The 5tt_nocoreg.mif I created is missing the frontal cortex and seems to be squished along the anterior-posterior direction. Any guesses what might have gone wrong? I have checked all of my input volumes (B0, T1, and all the co-registered versions) and they all look good.
Check out the following post.
Does it happen systematically, or is this occurrence only in a single subject? Screenshots of the input T1 into
5ttgen might be helpful in identifying a solution
Hope this helps!