Hi Judy,
On 04/10/2006 12:18 PM, Judy Smith wrote:
can I use Caret for subcortical labeling, parcellating, and segmentation?
No -- Caret is designed for cortical analyses. It doesn't have any
features specifically targeted for subcortical structures. If you have
a segmentation generated from some other software, you might be able to
use Caret to generate a surface from it, but since most subcortical
structures are not sheet-like, Caret's surface-based features are less
likely to be useful.
Also, can I import other image stacks into Caret besides MRI? I want
to import a macaque brain image stack from http://brainmaps.org
<http://brainmaps.org> but am not sure how to do this.
Not easily. I'm not very familiar with brainmaps.org, but I just looked
at some nissl sections there. While the gray white contrast is
excellent, Caret/SureFit expects a dark/black CSF-like enclosure around
the pial surface (i.e., CSF darker than gray matter). It will be very
confused and misbehave catastrophically if CSF is white. There also are
distortion problems with histological sections.
That said, I'm pretty sure at least one user has managed to pull off a
reconstruction from cryosections by figuring out how to do the steps
outlined in the old Caret 4.6 tutorial 9 using Caret 5:
http://brainmap.wustl.edu/caret/pdf/CARET_UsersGuide.03-06.Part-II.pdf
This tutorial was authored almost three years ago for the now ancient
Caret 4.6 interface, but the functionality should still be there in
Caret 5.33. Give the old tutorial a read/scan before you attempt it,
just to see if you're up for the challenge; this isn't something people
try every day, but it can be done.
thanks.
Judy
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Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see
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