I'm new to FS and I'm having trouble with the flattening step. After making the cuts, the instructions in the FreeSurferGuide (p44) are to fill the non-midbrain regions and save the patch.
1. It's not clear to me what the difference is between the blue and the white fill.
2. I filled the non-midbrain areas (white fill) and did "save patch as". But when I load the patch, I get back all the brain regions including the midbrain. In other words I can't seem to make a midbrain-free image that looks like the last figure on page 44.
3. When I try to flatten the brain, it processes the data for a while, but doesn't seem to produce a flattened image (I suspect because I can't get rid of the midbrain).
Any ideas how I might solve these problems would be much appreciated. thanks,
jack grinband
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