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here is my code
img=read_LUM_all; Lmask=mean(img,3); Lmask(Lmask<415)=0; Lmask(Lmask~=0)=1; Lmask=logical(Lmask); for i=1:13 imgL(:,:,i)=read_LUM2; L(i)=mean2(imgL(Lmask)); % this line is only taking the mean of imgL(:,:,1), not imgL(:,:,i) end avgL=L(1:13)'
it reads in 13 files into a 3D array of size (1040x1392x13). I then average all the files to create a mask so that I can use that mask as an ROI to get an average value of each individual file over the ORI created by the average mask. I eventually want a 13x1 array (avgL) that has the average value over the ROI of each image and right now I am getting a 13x1 array that gives me the average of only the first frame.
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