%************************************************************************************************************

% "getpoints.m" creates a set of points corresponding to the average 

% ROI value in each slice  .

% inputs:

% im- the image from which the ROI is selected.

% num_s- the image's number of slices 

% ROI- an image with the same size of 'im':the pixels of the ROI equal 1

% and the others 0.

% output:

% points- the set of averaged points

% SD- the standard deviation 

% mask_size- the number of pixels in the chosen ROI

%************************************************************************************************************



function [points,SD, mask_size] = getpoints(im, num_s,ROI)



for j=1:num_s

    im_mask=im(:,:,j).*ROI;

    mask_temp=im_mask(im_mask>0);

    points(j)=mean(mask_temp);

    %     SD= std(im_mask(im_mask>0))/points(j);

    SD(j)= std(mask_temp);

end

mask_size=length(mask_temp);

end