rest_sliceviewer.m

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

	AConfig.hAxesColorbar  =hAxesColorbar;
	AConfig.hImageColorbar =hImageColorbar;	
	
	%Overlay Configuration
	%Data for Overlay
	AConfig.Overlay.Filename ='';
	AConfig.Overlay.Volume	 =zeros(61, 73, 61);
	AConfig.Overlay.VolumeThrd =AConfig.Overlay.Volume;%Volume Thresholded by Cluster Size	
	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.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.InfoAal='None';	%AAL descriptions
		
	%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
			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('Slice Viewer -- REST %s',rest_misc( 'GetRestVersion')));
	%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, 
		theSagittalImg	=imresize(theSagittalImg, theMagnifyCoefficient);
		theCoronalImg	=imresize(theCoronalImg, theMagnifyCoefficient);
		theTransverseImg=imresize(theTransverseImg, theMagnifyCoefficient);
	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),
		theSagittalImg =AddOverlay('Sagittal' ,AConfig, theSagittalImg);
		theCoronalImg =AddOverlay('Coronal', AConfig, theCoronalImg);
		theTransverseImg =AddOverlay('Transverse', AConfig, theTransverseImg);
	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;