MATLAB: Overlay mask on sequence of mri images to mark out tumor ROI

mri

I created a mask based on one frame to mark out my ROI region.

segment_mask = poly2mask(xi, yi, 256, 256);

Is there a way I can overlay this mask onto my sequence of frames stored in a 3d array(256 x 256 x #of frames)?

maskedImg = imgArray.*segment_mask;
% segment_mask is size [256,256]
% maskedImg is same size as imgArray 
[256, 256, #of frames]

If you are using an older version of Matlab you may have to use bsxfun().

You can store the mask in cell array and later call any mask as per requiremnets.

n=?? % define
mask=cell(1,n)
for i=1:n 
%Mask generation, say mask_data
mask{i}=mask_data
end

Noy you can any mask as later say mask{1}, mask{2}, so on.....

Threshold for black.

mask = grayImage == 0;

Extract the two largest regions

mask = bwareafilt(mask, 2);

Then find the centroid or bounding box

props = regionprops(mask, 'Centroid');

and extract the lower black region. See if you can do this yourself.

Call imerode() to shrink it. Then XOR the shrunken region with the original region to get just the edges.

mask = imerode(lowerMask, true(9)); % Increase from 9 to get a wider white region.
mask = xor(mask, lowerMask);

Then set those pixels in the original image to white:

grayImage(mask) = 255;