How can I select a ROI dynamically (automatically) ?

I deal with dental X-ray and want to segment the teeth from other tissue, I try canny, but unwanted results i got by using this code:

readim = imread('indiv1.jpg');
imwrite(readim,'indiv1.tif');
i=imread('indiv1.tif');
figure, imshow(i), title('original image');

 BW = im2bw(i,0.6);
  I = edge(BW,'canny');
  figure, imshowpair(BW,I,'montage'), title('binary gradient mask');

 [~, threshold] = edge(BW, 'canny');
  fudgeFactor = .5;
  BWs = edge(BW,'canny', threshold * fudgeFactor);
  imshowpair(BW,BWs,'montage')

 %%%%%%%%%%%%
  %dilate the image

 se90 = strel('line', 3, 90);%vertical structuring element// creates a flat linear structuring element
  se0 = strel('line', 3, 0);% horizontal structuring element.
  Idil = imdilate(I, [se90 se0]);
  figure, imshow(Idil), title('dilated gradient mask');

and then try to use two step threshold composed of iterative thresholding and adaptive thresholding the first one i try the code below:

readim = imread('indiv1.jpg');
imwrite(readim,'indiv1.tif');
a=imread('indiv1.tif');
figure, imshow(a), title('original image');
i=rgb2gray(a);
AverageGrayValue = mean(mean(i));%=0.2311
%iterative thresh.
[ n, m ]=size(i);
newAverageGrayValue = 0.5;
while (newAverageGrayValue -  AverageGrayValue)>0.1
for r=1:n
    for c=1:m
       if i(r,c) >= AverageGrayValue
        R1 = i(r,c);

         else
           R2= i(r,c);
         end
      end
  end
  AverageGrayValue=newAverageGrayValue;

R1mean = mean( mean(R1));
R2mean = mean(mean(R2));
newAverageGrayValue=1/2 *(R1mean+R2mean );
end
T = AverageGrayValue;
bim=(i>T);

imshow(bim);

but the other threshold error message will appear after running this code:

readim = imread('indiv1.jpg');
imwrite(readim,'indiv1.tif');
a=imread('indiv1.tif');
figure, imshow(a), title('original image');
%AdaptiveT hreshold%%%%%%%%%
 [R, C]=size(a);
 for x = 0 : R 
     sumation = 0;
    for y = 0 : C
        sumation = sumation+a(x, y);
         if x == 0 
            intImg(x, y)= sumation;
         else
            intImg(x, y)= ( intImg(x-1, y) +sumation);
         end
    end
 end 
%%%%%%%%%%%%%%%%%

error message is:

>> Untitled5
Subscript indices must either be real positive integers or logicals.

Error in Untitled5 (line 44)
        sumation = sumation+a(x, y);
thanks for all

Answer 1

[Image Analyst]

See the FAQ: http://matlab.wikia.com/wiki/FAQ#How_do_I_fix_the_error_.22Subscript_indices_must_either_be_real_positive_integers_or_logicals..22.3F and then use the debugger and you'll be able to solve it yourself. Hint: there is no 0'th row or 0'th column - numbering starts at 1.

By the way, why are you calling rows x and calling columns y? Usually x is the horizontal direction and so x is columns, not rows. Using the most used convention, you do not index arrays as (x,y) but as (y, x) which is (rows, columns).