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Ah, this is a bit of a bug I suppose in the histogram plotting logic. Because you're passing in the tissue mask directly, it's using that as the brain mask when creating the histogram. So the individual histogram represents the WM of the image after normalization—since it's T1-w it seems correct to have the gap between 0 and the start of the foreground. I assume you're using the brain mask when calling plot-histograms which is why that looks normal.
Ah, this is a bit of a bug I suppose in the histogram plotting logic. Because you're passing in the tissue mask directly, it's using that as the brain mask when creating the histogram. So the individual histogram represents the WM of the image after normalization—since it's T1-w it seems correct to have the gap between 0 and the start of the foreground. I assume you're using the brain mask when calling
plot-histograms
which is why that looks normal.Originally posted by @jcreinhold in #78 (reply in thread)
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