig =DPARSF_rest_sliceviewer_Cfg.Config(GetDisplayCount(DPARSF_rest_sliceviewer_Cfg)).hFig;

			%I don't display the information defaultly
			ToggleInfoDisplay(DPARSF_rest_sliceviewer_Cfg.Config(GetDisplayCount(DPARSF_rest_sliceviewer_Cfg)));
			% end
			figure(theFig);
			varargout{1} =theFig;

			case 'UPDATECALLBACK', %UpdateCallback
			if nargin==2,
			AFigHandle =varargin{1};
			ACallback ='';
			ACallbackCaption='';
			elseif nargin==3,
			AFigHandle =varargin{1};
			ACallback =varargin{2};
			ACallbackCaption='';
			elseif nargin==4,
			AFigHandle =varargin{1};
			ACallback =varargin{2};
			ACallbackCaption=varargin{3};
			else
			error('Usage: DPARSF_rest_sliceviewer(''UpdateCallback'', AFigureHandle, ACallback, ACallbackCaption);');
			end
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =UpdateCallback(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal), ACallback, ACallbackCaption);
			ResizeFigure(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			end


			case 'DELETE', % Delete specific figure
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''Delete'', AFigHandle);'); end
			AFigHandle =varargin{1};
			DPARSF_rest_sliceviewer_Cfg =DeleteFigure(DPARSF_rest_sliceviewer_Cfg, AFigHandle);

			if ~GetDisplayCount(DPARSF_rest_sliceviewer_Cfg),
			DPARSF_rest_sliceviewer('QuitAllSliceViewer');
			end

			case {'CLICKPOSITION', 'SETPOSITION'}, %ClickPosition %SetPosition
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''ClickPosition'', AFigHandle); or DPARSF_rest_sliceviewer(''SetPosition'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0
			if strcmpi(AOperation, 'ClickPosition'), % for Mouse click
			if strcmpi(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).ViewMode, 'Orthogonal'),
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =ClickPositionCrossHair(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			elseif strcmpi(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).ViewMode, 'Sagittal'),
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =ClickPositionInSagittalMode(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			elseif strcmpi(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).ViewMode, 'Coronal'),
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =ClickPositionInCoronalMode(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			elseif strcmpi(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).ViewMode, 'Transverse'),
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =ClickPositionInTransverseMode(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			end
			elseif strcmpi(AOperation, 'SetPosition'), % for [x y z] manual input
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =SetPositionCrossHair(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			end


			%If yoke, then update all yoked image
			isSelfYoked =get(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).hYoke, 'Value');
			if isSelfYoked ,
			theDistanceFromOrigin =(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).LastPosition -DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Origin) .* DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).VoxelSize;
			%Dawnsong 20071102 Revise to make sure the left image/Right brain is +
			theDistanceFromOrigin =[-1, 1, 1].* theDistanceFromOrigin;

			for x=1:GetDisplayCount(DPARSF_rest_sliceviewer_Cfg),
			if x~=theCardinal ,
			isYoked =get(DPARSF_rest_sliceviewer_Cfg.Config(x).hYoke, 'Value');
			if isYoked,
			DPARSF_rest_sliceviewer('SetPhysicalPosition', DPARSF_rest_sliceviewer_Cfg.Config(x).hFig, theDistanceFromOrigin);
			end
			end
			end
			end

			%Execute the Callback
			DPARSF_rest_sliceviewer('RunCallback', AFigHandle);
			end

			case 'SETPHYSICALPOSITION', %SetPhysicalPosition, for Yoke, the physical position(mm) from the origin
			if nargin~=3, error('Usage: DPARSF_rest_sliceviewer(''SetPhysicalPosition'', AFigHandle, ADistanceFromOrigin);'); end
			AFigHandle =varargin{1};
			ADistanceFromOrigin =varargin{2};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			%Dawnsong 20071102 Revise to make sure the left image/Right brain is +
			ADistanceFromOrigin =[-1, 1, 1].* ADistanceFromOrigin;

			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =SetDistanceFromOrigin(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal), ADistanceFromOrigin);

			%Execute the Callback
			DPARSF_rest_sliceviewer('RunCallback', AFigHandle);
			end
			case 'RUNCALLBACK', %RunCallback , 20070625
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''RunCallback'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0
			% Run the Callback
			if ~isempty(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Callback)
			if ischar(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Callback),
			eval(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Callback); %run callback for caller
			elseif isa(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Callback, 'function_handle')
			%I give 2 parameters, 20070624
			%1) position: X, Y , Z,
			%2) and 3-dim: XSize, YSize, ZSize
			thePos =DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).LastPosition;
			theSize=size(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Volume);
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Callback(thePos, theSize);
			end
			end
			end


			case 'GETPOSITION', %GetPosition, return Absolute position where current cross-hair stay
			if nargin~=2, error('Usage: Position =DPARSF_rest_sliceviewer(''GetPosition'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0
			varargout{1}=DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).LastPosition;
			end

			case 'GETPHYSICALPOSITION', %GetPhysicalPosition return Coordinate .* VoxelSize (mm)
			if nargin~=2, error('Usage: DistanceFromOrigin =DPARSF_rest_sliceviewer(''GetPhysicalPosition'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0
			thePosition =DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).LastPosition;
			theOrigin =DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Origin;
			theVoxelSize=DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).VoxelSize;
			varargout{1} =(thePosition - theOrigin) * theVoxelSize;
			end

			case 'SETMESSAGE', %SetMessage, update the Message, I don't contain the Copyright any more , 20070915
			if nargin~=3, error('Usage: DPARSF_rest_sliceviewer(''SetMessage'', AFigHandle, AMessage);'); end
			AFigHandle =varargin{1};
			AMessage =varargin{2};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Message =AMessage;
			SetMessage(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			ResizeFigure(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			end

			case 'MAGNIFY', %Magnify, x0.5 -x1 -x2 -x3 -x4 -x5 -x6
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''Magnify'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =SetImage(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			end

			case 'QUITALLSLICEVIEWER', %QuitAllSliceViewer
			if nargin~=1, error('Usage: DPARSF_rest_sliceviewer(''QuitAllSliceViewer'');'); end
			for x=GetDisplayCount(DPARSF_rest_sliceviewer_Cfg):-1:1, % DawnSong, revised 20070625
			DPARSF_rest_sliceviewer('DELETE', DPARSF_rest_sliceviewer_Cfg.Config(x).Filename);
			end
			if mislocked(mfilename),munlock; end
			clear DPARSF_rest_sliceviewer_Cfg;

			case 'MONTAGE', %Montage
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''Montage'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			prompt ={'Across: (i.e. the number of columns)', 'Down: (i.e. the number of rows)', 'Spacing(voxels): ', 'Whether to show coordinate''s label: (1=yes and 0=no.)'};
			def ={ int2str(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Montage.Across), ...
			int2str(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Montage.Down), ...
			int2str(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Montage.Spacing), ...
			int2str(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Montage.WantLabel)};
			answer =inputdlg(prompt, 'Montage Set', 1, def);
			if numel(answer)==4,
			theVal =abs(round(str2num(answer{1})));
			if theVal==0, theVal=1; end
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Montage.Across = theVal;
			theVal =abs(round(str2num(answer{2})));
			if theVal==0, theVal=1; end
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Montage.Down =theVal;
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Montage.Spacing = abs(round(str2num(answer{3})));
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Montage.WantLabel = abs(round(str2num(answer{4})));
			%Update Image Display
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =SetImage(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			end
			end;
			case 'DF'
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''Montage'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			if isfield(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.Header,'descrip')
			headinfo=DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.Header.descrip; %dong 090921AConfig.Df.Ttest=0;
			if ~isempty(strfind(headinfo,'{T_['))% dong 100331 begin
			testFlag='T';
			Tstart=strfind(headinfo,'{T_[')+length('{T_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			elseif ~isempty(strfind(headinfo,'{F_['))
			testFlag='F';
			Tstart=strfind(headinfo,'{F_[')+length('{F_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			elseif ~isempty(strfind(headinfo,'{R_['))
			testFlag='R';
			Tstart=strfind(headinfo,'{R_[')+length('{R_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			elseif ~isempty(strfind(headinfo,'{Z_['))
			testFlag='Z';
			Tstart=strfind(headinfo,'{Z_[')+length('{Z_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			end
			if exist('testFlag')
			if ~isempty(testFlag)
			if exist('testDf')
			if testFlag == 'T'
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Df.Ttest=testDf;
			elseif testFlag == 'F'
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Df.Ftest=testDf;
			elseif testFlag == 'R'
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Df.Rtest=testDf;
			elseif testFlag == 'Z'
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Df.Ztest=testDf;
			end
			end % dong 100331 end
			end
			end
			end
			prompt ={'T-test (1 df) (two-tailed). For one sample T-test or paired T-test: df=n-1; for two sample T-test: df=n1+n2-2. (0 means not T-test).', 'F-test (2 df) (one-tailed). For one-way ANOVA (with s levels and n subjects): df1=s-1, df2=n-s. (0 means not F-test).','Z-test (two-tailed). 1 means Z-test. (0 means not Z-test)','R-test (1 df) (two-tailed). For Pearson''s Correlation Coefficient (with n samples): df=n-2. (0 means not R-test)'};
			def ={ int2str(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Df.Ttest), ...
			int2str(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Df.Ftest), ...
			int2str(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Df.Ztest), ...
			int2str(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Df.Rtest), ...
			};
			options.Resize='on';
			options.WindowStyle='modal';
			options.Interpreter='tex';
			answer =inputdlg(prompt, 'Input DF manually ', 1, def,options);
			if numel(answer)==4,
			theVal =abs(round(str2num(answer{1})));
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Df.Ttest = theVal;
			theVal =abs(round(str2num(answer{2})));
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Df.Ftest = theVal;
			theVal =abs(round(str2num(answer{3})));
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Df.Ztest = theVal;
			theVal =abs(round(str2num(answer{4})));
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Df.Rtest = theVal;
			SetMessage(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			end
			end;
			case 'ORTHOGONALVIEW', %OrthogonalView
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''OrthogonalView'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).ViewMode ='Orthogonal';
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =SetImage(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			end;

			case 'TRANSVERSEVIEW', %TransverseView
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''TransverseView'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).ViewMode ='Transverse';
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =SetImage(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			end;

			case 'SAGITTALVIEW', %SagittalView
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''SagittalView'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).ViewMode ='Sagittal';
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =SetImage(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			end;

			case 'CORONALVIEW', %CoronalView
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''CoronalView'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).ViewMode ='Coronal';
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =SetImage(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			end;

			case 'REPAINT', %Repaint
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''Repaint'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =SetImage(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			end;
			case 'MNI/TALAIRACH', %MNI/Talairach
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''Repaint'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			Transforming_MNI_Talairach(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			DPARSF_rest_sliceviewer('SetPosition', AFigHandle);
			end;

			case 'CHANGEUNDERLAY', %ChangeUnderlay
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''ChangeUnderlay'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			%Get the changed Underlay file
			theNewUnderlay =get(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).hUnderlayFile, 'String');
			% if exist(theNewUnderlay,'file')==2,
			% if ~all(isspace(theNewUnderlay)), %20070918
			%Set the current underlay
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Filename =theNewUnderlay;
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =InitUnderlay(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			% YAN Chao-Gan and DONG Zhang-Ye, 100401.
			if all(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).VoxelSize~=[1 1 1])
			msgbox('The voxel size of the underlay is not 1x1x1. If you want to add functional overlay to this structural underlay, the location may be not correct, please be careful!','Warning!')
			end
			if isfield(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Header,'mat')
			matinfo=DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Header.mat;
			if ~(matinfo(1,2)==0&&matinfo(1,3)==0&&matinfo(2,1)==0&&matinfo(2,3)==0&&matinfo(3,1)==0&&matinfo(3,2)==0&&matinfo(4,1)==0&&matinfo(4,2)==0&&matinfo(4,3)==0);
			msgbox('This NIfTI image includes an rotation transformation. You should reslice this data before attempting to underlay the image.','Warning!')
			end
			end

			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =SetImage(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			set(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).hUnderlayFile, 'String', theNewUnderlay, 'TooltipString', theNewUnderlay);
			% end
			end;

			case 'UNDERLAYSELECTION', %UnderlaySelection
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''UnderlaySelection'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			[filename, pathname] = uigetfile({'.img', 'ANALYZE or NIFTI files (.img)';'.nii','NIFTI files (.nii)'}, ...
			'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 add \ or /
			pathname = [pathname filesep];
			end
			theBrainMap =[pathname filename];
			set(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).hUnderlayFile, 'String', theBrainMap);
			DPARSF_rest_sliceviewer('ChangeUnderlay', AFigHandle);
			end
			end;
			case 'CLICKRECENTUNDERLAY', %ClickRecentUnderlay
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''ClickRecentUnderlay'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			theIndex =get(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).hUnderlayRecent, 'Value');
			if theIndex>1,
			theBrainMap =DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Recent.Underlay{theIndex-1};
			set(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).hUnderlayFile, 'String', theBrainMap);
			set(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).hUnderlayRecent, 'Value', 1);
			DPARSF_rest_sliceviewer('ChangeUnderlay', AFigHandle);
			end
			end;

			case 'CHANGEOVERLAY', %ChangeOverlay
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''ChangeOverlay'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			%Get the changed Overlay file
			theNewOverlay =get(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).hOverlayFile, 'String');
			% if exist(theNewOverlay,'file')==2,
			% if ~all(isspace(theNewOverlay)),
			%Set the current Overlay
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =LoadOverlay(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal), theNewOverlay);
			% YAN Chao-Gan and DONG Zhang-Ye, 100401.
			if isfield(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.Header,'mat')
			matinfo=DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.Header.mat;
			if ~(matinfo(1,2)==0&&matinfo(1,3)==0&&matinfo(2,1)==0&&matinfo(2,3)==0&&matinfo(3,1)==0&&matinfo(3,2)==0&&matinfo(4,1)==0&&matinfo(4,2)==0&&matinfo(4,3)==0);
			msgbox('This NIfTI image includes an rotation transformation. You should reslice this data before attempting to overlay the image.','Warning!')
			end
			end
			set(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).hSeeOverlay, 'Value', 1);
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =SetImage(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			set(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).hOverlayFile, 'String', theNewOverlay, 'TooltipString', theNewOverlay);
			% end
			end;

			case 'OVERLAYSELECTION', %OverlaySelection
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''UnderlaySelection'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			[filename, pathname] = uigetfile({'.img', 'ANALYZE or NIFTI files (.img)';'.nii','NIFTI files (.nii)'}, ...
			'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 add \ or /
			pathname = [pathname filesep];
			end
			theBrainMap =[pathname filename];
			set(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).hOverlayFile, 'String', theBrainMap);
			set(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).hEdtPValue, 'String', '1'); %DONG 100118 change the init P value
			DPARSF_rest_sliceviewer('ChangeOverlay', AFigHandle);
			if isfield(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.Header,'descrip') %DONG 100118 to read the DF when overlay selected.
			headinfo=DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.Header.descrip; %dong 090921AConfig.Df.Ttest=0;
			if isfield(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.Header,'descrip')
			headinfo=DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.Header.descrip; %dong 090921AConfig.Df.Ttest=0;
			if ~isempty(strfind(headinfo,'{T_['))% dong 100331 begin
			testFlag='T';
			Tstart=strfind(headinfo,'{T_[')+length('{T_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			elseif ~isempty(strfind(headinfo,'{F_['))
			testFlag='F';
			Tstart=strfind(headinfo,'{F_[')+length('{F_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			elseif ~isempty(strfind(headinfo,'{R_['))
			testFlag='R';
			Tstart=strfind(headinfo,'{R_[')+length('{R_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			elseif ~isempty(strfind(headinfo,'{Z_['))
			testFlag='Z';
			Tstart=strfind(headinfo,'{Z_[')+length('{Z_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			end
			if exist('testFlag')
			if ~isempty(testFlag)
			if exist('testDf')
			if testFlag == 'T'
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Df.Ttest=testDf;
			elseif testFlag == 'F'
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Df.Ftest=testDf;
			elseif testFlag == 'R'
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Df.Rtest=testDf;
			elseif testFlag == 'Z'
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Df.Ztest=testDf;
			end
			end % dong 100331 end
			end
			end
			end
			end
			end
			end
			case 'CLICKRECENTOVERLAY', %ClickRecentOverlay
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''ClickRecentOverlay'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			theIndex =get(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).hOverlayRecent, 'Value');
			if theIndex>1,
			theBrainMap =DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Recent.Overlay{theIndex-1};
			set(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).hOverlayFile, 'String', theBrainMap);
			set(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).hOverlayRecent, 'Value', 1);
			DPARSF_rest_sliceviewer('ChangeOverlay', AFigHandle);
			end
			end;

			case 'OVERLAY_SETTHRDABSVALUE', %Overlay_SetThrdAbsValue, %Change from the Absolute value Edit control
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''Overlay_SetThrdAbsValue'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.ValueThrdAbsolute =SetThrdAbsValue(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =ThresholdOverlayVolume(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =SetImage(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			end
			case 'OVERLAY_SETTHRDCLUSTERSIZE', %Overlay_SetThrdClusterSize
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''Overlay_SetThrdClusterSize'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.PNflag=0;
			theConfig =DPARSF_rest_sliceviewer_Cfg.Config(theCardinal);
			prompt ={'Set Cluster Size(voxel) must be GREATER than: ', 'Set Volume (mm^3) must be GREATER than: (this value would be transformed to Cluster Size according to the Overlay''s size and its voxel''s size)','!!!Set rmm value as Connectivity Criterion. If your voxel size is 333, then rmm=4 means 6 voxels (surface connected), rmm=5 means 18 voxels (edge connected, SPM use this criterion), and rmm=6 means 26 voxels (corner connected). You also can type ''SPM_Criterion'' if you want to use SPM''s criterion (18 voxels, edge connected). Note: just suitable for cube voxels currently.'};
			def ={num2str(theConfig.Overlay.ClusterSizeThrd) ,...
			num2str(theConfig.Overlay.ClusterSizeThrd(theConfig.Overlay.VoxelSize(1)theConfig.Overlay.VoxelSize(2)*theConfig.Overlay.VoxelSize(3))) ,...
			num2str(theConfig.Overlay.ClusterConnectivityCriterionRMM)}; %Added Cluster Connectivity Criterion option by YAN Chao-Gan 090711.
			answer =inputdlg(prompt, 'Threshold by cluster size ', 1, def);
			if numel(answer)==3,
			theVal =abs(str2num(answer{1}));
			if theVal~=theConfig.Overlay.ClusterSizeThrd
			theConfig.Overlay.ClusterSizeThrd =round(theVal);
			else
			theVal =abs(str2num(answer{2}));
			theConfig.Overlay.ClusterSizeThrd =round(theVal/(theConfig.Overlay.VoxelSize(1)theConfig.Overlay.VoxelSize(2)theConfig.Overlay.VoxelSize(3)));
			end

			theVal =abs(str2num(answer{3}));
			if isempty (theVal)
			theConfig.Overlay.ClusterConnectivityCriterionRMM='SPM_Criterion';
			theConfig.Overlay.ClusterConnectivityCriterion=18;
			else
			theConfig.Overlay.ClusterConnectivityCriterionRMM=theVal;
			if theVal < theConfig.Overlay.VoxelSize(1)
			theConfig.Overlay.ClusterConnectivityCriterion = 0;
			elseif theVal < theConfig.Overlay.VoxelSize(1)*sqrt(2)
			theConfig.Overlay.ClusterConnectivityCriterion = 6;
			elseif theVal < theConfig.Overlay.VoxelSize(1)*sqrt(3)
			theConfig.Overlay.ClusterConnectivityCriterion = 18;
			else
			theConfig.Overlay.ClusterConnectivityCriterion = 26;
			end
			if theConfig.Overlay.ClusterConnectivityCriterion==0
			uiwait(msgbox('The Connectivity Criterion has been set to 0, no voxels would be considered as connected, thus no cluster can be found.','Warning for Cluster Connectivity Criterion','warn'));
			end
			end

			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =theConfig;
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =ThresholdOverlayVolume(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =SetImage(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			end
			end
			case 'OVERLAY_MISC', %Overlay_Misc
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''Overlay_Misc'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =Overlay_Misc(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			DPARSF_rest_sliceviewer('Repaint', AFigHandle);
			end
			case 'OPEN_TEMPLATE', %Open_Template
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''Overlay_Misc'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =Open_Template(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			DPARSF_rest_sliceviewer('Repaint', AFigHandle);
			end
			case 'CLUSTERSREPORT'
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''Clusters Report'', AFigHandle);'); end

			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			theConfig =DPARSF_rest_sliceviewer_Cfg.Config(theCardinal);
			if theConfig.Overlay.ClusterConnectivityCriterion==0 % Revised by YAN Chao-Gan 091126. Check if rmm is not zero.
			uiwait(msgbox({'Please set Cluster Connectivity Criterion (rmm value or SPM_Criterion) by clicking Cluser Size button first.';...
			},'Set Cluster Connectivity Criterion first!'));
			return;
			end
			if ~isempty(find(theConfig.Overlay.VolumeThrd))
			rest_report( theConfig.Overlay.VolumeThrd,theConfig.Overlay.Header,theConfig.Overlay.ClusterConnectivityCriterion);
			else
			disp('There is no Cluster !');
			end
			end
			case 'CURRENTTHRD2MASK', %dong save thrd2mask 2009-09-09
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''CurrentThrd2Mask'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			theConfig =DPARSF_rest_sliceviewer_Cfg.Config(theCardinal);
			theConfig.Overlay.VolumeThrd(theConfig.Overlay.VolumeThrd<0.0002)=0;
			if theConfig.Overlay.ClusterConnectivityCriterion==0 % Revised by YAN Chao-Gan 091126. Check if rmm is not zero.
			uiwait(msgbox({'Please set Cluster Connectivity Criterion (rmm value or SPM_Criterion) by clicking Cluser Size button first.';...
			},'Set Cluster Connectivity Criterion first!'));
			return;
			end
			theMask =CurrentThrd2Mask(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			if ~isempty(theMask),
			[filename, pathname] = uiputfile('*.img','Save all the survived clusters: ');
			if isequal(filename,0) \|\| isequal(pathname,0),
			else
			if length(filename)>4,
			if strcmpi(filename(end-3:end), '.img')
			filename = filename(1:end-4);
			end
			end
			theMaskFile =fullfile(pathname, filename);
			theConfig.Overlay.Header.Origin=theConfig.Overlay.Origin; %%Yan 080610
			rest_writefile(theMask, theMaskFile, size(theConfig.Overlay.Volume), ...
			theConfig.Overlay.VoxelSize, theConfig.Overlay.Header,'double');%'int16'); %%Yan 080610
			theConfig.LastSavedMask =[theMaskFile ,'.img'];
			if ~isempty(theConfig.Callback.Save2Mask),
			eval(theConfig.Callback.Save2Mask);
			end
			end
			DPARSF_rest_sliceviewer('Repaint', AFigHandle);
			else
			errordlg(sprintf('No cluster found at (%s)', ...
			num2str(Pos_Underlay2Overlay(theConfig, theConfig.LastPosition) -theConfig.Overlay.Origin)));
			end
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =theConfig;
			end
			case 'CURRENTCLUSTER2MASK', %CurrentCluster2Mask
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''CurrentCluster2Mask'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			theConfig =DPARSF_rest_sliceviewer_Cfg.Config(theCardinal);
			if theConfig.Overlay.ClusterConnectivityCriterion==0 % Revised by YAN Chao-Gan 091126. Check if rmm is not zero.
			uiwait(msgbox({'Please set Cluster Connectivity Criterion (rmm value or SPM_Criterion) by clicking Cluser Size button first.';...
			},'Set Cluster Connectivity Criterion first!'));
			return;
			end
			theMask =CurrentCluster2Mask(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			if ~isempty(theMask),
			[filename, pathname] = uiputfile('*.img','Save current point''s cluster: ');
			if isequal(filename,0) \| isequal(pathname,0),
			else
			if length(filename)>4,
			if strcmpi(filename(end-3:end), '.img')
			filename = filename(1:end-4);
			end
			end
			theMaskFile =fullfile(pathname, filename);
			theConfig.Overlay.Header.Origin=theConfig.Overlay.Origin; %%Yan 080610
			rest_writefile(theMask, theMaskFile, size(theConfig.Overlay.Volume), ...
			theConfig.Overlay.VoxelSize, theConfig.Overlay.Header,'double');%int16 %%Yan 080610
			%Added by YAN Chao-Gan 091127. Also save binary mask.
			theBinaryMaskFile=fullfile(pathname, ['BinaryMask_',filename]);
			rest_writefile(theMask~=0, theBinaryMaskFile, size(theConfig.Overlay.Volume), ...
			theConfig.Overlay.VoxelSize, theConfig.Overlay.Header,'double');
			theConfig.LastSavedMask =[theMaskFile ,'.img'];
			if ~isempty(theConfig.Callback.Save2Mask),
			eval(theConfig.Callback.Save2Mask);
			end
			end
			DPARSF_rest_sliceviewer('Repaint', AFigHandle);
			else
			errordlg(sprintf('No cluster found at (%s)', ...
			num2str(Pos_Underlay2Overlay(theConfig, theConfig.LastPosition) -theConfig.Overlay.Origin)));
			end

			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =theConfig;
			end

			case 'SAVERECENT', %SaveRecent
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''SaveRecent'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			SaveRecent(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal), 'RecentOverlay');
			SaveRecent(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal), 'RecentUnderlay');
			end

			case 'CHANGECOLORELEMENT', %ChangeColorElement
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''ChangeColorElement'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =SetColorElements(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =SetImage(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			end

			case 'TOGGLEINFODISPLAY', %ToggleInfoDisplay
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''ToggleInfoDisplay'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			ToggleInfoDisplay(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			end

			case 'UPDATECALLBACK_SAVE2MASK', %UpdateCallback_Save2Mask
			if nargin~=3, error('Usage: DPARSF_rest_sliceviewer(''UpdateCallback_Save2Mask'', AFigHandle, ACallback);'); end
			AFigHandle =varargin{1};
			ACallback =varargin{2};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Callback.Save2Mask =ACallback;
			end
			case 'GETSAVEDMASKFILENAME', %GetSavedMaskFilename
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''GetSavedMaskFilename'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			varargout{1} =DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).LastSavedMask;
			else
			varargout{1} ='';
			end

			case 'SHOWOVERLAY', %ShowOverlay
			if nargin>3, error('Usage: DPARSF_rest_sliceviewer(''ShowOverlay'', AOverlay); or DPARSF_rest_sliceviewer(''ShowOverlay'', AFigHandle, AOverlay);'); end
			AFigHandle =varargin{1};
			if ~ischar(AFigHandle),
			AOverlay =varargin{2};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			set(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).hOverlayFile, 'String', AOverlay);
			DPARSF_rest_sliceviewer('ChangeOverlay', AFigHandle);
			end
			else %I will create a new slice-viewer
			AOverlay =varargin{1};
			theFig = DPARSF_rest_sliceviewer; %I can't write "()" considering Matlab 6.5 compatiable
			DPARSF_rest_sliceviewer('ShowOverlay', theFig, AOverlay);
			varargout{1} =theFig;
			end

			case 'ONKEYPRESS', %OnKeyPress
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''OnKeyPress'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =OnKeyPress(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			%For Updating
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =SetImage(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			%For Yoke
			DPARSF_rest_sliceviewer('SetPosition', AFigHandle);
			end
			case 'ONLYPOSITIVE', %dong 2009-09-09
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''Overlay_SetThrdAbsValue'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			%dong 100327 beging
			if DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.PNflag==0
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.VolumeForFlag=DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.VolumeThrd;
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.PNflag=1;
			end
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.VolumeThrd(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.VolumeForFlag<0)=0;
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.VolumeThrd(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.VolumeForFlag>DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.ValueThrdAbsolute)=DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.VolumeForFlag(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.VolumeForFlag>DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.ValueThrdAbsolute);
			%dong 100327 end
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =SetImage(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			end
			case 'ONLYNEGATIVE', %dong 2009-09-09
			if nargin~=2, error('Usage: DPARSF_rest_sliceviewer(''Overlay_SetThrdAbsValue'', AFigHandle);'); end
			AFigHandle =varargin{1};
			theCardinal =ExistViewer(DPARSF_rest_sliceviewer_Cfg, AFigHandle);
			if theCardinal>0,
			%dong 100327 begin
			if DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.PNflag==0
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.VolumeForFlag=DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.VolumeThrd;
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.PNflag=1;
			end
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.VolumeThrd(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.VolumeForFlag>0)=0;
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.VolumeThrd(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.VolumeForFlag<-DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.ValueThrdAbsolute)=DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.VolumeForFlag(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.VolumeForFlag<-DPARSF_rest_sliceviewer_Cfg.Config(theCardinal).Overlay.ValueThrdAbsolute);
			%dong 100327 end
			DPARSF_rest_sliceviewer_Cfg.Config(theCardinal) =SetImage(DPARSF_rest_sliceviewer_Cfg.Config(theCardinal));
			end
			otherwise
			end
			catch
			rest_misc( 'DisplayLastException');
			end

			function Result =InitControls(AFilename, ACallback)
			%Initialization 20070525
			theFig =figure('Units', 'pixel', 'Toolbar', 'none', 'MenuBar', 'none', ...
			'NumberTitle', 'off', 'Name', AFilename, 'DoubleBuffer', 'on');
			set(theFig, 'DeleteFcn', sprintf('DPARSF_rest_sliceviewer(''Delete'', %g);', theFig) );
			set(theFig, 'KeyPressFcn', sprintf('DPARSF_rest_sliceviewer(''OnKeyPress'', %g);', theFig) );

			MarginX =10; MarginY =10;
			OffsetX =MarginX;
			OffsetY =MarginY +245;%OffsetY =MarginY +200; dong

			%Create Slice View options
			%Create uicontrols to config Yoke or [X Y Z] position to set current cross-hair to locate the voxel
			theLeft =OffsetX; theBottom =OffsetY;
			hFrameSetPos=uicontrol(theFig, 'Style','Frame', 'Visible','off', 'Units','pixels', ...
			'BackgroundColor', get(theFig,'Color'), ...
			'Position', [theLeft,theBottom,150,180]);
			%YAN Chao-Gan, 090919. Set the uicontrols visible off
			uicontrol(theFig, 'Style','pushbutton','Visible','off', 'Units','pixels', ...
			'String', 'Slice Viewer', ... %'BackgroundColor', get(theFig,'Color'), ...
			'Callback', 'DPARSF_rest_sliceviewer', ...
			'Position', [theLeft+35,theBottom+172,80,18]);

			theLeft =OffsetX+MarginX; theBottom =OffsetY+MarginY+20 +20+MarginY/2 +10 +MarginY;
			hYoke =uicontrol(theFig, 'Style','checkbox', 'Visible','off','Units','pixels', ...
			'String', 'Yoke', ...
			'BackgroundColor', get(theFig,'Color'), ...
			'Position',[theLeft, theBottom+75, 80,15]);
			theLeft =OffsetX+MarginX+56+MarginX; theBottom =OffsetY+MarginY+20 +20+MarginY/2 +10 +MarginY;
			hCrosshair =uicontrol(theFig, 'Style','checkbox', 'Visible','off','Units','pixels', ...
			'String', 'Crosshair', 'Value', 1,...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''Repaint'', %g);',theFig) , ...
			'BackgroundColor', get(theFig,'Color'), ...
			'Position',[theLeft, theBottom+75, 70,15]);


			theEditCallbackFcn =sprintf('DPARSF_rest_sliceviewer(''SetPosition'', %g);', theFig);
			theLeft =OffsetX+MarginX-5; theBottom =OffsetY+MarginY+35+MarginY/2;
			uicontrol(theFig, 'Style','text', 'Visible','off','Units','pixels', ...
			'String', 'X(mm)', ...
			'BackgroundColor', get(theFig,'Color'), ...
			'Position',[theLeft, theBottom+85, 46,15]);
			theLeft =OffsetX+MarginX-5; theBottom =OffsetY+MarginY+20;
			hEditPositionX =uicontrol(theFig, 'Style','edit', 'Visible','off','Units','pixels', ...
			'String', '0', ...
			'BackgroundColor', 'white', ...
			'Callback', theEditCallbackFcn, ...
			'Position',[theLeft, theBottom+85, 46,20]);

			theLeft =OffsetX+MarginX+36+MarginX-5; theBottom =OffsetY+MarginY+35+MarginY/2;
			uicontrol(theFig, 'Style','text', 'Visible','off','Units','pixels', ...
			'String', 'Y(mm)', ...
			'BackgroundColor', get(theFig,'Color'), ...
			'Position',[theLeft, theBottom+85, 46,15]);
			theLeft =OffsetX+MarginX+36+MarginX-5; theBottom =OffsetY+MarginY+20;
			hEditPositionY =uicontrol(theFig, 'Style','edit', 'Visible','off','Units','pixels', ...
			'String', '0', ...
			'BackgroundColor', 'white', ...
			'Callback', theEditCallbackFcn, ...
			'Position',[theLeft, theBottom+85, 46,20]);

			theLeft =OffsetX+MarginX+36+MarginX+36+MarginX-5; theBottom =OffsetY+MarginY+35+MarginY/2;
			uicontrol(theFig, 'Style','text', 'Visible','off','Units','pixels', ...
			'String', 'Z(mm)', ...
			'BackgroundColor', get(theFig,'Color'), ...
			'Position',[theLeft, theBottom+85, 46,15]);
			theLeft =OffsetX+MarginX+36+MarginX+36+MarginX-5; theBottom =OffsetY+MarginY+20;
			hEditPositionZ =uicontrol(theFig, 'Style','edit', 'Visible','off','Units','pixels', ...
			'String', '0', ...
			'BackgroundColor', 'white', ...
			'Callback', theEditCallbackFcn, ...
			'Position',[theLeft, theBottom+85, 46,20]);

			theLeft =OffsetX+MarginX-5; theBottom =OffsetY+MarginY+20;
			hMagnify =uicontrol(theFig, 'Style','popupmenu', 'Visible','off','Units','pixels', ...
			'String', {'x0.5', 'x1', 'x2', 'x3'}, ...
			'Value', 2, ...
			'BackgroundColor', get(theFig,'Color'), ...
			'Enable', 'off', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''Magnify'', %g);',theFig), ...
			'Position',[theLeft, theBottom+70, 70,10]);
			if license('test','image_toolbox')
			set(hMagnify, 'Enable', 'on');
			else
			warning('image_toolbox not valid');
			end

			theLeft =OffsetX+MarginX+60+MarginX-5; theBottom =OffsetY+MarginY+20;
			hMniTal =uicontrol(theFig, 'Style','popupmenu', 'Visible','off','Units','pixels', ...
			'String', {'MNI/Talairach Coordinates', 'From Talairach to MNI', 'From MNI to Talairach'}, ...
			'Value', 1, ...
			'BackgroundColor', get(theFig,'Color'), ...
			'Enable', 'on', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''MNI/Talairach'', %g);',theFig), ...
			'Position',[theLeft, theBottom+70, 68,10]);


			%OffsetY =OffsetY +30;%20070911, for complete information display
			theLeft =OffsetX+MarginX; theBottom =OffsetY+MarginY;
			hVoxelIntensity=uicontrol(theFig, 'Style','text', 'Visible','off','Units','pixels', ...
			'String', '', 'TooltipString', 'Intensity of the current point', ...
			'BackgroundColor', get(theFig,'Color'), ...
			'HorizontalAlignment', 'left', ... % 'Visible', 'off', ...
			'Position',[theLeft-5, theBottom+42, 110,32]);

			%Create a Message label to display some specific message, dawnsong 20070526
			theLeft =OffsetX+MarginX; theBottom =OffsetY +100 +MarginY;
			hMsgLabel =uicontrol(theFig, 'Style','text', 'Visible','off','Units','pixels', ...
			'String', sprintf('Dawnwei.Song Copyright 2007-2010, all rights reserved'), ...
			'BackgroundColor', get(theFig,'Color'), ...
			'HorizontalAlignment', 'left', 'Enable', 'inactive',...
			'ButtonDownFcn', sprintf('DPARSF_rest_sliceviewer(''ToggleInfoDisplay'', %g);',theFig), ...
			'Position',[theLeft, theBottom, 130,10]);

			% Create a Callback Button to do sth.
			theLeft =OffsetX+MarginX; theBottom =OffsetY +100 +MarginY +10;
			% hDoCallbackBtn =-1;
			% if ~isempty(ACallback) && ischar(ACallback)
			% hDoCallbackBtn =uicontrol(theFig, 'Style','pushbutton', ...
			% 'Units','pixels', 'String', 'Do sth.', ...
			% 'Callback', ACallback, ...
			% 'Position',[theLeft, theBottom, 130,10]);
			% end
			%View Buttons
			theLeft =OffsetX+MarginX-4; theBottom =OffsetY +MarginY-2;
			theIcon =imread(fullfile(rest_misc( 'WhereIsREST'), 'icoTransverse.jpg'));
			hViewTransverse =uicontrol(theFig, 'Style','pushbutton', ...
			'Visible','off','Units','pixels', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''TransverseView'', %g);',theFig) , ...
			'CData', theIcon,...
			'Position',[theLeft, theBottom, 34,36]);
			theLeft =OffsetX+MarginX+30; theBottom =OffsetY +MarginY-2;
			theIcon =imread(fullfile(rest_misc( 'WhereIsREST'), 'icoSagittal.jpg'));
			hViewSagittal =uicontrol(theFig, 'Style','pushbutton', ...
			'Visible','off','Units','pixels', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''SagittalView'', %g);',theFig) , ...
			'CData', theIcon,...
			'Position',[theLeft, theBottom, 34,36]);
			theLeft =OffsetX+MarginX+34+30; theBottom =OffsetY +MarginY-2;
			theIcon =imread(fullfile(rest_misc( 'WhereIsREST'), 'icoCoronal.jpg'));
			hViewCoronal =uicontrol(theFig, 'Style','pushbutton', ...
			'Visible','off','Units','pixels', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''CoronalView'', %g);',theFig) , ...
			'CData', theIcon,...
			'Position',[theLeft, theBottom, 34,36]);
			theLeft =OffsetX+MarginX+34+34+30; theBottom =OffsetY +MarginY-2;
			theIcon =imread(fullfile(rest_misc( 'WhereIsREST'), 'icoOrthogonal.jpg'));
			hViewOrthogonal =uicontrol(theFig, 'Style','pushbutton', ...
			'Visible','off','Units','pixels', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''OrthogonalView'', %g);',theFig) , ...
			'CData', theIcon,...
			'Position',[theLeft, theBottom, 34,36]);
			theLeft =OffsetX+MarginX+34+30; theBottom =OffsetY +MarginY+34;
			hViewMontage =uicontrol(theFig, 'Style','pushbutton', ...
			'Visible','off','Units','pixels', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''Montage'', %g);',theFig) , ...
			'String', 'Montage','TooltipString', 'Montage: Multislice',...
			'Position',[theLeft, theBottom, 68,24]);



			%Add Underlay file selection directly
			theLeft =OffsetX; theBottom =MarginY+225;%theBottom =MarginY+180; dong +100
			hUnderlayRecent =uicontrol(theFig, 'Style','popupmenu', 'Visible','off','Units','pixels', ...
			'String', {'Underlay: '}, 'Value', 1, ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''ClickRecentUnderlay'', %g);',theFig), ...
			'BackgroundColor', get(theFig,'Color'), ...
			'Position',[theLeft, theBottom, 75,20]);
			theLeft =OffsetX; theBottom =MarginY+205;
			hUnderlayFile =uicontrol(theFig, 'Style','edit', 'Visible','off','Units','pixels', ...
			'String', '', ...
			'BackgroundColor', 'white', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''ChangeUnderlay'', %g);',theFig), ...
			'Position',[theLeft, theBottom, 150,20]);
			theLeft =OffsetX+116; theBottom =MarginY+225;
			uicontrol(theFig, 'Style','pushbutton', 'Visible','off','Units','pixels', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''UnderlaySelection'', %g);',theFig) , ...
			'String', '...', 'FontWeight', 'bold', ...
			'Position',[theLeft, theBottom, 34,15]);
			%Add Overlay file selection directly
			theLeft =OffsetX; theBottom =MarginY+185;
			hOverlayRecent =uicontrol(theFig, 'Style','popupmenu', 'Visible','off','Units','pixels', ...
			'String', {'Overlay: '}, 'Value', 1, ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''ClickRecentOverlay'', %g);',theFig), ...
			'BackgroundColor', get(theFig,'Color'), ...
			'Position',[theLeft, theBottom, 75,20]);
			theLeft =OffsetX; theBottom =MarginY+165;
			hOverlayFile =uicontrol(theFig, 'Style','edit', 'Visible','off','Units','pixels', ...
			'String', '', ...
			'BackgroundColor', 'white', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''ChangeOverlay'', %g);',theFig), ...
			'Position',[theLeft, theBottom, 150,20]);
			theLeft =OffsetX+116; theBottom =MarginY+185;
			uicontrol(theFig, 'Style','pushbutton', 'Visible','off','Units','pixels', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''OverlaySelection'', %g);',theFig) , ...
			'String', '...','FontWeight', 'bold', ...
			'Position',[theLeft, theBottom, 34,15]);
			%Add Overlay Options, 20070913
			theLeft =OffsetX; theBottom =MarginY;
			hFrameOverlay=uicontrol(theFig, 'Style','Frame', 'Visible','off','Units','pixels', ...
			'BackgroundColor', get(theFig,'Color'), ...
			'Position', [theLeft,theBottom,150,145]); %dong
			hSeeOverlay =uicontrol(theFig, 'Style','checkbox', 'Visible','off','Units','pixels', ...
			'String', 'See Overlay', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''Repaint'', %g);',theFig), ...
			'BackgroundColor', get(theFig,'Color'), ...
			'Position',[theLeft+35, theBottom+140, 80,15]);
			uicontrol(theFig, 'Style','text', 'Visible','off','Units','pixels', ...
			'String', 'Threshold', ...
			'BackgroundColor', get(theFig,'Color'), ...
			'Position',[theLeft+5, theBottom+120, 50,18]);
			hEdtThrdValue =uicontrol(theFig, 'Style','edit', 'Visible','off','Units','pixels', ...
			'String', '', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''Overlay_SetThrdAbsValue'', %g);',theFig), ...
			'BackgroundColor', 'white', ...
			'Position',[theLeft+75, theBottom+120, 70,18]);

			hSliderThrdValue =uicontrol(theFig, 'Style','slider', 'Visible','off','Units','pixels', ...
			'TooltipString', 'Absolute Value for thresholding the overlay', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''Overlay_SetThrdAbsValue'', %g);',theFig), ...
			'BackgroundColor', get(theFig,'Color'), ...
			'Position',[theLeft+5, theBottom+101, 140,15]);


			uicontrol(theFig, 'Style','text', 'Visible','off','Units','pixels', ...%dong
			'String', 'P', ...
			'BackgroundColor', get(theFig,'Color'), ...
			'Position',[theLeft+5, theBottom+78, 10,18]);
			hEdtPValue =uicontrol(theFig, 'Style','edit', 'Visible','off','Units','pixels', ...%P-value need improve dong
			'String', '1', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''Overlay_SetThrdAbsValue'', %g);',theFig), ...
			'BackgroundColor', 'w', ...
			'Position',[theLeft+15, theBottom+80, 35,18]);
			hdf =uicontrol(theFig, 'Style','pushbutton', ... %add df dong 090921
			'Visible','off','Units','pixels', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''DF'', %g);',theFig),...
			'String', 'df', ...
			'Position',[theLeft+55, theBottom+80, 30,18]);
			uicontrol(theFig, 'Style','text', 'Visible','off','Units','pixels', ...%dong
			'String', 'Only', ...
			'BackgroundColor', get(theFig,'Color'), ...
			'Position',[theLeft+85, theBottom+78, 30,18]);
			uicontrol(theFig, 'Style','pushbutton', 'Visible','off','Units','pixels', ... %only + dong 090921
			'String', '+', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''OnlyPositive'', %g);',theFig),...
			'Position',[theLeft+112, theBottom+80, 15,18]);
			uicontrol(theFig, 'Style','pushbutton', 'Visible','off','Units','pixels', ... %only + dong 090921
			'String', '-', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''OnlyNegative'', %g);',theFig),...
			'Position',[theLeft+129, theBottom+80, 15,18]);

			uicontrol(theFig, 'Style','pushbutton', 'Visible','off','Units','pixels', ...
			'String', 'Cluster Size', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''Overlay_SetThrdClusterSize'', %g);',theFig),... %here dong
			'Position',[theLeft+5, theBottom+30, 70,24]);
			hOverlayMisc =uicontrol(theFig, 'Style','popupmenu', 'Visible','off','Units','pixels', ...
			'String', {'Misc', 'Set Overlay''s Opacity', ...
			'Set Range of Threshold', 'Set Label Color', 'Set Overlay''s Color bar','Save Image As','Correction Thresholds by AlphaSim',...%YAN Chao-Gan 081223: add "save image as" function %YAN CHao-Gan 090401: add "Correction Thresholds by AlphaSim"
			'False Discovery Rate (FDR) Correction'}, ... %Dong 100115 add False discovery rate(FDR) control, a statistical method used in multiple hypothesis testing to correct for multiple comparisons
			'Value', 1, ...
			'BackgroundColor', get(theFig,'Color'), ...
			'Enable', 'on', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''Overlay_Misc'', %g);',theFig), ...
			'Position',[theLeft+5, theBottom+55, 70,24]);
			hTemplate =uicontrol(theFig, 'Style','popupmenu', 'Visible','off','Units','pixels', ...
			'String', {'Template', 'Open AAL', 'Open Brodmann','Open Ch2','Open Ch2 Bet'}, ...
			'Value', 1, ...
			'BackgroundColor', get(theFig,'Color'), ...
			'Enable', 'on', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''Open_Template'', %g);',theFig), ...
			'Position',[theLeft+75, theBottom+55, 70,24]);
			uicontrol(theFig, 'Style','pushbutton', 'Visible','off','Units','pixels', ...
			'String', 'Save Cluster', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''CurrentCluster2Mask'', %g);',theFig),...
			'Position',[theLeft+75, theBottom+30, 70,24]);
			uicontrol(theFig, 'Style','pushbutton', 'Visible','off','Units','pixels', ...%dong 090920
			'String', 'Save Clusters', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''CurrentThrd2Mask'', %g);',theFig),...
			'Position',[theLeft+5, theBottom+5, 70,24]);
			uicontrol(theFig, 'Style','pushbutton', 'Visible','off','Units','pixels', ...%dong 090920
			'String', 'Cl. Report', ...
			'Callback', sprintf('DPARSF_rest_sliceviewer(''ClustersReport'', %g);',theFig),...
			'Position',[theLeft+75, theBottom+5, 70,24]);
			% uicontrol(theFig, 'Style','pushbutton', 'Units','pixels', ...
			% 'String', 'Thrd2Mask', ...
			% 'Callback', sprintf('DPARSF_rest_sliceviewer(''Overlay_SetThrdClusterSize'', %g);',theFig),...
			% 'Position',[theLeft+75, theBottom+5, 70,24]);

			%Colorbar for overlay, do as AFNI, 20070921
			theAxesButtonDownFcn =sprintf('DPARSF_rest_sliceviewer(''ChangeColorElement'', %g);',theFig);
			hAxesColorbar =axes('Parent', theFig, 'Box', 'on', ...
			'Units', 'pixel', 'DrawMode','fast', 'Visible', 'off', ...
			'Position', [1 1 1 1], ...
			'YDir','normal', 'XTickLabel',[],'XTick',[], ...
			'YTickLabel',[],'YTick',[], ...
			'ButtonDownFcn', theAxesButtonDownFcn);
			hImageColorbar =image('Tag','OverlayColorbar', 'Parent', hAxesColorbar);
			hImageCover=uicontrol(theFig, 'Style','text', 'Units','pixels', ...%dong 1130
			'String', '', 'Visible','off',...
			'BackgroundColor', get(theFig,'Color'), ...
			'Position',[theLeft+500, theBottom+578, 20,18]);
			set(hAxesColorbar,'YDir','normal','ButtonDownFcn', theAxesButtonDownFcn, 'XTickLabel',[],'XTick',[], 'YTickLabel',[],'YTick',[]);

			clear theLeft theBottom;% dong 2009-09-09 end GUI

			%Save to config
			AConfig.hFig =theFig; %handle of the config

			%Save parameters handles
			AConfig.hFrameSetPos =hFrameSetPos;
			AConfig.hYoke =hYoke;
			AConfig.hCrosshair =hCrosshair;
			AConfig.hMagnify =hMagnify;
			AConfig.hMniTal =hMniTal;
			AConfig.hEditPositionX =hEditPositionX;
			AConfig.hEditPositionY =hEditPositionY;
			AConfig.hEditPositionZ =hEditPositionZ;
			%Save Voxel intensity label handle
			AConfig.hVoxelIntensity=hVoxelIntensity;
			%Save message handle
			AConfig.hMsgLabel =hMsgLabel;
			AConfig.Message ='';
			%Save Do Callback button's handle
			% AConfig.hDoCallbackBtn =hDoCallbackBtn;

			%Save important variables
			AConfig.Filename =AFilename; %Default for underlay
			%AConfig.Callback =ACallback; %Default for click callback
			%Callback define series, 20070924
			AConfig.Callback.ChangingPosition =ACallback;
			AConfig.Callback.Save2Mask ='';

			%View Mode, 20070911
			AConfig.ViewMode ='Orthogonal'; %Default View mode
			AConfig.ViewSeries =[]; %Default no any view series
			AConfig.Montage.Across =1;
			AConfig.Montage.Down =1;
			AConfig.Montage.Spacing=3;
			AConfig.Montage.WantLabel=1;
			%P_value
			AConfig.Df.Ttest=0;
			AConfig.Df.Ftest=[0,0];
			AConfig.Df.Ztest=0;
			AConfig.Df.Rtest=0;
			AConfig.Overlay.Header='';
			%Underlay and Overlay, handles
			AConfig.hUnderlayFile =hUnderlayFile;
			AConfig.hUnderlayRecent =hUnderlayRecent;
			AConfig.hOverlayFile =hOverlayFile;
			AConfig.hOverlayRecent =hOverlayRecent;

			AConfig.hSeeOverlay =hSeeOverlay;
			AConfig.hSliderThrdValue =hSliderThrdValue;
			AConfig.hEdtThrdValue =hEdtThrdValue;
			AConfig.hEdtPValue=hEdtPValue; %dong 2009-09-09
			AConfig.hOverlayMisc =hOverlayMisc;
			AConfig.hTemplate =hTemplate;
			AConfig.hFrameOverlay =hFrameOverlay;

			AConfig.hAxesColorbar =hAxesColorbar;
			AConfig.hImageColorbar =hImageColorbar;
			AConfig.hImageCover=hImageCover;
			%Overlay Configuration
			%Data for Overlay
			AConfig.Overlay.Filename ='';
			AConfig.Overlay.Volume =zeros(61, 73, 61);

			AConfig.Overlay.PNflag =0;
			AConfig.Overlay.VolumeThrd =AConfig.Overlay.Volume;%Volume Thresholded by Cluster Size
			AConfig.Overlay.VolumeForFlag=AConfig.Overlay.Volume;
			AConfig.Overlay.VoxelSize=[3 3 3];
			AConfig.Overlay.Origin =[31 43 25];
			%Overlay's Info - statistics
			Result.Overlay.MinNegative =-Inf;
			Result.Overlay.MaxNegative =0;
			Result.Overlay.MinPositive =0;
			Result.Overlay.MaxPositive =Inf;
			Result.Overlay.AbsMin =0;
			Result.Overlay.AbsMax =Inf;
			%Options for Overlay
			AConfig.Overlay.Colormap =jet(64);
			AConfig.Overlay.ColorbarCmd ='jet(64)';
			%[0 0 1;1 0 0]; %Pure Blue and Pure Red
			%[0 0 0.5625;0 0 0.875;0 0 1;1 0 0;0.875 0 0;0.5 0 0];
			AConfig.Overlay.Opacity =1; %Default, 50% Opacity
			AConfig.Overlay.LabelColor ='white';
			AConfig.Overlay.ValueP =1; %P value dong 2009-09-09
			AConfig.Overlay.ValueThrdAbsolute =0; %Default, show all
			AConfig.Overlay.ValueThrdMin = -Inf; %Default, show all, not absolute, may be negative
			AConfig.Overlay.ValueThrdMax = Inf; %Default, show all, not absolute , may be negative, this allows me to set a range such as showing negative values only or positives only
			AConfig.Overlay.ValueThrdSeries = NaN; %Default, show all
			AConfig.Overlay.ClusterSizeThrd =0; %Default, 0 voxels, for not confining cluster-size
			AConfig.Overlay.ClusterRadiusThrd =0; %Default radius(mm) for Cluster size definition
			AConfig.Overlay.ClusterConnectivityCriterion =0; %Default Connectivity Criterionradius: 0.
			AConfig.Overlay.ClusterConnectivityCriterionRMM=0;
			AConfig.Overlay.InfoAal='None'; %AAL descriptions



			AConfig.Overlay.Qvalue=0.05;%For FDR
			AConfig.Overlay.Qmaskname='';
			AConfig.Overlay.Conproc=1;
			AConfig.Overlay.Tchoose=2; % YAN Chao-Gan, 100201
			%Load Recent Images/brains
			AConfig =InitRecent(AConfig);

			%Save Axes's handles
			AConfig.hAxesSagittal =-1;
			AConfig.hAxesCoronal =-1;
			AConfig.hAxesTransverse =-1;
			%Save Images' handles
			AConfig.hImageSagittal =-1;
			AConfig.hImageCoronal =-1;
			AConfig.hImageTransverse =-1;
			%Save Lines' handles
			AConfig.hXLineSagittal =-1; %x
			AConfig.hYLineSagittal =-1; %y
			AConfig.hXLineCoronal =-1; %x
			AConfig.hYLineCoronal =-1; %y
			AConfig.hXLineTransverse =-1; %x
			AConfig.hYLineTransverse =-1; %y
			AConfig.LastPosition =[90 126 72]; %Default
			AConfig.LastAxes ='Transverse'; %For slice previous/next by pressing up/down left/right j/k ... on keyboard
			AConfig.LastSavedMask =''; %For ROI define callback

			AConfig =InitUnderlay(AConfig);



			%Move Auto-Balance out of initialization just for speeding up for starting this slice-viewer
			%Save Maping Image parameters, Auto balance 20070911 revised
			% theSatMin=0; theSatMax =0; nBins=2^16; %Satuation Min/Max
			% theMaxVal=max(AConfig.Volume(:));
			% if theMaxVal<257,
			% nBins =256;
			% else
			% nBins =theMaxVal;
			% end
			% theSum =histc(AConfig.Volume(:), [1:nBins]);
			% theSum =cumsum(theSum);
			% theCdf =theSum/theSum(end);
			% if rest_misc('GetMatlabVersion')>=7.3
			% idxSatMin =find(theCdf>0.01, 1, 'first');
			% idxSatMax =find(theCdf>=0.99, 1, 'first');
			% else
			% idxSatMin =find(theCdf>0.01);
			% idxSatMin =idxSatMin(1);
			% idxSatMax =find(theCdf>=0.99);
			% idxSatMax =idxSatMax(1);
			% end
			% idxSatMin =find(theCdf>0.01, 1, 'first');
			% idxSatMax =find(theCdf>=0.99, 1, 'first');
			% theSatMin =(idxSatMin-1)/(nBins-1) *theMaxVal;
			% theSatMax =(idxSatMax-1)/(nBins-1) *theMaxVal;
			% AConfig.Contrast.GrayDepth =256;
			% AConfig.Contrast.SatMax =theSatMax;
			% AConfig.Contrast.SatMin =theSatMin;
			%20070911, AutoBalance for contrast
			% AConfig.Contrast.WindowWidth =theSatMax -theSatMin;
			% AConfig.Contrast.WindowCenter=(theSatMax +theSatMin)/2;
			%For debugging, 20070911
			% disp(AConfig.Contrast);


			%%Update the figure, the follow function called order shouldn't change
			%Display Images
			AConfig =SetImage(AConfig);

			Result =AConfig;
			return;

			function Result =DeleteFigure(AGlobalConfig, AFigHandle)
			x =ExistViewer(AGlobalConfig, AFigHandle);
			if x>0,
			theDisplayCount =GetDisplayCount(AGlobalConfig);
			isExistFig =rest_misc( 'ForceCheckExistFigure' , AGlobalConfig.Config(x).hFig);
			if isExistFig,
			%Save the recent menu
			DPARSF_rest_sliceviewer('SaveRecent', AFigHandle);

			%Delete the figure and rearrange the queue
			delete(AGlobalConfig.Config(x).hFig);
			if theDisplayCount>x
			for y=x:theDisplayCount-1
			AGlobalConfig.Config(x) =AGlobalConfig.Config(x+1);
			end
			end
			AGlobalConfig.Config(theDisplayCount)=[];
			end
			end
			Result =AGlobalConfig;

			function Result =GetDisplayCount(AGlobalConfig)
			%Get the Count of display, this program allow multi-view of brain like MRIcro
			if isempty(AGlobalConfig) \|\| isempty(AGlobalConfig.Config),
			Result =0;
			else
			Result =length(AGlobalConfig.Config);
			end
			return;

			function Result =ListViewerFigure(AGlobalConfig, AFilename)
			Result =[];
			if (isstruct(AGlobalConfig) && isstruct(AGlobalConfig.Config))
			for x=1:length(AGlobalConfig.Config)
			if strcmpi( AGlobalConfig.Config(x).Filename, AFilename)
			Result =[Result; AGlobalConfig.Config(x).hFig];
			end
			end
			else
			return;
			end

			function Result =ExistViewer(AGlobalConfig, AFigureHandle)
			Result =0;
			if (isstruct(AGlobalConfig) && isstruct(AGlobalConfig.Config))
			for x=1:length(AGlobalConfig.Config)
			if AGlobalConfig.Config(x).hFig==AFigureHandle,
			Result =x;
			return;
			end
			end
			else
			return;
			end

			function Result =SetImage(AConfig)
			if strcmpi(AConfig.ViewMode, 'Orthogonal'),
			Result =SetView_Orthogonal(AConfig);
			elseif strcmpi(AConfig.ViewMode, 'Transverse'),
			Result =SetView_Transverse(AConfig);
			elseif strcmpi(AConfig.ViewMode, 'Sagittal'),
			Result =SetView_Sagittal(AConfig);
			elseif strcmpi(AConfig.ViewMode, 'Coronal'),
			Result =SetView_Coronal(AConfig);
			end
			%Draw the color bar
			Result =DrawColorbar(Result);

			set(AConfig.hFig, 'Name', sprintf('REST Slice Viewer -- For DPARSF''s special use')); %YAN Chao-Gan, 090919.
			%Display Underlay Filename
			set(AConfig.hUnderlayFile, 'String', sprintf('%s', AConfig.Filename));
			%Display Overlay Filename
			set(AConfig.hOverlayFile, 'String', sprintf('%s', AConfig.Overlay.Filename));

			%Show Voxel's position [x y z]
			ShowPositionInEdit(AConfig);
			%Update the message
			SetMessage(AConfig);
			%Resize figure width and height
			ResizeFigure(AConfig);


			function Result =SetView_Orthogonal(AConfig)
			%Underlay Image manuplication, 20070913
			theSagittalImg =GetGrayImage('Sagittal', AConfig.Volume, AConfig.LastPosition(1)); %x
			theCoronalImg =GetGrayImage('Coronal', AConfig.Volume, AConfig.LastPosition(2)); %y
			theTransverseImg =GetGrayImage('Transverse', AConfig.Volume, AConfig.LastPosition(3));%z

			%Auto balance
			theSagittalImg =SaturateContrast(theSagittalImg, AConfig.Contrast.SatMin, AConfig.Contrast.SatMax);
			theCoronalImg =SaturateContrast(theCoronalImg, AConfig.Contrast.SatMin, AConfig.Contrast.SatMax);
			theTransverseImg =SaturateContrast(theTransverseImg, AConfig.Contrast.SatMin, AConfig.Contrast.SatMax);

			%Calculate the Result Image after Magnifying
			theMagnifyCoefficient =GetMagnifyCoefficient(AConfig);
			if license('test','image_toolbox')==1 && theMagnifyCoefficient~=1,
			if rest_misc('GetMatlabVersion')>=7.4 %YAN Chao-Gan 090401: The imresize function has been completely rewritten in Matlab R2007a. Fixed the bug of 'Set Overlay's Color bar' in Matlab R2007a or latter version.
			theSagittalImg =imresize_old(theSagittalImg, theMagnifyCoefficient);
			theCoronalImg =imresize_old(theCoronalImg, theMagnifyCoefficient);
			theTransverseImg=imresize_old(theTransverseImg, theMagnifyCoefficient);
			else
			theSagittalImg =imresize(theSagittalImg, theMagnifyCoefficient);
			theCoronalImg =imresize(theCoronalImg, theMagnifyCoefficient);
			theTransverseImg=imresize(theTransverseImg, theMagnifyCoefficient);
			end
			end

			% Revise the Axes position to make it comfort to Magnify
			theFramePosParamSet =get(AConfig.hFrameSetPos, 'Position');
			theLeft =theFramePosParamSet(1) +theFramePosParamSet(3) +5;
			theBottom =10; %theFramePosParamSet(2);
			theLeftTransverse =theLeft;
			theLeftCoronal =theLeftTransverse;
			theLeftSagittal =theLeftCoronal +size(theCoronalImg,2)+ 2;
			theBottomTransverse =theBottom;
			theBottomCoronal =theBottomTransverse +size(theTransverseImg,1) +2;
			theBottomSagittal =theBottomCoronal;

			thePosTransverse =[theLeftTransverse, theBottomTransverse, size(theTransverseImg,2), size(theTransverseImg,1)];
			thePosCoronal =[theLeftCoronal, theBottomCoronal, size(theCoronalImg,2), size(theCoronalImg,1)];
			thePosSagittal =[theLeftSagittal, theBottomSagittal, size(theSagittalImg,2), size(theSagittalImg,1)];
			clear theFramePosParamSet theLeft theBottom
			clear theLeftTransverse theLeftCoronal theLeftSagittal
			clear theBottomTransverse theBottomCoronal theBottomSagittal

			% Show Images
			%Clear Text labels first
			ClearTextLabels(AConfig);

			%Set Default color map for only Underlay
			%colormap(gray(AConfig.Contrast.GrayDepth));
			%Map images to true color
			theSagittalImg =repmat(theSagittalImg, [1 1 3]);
			theCoronalImg =repmat(theCoronalImg, [1 1 3]);
			theTransverseImg =repmat(theTransverseImg, [1 1 3]);

			%Add Overlay Images
			if SeeOverlay(AConfig),
			%dong 100331 begin
			theSagittalImg =AddOverlay('Sagittal' ,AConfig, theSagittalImg,theMagnifyCoefficient);
			theCoronalImg =AddOverlay('Coronal', AConfig, theCoronalImg,theMagnifyCoefficient);
			theTransverseImg =AddOverlay('Transverse', AConfig, theTransverseImg,theMagnifyCoefficient);
			%dong 100331 end
			end

			%Sagittal
			set(AConfig.hImageSagittal, 'CData', (theSagittalImg), 'HitTest', 'off','Visible', 'on');
			set(AConfig.hAxesSagittal,'Visible', 'on', ...
			'XLim', [1 size(theSagittalImg,2)], ...
			'YLim', [1 size(theSagittalImg,1)] , ...
			'Position', thePosSagittal);
			set(AConfig.hXLineSagittal, 'HitTest','off','Visible', IsCrosshairChecked(AConfig), ...
			'XData', [1 size(theSagittalImg,2)] , ...
			'YData', [1 1]AConfig.LastPosition(3) theMagnifyCoefficient);%Parallel to X-axis
			set(AConfig.hYLineSagittal, 'HitTest','off','Visible', IsCrosshairChecked(AConfig), ...
			'XData', [1 1]AConfig.LastPosition(2) theMagnifyCoefficient, ...
			'YData', [1 size(theSagittalImg,1)] );%Parallel to Y-axis

			%Coronal
			set(AConfig.hImageCoronal, 'CData', (theCoronalImg), 'HitTest', 'off','Visible', 'on');
			%colormap(gray(AConfig.Contrast.GrayDepth));
			set(AConfig.hAxesCoronal, 'Visible', 'on',...
			'XLim', [1 size(theCoronalImg,1)], ...
			'YLim', [1 size(theCoronalImg,2)], ...
			'Position', thePosCoronal);
			set(AConfig.hXLineCoronal, 'HitTest','off','Visible', IsCrosshairChecked(AConfig), ...
			'XData', [1 size(theCoronalImg,2)] , ...
			'YData', [1 1]AConfig.LastPosition(3) theMagnifyCoefficient );%Parallel to X-axis
			set(AConfig.hYLineCoronal, 'HitTest','off','Visible', IsCrosshairChecked(AConfig), ...
			'XData', [1 1]AConfig.LastPosition(1) theMagnifyCoefficient , ...
			'YData', [1 size(theCoronalImg,1)] );%Parallel to Y-axis

			%Transverse
			set(AConfig.hImageTransverse, 'CData', (theTransverseImg), 'HitTest', 'off','Visible', 'on');
			% colormap(gray(AConfig.Contrast.GrayDepth));
			set(AConfig.hAxesTransverse,'Visible', 'on', ...
			'XLim', [1 size(theTransverseImg,2)], ...
			'YLim', [1 size(theTransverseImg,1)], ...
			'Position', thePosTransverse);
			set(AConfig.hXLineTransverse, 'HitTest','off','Visible', IsCrosshairChecked(AConfig), ...
			'XData', [1 size(theTransverseImg,2)] , ...
			'YData', [1 1]AConfig.LastPosition(2) theMagnifyCoefficient );%Parallel to X-axis
			set(AConfig.hYLineTransverse, 'HitTest','off','Visible', IsCrosshairChecked(AConfig), ...
			'XData', [1 1]AConfig.LastPosition(1) theMagnifyCoefficient , ...
			'YData', [1 size(theTransverseImg,1)] );%Parallel to Y-axis

			%Reset View Series
			AConfig.ViewSeries =[];
			Result =AConfig;

			function Result =SetView_Transverse(AConfig)
			[nDim1 nDim2 nDim3] =size(AConfig.Volume);
			theCenterZ =AConfig.LastPosition(3);
			theCount =AConfig.Montage.Across *AConfig.Montage.Down ;

			theZSeries =theCenterZ -([(floor(theCount/2)) : -1 :(ceil(-theCount/2))]) *AConfig.Montage.Spacing;
			while ~isempty(find(theZSeries<=0)),
			theZSeries(find(theZSeries<=0)) = theZSeries(find(theZSeries<=0)) +nDim3;
			end
			while ~isempty(find(theZSeries>nDim3)),
			theZSeries(find(theZSeries>nDim3)) = theZSeries(find(theZSeries>nDim3)) -nDim3;
			end

			theTransverseImg = zeros(nDim2 * AConfig.Montage.Down, nDim1 *AConfig.Montage.Across);
			for theRow=AConfig.Montage.Down:-1:1,
			for theCol=1:AConfig.Montage.Across,
			%I don't draw the last image because it is used to indicate the positions
			theZIndex = theZSeries((AConfig.Montage.Down-theRow)*AConfig.Montage.Across +theCol); %DONG Zhang-Ye 090721 %
			theTransverseImg((theRow-1)nDim2 +(1:nDim2), (theCol-1)nDim1+(1:nDim1)) =GetGrayImage('Transverse', AConfig.Volume, theZIndex);%DONG Zhang-Ye 090721 %
			%YAN Chao-Gan 081229 theTransverseImg((theRow-1)nDim2 +(1:nDim2), (theCol-1)nDim1+(1:nDim1)) =GetGrayImage('Transverse', AConfig.Volume, theZIndex);
			%Write the Z Coordinates to the left-down corner
			%I have to move this code to the end of Setting Axis by using TEXT function

			%Save the Center image's Row and Col for CrossHair-line displaying
			if theZIndex==theCenterZ,
			theCenterZ_Row =theRow;
			theCenterZ_Col =theCol;
			end
			end
			end

			%Save View Series
			AConfig.ViewSeries = theZSeries;
			%Auto balance
			theTransverseImg =SaturateContrast(theTransverseImg, AConfig.Contrast.SatMin, AConfig.Contrast.SatMax);

			%Calculate the Result Image after Magnifying
			theMagnifyCoefficient =GetMagnifyCoefficient(AConfig);
			if license('test','image_toolbox')==1 && theMagnifyCoefficient~=1,
			if rest_misc('GetMatlabVersion')>=7.4 %YAN Chao-Gan 090401: The imresize function has been completely rewritten in Matlab R2007a. Fixed the bug of 'Set Overlay's Color bar' in Matlab R2007a or latter version.
			sizetheTI=size(theTransverseImg);%Dong 091026
			if theMagnifyCoefficient<1
			sizeTI=[floor(sizetheTI(1)theMagnifyCoefficient),floor(sizetheTI(2)theMagnifyCoefficient/10)*10];%Dong 091026
			else
			sizeTI=[floor(sizetheTI(1)theMagnifyCoefficient),floor(sizetheTI(2)theMagnifyCoefficient)];%Dong 091026
			end

			theTransverseImg=imresize_old(theTransverseImg,sizeTI);
			else
			sizetheTI=size(theTransverseImg);%Dong 091026
			if theMagnifyCoefficient<1
			sizeTI=[floor(sizetheTI(1)theMagnifyCoefficient),floor(sizetheTI(2)theMagnifyCoefficient/10)*10];%Dong 091026
			else
			sizeTI=[floor(sizetheTI(1)theMagnifyCoefficient),floor(sizetheTI(2)theMagnifyCoefficient)];%Dong 091026
			end
			theTransverseImg=imresize(theTransverseImg,sizeTI);%theMagnifyCoefficient);%Dong 091026
			end
			end

			% Revise the Axes position to make it comfort to Magnify
			theFramePosParamSet =get(AConfig.hFrameSetPos, 'Position');
			theLeft =theFramePosParamSet(1) +theFramePosParamSet(3) +5;
			theBottom =10; %theFramePosParamSet(2);
			thePosTransverse =[theLeft, theBottom, size(theTransverseImg,2), size(theTransverseImg,1)];

			%Map images to true color
			theTransverseImg =repmat(theTransverseImg, [1 1 3]);

			%Add overlay
			if SeeOverlay(AConfig),
			theTransverseImg =AddOverlaySeries(AConfig, theTransverseImg,theMagnifyCoefficient);
			end

			% Show Images
			%Sagittal
			set(AConfig.hAxesSagittal, 'Visible','off');
			set(AConfig.hImageSagittal,'Visible','off');
			set(AConfig.hXLineSagittal, 'Visible','off');
			set(AConfig.hYLineSagittal, 'Visible','off');
			%Coronal
			set(AConfig.hAxesCoronal, 'Visible','off');
			set(AConfig.hImageCoronal,'Visible','off');
			set(AConfig.hXLineCoronal, 'Visible','off');
			set(AConfig.hYLineCoronal, 'Visible','off');

			%Transverse
			%theTransverseImg =repmat(theTransverseImg, [1, 1, 3])/AConfig.Contrast.GrayDepth; % For true color display
			set(AConfig.hImageTransverse, 'CData', (theTransverseImg), 'HitTest', 'off', 'Visible','on');
			%colormap(gray(AConfig.Contrast.GrayDepth));
			set(AConfig.hAxesTransverse, 'Visible','on', ...
			'XLim', [1 size(theTransverseImg,2)], ...
			'YLim', [1 size(theTransverseImg,1)], ...
			'Position', thePosTransverse);
			set(AConfig.hXLineTransverse, 'HitTest','off','Visible', IsCrosshairChecked(AConfig), ...
			'XData', ([1 nDim1] +(theCenterZ_Col-1)nDim1 ) theMagnifyCoefficient, ...
			'YData', ([1 1]AConfig.LastPosition(2) + (theCenterZ_Row-1)nDim2) *theMagnifyCoefficient);%Parallel to X-axis
			set(AConfig.hYLineTransverse, 'HitTest','off','Visible', IsCrosshairChecked(AConfig), ...
			'XData', ([1 1]AConfig.LastPosition(1)+(theCenterZ_Col-1)nDim1) * theMagnifyCoefficient , ...
			'YData', ([1 nDim2]+(theCenterZ_Row-1)nDim2) theMagnifyCoefficient );%Parallel to Y-axis


			%Clear Text labels first
			ClearTextLabels(AConfig);

			%Write text label to indicate the Z value
			if AConfig.Montage.WantLabel,
			for theRow=AConfig.Montage.Down:-1:1,
			for theCol=1:AConfig.Montage.Across,
			%I don't draw the last image because it is used to indicate the positions
			theZIndex = theZSeries((AConfig.Montage.Down-theRow)*AConfig.Montage.Across +theCol);% DONG Zhang-Ye 090721 %
			theZIndex = theZIndex -AConfig.Origin(3);

			%Transform to Physical distance 20071102
			theZIndex = AConfig.VoxelSize(3) *theZIndex;

			theY =theRownDim2 theMagnifyCoefficient;
			%DONG Zhang-Ye 090721 %theY
			%=(AConfig.Montage.Down-theRow+1)nDim2 theMagnifyCoefficient;
			%YAN Chao-Gan 081229 theY =(theRow)nDim2 theMagnifyCoefficient;
			theX =(theCol-1)nDim1 theMagnifyCoefficient;

			text( theX,theY,sprintf('%+gmm',theZIndex), 'Parent', AConfig.hAxesTransverse, 'Color', AConfig.Overlay.LabelColor, 'HitTest', 'off', 'VerticalAlignment', 'top', 'Units', 'pixels');
			end
			end
			end

			Result =AConfig;

			function Result =SetView_Sagittal(AConfig)
			[nDim1 nDim2 nDim3] =size(AConfig.Volume);
			theCenterX =AConfig.LastPosition(1);
			theCount =AConfig.Montage.Across *AConfig.Montage.Down ;

			theXSeries =theCenterX -([floor(theCount/2) : -1 :ceil(-theCount/2)]) *AConfig.Montage.Spacing;
			while ~isempty(find(theXSeries<=0)),
			theXSeries(find(theXSeries<=0)) = theXSeries(find(theXSeries<=0)) +nDim1;
			end
			while ~isempty(find(theXSeries>nDim1)),
			theXSeries(find(theXSeries>nDim1)) = theXSeries(find(theXSeries>nDim1)) -nDim1;
			end

			theSagittalImg = zeros(nDim3 * AConfig.Montage.Down, nDim2 *AConfig.Montage.Across);
			for theRow=AConfig.Montage.Down:-1:1,
			for theCol=1:AConfig.Montage.Across,
			%I don't draw the last image because it is used to indicate the positions
			%DONG Zhang-Ye 090721 %theXIndex = theXSeries((theRow-1)*AConfig.Montage.Across +theCol);
			theXIndex = theXSeries((AConfig.Montage.Down-theRow)*AConfig.Montage.Across +theCol);
			theSagittalImg((theRow-1)nDim3 +(1:nDim3), (theCol-1)nDim2+(1:nDim2)) =GetGrayImage('Sagittal', AConfig.Volume, theXIndex);
			%Write the X Coordinates to the left-down corner
			%I have to move this code to the end of Setting Axis by using TEXT function

			%Save the Center image's Row and Col for CrossHair-line displaying
			if theXIndex==theCenterX,
			theCenterX_Row =theRow;
			theCenterX_Col =theCol;
			end
			end
			end
			%Save View Series
			AConfig.ViewSeries = theXSeries;
			%Auto balance
			theSagittalImg =SaturateContrast(theSagittalImg, AConfig.Contrast.SatMin, AConfig.Contrast.SatMax);

			%Calculate the Result Image after Magnifying
			theMagnifyCoefficient =GetMagnifyCoefficient(AConfig);
			if license('test','image_toolbox')==1 && theMagnifyCoefficient~=1,
			if rest_misc('GetMatlabVersion')>=7.4 %YAN Chao-Gan 090401: The imresize function has been completely rewritten in Matlab R2007a. Fixed the bug of 'Set Overlay's Color bar' in Matlab R2007a or latter version.
			sizetheTI=size(theSagittalImg);%Dong 091026
			if theMagnifyCoefficient<0.1
			sizeTI=[floor(sizetheTI(1)theMagnifyCoefficient),floor(sizetheTI(2)theMagnifyCoefficient/10)*10];%Dong 091026
			else
			sizeTI=[floor(sizetheTI(1)theMagnifyCoefficient),floor(sizetheTI(2)theMagnifyCoefficient)];%Dong 091026
			end
			theSagittalImg=imresize_old( theSagittalImg,sizeTI);
			else
			sizetheTI=size(theSagittalImg);%Dong 091026
			if theMagnifyCoefficient<0.1
			sizeTI=[floor(sizetheTI(1)theMagnifyCoefficient),floor(sizetheTI(2)theMagnifyCoefficient/10)*10];%Dong 091026
			else
			sizeTI=[floor(sizetheTI(1)theMagnifyCoefficient),floor(sizetheTI(2)theMagnifyCoefficient)];%Dong 091026
			end
			theSagittalImg=imresize( theSagittalImg,sizeTI);%Dong 091026
			end
			end

			% Revise the Axes position to make it comfort to Magnify
			theFramePosParamSet =get(AConfig.hFrameSetPos, 'Position');
			theLeft =theFramePosParamSet(1) +theFramePosParamSet(3) +5;
			theBottom =10; %theFramePosParamSet(2);
			thePosSagittal =[theLeft, theBottom, size(theSagittalImg,2), size(theSagittalImg,1)];

			%Map images to true color
			theSagittalImg =repmat(theSagittalImg, [1 1 3]);

			%Add overlay
			if SeeOverlay(AConfig),
			theSagittalImg =AddOverlaySeries(AConfig, theSagittalImg,theMagnifyCoefficient);
			end

			% Show Images
			%Transverse
			set(AConfig.hAxesTransverse, 'Visible','off');
			set(AConfig.hImageTransverse,'Visible','off');
			set(AConfig.hXLineTransverse, 'Visible','off');
			set(AConfig.hYLineTransverse, 'Visible','off');
			%Coronal
			set(AConfig.hAxesCoronal, 'Visible','off');
			set(AConfig.hImageCoronal,'Visible','off');
			set(AConfig.hXLineCoronal, 'Visible','off');
			set(AConfig.hYLineCoronal, 'Visible','off');

			%Transverse
			%theTransverseImg =repmat(theTransverseImg, [1, 1, 3])/AConfig.Contrast.GrayDepth; % For true color display
			set(AConfig.hImageSagittal, 'CData', (theSagittalImg), 'HitTest', 'off', 'Visible','on');
			%colormap(gray(AConfig.Contrast.GrayDepth));
			set(AConfig.hAxesSagittal, 'Visible','on', ...
			'XLim', [1 size(theSagittalImg,2)], ...
			'YLim', [1 size(theSagittalImg,1)], ...
			'Position', thePosSagittal);
			set(AConfig.hXLineSagittal, 'HitTest','off','Visible', IsCrosshairChecked(AConfig), ...
			'XData', ([1 nDim2] +(theCenterX_Col-1)nDim2 ) theMagnifyCoefficient, ...
			'YData', ([1 1]AConfig.LastPosition(3) + (theCenterX_Row-1)nDim3) *theMagnifyCoefficient);%Parallel to X-axis
			set(AConfig.hYLineSagittal, 'HitTest','off','Visible', IsCrosshairChecked(AConfig), ...
			'XData', ([1 1]AConfig.LastPosition(2)+(theCenterX_Col-1)nDim2) * theMagnifyCoefficient , ...
			'YData', ([1 nDim3]+(theCenterX_Row-1)nDim3) theMagnifyCoefficient );%Parallel to Y-axis

			%Clear Text labels first
			ClearTextLabels(AConfig);
			%Write text label to indicate the Z value
			if AConfig.Montage.WantLabel,
			for theRow=AConfig.Montage.Down:-1:1,
			for theCol=1:AConfig.Montage.Across,
			theXIndex = theXSeries((AConfig.Montage.Down-theRow)*AConfig.Montage.Across +theCol);
			%DONG Zhang-Ye 090721 %theXIndex = theXSeries((theRow-1)*AConfig.Montage.Across +theCol);
			theXIndex = theXIndex -AConfig.Origin(1);

			%Transform to Physical distance 20071102
			theXIndex = AConfig.VoxelSize(1) *theXIndex;
			%Dawnsong 20071102 Revise to make sure the left image/Right brain is +
			theXIndex =(-1) *theXIndex;

			theY =(theRow)nDim3theMagnifyCoefficient;
			%DONG Zhang-Ye 090721 %theY =(AConfig.Montage.Down-theRow+1)nDim3 theMagnifyCoefficient;
			% YAN Chao-Gan 090715, theY =(theRow)nDim3theMagnifyCoefficient;
			theX =(theCol-1)nDim2 theMagnifyCoefficient;
			text( theX,theY,sprintf('%+gmm',theXIndex), 'Parent', AConfig.hAxesSagittal, 'Color', AConfig.Overlay.LabelColor, 'HitTest', 'off', 'VerticalAlignment', 'top', 'Units', 'pixels');
			end
			end
			end

			Result =AConfig;

			function Result =SetView_Coronal(AConfig)
			[nDim1 nDim2 nDim3] =size(AConfig.Volume);
			theCenterY =AConfig.LastPosition(2);
			theCount =AConfig.Montage.Across *AConfig.Montage.Down ;

			theYSeries =theCenterY -([floor(theCount/2) : -1 :ceil(-theCount/2)]) *AConfig.Montage.Spacing;
			while ~isempty(find(theYSeries<=0)),
			theYSeries(find(theYSeries<=0)) = theYSeries(find(theYSeries<=0)) +nDim2;
			end
			while ~isempty(find(theYSeries>nDim2)),
			theYSeries(find(theYSeries>nDim2)) = theYSeries(find(theYSeries>nDim2)) -nDim2;
			end

			theCoronalImg = zeros(nDim3 * AConfig.Montage.Down, nDim1 *AConfig.Montage.Across);
			for theRow=AConfig.Montage.Down:-1:1,
			for theCol=1:AConfig.Montage.Across,
			%I don't draw the last image because it is used to indicate the positions AConfig.Montage.Down-theRow
			theYIndex = theYSeries((AConfig.Montage.Down-theRow)*AConfig.Montage.Across +theCol);
			%DONG Zhang-Ye 090721 %theYIndex = theYSeries((theRow-1)*AConfig.Montage.Across +theCol);
			theCoronalImg((theRow-1)nDim3 +(1:nDim3), (theCol-1)nDim1+(1:nDim1)) =GetGrayImage('Coronal', AConfig.Volume, theYIndex);
			%DONG Zhang-Ye 090721 %theCoronalImg((AConfig.Montage.Down-theRow)nDim3 +(1:nDim3), (theCol-1)nDim1+(1:nDim1)) =GetGrayImage('Coronal', AConfig.Volume, theYIndex);

			%Write the Z Coordinates to the left-down corner
			%I have to move this code to the end of Setting Axis by using TEXT function

			%Save the Center image's Row and Col for CrossHair-line displaying
			if theYIndex==theCenterY,
			theCenterY_Row =theRow;
			theCenterY_Col =theCol;
			end
			end
			end
			%Save View Series
			AConfig.ViewSeries = theYSeries;
			%Auto balance
			theCoronalImg =SaturateContrast(theCoronalImg, AConfig.Contrast.SatMin, AConfig.Contrast.SatMax);

			%Calculate the Result Image after Magnifying
			theMagnifyCoefficient =GetMagnifyCoefficient(AConfig);
			if license('test','image_toolbox')==1 && theMagnifyCoefficient~=1,
			if rest_misc('GetMatlabVersion')>=7.4 %YAN Chao-Gan 090401: The imresize function has been completely rewritten in Matlab R2007a. Fixed the bug of 'Set Overlay's Color bar' in Matlab R2007a or latter version.
			sizetheTI=size(theCoronalImg);%Dong 091026
			if theMagnifyCoefficient<1
			sizeTI=[floor(sizetheTI(1)theMagnifyCoefficient),floor(sizetheTI(2)theMagnifyCoefficient/10)*10];%Dong 091026
			else
			sizeTI=[floor(sizetheTI(1)theMagnifyCoefficient),floor(sizetheTI(2)theMagnifyCoefficient)];%Dong 091026
			end
			theCoronalImg=imresize_old(theCoronalImg,sizeTI);
			else
			sizetheTI=size(theCoronalImg);%Dong 091026
			if theMagnifyCoefficient<1
			sizeTI=[floor(sizetheTI(1)theMagnifyCoefficient),floor(sizetheTI(2)theMagnifyCoefficient/10)*10];%Dong 091026
			else
			sizeTI=[floor(sizetheTI(1)theMagnifyCoefficient),floor(sizetheTI(2)theMagnifyCoefficient)];%Dong 091026
			end
			theCoronalImg=imresize(theCoronalImg,sizeTI);%theMagnifyCoefficient);%Dong 091026
			end
			end

			% Revise the Axes position to make it comfort to Magnify
			theFramePosParamSet =get(AConfig.hFrameSetPos, 'Position');
			theLeft =theFramePosParamSet(1) +theFramePosParamSet(3) +5;
			theBottom =10; %theFramePosParamSet(2);
			thePosCoronal =[theLeft, theBottom, size(theCoronalImg,2), size(theCoronalImg,1)];

			%Map images to true color
			theCoronalImg =repmat(theCoronalImg, [1 1 3]);

			%Add overlay
			if SeeOverlay(AConfig),
			theCoronalImg =AddOverlaySeries(AConfig, theCoronalImg,theMagnifyCoefficient);
			end

			% Show Images
			%Transverse
			set(AConfig.hAxesTransverse, 'Visible','off');
			set(AConfig.hImageTransverse,'Visible','off');
			set(AConfig.hXLineTransverse, 'Visible','off');
			set(AConfig.hYLineTransverse, 'Visible','off');
			%Sagittal
			set(AConfig.hAxesSagittal, 'Visible','off');
			set(AConfig.hImageSagittal,'Visible','off');
			set(AConfig.hXLineSagittal, 'Visible','off');
			set(AConfig.hYLineSagittal, 'Visible','off');

			%Transverse
			%theTransverseImg =repmat(theTransverseImg, [1, 1, 3])/AConfig.Contrast.GrayDepth; % For true color display
			set(AConfig.hImageCoronal, 'CData', (theCoronalImg), 'HitTest', 'off', 'Visible','on');
			%colormap(gray(AConfig.Contrast.GrayDepth));
			set(AConfig.hAxesCoronal, 'Visible','on', ...
			'XLim', [1 size(theCoronalImg,2)], ...
			'YLim', [1 size(theCoronalImg,1)], ...
			'Position', thePosCoronal);

			set(AConfig.hXLineCoronal, 'HitTest','off','Visible', IsCrosshairChecked(AConfig), ...
			'XData', ([1 nDim1] +(theCenterY_Col-1)nDim1 ) theMagnifyCoefficient, ...
			'YData', ([1 1]AConfig.LastPosition(3) + (theCenterY_Row-1)nDim3) *theMagnifyCoefficient);%Parallel to X-axis
			set(AConfig.hYLineCoronal, 'HitTest','off','Visible', IsCrosshairChecked(AConfig), ...
			'XData', ([1 1]AConfig.LastPosition(1)+(theCenterY_Col-1)nDim1) * theMagnifyCoefficient , ...
			'YData', ([1 nDim3]+(theCenterY_Row-1)nDim3) theMagnifyCoefficient );%Parallel to Y-axis

			%Clear Text labels first
			ClearTextLabels(AConfig);
			%Write text label to indicate the Z value
			if AConfig.Montage.WantLabel,
			for theRow=AConfig.Montage.Down:-1:1,
			for theCol=1:AConfig.Montage.Across,
			%I don't draw the last image because it is used to indicate the positions
			theYIndex = theYSeries((theRow-1)*AConfig.Montage.Across +theCol);
			theYIndex = theYIndex -AConfig.Origin(2);

			%Transform to Physical distance 20071102
			theYIndex = AConfig.VoxelSize(2) *theYIndex;

			theY =(AConfig.Montage.Down-theRow+1)nDim3 theMagnifyCoefficient;
			% YAN Chao-Gan, 090715 %theY =theRownDim3 theMagnifyCoefficient;
			theX =(theCol-1)nDim1 theMagnifyCoefficient;
			text( theX,theY,sprintf('%+gmm',theYIndex), 'Parent', AConfig.hAxesCoronal, 'Color', AConfig.Overlay.LabelColor, 'HitTest', 'off', 'VerticalAlignment', 'top', 'Units', 'pixels');
			end
			end
			end
			Result =AConfig;

			function Result =GetGrayImage(AType, AVolume, APosition)
			%Return raw image data at specific position in the Volume
			if nargin~=3, error('Result =GetGrayImage(AVolume, AType)'); end
			switch lower(AType)
			case 'sagittal',
			Result =squeeze(AVolume(APosition, :, :));
			case 'coronal',
			Result =squeeze(AVolume(:,APosition, :));
			case 'transverse',
			Result =squeeze(AVolume(:, :, APosition));
			otherwise
			end
			Result =Result';

			function Result =ClickPositionCrossHair(AConfig)
			theFig =AConfig.hFig;
			hAxesSagittal =AConfig.hAxesSagittal;
			hAxesCoronal =AConfig.hAxesCoronal;
			hAxesTransverse =AConfig.hAxesTransverse;
			theAxes =get(theFig, 'CurrentObject');
			%Check legal click point in the axes
			thePoint =get(theAxes,'CurrentPoint');
			thePoint =thePoint(1, 1:2);
			theXLim =get(theAxes, 'XLim');
			theYLim =get(theAxes, 'YLim');
			if thePoint(1)<theXLim(1) \|\| thePoint(1)>theXLim(2) ...
			\|\| thePoint(2)<theYLim(1) \|\| thePoint(2)>theYLim(2) ,
			Result =AConfig;
			return;
			end

			thePosition =AConfig.LastPosition;
			theMagnifyCoefficient =GetMagnifyCoefficient(AConfig);
			switch theAxes,
			case hAxesSagittal,
			thePosition(2) =round(thePoint(1));% x is Y
			thePosition(3) =round(thePoint(2));%y is Z
			%Calculate the Result Position after Magnifying
			if license('test','image_toolbox')==1 && theMagnifyCoefficient~=1,
			thePosition(2) =round(thePosition(2) / theMagnifyCoefficient);
			thePosition(3) =round(thePosition(3) / theMagnifyCoefficient);
			end
			case hAxesCoronal,
			thePosition(1) =round(thePoint(1));%x is X
			thePosition(3) =round(thePoint(2));%x is Z
			%Calculate the Result Position after Magnifying
			if license('test','image_toolbox')==1 && theMagnifyCoefficient~=1,
			thePosition(1) =round(thePosition(1) / theMagnifyCoefficient);
			thePosition(3) =round(thePosition(3) / theMagnifyCoefficient);
			end
			case hAxesTransverse,
			thePosition(1) =round(thePoint(1));%x is X
			thePosition(2) =round(thePoint(2));%y is Y
			%Calculate the Result Position after Magnifying
			if license('test','image_toolbox')==1 && theMagnifyCoefficient~=1,
			thePosition(1) =round(thePosition(1) / theMagnifyCoefficient);
			thePosition(2) =round(thePosition(2) / theMagnifyCoefficient);
			end
			otherwise
			error(sprintf('Error call: It must be called by Axes''s ButtonDownFcn\nWhy did this occur?\nThere must be something wrong.\nrun "clear all" or re-start MATLAB to avoid this error.\n Dawnwei.song 20070526'));
			end

			% AConfig.LastPosition =thePosition;
			AConfig =UpdatePosition(AConfig, thePosition);
			%Display Images
			AConfig =SetImage(AConfig);

			Result =AConfig;

			function Result =ClickPositionInSagittalMode(AConfig)
			theFig =AConfig.hFig;
			[nDim1 nDim2 nDim3] =size(AConfig.Volume);
			theAxes =get(theFig, 'CurrentObject');
			%Check legal click point in the axes
			thePoint =get(theAxes,'CurrentPoint');
			thePoint =round(thePoint(1, 1:2));
			theXLim =get(theAxes, 'XLim');
			theYLim =get(theAxes, 'YLim');
			if thePoint(1)<theXLim(1) \|\| thePoint(1)>theXLim(2) ...
			\|\| thePoint(2)<theYLim(1) \|\| thePoint(2)>theYLim(2) ,
			Result =AConfig;
			return;
			end

			theMagnifyCoefficient =GetMagnifyCoefficient(AConfig);
			thePosition =AConfig.LastPosition;
			thePosition(2) =mod(thePoint(1), nDim2* theMagnifyCoefficient);% x is Y
			thePosition(3) =mod(thePoint(2), nDim3* theMagnifyCoefficient);%y is Z

			theSeries_RowId =ceil(thePoint(2)/ (theYLim(2)/AConfig.Montage.Down));
			theSeries_ColId =ceil(thePoint(1)/ (theXLim(2)/AConfig.Montage.Across));
			thePointId_inSeries =(theSeries_RowId -1)*AConfig.Montage.Across +theSeries_ColId;

			%Calculate the Result Position after Magnifying
			if license('test','image_toolbox')==1 && theMagnifyCoefficient~=1,
			thePosition(2) =round(thePosition(2) / theMagnifyCoefficient);
			thePosition(3) =round(thePosition(3) / theMagnifyCoefficient);
			theXLim =round(theXLim /theMagnifyCoefficient);
			theYLim =round(theYLim /theMagnifyCoefficient);
			end

			%Set the real position
			thePosition(1) = AConfig.ViewSeries(thePointId_inSeries);
			% AConfig.LastPosition =thePosition;
			AConfig =UpdatePosition(AConfig, thePosition);

			%Display Images
			AConfig =SetImage(AConfig);

			Result =AConfig;

			function Result =ClickPositionInCoronalMode(AConfig)
			theFig =AConfig.hFig;
			[nDim1 nDim2 nDim3] =size(AConfig.Volume);
			theAxes =get(theFig, 'CurrentObject');
			%Check legal click point in the axes
			thePoint =get(theAxes,'CurrentPoint');
			thePoint =round(thePoint(1, 1:2));
			theXLim =get(theAxes, 'XLim');
			theYLim =get(theAxes, 'YLim');
			if thePoint(1)<theXLim(1) \|\| thePoint(1)>theXLim(2) ...
			\|\| thePoint(2)<theYLim(1) \|\| thePoint(2)>theYLim(2) ,
			Result =AConfig;
			return;
			end

			theMagnifyCoefficient =GetMagnifyCoefficient(AConfig);
			thePosition =AConfig.LastPosition;
			thePosition(1) =mod(thePoint(1), nDim1* theMagnifyCoefficient);% x is Y
			thePosition(3) =mod(thePoint(2), nDim3* theMagnifyCoefficient);%y is Z


			theSeries_RowId =ceil(thePoint(2)/ (theYLim(2)/AConfig.Montage.Down));
			theSeries_ColId =ceil(thePoint(1)/ (theXLim(2)/AConfig.Montage.Across));
			thePointId_inSeries =(theSeries_RowId -1)*AConfig.Montage.Across +theSeries_ColId;

			%Calculate the Result Position after Magnifying
			if license('test','image_toolbox')==1 && theMagnifyCoefficient~=1,
			thePosition(1) =round(thePosition(1) / theMagnifyCoefficient);
			thePosition(3) =round(thePosition(3) / theMagnifyCoefficient);
			theXLim =round(theXLim /theMagnifyCoefficient);
			theYLim =round(theYLim /theMagnifyCoefficient);
			end

			%Set the real position
			thePosition(2) = AConfig.ViewSeries(thePointId_inSeries);
			% AConfig.LastPosition =thePosition;
			AConfig =UpdatePosition(AConfig, thePosition);

			%Display Images
			AConfig =SetImage(AConfig);

			Result =AConfig;

			function Result =ClickPositionInTransverseMode(AConfig)
			theFig =AConfig.hFig;
			[nDim1 nDim2 nDim3] =size(AConfig.Volume);
			theAxes =get(theFig, 'CurrentObject');
			%Check legal click point in the axes
			thePoint =get(theAxes,'CurrentPoint');
			thePoint =round(thePoint(1, 1:2));
			theXLim =get(theAxes, 'XLim');
			theYLim =get(theAxes, 'YLim');
			if thePoint(1)<theXLim(1) \|\| thePoint(1)>theXLim(2) ...
			\|\| thePoint(2)<theYLim(1) \|\| thePoint(2)>theYLim(2) ,
			Result =AConfig;
			return;
			end

			theMagnifyCoefficient =GetMagnifyCoefficient(AConfig);
			thePosition =AConfig.LastPosition;
			thePosition(1) =mod(thePoint(1), nDim1* theMagnifyCoefficient);% x is Y
			thePosition(2) =mod(thePoint(2), nDim2* theMagnifyCoefficient);%y is Z

			theSeries_RowId =ceil((theYLim(2)-thePoint(2))/ (theYLim(2)/AConfig.Montage.Down));
			%YAN Chao-Gan 081229 theSeries_RowId =ceil(thePoint(2)/ (theYLim(2)/AConfig.Montage.Down));
			theSeries_ColId =ceil(thePoint(1)/ (theXLim(2)/AConfig.Montage.Across));
			thePointId_inSeries =(theSeries_RowId -1)*AConfig.Montage.Across +theSeries_ColId;

			%Calculate the Result Position after Magnifying
			if license('test','image_toolbox')==1 && theMagnifyCoefficient~=1,
			thePosition(1) =round(thePosition(1) / theMagnifyCoefficient);
			thePosition(2) =round(thePosition(2) / theMagnifyCoefficient);
			theXLim =round(theXLim /theMagnifyCoefficient);
			theYLim =round(theYLim /theMagnifyCoefficient);
			end

			%Set the real position
			thePosition(3) = AConfig.ViewSeries(thePointId_inSeries);
			% AConfig.LastPosition =thePosition;
			AConfig =UpdatePosition(AConfig, thePosition);

			%Display Images
			AConfig =SetImage(AConfig);

			Result =AConfig;

			function Result =SetPositionCrossHair(AConfig)
			% theCurrentControl =gco;
			% uicontrol(AConfig.hYoke);
			%I must change the current focus to force the callback of the edit to run at once to make sure 'get' can return current string/value instead of old value
			% when I use KeyPressFcn. And KeyPressFcn didn't exist for uicontrol before Matlab 7. In Matlab 6.5, there is only KeyPressFcn for figure;

			thePosition =AConfig.LastPosition;
			theXLim =[1, size(AConfig.Volume, 1)];
			theYLim =[1, size(AConfig.Volume, 2)];
			theZLim =[1, size(AConfig.Volume, 3)];
			theX =str2num(get(AConfig.hEditPositionX, 'String'));
			theY =str2num(get(AConfig.hEditPositionY, 'String'));
			theZ =str2num(get(AConfig.hEditPositionZ, 'String'));

			%Revise Direction , dawnsong20071101
			theX = theX * (-1);


			theX =round(theX/AConfig.VoxelSize(1) +AConfig.Origin(1));
			theY =round(theY/AConfig.VoxelSize(2) +AConfig.Origin(2));
			theZ =round(theZ/AConfig.VoxelSize(3) +AConfig.Origin(3));



			% uicontrol(theCurrentControl);

			if ~isempty(theX) && theX>=theXLim(1) ...
			&& ~isempty(theY) && theY>=theYLim(1) ...
			&& ~isempty(theZ) && theZ>=theZLim(1) ...
			&& any(thePosition ~= [theX theY theZ]) ,

			if theX >theXLim(2), theX =theXLim(2); end
			if theY >theYLim(2), theY =theYLim(2); end
			if theZ >theZLim(2), theZ =theZLim(2); end

			thePosition =[theX theY theZ];
			% AConfig.LastPosition =thePosition;
			AConfig =UpdatePosition(AConfig, thePosition);
			end

			%Display Images
			AConfig =SetImage(AConfig);
			%Save LastPosition
			Result =AConfig;

			function Result =SetDistanceFromOrigin(AConfig, ADistanceFromOrigin);
			% Set current cross-hair position according to the Proportion Position among many size-not-equal brain images
			thePosition = ADistanceFromOrigin ./ AConfig.VoxelSize + AConfig.Origin;
			thePosition =round(thePosition);
			if any(thePosition ~= AConfig.LastPosition) ...
			&& thePosition(1)>=1 && thePosition(1)<=size(AConfig.Volume,1) ...
			&& thePosition(2)>=1 && thePosition(2)<=size(AConfig.Volume,2) ...
			&& thePosition(3)>=1 && thePosition(3)<=size(AConfig.Volume,3) , ...
			% AConfig.LastPosition =thePosition;
			AConfig =UpdatePosition(AConfig, thePosition);
			elseif any(thePosition ~= AConfig.LastPosition),
			for x=1:3,
			while thePosition(x)<1,
			thePosition(x) =thePosition(x) +size(AConfig.Volume,x);
			end
			while thePosition(x)>size(AConfig.Volume,x),
			thePosition(x) =thePosition(x) -size(AConfig.Volume,x);
			end
			end
			end

			%Display Images
			AConfig =SetImage(AConfig);
			%Save LastPosition
			Result =AConfig;

			function ShowPositionInEdit(AConfig)
			thePosition =AConfig.LastPosition;
			set(AConfig.hEditPositionX, 'String', num2str((thePosition(1)-AConfig.Origin(1))AConfig.VoxelSize(1) (-1) )); %Make sure Left is Right like BA, and Left-image is + or Right-Brain is +
			set(AConfig.hEditPositionY, 'String', num2str((thePosition(2)-AConfig.Origin(2) )*AConfig.VoxelSize(2) )); %Make sure Fore is +
			set(AConfig.hEditPositionZ, 'String', num2str((thePosition(3)-AConfig.Origin(3) )*AConfig.VoxelSize(3) )); %Make sure Top is +

			function SetMessage(AConfig)
			%Detect if I should hide the big information area
			theTitle ='Click to Toggle Hdr info';
			theOldMsg =get(AConfig.hMsgLabel, 'String');

			if SeeOverlay(AConfig),
			%Compute the cooresponding position according to physical distance(mm) from origin
			thePhysicalPos = (AConfig.LastPosition -AConfig.Origin) .* AConfig.VoxelSize;
			theOverlayPos = thePhysicalPos ./ AConfig.Overlay.VoxelSize +AConfig.Overlay.Origin;
			theOverlayPos =round(theOverlayPos);
			if all(theOverlayPos<=size(AConfig.Overlay.Volume)) ...
			&& all(theOverlayPos >=[1 1 1]),
			%Legal
			else%Illegal data
			warning(sprintf('Illegal Overlay Position: (%s)\nI will revise the underlay''s position to its origin.', num2str(theOverlayPos)));
			%Revise the LastPosition on the underlay to the origin
			AConfig.LastPosition =AConfig.Origin; %This line will not work because This fun didn't save the Global variable AConfig
			DPARSF_rest_sliceviewer('SetPhysicalPosition', AConfig.hFig, [0 0 0]);
			DPARSF_rest_sliceviewer('Repaint', AConfig.hFig);
			return;
			end

			theUnderlayIntensity =AConfig.Volume(AConfig.LastPosition(1),AConfig.LastPosition(2),AConfig.LastPosition(3));

			theOverlayIntensity =AConfig.Overlay.Volume(theOverlayPos(1),theOverlayPos(2),theOverlayPos(3));
			if prod(size(AConfig.Overlay.InfoAal))==116 ...
			&& theOverlayIntensity>0, %AAL template description
			theIntensity =sprintf('%s\n%g / %g', AConfig.Overlay.InfoAal{theOverlayIntensity},theUnderlayIntensity, theOverlayIntensity);
			else %Default
			%Show the voxel's intensity for underlay and overlay
			theIntensity =sprintf('\n%g / %g', theUnderlayIntensity, theOverlayIntensity);
			end

			set(AConfig.hVoxelIntensity, 'String', theIntensity, 'TooltipString', ['Value: Underlay/Overlay = ', theIntensity]);

			theUnderlayInfo =sprintf('Dimension: %dx%dx%d\nVoxel(mm): %gx%gx%g\nOrigin(vxl): %d,%d,%d',size(AConfig.Volume,1), size(AConfig.Volume, 2), size(AConfig.Volume, 3), AConfig.VoxelSize(1), AConfig.VoxelSize(2),AConfig.VoxelSize(3), AConfig.Origin(1), AConfig.Origin(2), AConfig.Origin(3));
			theUnderlayInfo =sprintf('Underlay:\n%s\n\n', theUnderlayInfo);
			theOverlayInfo =sprintf('Dimension: %dx%dx%d\nVoxel(mm): %gx%gx%g\nOrigin(vxl): %d,%d,%d',size(AConfig.Overlay.Volume,1), size(AConfig.Overlay.Volume, 2), size(AConfig.Overlay.Volume, 3), AConfig.Overlay.VoxelSize(1), AConfig.Overlay.VoxelSize(2),AConfig.Overlay.VoxelSize(3), AConfig.Overlay.Origin(1), AConfig.Overlay.Origin(2), AConfig.Overlay.Origin(3));
			theOverlayInfo =sprintf('Overlay: (%s)\n%s', num2str((Pos_Underlay2Overlay(AConfig, AConfig.LastPosition) -AConfig.Overlay.Origin).AConfig.Overlay.VoxelSize . [-1, 1, 1]),theOverlayInfo);
			if isfield(AConfig.Overlay.Header,'mat')
			theOverlayInfo =sprintf('%s\nNIfTI Image: Displayed in Radiology Convention',theOverlayInfo);
			end
			theInfo =[theUnderlayInfo theOverlayInfo];
			%set(AConfig.hMsgLabel, 'String', theInfo);
			else %Don't see Overlay
			theIntensity =sprintf('\n%g',AConfig.Volume(AConfig.LastPosition(1),AConfig.LastPosition(2),AConfig.LastPosition(3)));
			set(AConfig.hVoxelIntensity, 'String', theIntensity, 'TooltipString', ['Value: Underlay ', theIntensity]);

			theInfo =sprintf('Dimension: %dx%dx%d\nVoxel(mm): %gx%gx%g\nOrigin(vxl): %d,%d,%d',size(AConfig.Volume,1), size(AConfig.Volume, 2), size(AConfig.Volume, 3), AConfig.VoxelSize(1), AConfig.VoxelSize(2),AConfig.VoxelSize(3), AConfig.Origin(1), AConfig.Origin(2), AConfig.Origin(3));
			%set(AConfig.hMsgLabel, 'String', theInfo);
			end

			if ~isempty(AConfig.Message) && ~all(isspace(AConfig.Message)),
			theInfo =sprintf('%s\n\n%s', theInfo, AConfig.Message);
			end

			if strcmpi(theTitle, theOldMsg),
			%Hide the Information as the old
			%set(AConfig.hMsgLabel, 'String', theInfo);
			set(AConfig.hMsgLabel, 'TooltipString', theInfo);
			else %Normally showing the Hdr info
			set(AConfig.hMsgLabel, 'String', theInfo,'TooltipString', '');
			end
			%Threshhold value display
			set(AConfig.hEdtThrdValue, 'String', num2str(AConfig.Overlay.ValueThrdAbsolute));
			%hflag=AConfig.Overlay.Header;
			% if ExistViewer(AConfig.Overlay.Header.descrip)
			%AConfig.Overlay.ValueP=ThrdtoP(AConfig.Overlay.ValueThrdAbsolute,AConfig);
			%set(AConfig.hEdtPValue, 'String', sprintf('%.5f',AConfig.Overlay.ValueP)); % dong 090921
			return;

			function ResizeFigure(AConfig)
			MarginX =10; MarginY =10;
			[nDim1, nDim2, nDim3] =size(AConfig.Volume);
			if strcmpi(get(AConfig.hFrameSetPos, 'Visible'), 'on'),
			theFramePos =get(AConfig.hFrameSetPos, 'Position');
			else
			theFramePos =[0 0 0 0];
			end
			theMagnifyCoefficient =GetMagnifyCoefficient(AConfig); % Considering Magnifying result
			nDim1 =nDim1 *theMagnifyCoefficient;
			nDim2 =nDim2 *theMagnifyCoefficient;
			nDim3 =nDim3 *theMagnifyCoefficient;
			if strcmpi(AConfig.ViewMode, 'Orthogonal'),
			FigWidth =theFramePos(1) +theFramePos(3) +MarginX + nDim1 +2 +nDim2 + MarginX;
			FigHeight =10 + nDim2 +2 +nDim3 + MarginY;
			elseif strcmpi(AConfig.ViewMode, 'Transverse'),
			FigWidth =theFramePos(1) +theFramePos(3) +MarginX + nDim1 * AConfig.Montage.Across + MarginX;
			FigHeight =MarginY + nDim2 * AConfig.Montage.Down + MarginY;
			elseif strcmpi(AConfig.ViewMode, 'Sagittal'),
			FigWidth =theFramePos(1) +theFramePos(3) +MarginX + nDim2 * AConfig.Montage.Across + MarginX;
			FigHeight =MarginY + nDim3 * AConfig.Montage.Down + MarginY;
			elseif strcmpi(AConfig.ViewMode, 'Coronal'),
			FigWidth =theFramePos(1) +theFramePos(3) +MarginX + nDim1 * AConfig.Montage.Across + MarginX;
			FigHeight =MarginY + nDim3 * AConfig.Montage.Down + MarginY;
			end
			%Resize figure's width according to colorbar's visiblity
			if SeeOverlay(AConfig),
			theColorBarPos=get(AConfig.hAxesColorbar, 'Position');
			FigWidth = FigWidth +MarginX +theColorBarPos(3) +1.5*MarginX +MarginX;
			end
			%FigHeight =theFramePos(2) + nDim2 +2 +nDim3 + MarginY;


			% Revise the Intensity position
			% theMsgPos =get(AConfig.hVoxelIntensity, 'Position');
			% theMsgPos(1) =theFramePos(1) +theFramePos(3) +MarginX + nDim1 +5;
			% theMsgPos(2) =theFramePos(2);
			% theMsgPos(3) = FigWidth -theMsgPos(1) -MarginX;
			% set(AConfig.hVoxelIntensity, 'Position', theMsgPos); %Set first

			% theIntensity =get(AConfig.hVoxelIntensity, 'String');
			% [newMsg,newMsgPos]=textwrap(AConfig.hVoxelIntensity, {theIntensity});
			% set(AConfig.hVoxelIntensity, 'Position', newMsgPos);

			%Revise the Message's position
			if strcmpi(get(AConfig.hMsgLabel,'Visible'), 'on'),
			theMsgPos =get(AConfig.hMsgLabel, 'Position');
			theMsgPos(1) =theFramePos(1);
			theMsgPos(2) =theFramePos(2) +theFramePos(4) +MarginY;
			theMsgPos(3) =theFramePos(3);
			theMsgPos(4) =1;
			set(AConfig.hMsgLabel, 'Position', theMsgPos); %Set default position first

			theMsg =get(AConfig.hMsgLabel, 'String');
			[theMsg, theMsgPos] =textwrap(AConfig.hMsgLabel, cellstr(theMsg));
			set(AConfig.hMsgLabel, 'String', theMsg, 'Position', theMsgPos);
			end
			% Revise the Do Callback Button's position
			% if AConfig.hDoCallbackBtn>0
			% thePos =get(AConfig.hDoCallbackBtn, 'Position');
			% thePos(1) =theMsgPos(1);
			% thePos(2) =theMsgPos(2) +theMsgPos(4) +MarginY;
			% thePos(3) =theMsgPos(3);
			% thePos(4) =25;
			% set(AConfig.hDoCallbackBtn, 'Position', thePos);
			% end

			% Revise the figure's position according to the Brain Image's width and height
			thePos =get(AConfig.hFig, 'Position');
			theScrPos =get(0, 'ScreenSize');
			% if AConfig.hDoCallbackBtn>0
			% theBtnPos =get(AConfig.hDoCallbackBtn, 'Position');
			% if FigHeight< (theBtnPos(2) +theBtnPos(4) +MarginY)
			% FigHeight =theBtnPos(2) +theBtnPos(4) +MarginY;
			% end
			% else end
			if strcmpi(get(AConfig.hMsgLabel,'Visible'), 'on'),
			theMsgPos =get(AConfig.hMsgLabel, 'Position');
			if FigHeight< (theMsgPos(2) +theMsgPos(4) +MarginY)
			FigHeight =theMsgPos(2) +theMsgPos(4) +MarginY;
			end
			end
			if (thePos(2) +FigHeight +60) > theScrPos(4)
			thePos(2) = theScrPos(4) -FigHeight -60;
			end
			if thePos(3) <FigWidth
			thePos(3) =FigWidth;
			elseif thePos(3) >1.5*FigWidth
			thePos(3) =FigWidth;
			end
			thePos(4) =FigHeight;
			set(AConfig.hFig, 'Position', thePos);

			%Resize figure position according to the Message height
			if strcmpi(get(AConfig.hMsgLabel,'Visible'), 'on'),
			theMsgPos =get(AConfig.hMsgLabel, 'Position');
			if ( theMsgPos(2)+theMsgPos(4) )> thePos(4),
			thePos(3) =FigWidth;
			thePos(4) =theMsgPos(2)+theMsgPos(4) +MarginY;
			set(AConfig.hFig, 'Position', thePos);
			end
			end

			function Result =GetMagnifyCoefficient(AConfig)
			if license('test','image_toolbox')~=1 ,
			Result =1;
			return;
			end

			theStr =get(AConfig.hMagnify ,'String');
			theIdx =get(AConfig.hMagnify ,'Value');
			Result =1;
			switch upper(theStr{theIdx}),
			case 'X0.5',
			Result =0.5;
			case 'X1',
			Result =1;
			case 'X2',
			Result =2;
			case 'X3',
			Result =3;
			otherwise
			rest_misc( 'ComplainWhyThisOccur');
			end

			function Result =UpdateCallback(AConfig, ACallback, ACallbackCaption)
			Result =AConfig;
			Result.Callback =ACallback;
			% if ~isempty(ACallbackCaption) && ischar(ACallbackCaption)
			% theBtnCaption =ACallbackCaption;
			% else
			% theBtnCaption ='Do sth.';
			% end

			% if Result.hDoCallbackBtn>0
			% I have created the Button to respond to the click event
			% if ~isempty(ACallback) && ischar(ACallback) ,
			% set(Result.hDoCallbackBtn, 'Callback', ACallback, 'String', theBtnCaption);
			% else
			% Remove the button because the Callback is illegal or empty
			% delete(Result.hDoCallbackBtn);
			% Result.hDoCallbackBtn =-1;
			% Result.Callback ='';
			% end
			% else
			% Create a Button responding the click event
			% if ~isempty(ACallback) && (ischar(ACallback) \|\| isa(ACallback, 'function_handle')),
			% theCallback =sprintf('DPARSF_rest_sliceviewer(''RunCallback'', ''%s'');',AConfig.Filename);
			% Result.hDoCallbackBtn =uicontrol(Result.hFig, 'Style','pushbutton', ...
			% 'Units','pixels','String', theBtnCaption, ...
			% 'Callback', theCallback);
			% end
			% end

			function ClearTextLabels(AConfig)
			%Clear Text labels first for multislice mode
			theLabels =findobj(AConfig.hAxesSagittal, 'Type', 'text');
			for theX=1:length(theLabels), delete(theLabels(theX)); end
			theLabels =findobj(AConfig.hAxesCoronal, 'Type', 'text');
			for theX=1:length(theLabels), delete(theLabels(theX)); end
			theLabels =findobj(AConfig.hAxesTransverse, 'Type', 'text');
			for theX=1:length(theLabels), delete(theLabels(theX)); end

			function Result =AutoBalance(AConfig)
			Result =AConfig;
			%Save Maping Image parameters, Auto balance 20070911 revised, 20070914 revised for Statistical map which has negative values
			%Revise first
			Result.Volume(isnan(Result.Volume)) =0;
			Result.Volume(isinf(Result.Volume)) =0;
			%Begin computation, the following two lines are time-consuming up to 4.6 seconds!!!
			%But after replacing AConfig with Result, then their speed rocketed to 0.2 seconds!!!
			%Attention!!! Dawnwei.Song, 20070914
			theMaxVal=max(Result.Volume(:));
			theMinVal=min(Result.Volume(:));
			if theMaxVal>theMinVal,
			nBins=255;
			%Special processing just for very common images! 20071212
			if (theMaxVal<257) && (theMinVal>=0) && (theMaxVal-theMinVal>100), %not statistic map
			theSum =histc(Result.Volume(:), 1:ceil(theMaxVal));
			else
			theSum =histc(Result.Volume(:), theMinVal:(theMaxVal-theMinVal)/254:theMaxVal);
			end
			theSum =cumsum(theSum);
			theCdf =theSum/theSum(end);
			if rest_misc('GetMatlabVersion')>=7.3
			idxSatMin =find(theCdf>0.01, 1, 'first');
			idxSatMax =find(theCdf>=0.99, 1, 'first');
			else
			idxSatMin =find(theCdf>0.01);
			idxSatMin =idxSatMin(1);
			idxSatMax =find(theCdf>=0.99);
			idxSatMax =idxSatMax(1);
			end
			if idxSatMin==idxSatMax, idxSatMin =1; end %20070919, For mask file's display
			theSatMin =(idxSatMin-1)/(nBins-1) *(theMaxVal-theMinVal) +theMinVal;
			theSatMax =(idxSatMax-1)/(nBins-1) *(theMaxVal-theMinVal) +theMinVal;
			elseif theMaxVal==theMinVal,
			theSatMin =theMaxVal;
			theSatMax =theMaxVal;
			else
			end
			Result.Contrast.GrayDepth =255;
			Result.Contrast.SatMin =theSatMin;
			Result.Contrast.SatMax =theSatMax;
			%20070911, AutoBalance for contrast
			Result.Contrast.WindowWidth =theSatMax -theSatMin;
			Result.Contrast.WindowCenter=(theSatMax +theSatMin)/2;

			%For debug display
			% disp(Result.Contrast);



			function Result =IsCrosshairChecked(AConfig)
			Result ='off';
			if get(AConfig.hCrosshair, 'Value'),
			Result ='on';
			end

			function Transforming_MNI_Talairach(AConfig)
			isNeedUpdate =false;
			switch get(AConfig.hMniTal, 'Value'),
			case 1, %'MNI/Talairach Coordinates'
			%Do nothing
			case 2, %'From Talairach to MNI'
			% AConfig.LastPosition
			thePosition =round(rest_tal2mni(AConfig.LastPosition -AConfig.Origin) +AConfig.Origin);
			AConfig =UpdatePosition(AConfig, thePosition);
			isNeedUpdate =true;
			case 3, %'From MNI to Talairach'
			% AConfig.LastPosition
			thePosition=round(rest_mni2tal(AConfig.LastPosition -AConfig.Origin) +AConfig.Origin);
			AConfig =UpdatePosition(AConfig, thePosition);
			isNeedUpdate =true;
			otherwise
			end
			% disp(AConfig.LastPosition);
			% return;

			if isNeedUpdate,
			ShowPositionInEdit(AConfig);
			SetMessage(AConfig);
			DPARSF_rest_sliceviewer('SetPosition', AConfig.Filename);
			end
			%Reset position in Choice selection
			set(AConfig.hMniTal, 'Value', 1);


			function Result =SaturateContrast(AImage, ASatMin, ASatMax)
			Result =AImage;
			if ASatMin<ASatMax,
			Result(find(Result<ASatMin)) =ASatMin;
			Result(find(Result>ASatMax)) =ASatMax;
			Result =(Result -ASatMin)/(ASatMax - ASatMin);
			elseif ASatMin==ASatMax,
			Result(:) =0.01;
			else
			error('ASatMin>ASatMax ???');
			end

			%Map a indexed 2D image to a 2D * 3 image which is true color image and range is in [0 , 1]
			% Result =repmat(Result, [1 1 3]) /AGrayDepth;

			function Result =InitUnderlay(AConfig)
			%Input: Need AConfig.Filename specified
			try
			[theVolume,theVoxelSize, Header] =rest_readfile(AConfig.Filename); %%Yan 080610
			[pathstr, name, ext] = fileparts(AConfig.Filename); %YAN Chao-Gan 100420 added. Change the first voxel of ch2bet.nii since it can not be displayed in a right way.
			if strcmpi(name,'ch2bet')
			theVolume(1,1,1)=254;
			end %YAN Chao-Gan 100420 added.
			theOrigin=Header.Origin; %%Yan 080610
			AConfig =AddRecentUnderlay(AConfig, AConfig.Filename);
			AConfig.Header=Header; %%Yan 080610
			catch
			if ~(exist(AConfig.Filename, 'file')==2) ...
			&& ( ~all(isspace(AConfig.Filename)) && ~isempty(isspace(AConfig.Filename))),
			warning(sprintf('Please check whether Img/Hdr file "%s" exist!', AConfig.Filename));
			warndlg(sprintf('Please check whether Img/Hdr file "%s" exist!', AConfig.Filename));
			end
			theVolume =255*zeros(181,217,181); %theVolume(:) =round([1:prod(size(theVolume))]/2^16);
			theVoxelSize =[1 1 1];
			theOrigin =[90 126 72];
			end
			[nDim1, nDim2, nDim3] =size(theVolume);

			% Displaying Orthogonal images
			theFramePos =get(AConfig.hFrameSetPos, 'Position');
			MarginY =10; MarginX =10;
			OffsetX =theFramePos(1) +theFramePos(3) +MarginX;
			OffsetY =MarginY;

			%Delete old handles if exists any
			if ishandle(AConfig.hAxesSagittal), delete(AConfig.hAxesSagittal); end
			if ishandle(AConfig.hAxesCoronal), delete(AConfig.hAxesCoronal); end
			if ishandle(AConfig.hAxesTransverse), delete(AConfig.hAxesTransverse); end
			%Save Images' handles
			if ishandle(AConfig.hImageSagittal), delete(AConfig.hImageSagittal); end
			if ishandle(AConfig.hImageCoronal), delete(AConfig.hImageCoronal); end
			if ishandle(AConfig.hImageTransverse), delete(AConfig.hImageTransverse); end
			%Save Lines' handles
			if ishandle(AConfig.hXLineSagittal), delete(AConfig.hXLineSagittal); end %x
			if ishandle(AConfig.hYLineSagittal), delete(AConfig.hYLineSagittal); end %y
			if ishandle(AConfig.hXLineCoronal), delete(AConfig.hXLineCoronal); end %x
			if ishandle(AConfig.hYLineCoronal), delete(AConfig.hYLineCoronal); end %y
			if ishandle(AConfig.hXLineTransverse), delete(AConfig.hXLineTransverse); end %x
			if ishandle(AConfig.hYLineTransverse), delete(AConfig.hYLineTransverse); end %y


			%Create Axes and lines and images
			theAxesButtonDownFcn =sprintf('DPARSF_rest_sliceviewer(''ClickPosition'', %g);', AConfig.hFig);
			hAxesTransverse =axes('Parent', AConfig.hFig, 'Box', 'on', ...
			'Units', 'pixel', 'DrawMode','fast', ...
			'Position', [OffsetX OffsetY nDim1 nDim2], ...
			'YDir','normal', 'XTickLabel',[],'XTick',[], ...
			'YTickLabel',[],'YTick',[], 'DataAspectRatio',[1 1 1],...
			'ButtonDownFcn', theAxesButtonDownFcn);
			hImageTransverse =image('Tag','BrainImageTransverse', 'Parent', hAxesTransverse);
			set(hAxesTransverse,'YDir','normal','ButtonDownFcn', theAxesButtonDownFcn, 'XTickLabel',[],'XTick',[], ...
			'YTickLabel',[],'YTick',[]);
			hXLineTransverse =line(0, 0, 'Parent', hAxesTransverse, 'Color', 'red');
			hYLineTransverse =line(0, 0, 'Parent', hAxesTransverse, 'Color', 'red');

			hAxesCoronal =axes('Parent', AConfig.hFig, 'Box', 'on', ...
			'Units', 'pixel', 'DrawMode','fast', ...
			'Position', [OffsetX OffsetY+nDim2+2 nDim1 nDim3], ...
			'YDir','normal', 'XTickLabel',[],'XTick',[], ...
			'YTickLabel',[],'YTick',[], ...
			'ButtonDownFcn', theAxesButtonDownFcn);
			hImageCoronal =image('Tag','BrainImageCoronal', 'Parent', hAxesCoronal);
			set(hAxesCoronal,'YDir','normal','ButtonDownFcn', theAxesButtonDownFcn, 'XTickLabel',[],'XTick',[], ...
			'YTickLabel',[],'YTick',[]);
			hXLineCoronal =line(0, 0, 'Parent', hAxesCoronal, 'Color', 'red');
			hYLineCoronal =line(0, 0, 'Parent', hAxesCoronal, 'Color', 'red');

			hAxesSagittal =axes('Parent', AConfig.hFig, 'Box', 'on', ...
			'Units', 'pixel', 'DrawMode','fast', ...
			'Position', [OffsetX+nDim1+2 OffsetY+nDim2+2 nDim2 nDim3], ...
			'YDir','normal', 'XTickLabel',[],'XTick',[], ...
			'YTickLabel',[],'YTick',[], ...
			'ButtonDownFcn', theAxesButtonDownFcn);
			hImageSagittal =image('Tag','BrainImageSagittal', 'Parent', hAxesSagittal);
			set(hAxesSagittal,'YDir','normal','ButtonDownFcn', theAxesButtonDownFcn, 'XTickLabel',[],'XTick',[], ...
			'YTickLabel',[],'YTick',[]);
			hXLineSagittal =line(0, 0, 'Parent', hAxesSagittal, 'Color', 'red');
			hYLineSagittal =line(0, 0, 'Parent', hAxesSagittal, 'Color', 'red');


			%Save Axes's handles
			AConfig.hAxesSagittal =hAxesSagittal;
			AConfig.hAxesCoronal =hAxesCoronal;
			AConfig.hAxesTransverse =hAxesTransverse;
			%Save Images' handles
			AConfig.hImageSagittal =hImageSagittal;
			AConfig.hImageCoronal =hImageCoronal;
			AConfig.hImageTransverse =hImageTransverse;
			%Save Lines' handles
			AConfig.hXLineSagittal =hXLineSagittal; %x
			AConfig.hYLineSagittal =hYLineSagittal; %y
			AConfig.hXLineCoronal =hXLineCoronal; %x
			AConfig.hYLineCoronal =hYLineCoronal; %y
			AConfig.hXLineTransverse =hXLineTransverse; %x
			AConfig.hYLineTransverse =hYLineTransverse; %y

			AConfig.Volume =theVolume;
			AConfig.VoxelSize =reshape(theVoxelSize, [1 3]);

			AConfig.Origin =reshape(theOrigin, [1 3]);
			AConfig.Header.Origin=AConfig.Origin;
			if any(AConfig.Origin==[0 0 0]),
			%Auto-Revise the Origin to the half of the size of the brain
			theMsg =sprintf('Illegal origin: (%s)\n\nI presume the origin is (%s)',num2str(AConfig.Origin), num2str(round(size(AConfig.Volume)/2)));
			warning(theMsg);
			warndlg(theMsg);
			AConfig.Origin =round(size(AConfig.Volume)/2);
			end
			if (norm(theOrigin)==0 \|\| (any(round(theOrigin)~=theOrigin)) \|\| (any(theOrigin<0))) %YAN Chao-Gan 090401: If the origin of the image was not positive integer, then jump to the image center.
			AConfig.LastPosition =round([nDim1 nDim2 nDim3]/2); %[x y z] the position in Volume corresponding to the cross-hair position
			else
			if ~all(AConfig.LastPosition < size(theVolume)), %If legal
			AConfig.LastPosition =reshape(AConfig.Origin, [1 3]);
			end
			end

			%Auto balance
			AConfig=AutoBalance(AConfig);

			Result =AConfig;



			function Result =SeeOverlay(AConfig)
			Result =get(AConfig.hSeeOverlay, 'Value');

			function Result =GetOverlayImg(AType, AConfig, AUnderlayPosition)
			%Return raw overlay image data by computing the real physical distance(mm) from the origin % AUnderlayPosition is a scalar, result is a slice according to AType and AUnderlayPosition
			theVolume =AConfig.Overlay.VolumeThrd;
			switch lower(AType)
			case 'sagittal',
			thePhysicalPosition =(AUnderlayPosition -AConfig.Origin(1)) *AConfig.VoxelSize(1);
			thePhysicalPosition =thePhysicalPosition/AConfig.Overlay.VoxelSize(1) +AConfig.Overlay.Origin(1);
			if thePhysicalPosition>size(theVolume, 1),
			thePhysicalPosition =size(theVolume, 1);
			elseif thePhysicalPosition<1,
			thePhysicalPosition =1;
			end
			%Result =theVolume(round(thePhysicalPosition), :, :);
			Result =squeeze(theVolume(round(thePhysicalPosition), :, :));
			%dong 090918
			case 'coronal',
			thePhysicalPosition =(AUnderlayPosition -AConfig.Origin(2)) *AConfig.VoxelSize(2);
			thePhysicalPosition =thePhysicalPosition/AConfig.Overlay.VoxelSize(2) +AConfig.Overlay.Origin(2);
			if thePhysicalPosition>size(theVolume, 2),
			thePhysicalPosition =size(theVolume, 2);
			elseif thePhysicalPosition<1,
			thePhysicalPosition =1;
			end
			Result =squeeze(theVolume(:, round(thePhysicalPosition), :));
			%Result =theVolume(:, round(thePhysicalPosition), :);

			case 'transverse',
			thePhysicalPosition =(AUnderlayPosition -AConfig.Origin(3)) *AConfig.VoxelSize(3);
			thePhysicalPosition =thePhysicalPosition/AConfig.Overlay.VoxelSize(3) +AConfig.Overlay.Origin(3);
			if thePhysicalPosition>size(theVolume, 3),
			thePhysicalPosition =size(theVolume, 3);
			elseif thePhysicalPosition<1,
			thePhysicalPosition =1;
			end
			Result =squeeze(theVolume(:, :, round(thePhysicalPosition)));
			% Result =theVolume(:, :, round(thePhysicalPosition));
			otherwise
			end
			Result =Result';

			function Result =Pos_Underlay2Overlay(AConfig, AUnderlayPosition)
			% AUnderlayPosition is a 1by3 vector, result is the same
			Result =(AUnderlayPosition -AConfig.Origin) .*AConfig.VoxelSize;
			Result =Result./AConfig.Overlay.VoxelSize +AConfig.Overlay.Origin;
			Result =round(Result);

			function Result =SetThrdAbsValue(AConfig)
			%By default, I only set the Min absolute value to be the threshold, and renturn the Min, 20070918
			AConfig=CheckDf(AConfig);
			theObject =get(AConfig.hFig, 'CurrentObject');
			if strcmpi(get(theObject, 'Style'), 'edit'), %dong 090921 add p value input
			edtPosition=get(theObject, 'Position');
			if edtPosition(1) ==85
			Result =str2num(get(AConfig.hEdtThrdValue, 'String'));
			Pvalue=ThrdtoP(Result,AConfig);
			else
			Pvalue =str2num(get(AConfig.hEdtPValue, 'String'));
			Result =PtoThrd(Pvalue,AConfig);
			end
			elseif strcmpi(get(theObject, 'Style'), 'slider'),
			Result =get(AConfig.hSliderThrdValue, 'Value');
			Pvalue=ThrdtoP(Result,AConfig);
			else
			Result =-Inf;
			Pvalue = 1;
			return;
			end

			theMin =get(AConfig.hSliderThrdValue, 'Min');
			theMax =get(AConfig.hSliderThrdValue, 'Max');
			if Result<theMin,
			Result =theMin;
			Pvalue=ThrdtoP(theMin,AConfig);
			elseif Result>theMax,
			Result =theMax;
			Pvalue=1;
			end

			set(AConfig.hSliderThrdValue, 'Value', Result);
			set(AConfig.hEdtThrdValue, 'String', num2str(Result));
			set(AConfig.hEdtPValue, 'String', num2str(Pvalue)); %dong 090921


			function Result =ThrdOverlayAbsoluteValueAbove(AOverlayImg, AAbsoluteValueMin)
			%Threshold for Absolute value above the Min
			Result =AOverlayImg;
			tmp = abs(AOverlayImg)>=abs(AAbsoluteValueMin);
			Result(~tmp)=0;

			function Result =ThrdOverlayAbsoluteValueBelow(AOverlayImg, AAbsoluteValueMax)
			%Threshold for Absolute value above the Min
			Result =AOverlayImg;
			tmp = abs(AOverlayImg)<=abs(AAbsoluteValueMax);
			Result(~tmp)=0;
			function Result =ThrdOverlayValueAbove(AOverlayImg, AValueMin)
			%Threshold for Absolute value above the Min
			Result =AOverlayImg;
			tmp = (AOverlayImg)>=(AValueMin);
			Result(~tmp)=0;

			function Result =ThrdOverlayValueBelow(AOverlayImg, AValueMax)
			%Threshold for Absolute value above the Min
			Result =AOverlayImg;
			tmp = (AOverlayImg)<=(AValueMax);
			Result(~tmp)=0;

			function Result =ThrdOverlayValueIn(AOverlayImg, AValueSeries)
			%Threshold for a seiry of values
			Result =AOverlayImg;
			tmp =false(size(AOverlayImg));
			for x=1:length(AValueSeries),
			tmp = tmp \| ((AOverlayImg)==(AValueSeries(x)) );
			end
			Result(~tmp)=0;




			function Result =ThrdOverlayCluster(AConfig, AVolume)
			%Threshold for Cluster Size or calculated cluster size from cluster-Raidus %This function must be called after thresholding the Value already!
			%"AConfig.Overlay.VolumeThrd" must be thresholded before this function is called!
			Result =AVolume;
			%Raidus has Priority
			if AConfig.Overlay.ClusterRadiusThrd~=0, %Raidus(mm)
			%Calcute the cluster size according to the Raidus(mm)
			AConfig.Overlay.Header.Origin=AConfig.Overlay.Origin; %%Yan 080610
			maskROI =rest_SphereROI( 'BallDefinition2Mask' , sprintf('ROI Center(mm)=(0, 0, 0); Radius=%g mm.', AConfig.Overlay.ClusterRadiusThrd), size(AConfig.Overlay.Volume), AConfig.Overlay.VoxelSize, AConfig.Overlay.Header); %%Yan 080610 and 081223
			AConfig.Overlay.ClusterSizeThrd =length(find(maskROI));
			AConfig.Overlay.ClusterRadiusThrd =0;
			end
			if AConfig.Overlay.ClusterSizeThrd==0, return; end
			[theObjMask, theObjNum]=bwlabeln(Result,AConfig.Overlay.ClusterConnectivityCriterion); %DONG Zhang-Ye and YAN Chao-Gan 090711, make the Cluster Connectivity Criterion flexible. %[theObjMask, theObjNum]=bwlabeln(Result);
			for x=1:theObjNum,
			theCurrentCluster = theObjMask==x;
			if length(find(theCurrentCluster))<AConfig.Overlay.ClusterSizeThrd,
			Result(logical(theCurrentCluster))=0; %YAN Chao-Gan 081223, Original "Result(~logical(theCurrentCluster))=0;" was an error
			end
			end


			function Result =ThresholdOverlayVolume(AConfig)
			AConfig.Overlay.VolumeThrd =AConfig.Overlay.Volume;
			%First, thresholding by a range set by Min,Max
			if ~isinf(AConfig.Overlay.ValueThrdMin),
			AConfig.Overlay.VolumeThrd =ThrdOverlayValueAbove(AConfig.Overlay.VolumeThrd, AConfig.Overlay.ValueThrdMin);
			end
			if ~isinf(AConfig.Overlay.ValueThrdMax),
			AConfig.Overlay.VolumeThrd =ThrdOverlayValueBelow(AConfig.Overlay.VolumeThrd, AConfig.Overlay.ValueThrdMax);
			end

			%Absolute value thresholding without priority!
			%Threshold the Overlay by the Value or Range or Series
			if AConfig.Overlay.ValueThrdAbsolute>0,
			AConfig.Overlay.VolumeThrd =ThrdOverlayAbsoluteValueAbove(AConfig.Overlay.VolumeThrd, AConfig.Overlay.ValueThrdAbsolute);
			end

			if ~isnan(AConfig.Overlay.ValueThrdSeries),
			AConfig.Overlay.VolumeThrd =ThrdOverlayValueIn(AConfig.Overlay.VolumeThrd, AConfig.Overlay.ValueThrdSeries);
			end
			AConfig.Overlay.VolumeThrd =ThrdOverlayCluster(AConfig, AConfig.Overlay.VolumeThrd);
			Result =AConfig;

			function Result =ScaleOverlay2TrueColor(AConfig, AOverlayImg, AColorMap)
			[pathstr, name, ext] = fileparts(AConfig.Overlay.Filename);
			if strcmpi(name,'aal') \|\| strcmpi(name,'brodmann'),
			Result =ScaleTemplate2TrueColor(AConfig, AOverlayImg);
			else
			VolumeMax=max(AConfig.Overlay.VolumeThrd(:));%090919 dong ,revise the max and min color
			VolumeMin=min(AConfig.Overlay.VolumeThrd(:));
			Result =Overlay2TrueColor(AOverlayImg, AColorMap,VolumeMax,VolumeMin,AConfig.Overlay.ValueThrdAbsolute); %dong 091128
			end
			DrawColorbar(AConfig);

			function Result =Overlay2TrueColor(AOverlayImg, AColorMap,VolumeMax,VolumeMin,ValueThrdAbsolute) %090919 dong ,revise the max color
			Result =AOverlayImg;
			nColorLen =size(AColorMap, 1);
			%Attention:
			%Keep zero as zero always! 20070915

			%Mapping the Negative values
			ResultNegative =Result;
			ResultNegative(Result>0) =0;

			theNonZeroPos =find(ResultNegative~=0);
			theMax =-ValueThrdAbsolute;
			%YAN Chao-Gan and DONG Zhang-Ye, 090717 %theMax =max(ResultNegative(theNonZeroPos));
			theMin =VolumeMin;%min(ResultNegative(theNonZeroPos));
			if theMax>theMin,
			ResultNegative(theNonZeroPos) = (ResultNegative(theNonZeroPos)-theMin)/(theMax - theMin) (nColorLen/2) +1; %YAN Chao-Gan 091201. %ResultNegative(theNonZeroPos) = (ResultNegative(theNonZeroPos)-theMin)/(theMax - theMin) (nColorLen/2-1) +1;%Add one to make sure theMin be mapped not zero(i.e. to 1) and could be mapped to the first element in colormap
			ResultNegative =overlay_ind2rgb(floor(ResultNegative), AColorMap(1:nColorLen/2, :));
			else
			if theMax~=0,
			ResultNegative(theNonZeroPos) =1;
			ResultNegative =overlay_ind2rgb(floor(ResultNegative), AColorMap(1, :));
			else
			ResultNegative =zeros([size(Result), 3]);
			end
			end

			%Mapping the Positive values
			ResultPositive =Result;
			ResultPositive(Result<0) =0;

			theNonZeroPos =find(ResultPositive~=0);
			theMax =VolumeMax;
			theMin =ValueThrdAbsolute;
			if theMax>theMin,
			ResultPositive(theNonZeroPos) = (ResultPositive(theNonZeroPos)-theMin)/(theMax - theMin) (nColorLen/2) +1; %YAN Chao-Gan 091201. %ResultPositive(theNonZeroPos) = (ResultPositive(theNonZeroPos)-theMin)/(theMax - theMin) (nColorLen/2-1) +1;
			ResultPositive =overlay_ind2rgb(floor(ResultPositive), AColorMap(nColorLen/2+1:end, :)); %YAN Chao-Gan 091201 %ceil
			else
			if theMax~=0,
			ResultPositive(theNonZeroPos) =1;
			ResultPositive =overlay_ind2rgb(floor(ResultPositive), AColorMap(end, :));
			else
			ResultPositive =zeros([size(Result), 3]);
			end
			end

			Result =ResultNegative +ResultPositive;

			function Result =ScaleTemplate2TrueColor(AConfig, AOverlayImg)
			%Such as AAL, BRODMANN ...
			Result =AOverlayImg;
			[pathstr, name, ext] = fileparts(AConfig.Overlay.Filename);
			if strcmpi(name, 'aal'),
			AColorMap =rest_ReadLutColorScheme(fullfile(rest_misc( 'WhereIsREST'),'Template', 'aal.nii.lut')); %YAN Chao-Gan 081223: use the NIFTI image information from the MRIcroN
			theBlackPos=sum(AColorMap, 2)==0;
			AColorMap(theBlackPos, :) =1; %Black to White for I use black always as the background
			Result =overlay_ind2rgb(1+floor(Result), AColorMap);%Overpass the first color which may be backgound color
			elseif strcmpi(name, 'brodmann'),
			AColorMap =rest_ReadLutColorScheme(fullfile(rest_misc( 'WhereIsREST'),'Template', 'brodmann.nii.lut')); %YAN Chao-Gan 081223: use the NIFTI image information from the MRIcroN
			theBlackPos=sum(AColorMap, 2)==0;
			AColorMap(theBlackPos, :) =1; %Black to White for I use black always as the background
			Result =overlay_ind2rgb(1+floor(Result), AColorMap);%Overpass the first color which may be backgound color
			end


			function Result =AddOverlay(AType, AConfig, ATrueColorUnderlay,theMagnifyCoefficient)

			switch lower(AType)
			case 'sagittal',
			AUnderlayPosition =AConfig.LastPosition(1);
			case 'coronal',
			AUnderlayPosition =AConfig.LastPosition(2);
			case 'transverse',
			AUnderlayPosition =AConfig.LastPosition(3);
			otherwise
			end

			Result =ATrueColorUnderlay;
			if isempty(AConfig.Overlay.Filename),
			return;
			else %Add Overlay Image
			theOverlay =GetOverlayImg(AType, AConfig, AUnderlayPosition);
			%100325 dong begin
			Xvol=AConfig.Overlay.VoxelSize(1);
			Yvol=AConfig.Overlay.VoxelSize(2);
			Zvol=AConfig.Overlay.VoxelSize(3);
			%100325 dong end
			%Resize image to the same size with the Anatomical image
			if license('test','image_toolbox')==1,
			if rest_misc('GetMatlabVersion')>=7.4 %YAN Chao-Gan 090401: The imresize function has been completely rewritten in Matlab R2007a. Fixed the bug of 'Set Overlay's Color bar' in Matlab R2007a or latter version.
			switch lower(AType)
			case 'sagittal',
			theOverlay =imresize_old(theOverlay, floor([(size(theOverlay, 1)-1)Xvol+1, (size(theOverlay, 2)-1)Xvol+1]*theMagnifyCoefficient));
			case 'coronal',
			theOverlay =imresize_old(theOverlay, floor([(size(theOverlay, 1)-1)Yvol+1, (size(theOverlay, 2)-1)Yvol+1]*theMagnifyCoefficient));
			case 'transverse',
			theOverlay =imresize_old(theOverlay, floor([(size(theOverlay, 1)-1)Zvol+1, (size(theOverlay, 2)-1)Zvol+1]*theMagnifyCoefficient));
			otherwise
			end
			else
			switch lower(AType)
			case 'sagittal',
			theOverlay =imresize(theOverlay, floor([(size(theOverlay, 1)-1)Xvol+1, (size(theOverlay, 2)-1)Xvol+1]*theMagnifyCoefficient));
			case 'coronal',
			theOverlay =imresize(theOverlay, floor([(size(theOverlay, 1)-1)Yvol+1, (size(theOverlay, 2)-1)Yvol+1]*theMagnifyCoefficient));
			case 'transverse',
			theOverlay =imresize(theOverlay, floor([(size(theOverlay, 1)-1)Zvol+1, (size(theOverlay, 2)-1)Zvol+1]*theMagnifyCoefficient));
			otherwise
			end
			end
			else,
			error('You must install image_toolbox first!');
			end
			%100325 dong begin
			newOverlay=zeros(size(ATrueColorUnderlay,1),size(ATrueColorUnderlay,2));
			Xset=AConfig.Origin(1)-(AConfig.Overlay.Origin(1)-1)*Xvol;
			Yset=AConfig.Origin(2)-(AConfig.Overlay.Origin(2)-1)*Yvol;
			Zset=AConfig.Origin(3)-(AConfig.Overlay.Origin(3)-1)*Zvol;
			switch lower(AType)
			case 'sagittal',
			setFlag=0;%100421 dong changed setFlag
			while setFlag == 0
			D1st = min(size(newOverlay,1),size(theOverlay,1))+abs(floor(Zset*theMagnifyCoefficient));
			D2nd = min(size(newOverlay,2),size(theOverlay,2))+abs(floor(Yset*theMagnifyCoefficient));
			setFlag=1;
			if D1st>size(ATrueColorUnderlay,1)
			Zset=Zset-1;
			setFlag=0;
			end
			if D2nd>size(ATrueColorUnderlay,2)
			Yset=Yset-1;
			setFlag=0;
			end
			end
			case 'coronal',
			setFlag=0;
			while setFlag == 0
			D1st = min(size(newOverlay,1),size(theOverlay,1))+abs(floor(Zset*theMagnifyCoefficient));
			D2nd = min(size(newOverlay,2),size(theOverlay,2))+abs(floor(Xset*theMagnifyCoefficient));
			setFlag=1;
			if D1st>size(ATrueColorUnderlay,1)
			Zset=Zset-1;
			setFlag=0;
			end
			if D2nd>size(ATrueColorUnderlay,2)
			Xset=Xset-1;
			setFlag=0;
			end
			end
			case 'transverse',
			setFlag=0;
			while setFlag == 0
			D1st = min(size(newOverlay,1),size(theOverlay,1))+abs(floor(Yset*theMagnifyCoefficient));
			D2nd = min(size(newOverlay,2),size(theOverlay,2))+abs(floor(Xset*theMagnifyCoefficient));
			setFlag=1;
			if D1st>size(ATrueColorUnderlay,1)
			Yset=Yset-1;
			setFlag=0;
			end
			if D2nd>size(ATrueColorUnderlay,2)
			Xset=Xset-1;
			setFlag=0;
			end
			end
			otherwise
			end
			switch lower(AType)
			case 'sagittal',
			for i=1:min(size(newOverlay,1),size(theOverlay,1))
			for j=1:min(size(newOverlay,2),size(theOverlay,2))
			if Zset>=0&&Yset>=0
			newOverlay(i+floor(ZsettheMagnifyCoefficient),j+floor(YsettheMagnifyCoefficient))=theOverlay(i,j);
			else
			newOverlay(i,j)=theOverlay(i+abs(floor(ZsettheMagnifyCoefficient)),j+abs(floor(YsettheMagnifyCoefficient)));
			end
			end
			end
			case 'coronal',
			for i=1:min(size(newOverlay,1),size(theOverlay,1))
			for j=1:min(size(newOverlay,2),size(theOverlay,2))
			if Zset>=0&&Xset>=0
			newOverlay(i+floor(ZsettheMagnifyCoefficient),j+floor(XsettheMagnifyCoefficient))=theOverlay(i,j);
			else
			newOverlay(i,j)=theOverlay(i+abs(floor(ZsettheMagnifyCoefficient)),j+abs(floor(XsettheMagnifyCoefficient)));
			end
			end
			end
			case 'transverse',
			for i=1:min(size(newOverlay,1),size(theOverlay,1))
			for j=1:min(size(newOverlay,2),size(theOverlay,2))
			if Yset>=0&&Xset>=0
			newOverlay(i+floor(YsettheMagnifyCoefficient),j+floor(XsettheMagnifyCoefficient))=theOverlay(i,j);
			else
			newOverlay(i,j)=theOverlay(i+abs(floor(YsettheMagnifyCoefficient)),j+abs(floor(XsettheMagnifyCoefficient)));
			end
			end
			end
			otherwise
			end
			nonZeroPos =newOverlay~=0;
			newOverlay =ScaleOverlay2TrueColor(AConfig, newOverlay, AConfig.Overlay.Colormap);
			Result =AddRGBInMask(newOverlay, ATrueColorUnderlay,nonZeroPos,AConfig.Overlay.Opacity);
			%100325 dong end
			SetMessage(AConfig);
			%Result =theOverlay AConfig.Overlay.Opacity + ATrueColorUnderlay(1-AConfig.Overlay.Opacity);
			end

			function Result =AddOverlaySeries(AConfig, ATrueColorUnderlay,theMagnifyCoefficient)
			%Get the Magnified Brain Size
			%Make sure there will be no any fractional value if GetMagnifyCoefficient(AConfig)<1
			theSize= floor(GetMagnifyCoefficient(AConfig) * (size(AConfig.Volume)));
			nDim1=theSize(1); nDim2=theSize(2); nDim3=theSize(3);
			Result =ATrueColorUnderlay;
			if isempty(AConfig.Overlay.Filename),
			return;
			else %Add Overlay Image
			%100325 dong begin
			Xvol=AConfig.Overlay.VoxelSize(1);
			Yvol=AConfig.Overlay.VoxelSize(2);
			Zvol=AConfig.Overlay.VoxelSize(3);
			%100325 dong end
			for theRow=AConfig.Montage.Down:-1:1,
			for theCol=1:AConfig.Montage.Across,
			%Retrieve the underlay
			switch lower(AConfig.ViewMode)
			case 'sagittal',
			theUnderlay =Result((theRow-1)nDim3 +(1:nDim3), (theCol-1)nDim2+(1:nDim2), :);
			case 'coronal',
			theUnderlay =Result((theRow-1)nDim3 +(1:nDim3), (theCol-1)nDim1+(1:nDim1), :);
			case 'transverse',
			theUnderlay =Result((theRow-1)nDim2 +(1:nDim2), (theCol-1)nDim1+(1:nDim1), :);
			otherwise
			end
			%Get the overlay
			theIndex = AConfig.ViewSeries((AConfig.Montage.Down-theRow)*AConfig.Montage.Across +theCol);
			%YAN Chao-Gan 081229 theIndex = AConfig.ViewSeries((theRow-1)*AConfig.Montage.Across +theCol);
			theOverlay =GetOverlayImg(AConfig.ViewMode, AConfig, theIndex);

			if license('test','image_toolbox')==1,
			if rest_misc('GetMatlabVersion')>=7.4 %YAN Chao-Gan 090401: The imresize function has been completely rewritten in Matlab R2007a. Fixed the bug of 'Set Overlay's Color bar' in Matlab R2007a or latter version.
			switch lower(AConfig.ViewMode)
			case 'sagittal',
			theOverlay =imresize_old(theOverlay, floor([(size(theOverlay, 1)-1)Xvol+1, (size(theOverlay, 2)-1)Xvol+1]*theMagnifyCoefficient));
			case 'coronal',
			theOverlay =imresize_old(theOverlay, floor([(size(theOverlay, 1)-1)Yvol+1, (size(theOverlay, 2)-1)Yvol+1]*theMagnifyCoefficient));
			case 'transverse',
			theOverlay =imresize_old(theOverlay, floor([(size(theOverlay, 1)-1)Zvol+1, (size(theOverlay, 2)-1)Zvol+1]*theMagnifyCoefficient));
			otherwise
			end
			else
			switch lower(AConfig.ViewMode)
			case 'sagittal',
			theOverlay =imresize(theOverlay, floor([(size(theOverlay, 1)-1)Xvol+1, (size(theOverlay, 2)-1)Xvol+1]*theMagnifyCoefficient));
			case 'coronal',
			theOverlay =imresize(theOverlay, floor([(size(theOverlay, 1)-1)Yvol+1, (size(theOverlay, 2)-1)Yvol+1]*theMagnifyCoefficient));
			case 'transverse',
			theOverlay =imresize(theOverlay, floor([(size(theOverlay, 1)-1)Zvol+1, (size(theOverlay, 2)-1)Zvol+1]*theMagnifyCoefficient));
			otherwise
			end
			end%100325 dong end
			else
			error('You must install image_toolbox first!');
			end
			%100325 dong begin
			newOverlay=zeros(size(theUnderlay,1),size(theUnderlay,2));
			Xset=AConfig.Origin(1)-(AConfig.Overlay.Origin(1)-1)*Xvol;
			if Xset ==1
			Xset=0;
			end
			if Xset ==13
			Xset=12;
			end
			Yset=AConfig.Origin(2)-(AConfig.Overlay.Origin(2)-1)*Yvol;
			if Yset ==1
			Yset=0;
			end
			if Yset ==14
			Yset=13;
			end
			Zset=AConfig.Origin(3)-(AConfig.Overlay.Origin(3)-1)*Zvol;
			if Zset ==1
			Zset=0;
			end
			if Yset ==22
			Yset=21;
			end
			switch lower(AConfig.ViewMode)
			case 'sagittal',
			for i=1:min(size(newOverlay,1),size(theOverlay,1))
			for j=1:min(size(newOverlay,2),size(theOverlay,2))
			if Zset>=0&&Yset>=0
			newOverlay(i+floor(ZsettheMagnifyCoefficient),j+floor(YsettheMagnifyCoefficient))=theOverlay(i,j);
			else
			newOverlay(i,j)=theOverlay(i+abs(floor(ZsettheMagnifyCoefficient)),j+abs(floor(YsettheMagnifyCoefficient)));
			end
			end
			end
			case 'coronal',
			for i=1:min(size(newOverlay,1),size(theOverlay,1))
			for j=1:min(size(newOverlay,2),size(theOverlay,2))
			if Zset>=0&&Xset>=0
			newOverlay(i+floor(ZsettheMagnifyCoefficient),j+floor(XsettheMagnifyCoefficient))=theOverlay(i,j);
			else
			newOverlay(i,j)=theOverlay(i+abs(floor(ZsettheMagnifyCoefficient)),j+abs(floor(XsettheMagnifyCoefficient)));
			end
			end
			end
			case 'transverse',
			for i=1:min(size(newOverlay,1),size(theOverlay,1))
			for j=1:min(size(newOverlay,2),size(theOverlay,2))
			if Yset>=0&&Xset>=0
			newOverlay(i+floor(YsettheMagnifyCoefficient),j+floor(XsettheMagnifyCoefficient))=theOverlay(i,j);
			else
			newOverlay(i,j)=theOverlay(i+abs(floor(YsettheMagnifyCoefficient)),j+abs(floor(XsettheMagnifyCoefficient)));
			end
			end
			end
			otherwise
			end
			nonZeroPos =newOverlay~=0;
			newOverlay =ScaleOverlay2TrueColor(AConfig, newOverlay, AConfig.Overlay.Colormap);
			% nonZeroPos = theOverlay~=0;
			% theOverlay =ScaleOverlay2TrueColor(AConfig, theOverlay, AConfig.Overlay.Colormap);

			%Add r g b colors with mask
			theUnderlay =AddRGBInMask(newOverlay, theUnderlay, nonZeroPos, AConfig.Overlay.Opacity);
			%theUnderlay =AddRGBInMask(theOverlay, theUnderlay, nonZeroPos, AConfig.Overlay.Opacity);
			%100325 dong end

			%Save underlay to big series' map
			switch lower(AConfig.ViewMode)
			case 'sagittal',
			Result((theRow-1)nDim3 +(1:nDim3), (theCol-1)nDim2+(1:nDim2), :) =theUnderlay;
			case 'coronal',
			Result((theRow-1)nDim3 +(1:nDim3), (theCol-1)nDim1+(1:nDim1), :) =theUnderlay;
			case 'transverse',
			Result((theRow-1)nDim2 +(1:nDim2), (theCol-1)nDim1+(1:nDim1), :) =theUnderlay;
			otherwise
			end
			end %end for-loop theCol
			end %end for-loop theRow
			end %end if

			function Result =LoadOverlay(AConfig, AFilename)
			AConfig.Df.Ttest=0;
			AConfig.Df.Ftest=[0,0];
			AConfig.Df.Ztest=0;
			AConfig.Df.Rtest=0;
			Result =AConfig;
			try
			[theVolume,theVoxelSize, Header] =rest_readfile(AFilename); %%Yan 080610
			theOrigin=Header.Origin; %%Yan 080610
			Result =AddRecentOverlay(AConfig, AFilename);
			catch
			if ~(exist(AFilename, 'file')==2) ...
			&& ( ~all(isspace(AFilename)) && ~isempty(isspace(AFilename))),
			warning(sprintf('Please check whether Img/Hdr file "%s" exist!', AConfig.Filename));
			warndlg(sprintf('Please check whether Img/Hdr file "%s" exist!', AConfig.Filename));
			end

			theVolume =zeros(61, 73, 61); theVolume(33,33,33)=0.1;
			theVoxelSize=[3 3 3];
			theOrigin =[31 43 25];
			end
			Result.Overlay.Filename =AFilename;
			Result.Overlay.Volume =theVolume;
			Result.Overlay.VolumeThrd =theVolume;%Volume Thresholded as cache
			Result.Overlay.VoxelSize =reshape(theVoxelSize, [1 3]);
			Result.Overlay.Origin =reshape(theOrigin, [1 3]);
			Result.Overlay.Header=Header; %%Yan 080610
			if any(Result.Overlay.Origin==[0 0 0]),
			%Auto-Revise the Origin to the half of the size of the brain
			theMsg =sprintf('Illegal origin: (%s)\n\nI presume the origin is (%s)',num2str(Result.Overlay.Origin), num2str(round(size(Result.Overlay.Volume)/2)));
			warning(theMsg);
			warndlg(theMsg);
			Result.Overlay.Origin =round(size(Result.Overlay.Volume)/2);
			end

			%Calcute the min and max both in positive & negative field
			tmpVolume =theVolume(find(theVolume));
			theMinNegative = min(tmpVolume(tmpVolume<0));
			theMaxNegative = max(tmpVolume(tmpVolume<0));
			theMinPositive = min(tmpVolume(tmpVolume>0));
			theMaxPositive = max(tmpVolume(tmpVolume>0));
			clear tmpVolume;
			if isempty(theMinNegative), theMinNegative =0; end %Just For always zero map
			if isempty(theMaxNegative), theMaxNegative =0; end %Just For always zero map
			if isempty(theMinPositive), theMinPositive =0; end %Just For always zero map
			if isempty(theMaxPositive), theMaxPositive =0; end %Just For always zero map

			theAbsMax =max(abs([theMinNegative, theMaxPositive]));
			theAbsMin =min(abs([theMaxNegative, theMinPositive]));
			% theAbsVolume =abs(theVolume);
			% theAbsMax =max(theAbsVolume(find(theAbsVolume)));
			% theAbsMin =min(theAbsVolume(find(theAbsVolume)));
			% clear theAbsVolume;
			if theAbsMax<=theAbsMin, theAbsMax =theAbsMin+1; end
			set(AConfig.hSliderThrdValue, 'Max',theAbsMax,'Min',theAbsMin, 'Value',theAbsMin, 'SliderStep',[0.01, 0.05]);


			Result.Overlay.MinNegative =theMinNegative;%-10
			Result.Overlay.MaxNegative =theMaxNegative;%-1
			Result.Overlay.MinPositive =theMinPositive; %1
			Result.Overlay.MaxPositive =theMaxPositive; %10
			Result.Overlay.AbsMin =theAbsMin;
			Result.Overlay.AbsMax =theAbsMax;

			Result.Overlay.ValueThrdAbsolute =theAbsMin; %Default, show all
			Result.Overlay.ValueThrdMin =theMinNegative; %Default, show all
			Result.Overlay.ValueThrdMax =theMaxPositive; %Default, show all
			Result.Overlay.ClusterThrd =0; %Default, don't confine cluster size
			Result.Overlay.ClusterRadius =0; %Default radius(mm) for Cluster size definition



			[pathstr, name, ext] = fileparts(Result.Overlay.Filename);
			if strcmpi(name, 'aal'),
			theInfoTxt =fullfile(rest_misc( 'WhereIsREST'),'Template', 'aal.nii.txt'); %YAN Chao-Gan 081223: use the NIFTI image information from the MRIcroN
			[x,Result.Overlay.InfoAal,y] =textread(theInfoTxt,'%d %s %d');
			else
			Result.Overlay.InfoAal='None';
			end


			function [rout,g,b] = overlay_ind2rgb(a,cm)
			theImage =a;
			% Make sure A is in the range from 0 to size(cm,1)
			theImage = max(0,min(theImage,size(cm,1)));
			%Exclude any zero values, following is the Revision
			theColormap =[[-1 -1 -1]; cm];
			theImage =theImage+1;%Make any zero to one

			% Extract r,g,b components
			r = zeros(size(theImage)); r(:) = theColormap(theImage,1);
			g = zeros(size(theImage)); g(:) = theColormap(theImage,2);
			b = zeros(size(theImage)); b(:) = theColormap(theImage,3);

			if nargout==3,
			rout = r;
			else
			rout = zeros([size(r),3]);
			rout(:,:,1) = r;
			rout(:,:,2) = g;
			rout(:,:,3) = b;
			end
			%Revision finally
			rout(rout==-1) =0;

			function Result =GetDefaultColormap()
			theNegative =winter(128);
			thePositive =hot(128);
			thePositive =thePositive(128:-1:1, :);
			Result =[theNegative; thePositive];

			function Result =AddRGBInMask(AMapO, AMapU, AMask, AOpacityX)
			if ~isequal(size(AMapO),size(AMapU)),
			error('Non-same size are the two true-color maps');
			end
			if AOpacityX<0 \|\| AOpacityX>1,
			error('Non legal AOpacity value');
			end
			AMask = AMask~=0;

			rx =AMapO(:, :, 1);
			ry =AMapU(:, :, 1);
			r =zeros(size(rx));
			r(AMask) =rx(AMask)AOpacityX +ry(AMask)(1-AOpacityX);
			r(~AMask)=ry(~AMask);

			gx =AMapO(:, :, 2);
			gy =AMapU(:, :, 2);
			g =zeros(size(rx));
			g(AMask) =gx(AMask)AOpacityX +gy(AMask)(1-AOpacityX);
			g(~AMask)=gy(~AMask);

			bx =AMapO(:, :, 3);
			by =AMapU(:, :, 3);
			b =zeros(size(rx));
			b(AMask) =bx(AMask)AOpacityX +by(AMask)(1-AOpacityX);
			b(~AMask)=by(~AMask);

			Result= zeros(size(AMapO));
			Result(:, :, 1)=r;
			Result(:, :, 2)=g;
			Result(:, :, 3)=b;

			function Result =Overlay_Misc(AConfig)
			isNeedUpdate =false;
			% if SeeOverlay(AConfig),
			switch get(AConfig.hOverlayMisc, 'Value'),
			case 1, %Overlay Misc
			%Do nothing
			case 2, %'Set Overlay Opacity'
			prompt ={'Overlay''s Opacity: (1=opaque, 0=transparent and restricted in [0, 1])'};
			def ={ num2str(AConfig.Overlay.Opacity) };
			answer =inputdlg(prompt, 'Overlay Opacity', 1, def);
			if numel(answer)==1,
			theVal =abs(str2num(answer{1}));
			if theVal>1, theVal=1; end
			AConfig.Overlay.Opacity = theVal;
			end
			case 3, %Set Range of Threshold
			prompt ={'Threshold Value''s Range: Min, Max( Default=-Inf,Inf.)', sprintf('\nSet Threshold Value''s Series, such as 25,1,7,31 for only showing Brodmann''s area BA25, BA1, BA7, BA31 when overlay is BA template. This also works for AAL template. This supports MATLAB array defination syntax. NaN means not confined in any series.')};
			def ={sprintf('%d, %d',AConfig.Overlay.ValueThrdMin,AConfig.Overlay.ValueThrdMax) ,...
			num2str(AConfig.Overlay.ValueThrdSeries)};
			answer =inputdlg(prompt, 'Set a range for thresholding', 2, def);
			if numel(answer)==2,
			theVal =(str2num(answer{1}));
			if length(theVal)==2,
			if theVal(1)>theVal(2), theVal=theVal([2,1]); end

			if theVal(1)<AConfig.Overlay.MinNegative,
			theVal(1) =AConfig.Overlay.MinNegative;
			end
			if theVal(2)>AConfig.Overlay.MaxPositive,
			theVal(2) =AConfig.Overlay.MaxPositive;
			end

			AConfig.Overlay.ValueThrdMin =theVal(1);
			AConfig.Overlay.ValueThrdMax =theVal(2);
			end
			theVal =(str2num(answer{2}));
			if ~isempty(theVal),
			AConfig.Overlay.ValueThrdSeries =theVal;
			else
			AConfig.Overlay.ValueThrdSeries =NaN;
			end
			AConfig =ThresholdOverlayVolume(AConfig);
			end
			case 4, %Set AConfig.Overlay.LabelColor
			theColor =uisetcolor;
			if numel(theColor)==1 && theColor==0,
			%User canceled the color selection
			else
			AConfig.Overlay.LabelColor =theColor;
			end
			case 5, %Set Color map parameters
			prompt ={sprintf('Overlay''s Color command: ( i.e. about how to generate the color map for overlay.)\n\n1. You can input 2 or 4 or 6...16 or 18 or 20... and so on. This way would generate a N-elements colorbar similar as AFNI''s colorbar.\n2. "jet(64)" or other MATLAB command(such as "Winter(20)" and so on) would generate a smooth colorbar.\n3. ** means using default colormap that''s generated by command jet(64).)')};
			def ={ AConfig.Overlay.ColorbarCmd };
			answer =inputdlg(prompt, 'Set color bar definition', 1, def);
			if numel(answer)==1,
			AConfig =DefineColorMap(AConfig, answer{1});
			end
			case 6, %Save Image
			%YAN Chao-Gan 081223: add "save image as" function
			[filename, pathname] = uiputfile({'.tiff';'.jpeg';'.png';'.bmp'}, 'Save Image As');
			if filename~=0,%dong 090919
			[tempPath, fileN, extn] = fileparts(filename);
			while isempty(strmatch(extn, strvcat('.tiff', '.jpeg', '.png','.bmp'),'exact'))
			[filename, pathname] = uiputfile({'.tiff';'.jpeg';'.png';'.bmp'}, 'Save Image As');
			[tempPath, fileN, extn] = fileparts(filename);
			end
			theFilename =fullfile(pathname,filename);
			set(gcf,'PaperPositionMode','auto')
			eval(['print -r600 -dtiff -noui ''',theFilename,''';']);
			end
			case 7, %Correction Thresholds by AlphaSim
			%YAN Chao-Gan 090401: add "Correction Thresholds by AlphaSim"
			% msgbox({'The Correction Thresholds correspond to a corrected P < 0.05 determined by the Monte Carlo simulations with the program AlphaSim in AFNI.';...
			% '';...
			% 'Mask File: BrainMask_05_61x73x61.img (70831 voxels, under /mask directory)';...
			% '';...
			% 'Gaussian kernel of spatially smooth: 4mm';...
			% ' p on individual voxel Cluster size (voxels)';...
			% ' 0.05 54';...
			% ' 0.01 16';...
			% ' 0.005 11';...
			% ' 0.001 6';...
			% '';...
			% 'Gaussian kernel of spatially smooth: 6mm';...
			% ' p on individual voxel Cluster size (voxels)';...
			% ' 0.05 165';...
			% ' 0.01 39';...
			% ' 0.005 27';...
			% ' 0.001 13';...
			% '';...
			% 'Gaussian kernel of spatially smooth: 8mm';...
			% ' p on individual voxel Cluster size (voxels)';...
			% ' 0.05 324';...
			% ' 0.01 71';...
			% ' 0.005 48';...
			% ' 0.001 22';...
			% '';...
			% 'Gaussian kernel of spatially smooth: 10mm';...
			% ' p on individual voxel Cluster size (voxels)';...
			% ' 0.05 524';...
			% ' 0.01 119';...
			% ' 0.005 78';...
			% ' 0.001 34';...
			% },'Correction Thresholds by AlphaSim');
			rest_CorrectionThresholdsByAlphaSim; %Revised by YAN Chao-Gan 091108: add situation in rmm=5 and rmm=6
			case 8 % DONG FDR 100118
			[AConfig.Overlay.Qvalue,AConfig.Overlay.Qmaskname,AConfig.Overlay.Conproc,AConfig.Overlay.Tchoose]=rest_FDR_gui(AConfig.Overlay.Qvalue,AConfig.Overlay.Qmaskname,AConfig.Overlay.Conproc,AConfig.Overlay.Tchoose);

			if AConfig.Overlay.Tchoose == 2 % Two-tailed % YAN Chao-Gan, 100201
			if AConfig.Df.Ttest~=0 ,
			ValueP=2*(1-tcdf(abs(AConfig.Overlay.Volume),AConfig.Df.Ttest)); %DONG AConfig.Overlay.Volume can change to AConfig.Overlay.VolumeThrd, if needed 100118
			elseif numel(find(AConfig.Df.Ftest))~=0 ,
			ValueP =2*(1-fcdf(abs(AConfig.Overlay.Volume),AConfig.Df.Ftest(1),AConfig.Df.Ftest(2)));
			elseif AConfig.Df.Ztest~=0 ,
			ValueP=2*(1-normcdf(abs(AConfig.Overlay.Volume)));
			elseif AConfig.Df.Rtest ~= 0 ,
			ValueP=2(1-tcdf(abs(AConfig.Overlay.Volume).sqrt((AConfig.Df.Rtest)./(1-AConfig.Overlay.Volume.*AConfig.Overlay.Volume)),AConfig.Df.Rtest));
			else
			msgbox('FDR only take effects on the statistical map!');
			Result =AConfig;
			return;
			end
			else % One-Tailed
			if AConfig.Df.Ttest~=0 ,
			ValueP=(1-tcdf(AConfig.Overlay.Volume,AConfig.Df.Ttest)); %DONG AConfig.Overlay.Volume can change to AConfig.Overlay.VolumeThrd, if needed 100118
			elseif numel(find(AConfig.Df.Ftest))~=0 ,
			ValueP =(1-fcdf(AConfig.Overlay.Volume,AConfig.Df.Ftest(1),AConfig.Df.Ftest(2)));
			elseif AConfig.Df.Ztest~=0 ,
			ValueP=(1-normcdf(AConfig.Overlay.Volume));
			elseif AConfig.Df.Rtest ~= 0,
			ValueP=(1-tcdf(AConfig.Overlay.Volume.sqrt((AConfig.Df.Rtest)./(1-AConfig.Overlay.Volume.AConfig.Overlay.Volume)),AConfig.Df.Rtest));
			else
			msgbox('FDR only take effects on the statistical map!');
			Result =AConfig;
			return;
			end
			end

			if ~isempty(AConfig.Overlay.Qmaskname)
			[MaskData MaskVox MaskHead]=rest_readfile(AConfig.Overlay.Qmaskname);
			[pID,pN] = rest_FDR(ValueP(find(MaskData)),AConfig.Overlay.Qvalue);
			else
			[pID,pN] = rest_FDR(ValueP,AConfig.Overlay.Qvalue);
			end
			if AConfig.Overlay.Conproc == 1
			AConfig.Overlay.ValueP =pID;
			else
			AConfig.Overlay.ValueP =pN;
			end
			if isempty(AConfig.Overlay.ValueP)
			AConfig.Overlay.ValueP = 0;
			end
			if AConfig.Overlay.ValueP == 0
			msgbox('No voxel exists after FDR !');
			end
			AConfig.Overlay.ValueThrdAbsolute =SetThrdAbsValueFDR(AConfig);
			AConfig =ThresholdOverlayVolume(AConfig);
			AConfig=SetImage(AConfig); %DONGFDR 100118
			case 99, %Save current map,
			%Todo, 20070916
			[filename, pathname] = uiputfile('*.jpg','Save current view: ');
			if isequal(filename,0) \| isequal(pathname,0)
			else
			theFilename =fullfile(pathname,filename);
			SaveCurrentView(AConfig, AFilename);
			end
			otherwise
			end
			% else
			% warndlg('Please Check on "SeeOverlay" before changing Overlay options!');
			% end%end if SeeOverlay(AConfig)
			%Reset position in Choice selection
			set(AConfig.hOverlayMisc, 'Value', 1);
			Result =AConfig;
			function Result =Open_Template(AConfig)
			isNeedUpdate =false;
			switch get(AConfig.hTemplate, 'Value'),
			case 1, %Overlay Misc
			%Do nothing
			case 2, %'Open Template AAL'
			rest_misc( 'CheckTemplate');
			theNewOverlay =fullfile(rest_misc( 'WhereIsREST'), 'Template', 'aal.nii'); %YAN Chao-Gan 081223: use the NIFTI image information from the MRIcroN
			set(AConfig.hOverlayFile, 'String', theNewOverlay);
			% DPARSF_rest_sliceviewer('ChangeOverlay', AConfig.hFig);
			AConfig =LoadOverlay(AConfig, theNewOverlay);
			set(AConfig.hSeeOverlay, 'Value', 1);
			case 3, %'Open Template Brodmann'
			rest_misc( 'CheckTemplate');
			theNewOverlay =fullfile(rest_misc( 'WhereIsREST'), 'Template', 'brodmann.nii'); %YAN Chao-Gan 081223: use the NIFTI image information from the MRIcroN
			set(AConfig.hOverlayFile, 'String', theNewOverlay);
			% DPARSF_rest_sliceviewer('ChangeOverlay', AConfig.hFig);
			AConfig =LoadOverlay(AConfig, theNewOverlay);
			set(AConfig.hSeeOverlay, 'Value', 1);
			case 4, %'Open Template Ch2'
			rest_misc( 'CheckTemplate');
			theNewUnderlay =fullfile(rest_misc( 'WhereIsREST'), 'Template', 'ch2.nii'); %YAN Chao-Gan 100403: use the ch2 bet image information from the MRIcroN
			set(AConfig.hUnderlayFile, 'String', theNewUnderlay);
			% DPARSF_rest_sliceviewer('ChangeOverlay', AConfig.hFig);
			AConfig.Filename =theNewUnderlay;
			AConfig =InitUnderlay(AConfig);
			case 5, %'Open Template Ch2'
			rest_misc( 'CheckTemplate');
			theNewUnderlay =fullfile(rest_misc( 'WhereIsREST'), 'Template', 'ch2bet.nii'); %YAN Chao-Gan 100403: use the ch2 bet image information from the MRIcroN
			set(AConfig.hUnderlayFile, 'String', theNewUnderlay);
			% DPARSF_rest_sliceviewer('ChangeOverlay', AConfig.hFig);
			AConfig.Filename =theNewUnderlay;
			AConfig =InitUnderlay(AConfig);
			otherwise
			end
			set(AConfig.hTemplate, 'Value', 1);
			Result =AConfig;
			function Result =CurrentThrd2Mask(AConfig)%dong 2009-09-09
			Result =AConfig.Overlay.VolumeThrd;

			function Result =CurrentCluster2Mask(AConfig)
			%Retrieve the cluster containing current point!
			% Result =ThresholdOverlayVolume(AConfig); %ThrdOverlayValue(AConfig, AConfig.Overlay.Volume);
			Result =AConfig.Overlay.VolumeThrd;
			[theCluster, theCount] =bwlabeln(Result, AConfig.Overlay.ClusterConnectivityCriterion); %DONG Zhang-Ye and YAN Chao-Gan 090711, make the Cluster Connectivity Criterion flexible. %[theCluster, theCount] =bwlabeln(Result);
			%Get the current point's position
			thePosition =Pos_Underlay2Overlay(AConfig, AConfig.LastPosition);
			if Result(thePosition(1),thePosition(2),thePosition(3))~=0, %Current point is valid and must reside in some cluster
			[pathstr, name, ext] = fileparts(AConfig.Overlay.Filename);
			%if strcmpi(name, 'aal') \|\| strcmpi(name, 'brodmann'),
			% theCurrentCluster = Result==Result(thePosition(1),thePosition(2),thePosition(3));
			% Result(~theCurrentCluster)=0;
			% return;
			%else %BwlabelN not work for AAL or Brodmann whose clusters are adjacent
			%Get the current point's cluster's label and return the current cluster
			theCurrentCluster = theCluster==theCluster(thePosition(1),thePosition(2),thePosition(3));
			theCluster(~theCurrentCluster)=0;
			%transform the Result to a binary mask
			Result(~logical(theCluster))=0;
			%Result =ceil(abs(Result)); %Revise for t-map just for not rounding to zero!
			return;
			%end
			else
			Result =[];
			end

			%Todo, 20070919
			function SaveCurrentView(AConfig, AFilename)
			%Hide most components and save the result
			theObjects =allchild(AConfig.hFig);
			for x=1:length(AConfig.hFig),
			if strcmpi(get(theObjects,'Type'), 'axes'),
			end
			end

			saveas(AConfig.hFig,theFilename);

			function Result =InitRecent(AConfig)
			Result =AConfig;
			theRecentCfg =fullfile(tempdir,['RecentUnderlay','_',rest_misc('GetCurrentUser'),'.txt']); %YAN Chao-Gan, 100420. %theRecentCfg =fullfile(rest_misc( 'WhereIsREST'), 'RecentUnderlay.txt');
			if exist(theRecentCfg, 'file')==2,
			[Result.Recent.Underlay] =textread(theRecentCfg,'%s', 'delimiter','\n');
			else
			Result.Recent.Underlay={};
			end
			theRecentCfg =fullfile(tempdir,['RecentOverlay','_',rest_misc('GetCurrentUser'),'.txt']); %YAN Chao-Gan, 100420. %theRecentCfg =fullfile(rest_misc( 'WhereIsREST'), 'RecentOverlay.txt');
			if exist(theRecentCfg, 'file')==2,
			[Result.Recent.Overlay] =textread(theRecentCfg,'%s', 'delimiter','\n');
			else
			Result.Recent.Overlay={};
			end
			set(AConfig.hUnderlayRecent, 'String', [{'Underlay: '}; Result.Recent.Underlay], 'Value',1);
			set(AConfig.hOverlayRecent, 'String', [{'Overlay: '}; Result.Recent.Overlay], 'Value',1);

			function Result =AddRecentUnderlay(AConfig, AFilename)
			Result =AConfig;

			%20071102
			%Check whether there is space in the AFilename to prevent from problem TextRead not-function when space contained !
			if any(isspace(AFilename)), return; end;

			%check whether the same menu item exist
			theIndex =strmatch(lower(AFilename), lower(Result.Recent.Underlay), 'exact');
			if ~isempty(theIndex),
			%Move the item to the first
			for x=theIndex-1:-1:1,
			Result.Recent.Underlay{x+1} =Result.Recent.Underlay{x};
			end
			else
			%Add
			if length(Result.Recent.Underlay)<6,%few
			Result.Recent.Underlay =[Result.Recent.Underlay; {''}];
			end
			for x=length(Result.Recent.Underlay):-1:2,
			Result.Recent.Underlay{x} =Result.Recent.Underlay{x-1};
			end
			end
			Result.Recent.Underlay{1} =AFilename;
			set(AConfig.hUnderlayRecent, 'String', [{'Underlay: '}; Result.Recent.Underlay], 'Value',1);

			function Result =AddRecentOverlay(AConfig, AFilename)
			Result =AConfig;
			%20071102
			%Check whether there is space in the AFilename to prevent from problem TextRead not-function when space contained !
			if any(isspace(AFilename)), return; end;


			%check whether the same menu item exist
			theIndex =strmatch(lower(AFilename), lower(Result.Recent.Overlay), 'exact' );
			if ~isempty(theIndex),
			%Move the item to the first
			for x=theIndex-1:-1:1,
			Result.Recent.Overlay{x+1} =Result.Recent.Overlay{x};
			end
			else
			%Add
			if length(Result.Recent.Overlay)<6,%few
			Result.Recent.Overlay =[Result.Recent.Overlay; {''}];
			end
			for x=length(Result.Recent.Overlay):-1:2,
			Result.Recent.Overlay{x} =Result.Recent.Overlay{x-1};
			end
			end
			Result.Recent.Overlay{1} =AFilename;
			set(AConfig.hOverlayRecent, 'String', [{'Overlay: '}; Result.Recent.Overlay], 'Value',1);

			function SaveRecent(AConfig, AType)
			%AType = RecentUnderlay.txt or RecentOverlay.txt
			theRecentCfg =fullfile(tempdir,[AType,'_',rest_misc('GetCurrentUser'),'.txt']); % YAN Chao-Gan, 100420. %theRecentCfg =fullfile(rest_misc( 'WhereIsREST'), [AType, '.txt']);
			if strcmpi(AType, 'RecentUnderlay'),
			theList =AConfig.Recent.Underlay;
			elseif strcmpi(AType, 'RecentOverlay'),
			theList =AConfig.Recent.Overlay;
			end
			hFile =fopen(theRecentCfg, 'w');
			if hFile>0,
			for x=1:length(theList),
			fprintf(hFile, '%s\r\n', theList{x});
			end
			fclose(hFile);
			else
			error(sprintf('Can''t write config file: %s', theRecentCfg));
			end

			%20070921, Colorbar definition/regeneratioin
			function Result =DefineColorMap(AConfig, AColorDefCmd)
			Result =AConfig;
			try
			theNumberCmd =str2double(AColorDefCmd);
			if ~isnan(theNumberCmd), %2,4,6...20 and is even!
			if mod(theNumberCmd,2)==1 \|\| theNumberCmd>20,
			errordlg(sprintf('The number must be even because there must be even numbers of colors in the colormap.\n\n And the Number must be less than 20. \n\nIllegal for your input: %d.', theNumberCmd), rest_misc( 'GetRestVersion'));
			return;
			else
			if theNumberCmd<2, theNumberCmd =2; AColorDefCmd='2'; end %for not zero encountered!
			theColormap =AFNI_ColorMap(theNumberCmd); %Changed to AFNI color map, YAN Chao-Gan, 090601 %theColormap =jet(theNumberCmd);
			end
			else %It is an USER DEFINED MATLAB command to generate the color map
			if strcmpi(AColorDefCmd, '**'), %Use default color map
			theColormap =jet(64);
			else %Evaluate the user's command in MATLAB
			theColormap=eval(AColorDefCmd);
			end
			end
			%Save the color-bar's definition
			AConfig.Overlay.ColorbarCmd =AColorDefCmd;
			AConfig.Overlay.Colormap =theColormap;
			Result =DrawColorbar(AConfig);
			catch
			rest_misc( 'DisplayLastException');
			errordlg('Error occured! Input may be illegal!');
			end

			function Result =DrawColorbar(AConfig)
			Result =AConfig;
			%Set whether to show the color bar
			[pathstr, name, ext] = fileparts(AConfig.Overlay.Filename);
			if SeeOverlay(AConfig) && ~strcmpi(name,'aal') && ~strcmpi(name,'brodmann'),
			set(AConfig.hAxesColorbar, 'Visible', 'on');
			set(AConfig.hImageColorbar,'Visible', 'on');
			set(AConfig.hImageCover,'Visible', 'on');

			else
			set(AConfig.hAxesColorbar, 'Visible', 'off');
			set(AConfig.hImageColorbar,'Visible', 'off');
			set(AConfig.hImageCover,'Visible', 'off');
			%Clear old labels
			theLabels =findobj(AConfig.hAxesColorbar, 'Type', 'text');
			for theX=1:length(theLabels), delete(theLabels(theX)); end
			return;
			end


			theColorbarWidth =20;
			%Set the colorbar's position according to the figure's height
			MarginX =10; MarginY =10;
			thePos =get(AConfig.hFig, 'Position');
			if strcmpi(AConfig.ViewMode, 'Orthogonal'),
			theAxesPosTop =get(AConfig.hAxesSagittal, 'Position');
			theAxesPosDown =get(AConfig.hAxesTransverse, 'Position');
			theLeft =theAxesPosTop(1) +theAxesPosTop(3) +MarginX;
			theHeight =theAxesPosTop(4) +theAxesPosDown(4);
			theColorBarPos =[theLeft, MarginY, theColorbarWidth, theHeight];
			elseif strcmpi(AConfig.ViewMode, 'Sagittal'),
			theAxesPos =get(AConfig.hAxesSagittal, 'Position');
			theLeft =theAxesPos(1) +theAxesPos(3) +MarginX;
			theHeight =theAxesPos(4);
			theColorBarPos =[theLeft, MarginY, theColorbarWidth, theHeight];
			elseif strcmpi(AConfig.ViewMode, 'Transverse'),
			theAxesPos =get(AConfig.hAxesTransverse, 'Position');
			theLeft =theAxesPos(1) +theAxesPos(3) +MarginX;
			theHeight =theAxesPos(4);
			theColorBarPos =[theLeft, MarginY, theColorbarWidth, theHeight];
			elseif strcmpi(AConfig.ViewMode, 'Coronal'),
			theAxesPos =get(AConfig.hAxesCoronal, 'Position');
			theLeft =theAxesPos(1) +theAxesPos(3) +MarginX;
			theHeight =theAxesPos(4);
			theColorBarPos =[theLeft, MarginY, theColorbarWidth, theHeight];
			end
			set(AConfig.hAxesColorbar, 'Position', theColorBarPos);
			theColorBarPosCover=[theLeft,MarginY + theHeight/2,theColorbarWidth+5,3];
			set(AConfig.hImageCover, 'Position', theColorBarPosCover,'Visible','on') %dong 1130


			theNumberCmd =str2double(AConfig.Overlay.ColorbarCmd);
			if ~isnan(theNumberCmd), %2,4,6...20 and is even!
			%Draw a element-divided colorbar, each element-color is defined by the coordesponding color in jet(theNumberColorElements)
			theColormap =reshape(AConfig.Overlay.Colormap, [size(AConfig.Overlay.Colormap,1), 1, size(AConfig.Overlay.Colormap,2)]);
			theColormap =repmat(theColormap, [1 theColorbarWidth 1]);
			if rest_misc('GetMatlabVersion')>=7.4 %YAN Chao-Gan 090401: The imresize function has been completely rewritten in Matlab R2007a. Fixed the bug of 'Set Overlay's Color bar' in Matlab R2007a or latter version.
			theColormap =imresize_old(theColormap, [theColorBarPos(4), theColorbarWidth]);
			else
			theColormap =imresize(theColormap, [theColorBarPos(4), theColorbarWidth]);
			end
			theDivideLine =reshape(get(AConfig.hFig, 'Color'), [1 1 3]);
			theDivideLine =repmat(theDivideLine, [3, theColorbarWidth, 1]);
			for x=1:theNumberCmd, % YAN Chao-Gan, 091201. %theNumberCmd-1,
			theGrayLinePos = floor(x*(theColorBarPos(4)/theNumberCmd) +[-1 0 1]);
			theColormap(theGrayLinePos, :, :) = theDivideLine;
			end
			set(AConfig.hImageColorbar, 'CData', (theColormap), 'HitTest', 'off','Visible', 'on');
			set(AConfig.hAxesColorbar,'Visible', 'on', 'XLim', [1 size(theColormap,2)], ...
			'YLim', [1 size(theColormap,1)]);
			else %Evaluate the user's command in MATLAB and %Draw a smooth colorbar
			%Build the image to show
			theColormap =reshape(AConfig.Overlay.Colormap, [size(AConfig.Overlay.Colormap,1), 1, size(AConfig.Overlay.Colormap,2)]);
			theColormap =repmat(theColormap, [1 theColorbarWidth 1]);

			theColormaptmp=theColormap;

			set(AConfig.hImageColorbar, 'CData', (theColormaptmp), 'HitTest', 'off','Visible', 'on');
			set(AConfig.hAxesColorbar,'Visible', 'on', 'XLim', [1 size(theColormap,2)], ...
			'YLim', [1 size(theColormap,1)]);
			end


			%Clear old labels
			theLabels =findobj(AConfig.hAxesColorbar, 'Type', 'text');
			for theX=1:length(theLabels), delete(theLabels(theX)); end
			%Add new labels
			if ~isnan(theNumberCmd), %2,4,6...20 and is even!
			%Draw a element-divided colorbar, each element-color is defined by the coordesponding color in jet(theNumberColorElements)
			% for x=1:(theNumberCmd+1),
			%Draw negative lables
			for x=1:theNumberCmd/2+1, %YAN Chao-Gan 091201. %x=1:theNumberCmd/2
			theGrayLinePos = floor((x-1)(theColorBarPos(4)/theNumberCmd))-8; %YAN Chao-Gan 091201. Move the negative labels down 8 pixels. %theGrayLinePos = floor((x-1)(theColorBarPos(4)/theNumberCmd));
			if x==theNumberCmd/2+1
			theGrayLinePos=theGrayLinePos-8;
			end%YAN Chao-Gan 091201. Move the negative labels down 8 pixels.
			% if theNumberCmd/2 >1, % YAN Chao-Gan 091201.
			if AConfig.Overlay.ValueThrdAbsolute<abs(AConfig.Overlay.MinNegative)
			thePercentValue = AConfig.Overlay.MinNegative +(-AConfig.Overlay.ValueThrdAbsolute -AConfig.Overlay.MinNegative) /(theNumberCmd/2) * (x-1); %YAN Chao-Gan 091201. %AConfig.Overlay.MinNegative +(-AConfig.Overlay.ValueThrdAbsolute -AConfig.Overlay.MinNegative) /(theNumberCmd/2-1) * (x-1);
			else
			thePercentValue = AConfig.Overlay.MinNegative;
			end
			%thePercentValue = AConfig.Overlay.MinNegative +(AConfig.Overlay.MaxNegative -AConfig.Overlay.MinNegative) /(theNumberCmd/2 -1) * (x-1);
			% elseif theNumberCmd/2 ==1,
			% thePercentValue = AConfig.Overlay.MinNegative;
			% end

			text( 1.5* theColorbarWidth, theGrayLinePos, sprintf('%.2f',thePercentValue), 'Parent', AConfig.hAxesColorbar, 'Color', 'black', 'HitTest', 'off', 'Units', 'pixels', 'VerticalAlignment', 'bottom', 'FontName','FixedWidth', 'FontSize', 10);
			end
			%Draw positive lables
			for x=(theNumberCmd/2):theNumberCmd, %YAN Chao-Gan 091201, %x=(theNumberCmd/2+1):theNumberCmd
			theGrayLinePos = floor((x)(theColorBarPos(4)/theNumberCmd)); %YAN Chao-Gan %theGrayLinePos = floor((x-1+1)(theColorBarPos(4)/theNumberCmd));

			% if theNumberCmd/2 >1, % YAN Chao-Gan 091201.
			if AConfig.Overlay.ValueThrdAbsolute<abs(AConfig.Overlay.MaxPositive)
			%thePercentValue = AConfig.Overlay.MinPositive +(AConfig.Overlay.MaxPositive -AConfig.Overlay.MinPositive) /(theNumberCmd -1 -theNumberCmd/2) * (x-1 -theNumberCmd/2);
			thePercentValue = AConfig.Overlay.ValueThrdAbsolute +(AConfig.Overlay.MaxPositive -AConfig.Overlay.ValueThrdAbsolute) /(theNumberCmd/2) * (x -theNumberCmd/2); % YAN Chao-Gan 091201. %thePercentValue = AConfig.Overlay.ValueThrdAbsolute +(AConfig.Overlay.MaxPositive -AConfig.Overlay.ValueThrdAbsolute) /(theNumberCmd -1 -theNumberCmd/2) * (x-1 -theNumberCmd/2);
			else
			thePercentValue = AConfig.Overlay.MaxPositive;
			end
			% elseif theNumberCmd/2 ==1,
			% thePercentValue = AConfig.Overlay.MaxPositive;
			% end

			text( 1.5* theColorbarWidth, theGrayLinePos, sprintf('%.2f',thePercentValue), 'Parent', AConfig.hAxesColorbar, 'Color', 'black', 'HitTest', 'off', 'Units', 'pixels', 'VerticalAlignment', 'bottom', 'FontName','FixedWidth', 'FontSize', 10);
			end
			else %Draw labels for smooth display
			%dong did for the color bar 091128 ValueThrdAbsolute
			% %Draw negative lables
			if AConfig.Overlay.ValueThrdAbsolute<abs(AConfig.Overlay.MinNegative)
			text( 1.5* theColorbarWidth, 0, sprintf('%.2f',AConfig.Overlay.MinNegative), 'Parent', AConfig.hAxesColorbar, 'Color', 'black', 'HitTest', 'off', 'Units', 'pixels', 'VerticalAlignment', 'bottom');
			text( 1.5* theColorbarWidth, floor(theColorBarPos(4)/2)-10, sprintf('-%.2f',AConfig.Overlay.ValueThrdAbsolute), 'Parent', AConfig.hAxesColorbar, 'Color', 'black', 'HitTest', 'off', 'Units', 'pixels', 'VerticalAlignment', 'bottom');
			else
			text( 1.5* theColorbarWidth, 0, sprintf('%.2f',AConfig.Overlay.MinNegative), 'Parent', AConfig.hAxesColorbar, 'Color', 'black', 'HitTest', 'off', 'Units', 'pixels', 'VerticalAlignment', 'bottom');
			end
			%Draw positive lables
			text( 1.5* theColorbarWidth, ceil(theColorBarPos(4)/2)+10, sprintf('%.2f',AConfig.Overlay.ValueThrdAbsolute), 'Parent', AConfig.hAxesColorbar, 'Color', 'black', 'HitTest', 'off', 'Units', 'pixels', 'VerticalAlignment', 'bottom');
			text( 1.5* theColorbarWidth, theColorBarPos(4),...
			sprintf('%.2f',AConfig.Overlay.MaxPositive), 'Parent', AConfig.hAxesColorbar, 'Color', 'black', 'HitTest', 'off', 'Units', 'pixels', 'VerticalAlignment', 'bottom');

			% %Draw negative lables
			% text( 1.5* theColorbarWidth, 0, sprintf('%.2f',AConfig.Overlay.MinNegative), 'Parent', AConfig.hAxesColorbar, 'Color', 'black', 'HitTest', 'off', 'Units', 'pixels', 'VerticalAlignment', 'bottom');
			% text( 1.5* theColorbarWidth, floor(theColorBarPos(4)/2)-10, sprintf('%.2f',AConfig.Overlay.MaxNegative), 'Parent', AConfig.hAxesColorbar, 'Color', 'black', 'HitTest', 'off', 'Units', 'pixels', 'VerticalAlignment', 'bottom');
			% %Draw positive lables
			% text( 1.5* theColorbarWidth, ceil(theColorBarPos(4)/2)+10, sprintf('%.2f',AConfig.Overlay.MinPositive), 'Parent', AConfig.hAxesColorbar, 'Color', 'black', 'HitTest', 'off', 'Units', 'pixels', 'VerticalAlignment', 'bottom');
			% text( 1.5* theColorbarWidth, theColorBarPos(4), sprintf('%.2f',AConfig.Overlay.MaxPositive), 'Parent', AConfig.hAxesColorbar, 'Color', 'black', 'HitTest', 'off', 'Units', 'pixels', 'VerticalAlignment', 'bottom');
			end

			ResizeFigure(AConfig);

			function Result =SetColorElements(AConfig)
			%Callback by clicking the color element on the color bar
			%1. Detect which element was clicked
			%2. Change the color and save

			theAxes =get(AConfig.hFig, 'CurrentObject');
			%Check legal click point in the axes
			thePoint =get(theAxes,'CurrentPoint');
			thePoint =round(thePoint(1, 1:2));
			theXLim =get(theAxes, 'XLim');
			theYLim =get(theAxes, 'YLim');
			if thePoint(1)<theXLim(1) \|\| thePoint(1)>theXLim(2) ...
			\|\| thePoint(2)<theYLim(1) \|\| thePoint(2)>theYLim(2) ,
			Result =AConfig;
			return;
			end

			theColorBarPos =get(AConfig.hAxesColorbar, 'Position');
			theNumberCmd =str2double(AConfig.Overlay.ColorbarCmd);
			if ~isnan(theNumberCmd), %2,4,6...20 and is even!
			% theColorbar =get(AConfig.hImageColorbar, 'CData');
			% uisetcolor(theColorbar(thePoint(2), 1, :));
			theColorIndex =1+ floor(thePoint(2)/(theColorBarPos(4)/theNumberCmd));
			theColor =uisetcolor(AConfig.Overlay.Colormap(theColorIndex, :));
			if numel(theColor==3),%User defined a color, didn't clicked Cancel btn
			AConfig.Overlay.Colormap(theColorIndex, :) =theColor;
			end
			end
			Result =AConfig;
			return;



			function ToggleInfoDisplay(AConfig);
			theTitle ='Click to Toggle Hdr info';
			theOldMsg =get(AConfig.hMsgLabel, 'String');
			if strcmpi(theTitle, theOldMsg),
			set(AConfig.hMsgLabel, 'String', 'Anything not same with theTitle');
			else
			set(AConfig.hMsgLabel, 'String', theTitle);
			end
			SetMessage(AConfig);
			ResizeFigure(AConfig);






			function Result =OnKeyPress(AConfig)
			%Processing up/down left/right J/K F1/F2... to responding previous slice or next slice
			%left=0x1C, right=0x1D, up=0x1E, down=0x1F
			%j =0x6A, k=0x6B;
			%J=0x4A, K=0x4B
			%F1, F2 not known! MATLAB not responding!
			%disp(sprintf('%x',(get(AConfig.hFig, 'CurrentCharacter'))));
			Result =AConfig;
			theKey =get(AConfig.hFig, 'CurrentCharacter');
			if isempty(theKey), return; end
			% Revised by DONG Zhang-Ye 090721, adding new corresponding fuctions to key pressing
			if any(theKey==hex2dec(['6a';'4a';])), %if any(theKey==hex2dec(['1c';'1f';'6a';'4a';])),
			Result =Slice2Previous(AConfig);
			elseif any(theKey==hex2dec(['6b';'4b';'20';])), %elseif any(theKey==hex2dec(['1d';'1e';'6b';'4b';])),
			Result =Slice2Next(AConfig);
			elseif any(theKey==hex2dec(['1c';])),
			Result =Slice2Left(AConfig);
			elseif any(theKey==hex2dec(['1d';])),
			Result =Slice2Right(AConfig);
			elseif any(theKey==hex2dec(['1f';])),
			Result =Slice2Down(AConfig);
			elseif any(theKey==hex2dec(['1e';])),
			Result =Slice2Up(AConfig);
			end

			function Result =Slice2Previous(AConfig)
			Result =AConfig;
			switch lower(AConfig.LastAxes),
			case 'transverse',
			AConfig.LastPosition(1) =AConfig.LastPosition(1)-1;
			while AConfig.LastPosition(1) <1,
			AConfig.LastPosition(1) = AConfig.LastPosition(1) +size(AConfig.Volume, 1);
			end
			case 'coronal',
			AConfig.LastPosition(2) =AConfig.LastPosition(2)-1;
			while AConfig.LastPosition(2) <1,
			AConfig.LastPosition(2) = AConfig.LastPosition(2) +size(AConfig.Volume, 2);
			end
			case 'sagittal',
			AConfig.LastPosition(3) =AConfig.LastPosition(3)-1;
			while AConfig.LastPosition(3) <1,
			AConfig.LastPosition(3) = AConfig.LastPosition(3) +size(AConfig.Volume, 3);
			end
			end
			Result =AConfig;

			function Result =Slice2Next(AConfig)
			Result =AConfig;
			switch lower(AConfig.LastAxes),
			case 'transverse',
			AConfig.LastPosition(1) =AConfig.LastPosition(1)+1;
			while AConfig.LastPosition(1) >size(AConfig.Volume, 1),
			AConfig.LastPosition(1) = AConfig.LastPosition(1) -size(AConfig.Volume, 1);
			end
			case 'coronal',
			AConfig.LastPosition(2) =AConfig.LastPosition(2)+1;
			while AConfig.LastPosition(2) >size(AConfig.Volume, 2),
			AConfig.LastPosition(2) = AConfig.LastPosition(2) -size(AConfig.Volume, 2);
			end
			case 'sagittal',
			AConfig.LastPosition(3) =AConfig.LastPosition(3)+1;
			while AConfig.LastPosition(3) >size(AConfig.Volume, 3),
			AConfig.LastPosition(3) = AConfig.LastPosition(3) -size(AConfig.Volume, 3);
			end
			end
			Result =AConfig;

			function Result =Slice2Left(AConfig)
			% Added by DONG Zhang-Ye 090721, adding new corresponding fuctions to key pressing
			Result =AConfig;
			switch lower(AConfig.LastAxes),
			case 'transverse',
			AConfig.LastPosition(2) =AConfig.LastPosition(2)-1;
			while AConfig.LastPosition(2) <1,
			AConfig.LastPosition(2) = AConfig.LastPosition(2) +size(AConfig.Volume, 1);
			end
			case 'coronal',
			AConfig.LastPosition(1) =AConfig.LastPosition(1)-1;
			while AConfig.LastPosition(1) <1,
			AConfig.LastPosition(1) = AConfig.LastPosition(1) +size(AConfig.Volume, 2);
			end
			case 'sagittal',
			AConfig.LastPosition(1) =AConfig.LastPosition(1)-1;
			while AConfig.LastPosition(1) <1,
			AConfig.LastPosition(1) = AConfig.LastPosition(1) +size(AConfig.Volume, 3);
			end
			end
			Result =AConfig;

			function Result =Slice2Right(AConfig)
			% Added by DONG Zhang-Ye 090721, adding new corresponding fuctions to key pressing
			Result =AConfig;
			switch lower(AConfig.LastAxes),
			case 'transverse',
			AConfig.LastPosition(2) =AConfig.LastPosition(2)+1;
			while AConfig.LastPosition(2) >size(AConfig.Volume, 1),
			AConfig.LastPosition(2) = AConfig.LastPosition(2) -size(AConfig.Volume, 1);
			end
			case 'coronal',
			AConfig.LastPosition(1) =AConfig.LastPosition(1)+1;
			while AConfig.LastPosition(1) >size(AConfig.Volume, 2),
			AConfig.LastPosition(1) = AConfig.LastPosition(1) -size(AConfig.Volume, 2);
			end
			case 'sagittal',
			AConfig.LastPosition(1) =AConfig.LastPosition(1)+1;
			while AConfig.LastPosition(1) >size(AConfig.Volume, 3),
			AConfig.LastPosition(1) = AConfig.LastPosition(1) -size(AConfig.Volume, 3);
			end
			end
			Result =AConfig;
			function Result =Slice2Down(AConfig)
			% Added by DONG Zhang-Ye 090721, adding new corresponding fuctions to key pressing
			Result =AConfig;
			switch lower(AConfig.LastAxes),
			case 'transverse',
			AConfig.LastPosition(3) =AConfig.LastPosition(3)-1;
			while AConfig.LastPosition(3) <1,
			AConfig.LastPosition(3) = AConfig.LastPosition(3) +size(AConfig.Volume, 1);
			end
			case 'coronal',
			AConfig.LastPosition(3) =AConfig.LastPosition(3)-1;
			while AConfig.LastPosition(3) <1,
			AConfig.LastPosition(3) = AConfig.LastPosition(3) +size(AConfig.Volume, 2);
			end
			case 'sagittal',
			AConfig.LastPosition(2) =AConfig.LastPosition(2)-1;
			while AConfig.LastPosition(2) <1,
			AConfig.LastPosition(2) = AConfig.LastPosition(2) +size(AConfig.Volume, 3);
			end
			end
			Result =AConfig;
			function Result =Slice2Up(AConfig)
			% Added by DONG Zhang-Ye 090721, adding new corresponding fuctions to key pressing
			Result =AConfig;
			switch lower(AConfig.LastAxes),
			case 'transverse',
			AConfig.LastPosition(3) =AConfig.LastPosition(3)+1;
			while AConfig.LastPosition(3) >size(AConfig.Volume, 1),
			AConfig.LastPosition(3) = AConfig.LastPosition(3) -size(AConfig.Volume, 1);
			end
			case 'coronal',
			AConfig.LastPosition(3) =AConfig.LastPosition(3)+1;
			while AConfig.LastPosition(3) >size(AConfig.Volume, 2),
			AConfig.LastPosition(3) = AConfig.LastPosition(3) -size(AConfig.Volume, 2);
			end
			case 'sagittal',
			AConfig.LastPosition(2) =AConfig.LastPosition(2)+1;
			while AConfig.LastPosition(2) >size(AConfig.Volume, 3),
			AConfig.LastPosition(2) = AConfig.LastPosition(2) -size(AConfig.Volume, 3);
			end
			end
			Result =AConfig;

			function Result =UpdatePosition(AConfig, ACurrentPosition)
			%Set the last axes by comparing the last position's value change
			theV =sum(AConfig.LastPosition==ACurrentPosition);
			if theV==1,
			%Clicking one image/axes
			switch find(AConfig.LastPosition==ACurrentPosition),
			case 1,
			AConfig.LastAxes ='Transverse';
			case 2,
			AConfig.LastAxes ='Coronal';
			case 3,
			AConfig.LastAxes ='Sagittal';
			end
			elseif theV==2,
			%Directly Setting the value in the edit control
			switch find(AConfig.LastPosition~=ACurrentPosition),
			case 1,
			AConfig.LastAxes ='Transverse';
			case 2,
			AConfig.LastAxes ='Coronal';
			case 3,
			AConfig.LastAxes ='Sagittal';
			end
			end
			AConfig.LastPosition =ACurrentPosition;
			Result =AConfig;


			function ColorMap =AFNI_ColorMap(SegmentNum)
			% Generate the color map like AFNI. Written by YAN Chao-Gan, 090601
			% Input: SegmentNum - the number of segments. it should be 2,4,6,8,9,10,11,12,13,14,15,16,17,18,19,20 or 256
			% Output: ColorMap - the generated color map, an x by 3 matrix.
			switch SegmentNum
			case 2,
			ColorMap=[1,1,0;0,0.8,1;];
			case 4,
			ColorMap=[1,1,0;1,0.4118,0;0,0.2667,1;0,0.8,1;];
			case 6,
			ColorMap=[1,1,0;1,0.6,0;1,0.2667,0;0,0,1;0,0.4118,1;0,0.8,1;];
			case 8,
			ColorMap=[1,1,0;1,0.8,0;1,0.4118,0;1,0.2667,0;0,0.2667,1;0,0.4118,1;0,0.6,1;0,0.8,1;];
			case 9,
			ColorMap=[1,1,0;1,0.8,0;1,0.4118,0;1,0.2667,0;0,0.2667,1;0,0.4118,1;0,0.6,1;0,0.8,1;];
			case 10,
			ColorMap=[1,1,0;1,0.8,0;1,0.6,0;1,0.4118,0;1,0.2667,0;0,0,1;0,0.2667,1;0,0.4118,1;0,0.6,1;0,0.8,1;];
			case 11,
			ColorMap=[1,1,0;1,0.8,0;1,0.6,0;1,0.4118,0;1,0.2667,0;1,0,0;0,0,1;0,0.2667,1;0,0.4118,1;0,0.6,1;0,0.8,1;];
			case 12,
			ColorMap=[1,1,0;1,0.8,0;1,0.6,0;1,0.4118,0;1,0.2667,0;1,0,0;0,0,1;0,0.2667,1;0,0.4118,1;0,0.6,1;0,0.8,1;0,1,1;];
			case 13,
			ColorMap=[1,1,0;1,0.8,0;1,0.6,0;1,0.4118,0;1,0.2667,0;1,0,0;0,0,1;0,0.2667,1;0,0.4118,1;0,0.6,1;0,0.8,1;0,1,1;0,1,0;];
			case 14,
			ColorMap=[1,1,0;1,0.8,0;1,0.6,0;1,0.4118,0;1,0.2667,0;1,0,0;0,0,1;0,0.2667,1;0,0.4118,1;0,0.6,1;0,0.8,1;0,1,1;0,1,0;0.1961,0.8039,0.1961;];
			case 15,
			ColorMap=[1,1,0;1,0.8,0;1,0.6,0;1,0.4118,0;1,0.2667,0;1,0,0;0,0,1;0,0.2667,1;0,0.4118,1;0,0.6,1;0,0.8,1;0,1,1;0,1,0;0.1961,0.8039,0.1961;0.3098,0.1843,0.3098;];
			case 16,
			ColorMap=[1,1,0;1,0.8,0;1,0.6,0;1,0.4118,0;1,0.2667,0;1,0,0;0,0,1;0,0.2667,1;0,0.4118,1;0,0.6,1;0,0.8,1;0,1,1;0,1,0;0.1961,0.8039,0.1961;0.3098,0.1843,0.3098;1,0.4118,0.7059;];
			case 17,
			ColorMap=[1,1,0;1,0.8,0;1,0.6,0;1,0.4118,0;1,0.2667,0;1,0,0;0,0,1;0,0.2667,1;0,0.4118,1;0,0.6,1;0,0.8,1;0,1,1;0,1,0;0.1961,0.8039,0.1961;0.3098,0.1843,0.3098;1,0.4118,0.7059;1,1,1;];
			case 18,
			ColorMap=[1,1,0;1,0.8,0;1,0.6,0;1,0.4118,0;1,0.2667,0;1,0,0;0,0,1;0,0.2667,1;0,0.4118,1;0,0.6,1;0,0.8,1;0,1,1;0,1,0;0.1961,0.8039,0.1961;0.3098,0.1843,0.3098;1,0.4118,0.7059;1,1,1;0.8667,0.8667,0.8667;];
			case 19,
			ColorMap=[1,1,0;1,0.8,0;1,0.6,0;1,0.4118,0;1,0.2667,0;1,0,0;0,0,1;0,0.2667,1;0,0.4118,1;0,0.6,1;0,0.8,1;0,1,1;0,1,0;0.1961,0.8039,0.1961;0.3098,0.1843,0.3098;1,0.4118,0.7059;1,1,1;0.8667,0.8667,0.8667;0.7333,0.7333,0.7333;];
			case 20,
			ColorMap=[0.8,0.0627,0.2;0.6,0.1255,0.4;0.4,0.1922,0.6;0.2,0.2549,0.8;0,0.3176,1;0,0.4549,0.8;0,0.5922,0.6;0,0.7255,0.4;0,0.8627,0.2;0,1,0;0.2,1,0;0.4,1,0;0.6,1,0;0.8,1,0;1,1,0;1,0.8,0;1,0.6,0;1,0.4,0;1,0.2,0;1,0,0;];
			otherwise,
			ColorMap=[1,0,0.1373;1,0,0.1176;1,0,0.0941;1,0,0.0706;1,0,0.0471;1,0.0667,0;1,0.0902,0;1,0.1137,0;1,0.1333,0;1,0.1569,0;1,0.1765,0;1,0.1961,0;1,0.2118,0;1,0.2314,0;1,0.251,0;1,0.2667,0;1,0.2863,0;1,0.302,0;1,0.3176,0;1,0.3373,0;1,0.3529,0;1,0.3686,0;1,0.3843,0;1,0.4,0;1,0.4157,0;1,0.4314,0;1,0.4471,0;1,0.4627,0;1,0.4784,0;1,0.4941,0;1,0.5098,0;1,0.5255,0;1,0.5412,0;1,0.5529,0;1,0.5686,0;1,0.5843,0;1,0.6,0;1,0.6118,0;1,0.6275,0;1,0.6431,0;1,0.6549,0;1,0.6706,0;1,0.6824,0;1,0.698,0;1,0.7098,0;1,0.7255,0;1,0.7373,0;1,0.7529,0;1,0.7647,0;1,0.7804,0;1,0.7922,0;1,0.8078,0;1,0.8196,0;1,0.8353,0;1,0.8471,0;1,0.8588,0;1,0.8745,0;1,0.8863,0;1,0.898,0;1,0.9137,0;1,0.9255,0;1,0.9373,0;1,0.9529,0;1,0.9647,0;1,0.9765,0;1,0.9882,0;0.9961,1,0;0.9843,1,0;0.9725,1,0;0.9608,1,0;0.9451,1,0;0.9333,1,0;0.9216,1,0;0.9059,1,0;0.8941,1,0;0.8824,1,0;0.8667,1,0;0.8549,1,0;0.8431,1,0;0.8275,1,0;0.8157,1,0;0.8,1,0;0.7882,1,0;0.7765,1,0;0.7608,1,0;0.749,1,0;0.7333,1,0;0.7216,1,0;0.7059,1,0;0.6941,1,0;0.6784,1,0;0.6627,1,0;0.651,1,0;0.6353,1,0;0.6235,1,0;0.6078,1,0;0.5922,1,0;0.5765,1,0;0.5647,1,0;0.549,1,0;0.5333,1,0;0.5176,1,0;0.5059,1,0;0.4902,1,0;0.4745,1,0;0.4588,1,0;0.4431,1,0;0.4275,1,0;0.4118,1,0;0.3961,1,0;0.3804,1,0;0.3647,1,0;0.3451,1,0;0.3294,1,0;0.3137,1,0;0.2941,1,0;0.2784,1,0;0.2627,1,0;0.2431,1,0;0.2235,1,0;0.2078,1,0;0.1882,1,0;0.1686,1,0;0.149,1,0;0.1255,1,0;0.1059,1,0;0.0824,1,0;0.0549,1,0;0,1,0.0549;0,1,0.0824;0,1,0.1059;0,1,0.1255;0,1,0.149;0,1,0.1686;0,1,0.1882;0,1,0.2078;0,1,0.2235;0,1,0.2431;0,1,0.2627;0,1,0.2784;0,1,0.2941;0,1,0.3137;0,1,0.3294;0,1,0.3451;0,1,0.3647;0,1,0.3804;0,1,0.3961;0,1,0.4118;0,1,0.4275;0,1,0.4431;0,1,0.4588;0,1,0.4745;0,1,0.4902;0,1,0.5059;0,1,0.5176;0,1,0.5333;0,1,0.549;0,1,0.5647;0,1,0.5765;0,1,0.5922;0,1,0.6078;0,1,0.6235;0,1,0.6353;0,1,0.651;0,1,0.6627;0,1,0.6784;0,1,0.6941;0,1,0.7059;0,1,0.7216;0,1,0.7333;0,1,0.749;0,1,0.7608;0,1,0.7765;0,1,0.7882;0,1,0.8;0,1,0.8157;0,1,0.8275;0,1,0.8431;0,1,0.8549;0,1,0.8667;0,1,0.8824;0,1,0.8941;0,1,0.9059;0,1,0.9216;0,1,0.9333;0,1,0.9451;0,1,0.9608;0,1,0.9725;0,1,0.9843;0,1,0.9961;0,0.9882,1;0,0.9765,1;0,0.9647,1;0,0.9529,1;0,0.9373,1;0,0.9255,1;0,0.9137,1;0,0.898,1;0,0.8863,1;0,0.8745,1;0,0.8588,1;0,0.8471,1;0,0.8353,1;0,0.8196,1;0,0.8078,1;0,0.7922,1;0,0.7804,1;0,0.7647,1;0,0.7529,1;0,0.7373,1;0,0.7255,1;0,0.7098,1;0,0.698,1;0,0.6824,1;0,0.6706,1;0,0.6549,1;0,0.6431,1;0,0.6275,1;0,0.6118,1;0,0.6,1;0,0.5843,1;0,0.5686,1;0,0.5529,1;0,0.5412,1;0,0.5255,1;0,0.5098,1;0,0.4941,1;0,0.4784,1;0,0.4627,1;0,0.4471,1;0,0.4314,1;0,0.4157,1;0,0.4,1;0,0.3843,1;0,0.3686,1;0,0.3529,1;0,0.3373,1;0,0.3176,1;0,0.302,1;0,0.2863,1;0,0.2667,1;0,0.251,1;0,0.2314,1;0,0.2118,1;0,0.1961,1;0,0.1765,1;0,0.1569,1;0,0.1333,1;0,0.1137,1;0,0.0902,1;0,0.0667,1;0.0471,0,1;0.0706,0,1;0.0941,0,1;0.1176,0,1;0.1373,0,1;];
			end
			ColorMap=flipdim(ColorMap,1);


			function rest_report(data,head,ClusterConnectivityCriterion)
			% Generate the report of the thresholded clusters.
			% Based on CUI Xu's xjview. (http://www.alivelearn.net/xjview/)
			% Revised by YAN Chao-Gan and ZHU Wei-Xuan 20091108: suitable for different Cluster Connectivity Criterion: surface connected, edge connected, corner connected.

			if ~(exist('TDdatabase.mat'))
			uiwait(msgbox('This function is based on CUI Xu''s xjview, please install xjview8 or later version at first (http://www.alivelearn.net/xjview/).','REST Slice Viewer'));
			return
			end

			disp('This report is based on CUI Xu''s xjview. (http://www.alivelearn.net/xjview/)');
			disp('Revised by YAN Chao-Gan and ZHU Wei-Xuan 20091108: suitable for different Cluster Connectivity Criterion: surface connected, edge connected, corner connected.');
			nozeropos=find(data~=0);
			[i j k]=ind2sub(size(data),nozeropos);
			cor=[i j k];
			mni=cor2mni(cor,head.mat);

			if isempty(mni)
			%errordlg('No cluster is picked up.','oops');
			disp( 'No cluster is found. So no report will be generated.');
			return;
			end

			intensity=data(nozeropos);


			L=cor';
			dim = [max(L(1,:)) max(L(2,:)) max(L(3,:))];
			vol = zeros(dim(1),dim(2),dim(3));
			indx = sub2ind(dim,L(1,:)',L(2,:)',L(3,:)');
			vol(indx) = 1;
			[cci,num] = bwlabeln(vol,ClusterConnectivityCriterion);
			A = cci(indx');

			clusterID = unique(A);
			numClusters = length(clusterID);
			disp(['Number of clusters found: ' num2str(numClusters)]);

			for mm = clusterID
			pos = find(A == clusterID(mm));
			numVoxels = length(pos);
			tmpmni = mni(pos,:);
			tmpintensity = intensity(pos);

			peakpos = find(abs(tmpintensity) == max(abs(tmpintensity)));
			peakcoord = tmpmni(peakpos,:);
			peakintensity = tmpintensity(peakpos);

			% list structure of voxels in this cluster
			x = load('TDdatabase.mat');
			[a, b] = cuixuFindStructure(tmpmni, x.DB);
			names = unique(b(:));
			index = NaN*zeros(length(b(:)),1);
			for ii=1:length(names)
			pos = find(strcmp(b(:),names{ii}));
			index(pos) = ii;
			end

			report = {};

			for ii=1:max(index)
			report{ii,1} = names{ii};
			report{ii,2} = length(find(index==ii));
			end
			for ii=1:size(report,1)
			for jj=ii+1:size(report,1)
			if report{ii,2} < report{jj,2}
			tmp = report(ii,:);
			report(ii,:) = report(jj,:);
			report(jj,:) = tmp;
			end
			end
			end
			report = [{'structure','# voxels'}; {'--TOTAL # VOXELS--', length(a)}; report];

			report2 = {sprintf('%s\t%s',report{1,2}, report{1,1}),''};
			for ii=2:size(report,1)
			if strcmp('undefined', report{ii,1}); continue; end
			report2 = [report2, {sprintf('%5d\t%s',report{ii,2}, report{ii,1})}];
			end

			disp(['----------------------'])
			disp(['Cluster ' num2str(mm)])
			disp(['Number of voxels: ' num2str(numVoxels)])
			disp(['Peak MNI coordinate: ' num2str(peakcoord)])
			[a,b] = cuixuFindStructure(peakcoord, x.DB);
			disp(['Peak MNI coordinate region: ' a{1}]);
			disp(['Peak intensity: ' num2str(peakintensity)])
			for kk=1:length(report2)
			disp(report2{kk});
			end
			end
			return


			function mni = cor2mni(cor, T)
			% function mni = cor2mni(cor, T)
			% convert matrix coordinate to mni coordinate
			%
			% cor: an Nx3 matrix
			% T: (optional) rotation matrix
			% mni is the returned coordinate in mni space
			%
			% caution: if T is not given, the default T is
			% T = ...
			% [-4 0 0 84;...
			% 0 4 0 -116;...
			% 0 0 4 -56;...
			% 0 0 0 1];
			%
			% xu cui
			% 2004-8-18
			% last revised: 2005-04-30

			if nargin == 1
			T = ...
			[-4 0 0 84;...
			0 4 0 -116;...
			0 0 4 -56;...
			0 0 0 1];
			end

			cor = round(cor);
			mni = T*[cor(:,1) cor(:,2) cor(:,3) ones(size(cor,1),1)]';
			mni = mni';
			mni(:,4) = [];
			return;

			function coordinate = mni2cor(mni, T)
			% function coordinate = mni2cor(mni, T)
			% convert mni coordinate to matrix coordinate
			%
			% mni: a Nx3 matrix of mni coordinate
			% T: (optional) transform matrix
			% coordinate is the returned coordinate in matrix
			%
			% caution: if T is not specified, we use:
			% T = ...
			% [-4 0 0 84;...
			% 0 4 0 -116;...
			% 0 0 4 -56;...
			% 0 0 0 1];
			%
			% xu cui
			% 2004-8-18
			%

			if isempty(mni)
			coordinate = [];
			return;
			end

			if nargin == 1
			T = ...
			[-4 0 0 84;...
			0 4 0 -116;...
			0 0 4 -56;...
			0 0 0 1];
			end

			coordinate = [mni(:,1) mni(:,2) mni(:,3) ones(size(mni,1),1)]*(inv(T))';
			coordinate(:,4) = [];
			coordinate = round(coordinate);
			return;

			function [onelinestructure, cellarraystructure] = cuixuFindStructure(mni, DB)
			% function [onelinestructure, cellarraystructure] = cuixuFindStructure(mni, DB)
			%
			% this function converts MNI coordinate to a description of brain structure
			% in aal
			%
			% mni: the coordinates (MNI) of some points, in mm. It is Nx3 matrix
			% where each row is the coordinate for one point
			% LDB: the database. This variable is available if you load
			% TDdatabase.mat
			%
			% onelinestructure: description of the position, one line for each point
			% cellarraystructure: description of the position, a cell array for each point
			%
			% Example:
			% cuixuFindStructure([72 -34 -2; 50 22 0], DB)
			%
			% Xu Cui
			% 2007-11-20
			%

			N = size(mni, 1);

			% round the coordinates
			mni = round(mni/2) * 2;

			T = [...
			2 0 0 -92
			0 2 0 -128
			0 0 2 -74
			0 0 0 1];

			index = mni2cor(mni, T);

			cellarraystructure = cell(N, length(DB));
			onelinestructure = cell(N, 1);

			for ii=1:N
			for jj=1:length(DB)
			graylevel = DB{jj}.mnilist(index(ii, 1), index(ii, 2),index(ii, 3));
			if graylevel == 0
			thelabel = 'undefined';
			else
			if jj==length(DB); tmp = ' (aal)'; else tmp = ''; end
			thelabel = [DB{jj}.anatomy{graylevel} tmp];
			end
			cellarraystructure{ii, jj} = thelabel;
			onelinestructure{ii} = [ onelinestructure{ii} ' // ' thelabel ];
			end
			end

			function P=ThrdtoP(Thrd,AConfig)
			if isfield(AConfig.Overlay.Header,'descrip')
			headinfo=AConfig.Overlay.Header.descrip; %dong 090921AConfig.Df.Ttest=0;
			if ~isempty(strfind(headinfo,'{T_['))% dong 100331 begin
			testFlag='T';
			Tstart=strfind(headinfo,'{T_[')+length('{T_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			elseif ~isempty(strfind(headinfo,'{F_['))
			testFlag='F';
			Tstart=strfind(headinfo,'{F_[')+length('{F_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			elseif ~isempty(strfind(headinfo,'{R_['))
			testFlag='R';
			Tstart=strfind(headinfo,'{R_[')+length('{R_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			elseif ~isempty(strfind(headinfo,'{Z_['))
			testFlag='Z';
			Tstart=strfind(headinfo,'{Z_[')+length('{Z_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			end
			if exist('testFlag')
			if ~isempty(testFlag)
			if exist('testDf')
			if testFlag == 'T'
			AConfig.Df.Ttest=testDf;
			elseif testFlag == 'F'
			AConfig.Df.Ftest=testDf;
			elseif testFlag == 'R'
			AConfig.Df.Rtest=testDf;
			elseif testFlag == 'Z'
			AConfig.Df.Ztest=testDf;
			end
			end % dong 100331 end
			end
			end
			end
			if AConfig.Df.Ttest~=0 ,
			AConfig.Overlay.ValueP=2*(1-tcdf(Thrd,AConfig.Df.Ttest));
			elseif numel(find(AConfig.Df.Ftest))~=0 ,
			AConfig.Overlay.ValueP =1-fcdf(Thrd,AConfig.Df.Ftest(1),AConfig.Df.Ftest(2));
			elseif AConfig.Df.Ztest~=0 ,
			AConfig.Overlay.ValueP=2*(1-normcdf(Thrd));
			elseif AConfig.Df.Rtest ~= 0 ,
			AConfig.Overlay.ValueP=2(1-tcdf(abs(Thrd)sqrt((AConfig.Df.Rtest)/(1-Thrd*Thrd)),AConfig.Df.Rtest));
			end
			if (AConfig.Df.Ttest ==0 && numel(find(AConfig.Df.Ftest)) ==0) && numel(find(AConfig.Df.Ztest)) ==0 && numel(find(AConfig.Df.Rtest)) ==0,AConfig.Overlay.ValueP = 1;end
			P=AConfig.Overlay.ValueP;



			function Thrd=PtoThrd(Pvalue,AConfig);
			if isfield(AConfig.Overlay.Header,'descrip')
			headinfo=AConfig.Overlay.Header.descrip; %dong 090921AConfig.Df.Ttest=0;
			if isfield(AConfig.Overlay.Header,'descrip')
			headinfo=AConfig.Overlay.Header.descrip; %dong 090921AConfig.Df.Ttest=0;
			if ~isempty(strfind(headinfo,'{T_['))% dong 100331 begin
			testFlag='T';
			Tstart=strfind(headinfo,'{T_[')+length('{T_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			elseif ~isempty(strfind(headinfo,'{F_['))
			testFlag='F';
			Tstart=strfind(headinfo,'{F_[')+length('{F_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			elseif ~isempty(strfind(headinfo,'{R_['))
			testFlag='R';
			Tstart=strfind(headinfo,'{R_[')+length('{R_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			elseif ~isempty(strfind(headinfo,'{Z_['))
			testFlag='Z';
			Tstart=strfind(headinfo,'{Z_[')+length('{Z_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			end
			if exist('testFlag')
			if ~isempty(testFlag)
			if exist('testDf')
			if testFlag == 'T'
			AConfig.Df.Ttest=testDf;
			elseif testFlag == 'F'
			AConfig.Df.Ftest=testDf;
			elseif testFlag == 'R'
			AConfig.Df.Rtest=testDf;
			elseif testFlag == 'Z'
			AConfig.Df.Ztest=testDf;
			end
			end % dong 100331 end
			end
			end
			end
			end
			if AConfig.Df.Ttest~=0 ,
			if AConfig.Overlay.Tchoose == 2 % YAN Chao-Gan, 100201
			Thrd=tinv(1 - Pvalue/2,AConfig.Df.Ttest);%2*(1-tcdf(Pvalue,AConfig.Df.Ttest));
			else
			Thrd=tinv(1 - Pvalue,AConfig.Df.Ttest);%2*(1-tcdf(Pvalue,AConfig.Df.Ttest));
			end
			elseif numel(find(AConfig.Df.Ftest))~=0 ,
			Thrd =finv(1-Pvalue,AConfig.Df.Ftest(1),AConfig.Df.Ftest(2));%1-fcdf(Pvalue,AConfig.Df.Ftest(1),AConfig.Df.Ftest(2));
			elseif AConfig.Df.Ztest~=0 ,
			if AConfig.Overlay.Tchoose == 2 % YAN Chao-Gan, 100201
			Thrd=norminv(1 - Pvalue/2);%2*(1-normcdf(Pvalue));
			else
			Thrd=norminv(1 - Pvalue);%2*(1-normcdf(Pvalue));
			end
			elseif AConfig.Df.Rtest ~= 0 ,
			if AConfig.Overlay.Tchoose == 2 % YAN Chao-Gan, 100201
			TRvalue=tinv(1 - Pvalue/2,AConfig.Df.Rtest);
			Thrd=sqrt(TRvalue^2/(AConfig.Df.Rtest+TRvalue^2));%2(1-tcdf(abs(Pvalue)sqrt((AConfig.Df.Rtest)/(1-Pvalue*Pvalue)),AConfig.Df.Rtest));
			else
			TRvalue=tinv(1 - Pvalue,AConfig.Df.Rtest);
			Thrd=sqrt(TRvalue^2/(AConfig.Df.Rtest+TRvalue^2));%2(1-tcdf(abs(Pvalue)sqrt((AConfig.Df.Rtest)/(1-Pvalue*Pvalue)),AConfig.Df.Rtest));
			end
			end
			if (AConfig.Df.Ttest ==0 && numel(find(AConfig.Df.Ftest)) ==0) && numel(find(AConfig.Df.Ztest)) ==0 && numel(find(AConfig.Df.Rtest)) ==0,Thrd = 0;end





			function Result=CheckDf(AConfig)
			Result=AConfig;
			if isfield(AConfig.Overlay,'Header')
			if isfield(AConfig.Overlay.Header,'descrip')
			headinfo=AConfig.Overlay.Header.descrip; %dong 090921AConfig.Df.Ttest=0;
			if ~isempty(strfind(headinfo,'{T_['))% dong 100331 begin
			testFlag='T';
			Tstart=strfind(headinfo,'{T_[')+length('{T_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			elseif ~isempty(strfind(headinfo,'{F_['))
			testFlag='F';
			Tstart=strfind(headinfo,'{F_[')+length('{F_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			elseif ~isempty(strfind(headinfo,'{R_['))
			testFlag='R';
			Tstart=strfind(headinfo,'{R_[')+length('{R_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			elseif ~isempty(strfind(headinfo,'{Z_['))
			testFlag='Z';
			Tstart=strfind(headinfo,'{Z_[')+length('{Z_[');
			Tend=strfind(headinfo,']}')-1;
			testDf = str2num(headinfo(Tstart:Tend));
			end
			if exist('testFlag')
			if ~isempty(testFlag)
			if exist('testDf')
			if testFlag == 'T'
			AConfig.Df.Ttest=testDf;
			elseif testFlag == 'F'
			AConfig.Df.Ftest=testDf;
			elseif testFlag == 'R'
			AConfig.Df.Rtest=testDf;
			elseif testFlag == 'Z'
			AConfig.Df.Ztest=testDf;
			end
			end % dong 100331 end
			end
			end
			end
			end
			Result=AConfig;

			function [pID,pN] = rest_FDR(p,q)
			% FORMAT [pID,pN] = FDR(p,q)
			%
			% p - vector of p-values
			% q - False Discovery Rate level
			%
			% pID - p-value threshold based on independence or positive dependence
			% pN - Nonparametric p-value threshold
			%______________________________________________________________________________
			% @(#)FDR.m 1.3 Tom Nichols 02/01/18
			%
			% example: [pID pN] = FDR(p,0.05)
			% DONG FDR 100117 added Tom's FDR routine for REST
			p = sort(p(:));
			V = length(p);
			I = (1:V)';

			cVID = 1;
			cVN = sum(1./(1:V));

			pID = p(max(find(p<=I/V*q/cVID)));
			pN = p(max(find(p<=I/V*q/cVN)));

			function Result =SetThrdAbsValueFDR(AConfig)
			%DONG FDR added 100117, for the FDR displays
			AConfig=CheckDf(AConfig);
			Pvalue =AConfig.Overlay.ValueP;
			Result =PtoThrd(Pvalue,AConfig);

			theMin =get(AConfig.hSliderThrdValue, 'Min');
			theMax =get(AConfig.hSliderThrdValue, 'Max');
			if Result<theMin,
			Result =theMin;
			Pvalue=ThrdtoP(theMin,AConfig);
			elseif Result>theMax,
			Result =theMax;
			Pvalue=0;
			end
			set(AConfig.hSliderThrdValue, 'Value', Result);
			set(AConfig.hEdtThrdValue, 'String', num2str(Result));
			set(AConfig.hEdtPValue, 'String', num2str(Pvalue)); %DONG FDR added 100117, for the FDR displays

Slepi/Code/Utilities/DPARSF_V2.3_130615/Subfunctions/DPARSF_rest_sliceviewer.m22f22bf83060master

DPARSF_rest_sliceviewer.mView Options

Slepi/Code/Utilities/DPARSF_V2.3_130615/Subfunctions/DPARSF_rest_sliceviewer.m
22f22bf83060master

DPARSF_rest_sliceviewer.m
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