Hi Timothy,
Hmmm. I just to recreate your problem using the output of 3dAFNItoMINC
Human.colin.LR.TLRC-711-2B.111+tlrc.HEAD, and my initial segmentation
after filling ventricles, but before automatic error correction, had no
missing chunks like yours. I'd like to see your cropped structural
*.L.full*sMRI.mnc file and .params file. Could you upload them here:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
How did you convert the dataset to minc?
There are some significant non-uniformity issues that relate to what I
call the "stripey minc" problem
(http://brainmap.wustl.edu/SureFit/RELEASE_NOTES.html#mincscaling),
which has since been fixed in SureFit, but which remain in our atlas
dataset. But based on my trial, this is not causing the problem you report.
Thanks,
Donna
On 06/23/2004 11:16 AM, jarv0075 wrote:
Hi,
I'm currently testing out the surface extraction using the Colin dataset.
Everything comes out satisfactory - except, the segmentation generated
tends to leave out a large chunk towards the anterior end of the brain.
http://www.cs.umn.edu/~tjarvis/colin1.gif
http://www.cs.umn.edu/~tjarvis/colin2.gif
I'm using a talirach coordinate space volume, so cropping the hemisphere,
and seting the AC is fairly straight forward. I have error correction on,
'extract cerebellum and segment' on, and 'do not identify sulci'.
also the volume orientation is correct, peaks are set correctly, and any
other option I see
Any idea what I could be missing here? (I don't think it's the dataset)
Thanks!
---------------------------------------
Timothy R. Jarvis
---------------------------------------
Graduate Research Assistant
International Neuroimaging Consortium
VA Medical Center
612-467-2619
http://www.neurovia.umn.edu
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