Hi Julia,
It is not unusual for there a few red highlights around the edges at
this stage of the flattening process. You could continue the
flattening process and it might turn out okay.
If there are no topological problems with the original 3D fiducial
surface, then all surfaces derived from it (spherical, etc) should be
topologically correct. Load the original 3D surface into Caret's
main window and select Surface Menu->Topology->Topology Error Report
(it may take a minute to execute). If the "Number of Handles" is
zero, then the 3D surface and the "derived" surfaces (spherical,
flat) are topologically correct and you can proceed with flattening.
If the 3D surface does contain handles, the best solution is to go
back to the original segmentation volume and make corrections.
However, since your surface was not generated within Caret, there is
a new feature in Caret that may help. With the original 3D surface
in Caret's main window, Select Surface Menu->Topology->Correct
Fiducial Surface Topology (Remove Handles). This process will
attempt to re-tessellate the surface in order to remove any handles
and will create new coordinate and topology files that will need to
be saved. This is a new process, so examine the corrected surface to
verify that the process has not done anything bad. If things look
good, use the new coordinate and topology file and restart the
flattening process.
When I have time, I will modify Caret so that the beginning of the
flattening process will check for topological problems.
----------------------------------------------------------
John Harwell
[EMAIL PROTECTED]
314-362-3467
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave. Box 8108
St. Louis, MO 63110 USA
On Jul 3, 2007, at 10:22 AM, Julia Molony wrote:
John,
Your answer was very helpful. Now I'm stuck with an initial flat
map that has red highlights on a few of the edges. The tutorial
says this means there are handles that need to be corrected in the
segmentation volume. I don't have a volume. I have Freesurfer
surfaces that I'm using to compare warping methods. Is there any
solution to this cross over correction problem for already created
surfaces?
There's just a little bit of red. Here's a picture. I can send
more information, if that would be helpful.
Thank you.
Julia
--
Julia Molony
SSCC/NIMH/NIH
<Init.Surf.crossovers 5.5_Figure40.jpg>
On Jul 2, 2007, at 12:21 PM, John Harwell wrote:
Hi Julia,
During the flattening process, the medial wall border is normally
drawn on the Compressed Medial Wall Surface. The CMW surface is a
sphere with the medial portion made flat so that 2D borders can be
drawn on it. This surface should be selected from the model
selection control in the main window's toolbar.
The "Smooth Fiducial Medial Wall" option results in the fiducial
surface's medial wall being smoothed during the flattening
process. Smoothing will change the shape of the medial wall so
that it is relatively flat. This option does not affect the
sphere. There is normally some distortion around on the sphere
that should be removed by the morphing process that is part of
flattening.
----------------------------------------------------------
John Harwell
[EMAIL PROTECTED]
314-362-3467
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave. Box 8108
St. Louis, MO 63110 USA
On Jul 2, 2007, at 10:09 AM, Julia Molony wrote:
I'm attempting to go through Caret's spherical registration stuff
but first I need to work out how to draw all the borders. I'm
following the 5.5 tutorial and I'm stuck trying to draw the
medial wall borders. When I open the draw borders dialogue,
choose the border name, set type to closed and dimension to 2D,
and press apply, I can't draw the border. I click on the sphere
and hold the left mouse button and nothing is drawn. Any ideas
on what's going on? I checked the D/C to see if "show borders"
was selected and it is. I've drawn borders in the past with no
trouble, so I'm not sure what's happening here.
Also, what does it mean in the "Flatten Full or Partial
Hemisphere" box when it says "Smooth Fiducial Medial Wall". It
looks like this smoothing is causing distortions in the sphere.
It makes the sphere look sort of swirly around the medial wall area.
Julia
--
Julia Molony
SSCC/NIMH/NIH
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