Hi Ed,
It would have mattered if you had not already cut out the cut face nodes
-- i.e., the difference between the following coord files:
Macaque.m17.L.coordinate_file_47.2005-10-20.12400.coord
Macaque.m17.L.coordinate_file_47.2005-10-20.12400.CUT03coord.coord
You had already done the hard work of disconnecting these nodes, so in
this case, it was really only necessary to identify a single node on the
perimeter of the surface, just to satisfy the Caret check. If you had
not already disconnected these nodes, then it would have been necessary
to identify the three faces that appeared to be cut:
Dorsal
Ventral
Posterior
(Since I could not recognize the actual structure, I'm not sure whether
these labels correspond to the actual anatomical faces, but these are
the faces that appeared to be cut when switching among the caret views
-- i.e., M,L,A,P,D,V.)
In this case, it didn't matter much which node you chose, as long as it
was along the perimeter. I chose a corner node, guessing that deleting
it would cause less trouble.
Donna
On 11/14/2005 08:39 AM, Edward Craft wrote:
Terrific--thanks! I'm a little confused about one thing, though: You only
need to specify one node as CUT.FACE, not the entire perimeter of the
surface? Does it matter which node you choose?
-- Ed
----- Original Message -----
From: "Donna Hanlon" <[EMAIL PROTECTED]>
To: "Edward Craft" <[EMAIL PROTECTED]>; "Caret, SureFit, and SuMS software
users" <caret-users@brainvis.wustl.edu>
Sent: Friday, November 11, 2005 12:08 PM
Subject: Re: [caret-users] CUT.FACE Error
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
login pub
password download
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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