Hi Donna,
This is exactly what I thought it was happening. Answering your question, I don´t know if I can export the cells separately as 3D coords. Or at least I don´t know how to do it. What is interesting is that this problem happens only when I export the sections as a unique serial section file. When I export those sections to CARET separately, both contour and cells are exported. Therefore, it seems that the problem is in the way I´m saving the serial section file (XML format) in Neurolucida. Do you know how it´s done in Mdplot? Thanks, Andrei 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 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
