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
<<attachment: Reconstr1-40.JPG>>
