Hi Isabelle, Have you tried projecting the cells (something like Layers: Cells: Project Fiducial Cells -- or the foci equivalent of cells)?
I'm not sure caret5 has the opacity feature you seek, but look under D/C: Page Selection: Surface Miscellaneous. You can select Hide Surface from the Drawing Mode drop-down menu, but then you can't see it at all. But at least this is a sanity check when you can't see the cells and want to make sure they are really there. You can try a drawing mode like nodes or links, and then zoom on the region where the cells are located. This will reduce the surface obstruction, but probably still not be the opacity reduction you seek. Again, not sure this is quite what you want, but it points to some features worth exploring as a work-around. Donna On Feb 13, 2013, at 2:14 PM, Isabelle wrote: > my question is to know whether there is a way in Caret that would allow me to > see labeled cells that are initially ‘below’ the surface of the brain at the > surface of the brain. > > This is why: > Initially, I plot section outlines and labeled cells using a computer based > charting system. Software written in our lab allows me then to reconstruct > 2D maps showing the location of labeled cells in the cerebral cortex. > > For the purpose of 3D reconstruction of brains in Caret, this customized > software also allows me to draw a ‘fictive’ layer IV in each section of a > dataset that will be converted in files readable in Caret. I draw the > ‘fictive’ layer IV between layer III and layer V. > > In Caret, once I have reconstructed the contours into surface, I can only see > labeled cells that are located in supra-granular layers (‘above’ the fictive > layer IV, namely labeling in layers 2 and 3) at the surface of the brain. In > order to see labeled cells located in infra-granular layers (‘below’ the > fictive layer IV, namely labeling in layers 5 and 6), I need to decrease the > opacity of the brain. > > Thank you for your help in this matter-- Isabelle. > > > > > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users
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