Hi Alex,
I recognize your name from other mailing lists, but don't recall you
posting on caret-users before -- welcome!
Yes, this post reminds me of our need to update the old Caret 4.6
Tutorial 11 (Freesurfer-to-Caret), because this is something several
users are going to want to do (e.g., so you can register your
Freesurfer-generated surfaces using Caret's landmark-based registration
algorithm, which is useful in ways that differ from Freesurfer's
intensity/convexity-based registration algorithm). At some point, both
tools may support multiple registration algorithms, but I'm guessing
this is a ways off.
Reading this passage, it's amazing how little I recall of the way Caret
4.6 used to work. ;-) But I don't think this step is necessary in
Caret5. The smoothing will operate on the surface in the main window,
whatever surface that is (presumably the rh.orig.asc surface).
One thing that bears attention from David, my boss, however, is whether
it is generally good practice to import both the rh.orig.asc and
rh.pial.asc surfaces, and then use the Surface: Create Average Coord
File, the result of which should be more like our SureFit-generated
fiducial surfaces. I suppose this depends on what your objectives are,
but David feels it is important to aim for layer 4, because then the
surface area along gyral crests is not underestimated and the area along
sulcal fundi is not overestimated. Since many of our analysis
techniques depend on surface area, this is an important consideration
for us.
Please bear with our current state of documentation. We're juggling
many priorities right now, but at some point we will turn our attention
to updating the tutorials. Users who update them for us get stickers.
;-) Seriously, if you run into more trouble, let us know, because other
users will soon feel your pain.
Donna
On 12/16/2005 01:55 AM, Fornito, Alexander wrote:
Hi,
I'm new to Caret and have just downloaded version 5.3.
I'm trying to work with surfaces generated in freesurfer, and have been following the tutotial, but have become stuck at a point where I think the new version differs to older ones.
After improting the surfaces and smoothing it, the tutorial (p. 71) says Select Surface: Load AUXconfig into REFconfig.
The config files (?) did not come up before, so i don't know what this refers
to. Also, I can't seem to find anything that might resemble this option in the
usrface (or any other) pull-down menu.
Any help on how to proceed is much appreciated. My goal is to used caret
registration with freesurfer surfaces.
Thanks,
Alex
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
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