Hi Eric,
We haven't updated the old Freesurfer-to-Caret tutorial, but you might
find these caret-users posts helpful:
http://brainvis.wustl.edu/pipermail/caret-users/2006-February/000686.html
http://brainvis.wustl.edu/pipermail/caret-users/2006-February/000687.html
Entering caret_command -help at the command line will spew 954 lines of
helpful text, as well.
If these don't cover what you want to do, post back here and we'll see
if we can help.
On 06/13/2006 08:31 AM, Faden, Eric (NIH/NIMH) [F] wrote:
Are there instructions somewhere for importing from FreeSurfer to Caret 5.4
somewhere? The only instructions seem to be fairly old and it looks like
things have changed a bit since then.
-Eric
-----Original Message-----
From: Donna Dierker [mailto:[EMAIL PROTECTED]
Sent: Tue 6/13/2006 8:36 AM
To: [EMAIL PROTECTED]; Caret, SureFit,and SuMS software users
Subject: Re: [caret-users] Cortical Thickness Measurement
Hi Darren,
Sorry to be the bearer of bad news, but no: Caret/SureFit doesn't
compute cortical thickness. For a while, a student was working on it,
but it never went anywhere. Occasionally, people mistake our sulcal
depth measure for cortical thickness, but the two are completely
different measures. (See David's PALS paper
(http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WNP-4H4T34K-1-3&_cdi=6968&_user=4275&_orig=browse&_coverDate=11%2F15%2F2005&_sk=999719996&view=c&wchp=dGLbVzb-zSkzk&md5=0920fddff1134928d23f0a23d746935f&ie=/sdarticle.pdf),
figure 1, for a description of sulcal depth.)
The only good news I can give those who are interested in cortical
thickness is that you can import your freesurfer surfaces and thickness
maps into Caret in a mostly automated way, and generate sulcal depth on
them, if desired. You can then register them to the PALS_B12 atlas,
although this requires drawing our Core6 landmark borders:
http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html
Due to algorithmic differences between Freesurfer's and Caret's
registration algorithms, seeking a "second opinion" can be useful,
depending on the nature of your study. For example, the algorithm that
best aligns intrasubject anatomy across multiple timepoints may not be
ideal for finding group anatomical differences.
On 06/12/2006 09:09 PM, Darren Weber wrote:
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Hi,
I have been using FreeSurfer for a while, to obtain cortical thickness
measures. Is it now possible to obtain thickness measures with caret?
There is a previous thread from 2003 indicating this feature was on a
wish-list:
http://brainvis.wustl.edu/pipermail/caret-users/2003-September/000076.html
Thanks, Darren
- --
Darren L. Weber, Ph.D.
Postdoctoral Scholar
Dynamic Neuroimaging Laboratory,
UCSF Department of Radiology,
185 Berry Street, Suite 350, Box 0946,
San Francisco, CA 94107, USA.
Tel: +1 415 353-9444
Fax: +1 415 353-9421
www: http://dnl.ucsf.edu/users/dweber
"To explicate the uses of the brain seems as difficult
a task as to paint the soul, of which it is commonly
said, that it understands all things but itself."
Thomas Willis (The Anatomy of the Brain and Nerves, 1664)
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--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see
http://home.att.net/~donna.hanlon for details.)
