Jason,I'm getting ready to walk out the door (I get in around 7am), and a file named fordonna.tar.gz was just uploaded -- presumably from you. I looked at it, and with sane file selections, I don't see the black hole you described. Make sure you're using the topo that doesn't begin with deformed, but use the inflated and fiducial coords that are named like deformed*. I do see something funky with the topology, though, at the location indicated on the attached capture. I suspect it stems from your original surface, and has nothing to do with registration. Could you upload your original surface directory (using the same copy spec file, archive, upload approach), so I can be sure?
It occurred to me: By black, you're not referring to the sulcal depth underlay, which makes deeper nodes appear darker, are you? You can turn this off, but we find it informative.
On 04/19/2006 08:01 AM, Donna Dierker wrote:
On 04/18/2006 03:50 PM, Jason D Connolly wrote:Make a "fordonna" subdirectory and use Copy Spec file to copy the spec file you are viewing to that subdirectory. Then, create a zip or tar.gz archive of that subdirectory and upload it here:Dear David and Donna, I re-ran the left hemisphere deformation and I noticed that the deformed flat maps look alright. It is only the fiducial, inflated and spheres that are black.http://pulvinar.wustl.edu/cgi-bin/upload.cgiI need to know exactly which CLOSED topo and fiducial, inflated, and spherical coord files you have loaded. Make sure only one CLOSED topo file is loaded.I also noticed that when the spherical deformation is run, the central sulcus appears on the right side and the medial wall on the left duringwarping.This is normal. During registration, left hemispheres are flipped and treated as if they were right hemispheres. This is normal behavior and causes no problems.Sounds to me like you have the target border file Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.SPHERE.border selected.Following deformation there are 2 sets of borders that appear on the spheres the "left" set and also concurrently a "right" (or perhaps target) set. The two sets are overlaid on the spheres.I'm still in the dark as to what your goal is -- the type of data you're trying to register to PALS (e.g., sulcal depth? functional data?).Jason. ------------------------------------------------------------ Jason D. Connolly, PhD Center for Neural Science, New York University 6 Washington Place Room 875, New York, NY 10003cell:646.417.2937 lab:212.998.8347 fax:212.995.4562 http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html_______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
-- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.)
<<inline: funky_topo.jpg>>
<<inline: funky_topo_on_sphere.jpg>>
