Hi Ed, Maybe John and/or David will have better answers, but here's my stab:
1) Smoothing should have helped at least somewhat. You can increase the smoothing strength and/or iterations, but at some point it should look smoother.
2) Caret is going to try to make a single surface. It assumes the slices form a single object, so it will connect them where the bridge is shortest. I'm not sure how to get around that problem other than to include enough sections so that they really do join, if that makes sense.
There's a chance that David/John may want to see your dataset, so if you could upload your spec file and the files it cites in a zipped or gzipped tar file, it might be helpful:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi Donna On 03/25/2005 12:30 PM, Edward Craft wrote:
Hi, The attached image is a reconstruction I generated in Caret4.6 from 40 histological slices (50um each, 2mm total depth) taken tangential to the cortical surface surrounding the lunate sulcus in the left hemisphere of a macaque brain. I have many more slices to trace, but did this trial reconstruction to see how it was working and encountered two problems: the reconstructed surface has a rough, stair-stepped appearance, and nodes in the pre-lunate (left-hand side of image) and post-lunate (right-hand side) gyri have been linked together. I didn't find much discussion of topology clean-up in the tutorials, so I was hoping you could offer some advice. (1) How can I make the reconstructed surface fit the section contours more smoothly? (Using the Surface: Smoothing option as described in Tutorial 9 did not seem to help.) Is it possible to generate a surface as smooth as that in your macaque atlas from histological slices? (2) In addition to the separate gyri visible in the attached image, my sections include buried folds of cortex near the base of the lunate sulcus. How can I ensure that the surface topology is reconstructed correctly when there are two or more distinct sets of contours, such as these, in a sequence of slice images? Any help you can provide will be greatly appreciated. -- Ed Craft------------------------------------------------------------------------ ------------------------------------------------------------------------ _______________________________________________ caret-users mailing list [email protected] http://pulvinar.wustl.edu/mailman/listinfo/caret-users
