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I assume you used the Trainable Weka Segmentation plugin in Fiji to get this? (It helps to provide all the information, so others don't waste time suggesting you things that won't help you.)
The result you get from this plugin is actually not an RGB image, but an indexed 8-bit color image. That means each class (color) has a pixel index value between 0 and 255.
You can get a binary mask for each class by simple thresholding, e.g. with these lines of macro code:
run("Convert to Mask");
Just change the
setThreshold command to the index you'd like to have.