Hi Julia, plus others interested in registering surfaces (FreeSurfer-
as well as SureFit-generated) to the PALS human atlas,
John and Donna have already provided useful technical comments that
have hopefully addressed the specific questions you raised.
This email provides a heads-up on two parallel efforts we are
currently undertaking to expedite surface-based registration,
particularly mapping FreeSurfer surfaces onto PALS.
1) A revised process will bypass flat maps altogether and instead
draw the 'Core 6' landmark contours directly on inflated surfaces.
The requisite tools are already in place; we're currently revising
the instructions appropriately. This should save a fair amount of time.
2) A more ambitious effort is to fully automate the process of
drawing landmark contours. There are many steps to doing this with
high fidelity, but what we've implemented so far look quite encouraging.
The objective is to allow batch process mapping of FreeSurfer to PALS
- fully automatically, but with quality control checks included.
David VE
On Jul 5, 2007, at 9:30 AM, Donna Dierker wrote:
Hi Julia,
On your initial flat map, none of the red patches along the edges
would worry me, but we would check the ones I've circled in the
attached capture. By check, I mean click on the red patch in the
main window, but use an inflated view in Window 2 to locate the
crossover region in the inflated surface. The patch in the upper
left may end up being nothing, but the one in the lower right looks
like a handle connecting cortical regions that are separated by a
significant geodesic distance.
If you're processing enough subjects that a case or two like this
is down in the noise, then this isn't a show stopper. But this is
something we'd fix in the segmentation and regenerate the surface,
for one of our own studies.
Donna
On 07/03/2007 02:01 PM, John Harwell wrote:
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
<Init.Surf.crossovers_check.jpg>
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