Create 3D Volume of interest (VOI)

Hi all,

I am trying to create a 3D volume of interest (VOI), using imfreehand as in the script below. At the moment it's working but i have to draw my ROI at every single slide. Does anybody know whether it is possible to keep the region of the first slide and adjust it in the next slides?

if true
  % 
s = size (MRI1);
for i = 1:s(3);
  A = MRI1(:,:,i);
  imshow (A,[]);
  h = imfreehand(gca);
  BW = createMask(h);
  BWs = imcomplement (BW);
  A(BWs)=0;
  MRIm (:,:,i) = A;
end

end

Answer 1

[Sean de Wolski]

A thought:

You could use imfreehand on the first slice. imfreehand does not have a 'Position' option that you can set. However, impoly does, so use impoly on the subsequent slices.

I = imread('cameraman.tif');
imshow(I);
hax=gca;
hf = imfreehand(hax);
wait(hf);
for ii = 2:2    
  pos = getPosition(hf);
  %You would create mask etc. before deleting
  delete(hf);    
  hf = impoly(hax,pos);        
end

Can you post an example image? Perhaps there's a way to automate or semi-automate this process so you don't have to repeat this at each slice.

[Hugo]

do you know whether it's possible to adjust the size of the ROI using impoly?

What i want is to extract the brain from all of the surrounding intensity's, so i want to create a basic ROI which i can resize adjust for every image in my volume.

I attached an example of (my already partially rectangular cropped image) with the region i would like to extract in 3 dimensions.

[Hugo]

I tried using impoly in the mean time, and it enables me to change the roi afterwards, so it's major improvement already.

Thanks

[Sean de Wolski]

If I had to do this and only needed semi automation, I would take your freehand mask from above and use that as the initial mask in activecontour. Then let active contour do the work. For each subsequent slice, I'd use the previous slice's mask as the initial mask for the active contours.

Or you could fully automate this using a threshold and morphological operations. It's hard to say without knowing your requirements.

[Hugo]

Basically the only requirement is to extract the brain from everything else, which doesn't have to be automatically.

Unfortunately i want to be enabled to change my roi in every loop, i understood getPosition gives me the coordinates of my ROI, but how do i create a line which gives me my previous MRI, but adaptable, and transfers me to the next slide when i complete my roi.

The script below is what i have at the moment, but i need to implement a specific instruction which allows me to close one slide, save the roi, go to the next slide and start there with the saved ROI, which should be adaptable, i tried to use getPosition and setPosition for this but i'm not sure how to implement them.

if true
  % 
s=size (MRIsag);
for i = 1:s(3)
  A = MRIsag(:,:,i);
  imshow (A,[]);
  h = impoly(gca);
  BW = createMask(h);
  BWs = imcomplement (BW);
  A(BWs) = 0;
  Brain(:,:,i)= A;   
end
end