From what I understand, the --cortex flag is simply supposed to zero out any signal in the medial wall with a mask, I checked mask.mgh, it is 0 on the medial wall and 1 everywhere else as expected... however when I analyze the data without this flag, the resulting sig.mgh file has completely changed. Areas on the cortex that were "lit up" disappear, and other areas light up that were silent before. This should not be happening right?
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