Jason:  See inline replies below.

On 04/19/2006 04:40 PM, Jason D Connolly wrote:

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.
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?

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):


One important point is that when you click on the deformed lateral view,
you get a medial view, so something is wrong here.
Solve this problem by entering this command in the directory where the spec is located:

echo hem_flag left >> deformed_Human.6.L.spec

It 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.

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 you
will 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:


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.
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:


What 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 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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Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)

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