Hi Ed,
The volume route didn't work, because it generates a surface from the
volume when it creates the paint file (i.e., no way in Caret to turn off
surface generation when you generate curvature and paint, even though I
was happy with your fiducial surface), and that fiducial was much
smoother than yours (not as good).
So, I went the label-an-edge-node-CUT-FACE route. I zoomed way up;
switched from Surface Miscellaneous tiles and lights view to nodes and
links; ID's a node at a corner; and used Draw Borders to label it
CUT.FACE. My Draw Borders failed to actually capture the node, though,
so I saved the paint file as ASCII and used File: Text Editor to
actually change the paint number for node 6685 from 0 to 1. Then, I
saved the paint file; reopened it; and Caret flattening was happy.
I don't know if you're happy with the result, but you can tweak on your
end. Here is a capture; the paint; and my cut topo (removed corners and
stragglers):
http://brainmap.wustl.edu/pub/donna/IEEE/flat.jpg
http://brainmap.wustl.edu/pub/donna/IEEE/Macaque.m17.L.geography2.paint
http://brainmap.wustl.edu/pub/donna/IEEE/Macaque.m17.L.topology_file_46.2005-10-20.12400.CUTdh.topo
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Donna
On 11/11/2005 09:18 AM, Edward Craft wrote:
Hi,
Thank you both for your suggestions--I'll give them a try. Per Donna's
suggestion I've also uploaded my files, as ECraftDataset_11-10-2005.tar.gz
(includes both the uncut and cut surfaces).
This is a bit tough, because you didn't generate your surface from a
segmentation using the SureFit segmentation feature ....
I never considered using SureFit, because (unfortunately) I only have
histological sections--no MRI data. I got the impression from Tutorial 9
(Caret4.6 Documentation) that it wouldn't be a problem to flatten a surface
reconstructed from traced contours, though. Was the "Draw Cuts" feature
supposed to label the cut face? Any idea why it was sampling the cuts I drew
so sparsely?
job of identifying the cut face, and you can use spherical registration
rather than flat registration, assuming you want to register your
surface to our atlas (which you may not need to do).
I was aiming for a flatmap because I want to reconstruct a partial
visuotopic map (by pairing electrode recording positions in the histological
sections with their associated receptive field positions) and make some
cortical distance measurements. I'm hoping my small portion of cortex is
topologically well-behaved enough to flatten without "too much" distortion.
-- Ed
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