The following sample code will extract the segment of image that you could use for classification.
Here I assumed you wanted to threshold an RGB image and you are using grey scale intensity of the RGB image for Otsu’s thresholding.
grayVersion = rgb2gray(colorImage);
thresholded = imbinarize(grayVersion);
thresholded(:,:,2) = thresholded;
thresholded(:,:,3) = thresholded(:,:,1);
colorImage(thresholded == 0) = 0;