function [tc, sel_roi] = mri_roi_timecourse(images, tmap, scale, sgn);

% function [tc, sel_roi] = mri_roi_timecourse(images, tmap, scale, sgn);
%
% Aug 2003, Farshad Moradi
% California Institute of Technology
%
% User may define the region of interest by zooming the areas of
% interest. Figure 1 shows the original t-map. Figure 2 depicts the
% selected regions. Only voxels with significant t are selected. 
% 
% Example:
%   mri_roi_timecourse(images, t, [0 1.5 3], 1);
%       After user defines roi, plots the roi
%   tc = mri_roi_timecourse(images, t, [0 1.5 3], 1);
%   [tc, roi] = mri_roi_timecourse(images, t, [0 1.5 3], 1);
%
% Also saves ROI in a global variable (roi)

global roi

figure(1);
if nargin<3,
    scale = [0, 3, 8];
    sgn = 1;
end;
mri_display(images(1).data, tmap, scale);

f = find(isnan(tmap)); tmap(f) = 0;
roi = zeros(size(tmap));
keep = 1;

while keep,
	disp('Zoom ROI');
    zoom on;
	pause;
	ax = round(axis);
    [x1,y2,slice] = MosaicTo3D(images(1), ax(1), ax(3));
    x2 = min(x1+max(ax(2)-ax(1),1), images(1).w);
    y1 = max(y2-(ax(4)-ax(3)), 1);
	%disp([ax x1 x2 y1 y2 slice]);
	
	figure(2); ax = floor(ax);
    keep = ax(1)~=0 | ax(3)~=0;
    if keep,
	    t = images(1).data*0; t(x1:x2,y1:y2, slice) = 1;
	    f = find(sgn*tmap<scale(2)); t(f) = 0;
        roi = roi | t;
    end;
	mri_display(images(1).data, roi*4);
    title('Selected ROI');
	figure(1);
    axis auto;
end;

tc = mri_timecourse(images, roi, 1);
if nargin<1,
    figure(3); clf;
    plot(tc);
    title(['Activity, %BOLD change #voxels: ' num2str(length(find(roi>0)))]);
end;

if nargout>=2,
    sel_roi = roi;
end;

function [x,y,slice] = MosaicTo3D(image, X, Y);

if size(image.data, 3)>1,
    [a,b, mn] = size(image.data);
    m = floor(sqrt(mn));
    n = ceil(mn / m);
    X = X-1; Y = b*n-Y;
    x = mod(X, a)+1;
    y = mod(Y, b)+1;
    i = floor(X/a);
    j = floor(Y/b);
    slice = i+j*m+1;
else,
    x = X;
    y = Y;
    slice = 1;
end;
x = max(min(x, image.w),1);
y = max(min(y, image.h),1);
slice = max(min(slice, image.nslice),1);