I created a 3D mask, saved it, and re-loaded it. VIsually it looks to be what I expected with two small regions I had marked showing up in grayscale and the background black. I would expect the histogram to show mainly zeros, with a few tens of voxels set to 1. But when I plot the histogram, it shows a linear mapping between intensity and # of voxels.
When I apply this mask to another image fith fslmaths, the resul is a gray field with the masked area showing whiter, and again the histogram is a simple linear graph.
???
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