Hi,
Unfortunately the brainstem segmentation finishes just underneath the
level of the cerebellum, and your scan is right on the verge of this
being too little. This certainly isn't ideal behaviour and we are
working
on fixing it, but I believe that your scans are just close enough to the
inferior border of the FIRST brainstem definition that it is probably
running over in some of the scans. We will hopefully have a fix out for
this in the next patch. Until then, you can get all the other
structures
segmented by using the -s option and omitting the brainstem. If you
also really need the brainstem then it is possible to cheat a little and
just copy the last slice of your image a few times (appending it to the
bottom of the scan) and then run this through FIRST instead. That
should give it just enough padding in the inferior direction to avoid it
crashing.
All the best,
Mark
On 31 Jul 2010, at 20:13, Allison Nugent wrote:
> I did indeed discover that this runs fine when I don't include the
> brainstem. However, like the person in the original post I
> referenced, I do seem to have sufficient field of view in the
> inferior direction. I attached a sagital image.
> <sagital.jpg>
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