Hi Andrei, Because I have no Neurolucida experience, I feel pretty helpless to help you. But my hunch is that Caret would need two different files to open/import -- the contours and the cells. (And cellcolor, too, but I'd think you'd at least see black dots of the cells were there.)
First things first: Make sure a .cell or .foci file exists after you export the Neurolucida files to Caret or import them. I assume you mean this tutorial: http://brainvis.wustl.edu/wiki_linked_files/documentation/caret5.5_contours_tutorial.pdf I haven't done this myself, but it appears that just the contours are coming in and the cells are being added later. Is it possible the cells can be exported separately as 3D coords from Neurolucida? Donna On Nov 30, 2011, at 7:31 AM, [email protected] wrote: > Dear CARET experts, > > My name is Andrei Mayer and I´m currently trying to do a 3D > reconstruction of Cebus monkey brain in which we injected > neurotracers. The plotting of labeled neurons was made in Neurolucida > and to do the 3D reconstruction I´m going to use the mid-thickness > contour of the cortex. I´m having troubles to export the XML > Neurolucida files to CARET. The problem is that after doing it the > plotted cells disappeared (in CARET). I can see and edit the contours, > but for some reason the cells aren´t there. > > That´s how I´m proceeding: > In Neurolúcida I´m opening all contour files as a unique serial > sections file. That way I can organize the sections, putting them in > order and setting the distance between them. At this point I still can > see both contours and cells. I then save this file in the XML format > like it is described in the tutorial. The problem is when I Upload > this XML file into CARET. It seems that only the contours were > uploaded. I can´t see the cells. Therefore I can´t project them to the > surface. > > Best, > > Andrei > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
