I have a T1 scan of a rhesus macaque from which I’d like to extract an outer skull surface for 3d printing.
The standard process for extracting this from human mri data doesn’t work well at all. The musculature on the outside of the skull interferes with the brain mask, yielding a grotesque brain with bulges where portions of the outer musculature are incorporated into the brain.
I have taken the resulting mask and modified it heavily using the masking tool – to narrow down the mask to encompass the brain only. This is relatively easy, though tedious, as the brain is easily picked out visually.
At the next step, however, the extraction of the surfaces fails miserably. The inner skull surface is incorrect, and the outer skull surface seems as if it cannot be viewed — it doesn’t show up at all on the resulting 3D image, even when I change its color to something obvious.
Am I right to modify the brain mask before running “Skull and Scalp” (I do this after the BSE has run, but before the “Skull and Scalp” step)