Hi Donna,
I am trying to get AFNI and Caret to lock together, and I am having
trouble understanding how to generate a metric file from AFNI in
order to open it in Caret. Also do you know why when I use the
tutorial and try to import an image, the AFNI format is not supported
(I saw hdr and that's what I used, and the option of saving as
a .HEAD file is available but no AFNI when I try to import) - just
curious. If you could help me understand how Caret uses the metric
through AFNI and how I can generate one.
Thank you.
Best,
Alan
Alan Anticevic
Barch (CCP) Lab
Washington University
(314) 935-8547
[EMAIL PROTECTED]
On Oct 13, 2005, at 8:51 AM, Donna Hanlon wrote:
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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