Hi Mark,
Thanks for your response. If you wouldn't mind taking a look at the data
that I put on your server that would be great. So you can see my responses,
I've put them in CAPS.
Your previous response: I haven't heard about that problem of one run
failing but
a re-run working. If you have a dataset where you can replicate this (by
taking a fresh copy of the original data and doing it all again) then please
upload it for us to have
a look at.
I COULDN'T REPLICATE THIS PROBLEM AS YOU HAVE SUGGESTED HERE WITH THE
ORIGINAL DATA, SO I UPLOADED A SUBJECT WHO INITIALLY DISPLAYED THIS PROBLEM.
UPLOAD NUMBER: 701725. YOU WILL SEE THAT IN THE 313_all_fast_firstseg file
THE RIGHT AMYDALA APPEARS APPROXIMATELY IN THE JAW AREA.
Any help is greatly appreciated!
Thanks again and have a good weekend!
Dana
All the best,
Mark
On 29 Jan 2010, at 14:23, Dana Eldreth wrote:
> I was wondering if anyone else noticed this problem with FIRST on
> the newest
> release 4.1.5.
>
> First, I'd like to note that FSL 4.1.5 does an excellent job at
> boundary
> correction on our older brains. It's extremely impressive.
>
> 1. For some reason, this newest release occasionally does not
> accurately
> parcellate some structures correctly (e.g., hippocampus in the brain
> stem),
> but when I rerun it again it appears to fix the problem and the
> volumes are
> where they should be in the brain. The volume sizes are also
> relatively
> close to the volume sizes that I had in the earlier version of FIRST.
> Interestingly, the volumes that appear to be parcellated in the
> wrong area
> produce the same volume size as when FIRST produces the volumes in the
> correct location. Has anyone else noticed this, and should this be
> something that I should be concerned about?
>
> I also had another question associated with FIRST:
> 1. How can I tell how confident the program is that it has accurately
> identified a specific structure, or can I only tell via visual
> inspection
> using a neuroantaomical atlas?
>
> As always, thank you so much!
>
> Dana
>
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