Jason,
I suspect that somewhere along the line, the deformed left hemisphere
surfaces got linked to an inappropriate topology file. However, the
atlas spec file you used should be valid - It is a left-right hybrid
target that is viewed with a right hemisphere topology. We have done
many Caret registrations from both hemispheres ('left to LR' and
'right to LR') to this target.
All I can suggest is that you view the left hemisphere files (pre-
deformation) in Caret and make sure they all have proper topology and
hemisphere assignments (e.g., coord files should be designated as
left hem and should show a lateral view when you click Toolbar: L).
Donna Dierker or John Harwell may be able to troubleshoot in more
detail based on what you've said. (But Donna is out Monday morning.)
If necessary, we'll ask you to upload the files so we can decipher
the problem with the data at hand.
David
On Apr 14, 2006, at 9:06 PM, Jason D Connolly wrote:
Dear Donna or David,
Thank you very much for your timely assistance thus far.
We have successfully morphed a right hemisphere to the B12 atlas. My
question concerns the left hemisphere deformation. When I run the
spherical deformation, the output left hemisphere deform_ files (flat,
inflated, fiducial etc.) have cortex that appears "black" in
appearance,
very similar in color to the background. Obviously, some error has
occurred. Could this have to do with the atlas .spec file that was
used
for the deformation? I used:
Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730.spec
as I may have incorrectly assumed the 'LR' refers to left and right
and
thus the same spec file is to be used for both hemispheres ...
------------------------------------------------------------
Jason D. Connolly, PhD
Center for Neural Science, New York University
6 Washington Place Room 875, New York, NY 10003
cell:646.417.2937 lab:212.998.8347 fax:212.995.4562
http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html
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