Hi Nina,
After trying a couple of peak settings with the low hindbrain threshold,
I got a pretty decent result:
GMpeak 39
WMpeak 53
I suspect you can do even better with some peak tweaking. The downside
is that much of the hindbrain remains connected, but you can run it
again with the high hindbrain option and use the Copy Subvolume trick to
erase the hindbrain out of the low hindbrain segmentation. Mike Todd
can teach you this trick.
Based on your message below, I'm betting you used the Caret version off
our official download site. Like many labs, we don't update our
official release until we release a major revision. But John made some
changes in August 2005 to the hindbrain routine that will be of great
benefit to you, so you'll definitely want to grab the updated caret5
executable from the site below. It's just the executable -- not the
whole distribution.
Let me know how it goes,
Donna
On 10/12/2005 04:10 PM, Donna Hanlon wrote:
Hi Nina,
I'm about to leave for the day, but I'll look at this tomorrow.
Meanwhile, a couple of questions:
1. Are you using a version of Caret from August 2005 or later that
has the fix John made to the hindbrain routine? I suspect you are,
since it was your lab's data that prompted that change. In case not,
here is the download site:
http://brainvis.wustl.edu/pub/john/
login pub
password download
2. Are you using the low or high option for hindbrain removal?
Thanks,
Donna
On 10/12/2005 03:50 PM, Nina del Rosario wrote:
Hi,
I've been trying to segment a hemisphere in Caret 5.31, and depending on
where I set the peaks I either get a hindbrain segmentation error or a
segmentation that finishes but misses some DL white matter.
I uploaded the files under the name s2s1_mprage.L and here are the
different
peak values I tried:
Gray 30, White 48; Gray 27, White 51 => Hindbrain Error
Gray 31, White 53; Gray 35, White 53 => DL Limbs Missing
Any suggestions would be appreciated. Thanks in advance.
Nina del Rosario
Poldrack Lab Manager
(310) 794-1139
[EMAIL PROTECTED]
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