Jason: See inline replies below. On 04/19/2006 04:40 PM, Jason D Connolly wrote:
A picture is worth a thousand words. Try this when viewing these same surfaces: Surface: Normals: Flip Normals. I'll bet the problem disappears. How your normals got flipped is another question; I don't know the answer, but it happens now and then. These were Caret-generated surfaces, right?Dear Donna, I have uploaded the .spec file containing the "black" inflated, fiducial and spherical left hemisphere datasets. The file is a tar.gz format labelled "fordonna". Thank you again for your help. We are trying to deform the sulcal depth maps of subjects left hemispheres to the PALS atlas. Again, following spherical deformation, the left - but not right - fiducial, inflated and spherical hemispheres appear "black", as shown in the screen captures that are appended in jpg format.
I can't replicate the problem on my end; when I select only these files, the surface looks fine, other than the topology issue (see green ID node in attached capture):
deformed_Human.6.L.Fiducial.2006-02-13.64283.coord Human.sphere_6.73730.topo deformed_Human.6.L.surface_shape_file_24.2006-02-13.64283.surface_shape
Solve this problem by entering this command in the directory where the spec is located:One important point is that when you click on the deformed lateral view,you get a medial view, so something is wrong here.
echo hem_flag left >> deformed_Human.6.L.specIt would be nice if Caret inserted the hem_flag into the deformed spec file, but to be honest, we don't use these deformed spec files much. Instead, we create composite files of the deformed*shape and deformed*metric, and then use an analysis/visualization spec.
It is almost certainly a case of flipped normals, and my guess is that the impact is 0, other than the visualization anomaly that is easily corrected. If you are using the atlas target dataset linked here, then you're using what we're using, and your deformed shape files are fine:There is a dorsal view of the deformed depth fiducial map; a dorsal view of the deformed sphere, and the medial view of the deformed inflated surface. As youwill see, the appended and deformed flat maps look fine.Indeed, only one CLOSED topo file is loaded. The CLOSED topo file is: CLOSED Human.sphere_6.73730.topo The fiducial, inflated and spherical coord files are: deformed_Human.6.L.Fiducial.2006-02-13.64283.coord deformed_Human.6.L.Inflated.2006-02-13.64283.coord deformed_Human.6.L.SPHERE_ALIGN.2006-02-13.64283.coord We have tried troubleshooting this by performing this deform on other subjects left hemispheres, and the results are the same (so it cannot be due to a "bad" subjects dataset. We have also tried this on the right hemisphere using the same target atlas, so the atlas files are not corrupted. Finally, we have tried this on both the Linux and Mac platforms and we get the same results, i.e. "bad" left - but not right - hemisphere images.
http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.htmlWhat I need to add, though, are links to the visualization and analysis specs (e.g., including the latest/greatest average fiducials and the distortion metric files needed to run processes like Attributes: Surface Shape: Find Significant Cluster).
Best, Jason. ------------------------------------------------------------Jason D. Connolly, PhD Center for Neural Science, New York University6 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.)
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