> > 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 > > > 2011/11/30 Donna Dierker <[email protected]> > >> 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 >> > > > > -- > *Andrei Mayer de Oliveira* > MSc Student (Physiology) > Laboratório de Neurobiologia II > Instituto de Biofísica Carlos Chagas Filho > Universidade Federal do Rio de Janeiro - UFRJ > Cidade Universitária, Ilha do Fundão, RJ > Phone: 55 - 21 - 2562-6514 >
-- *Andrei Mayer de Oliveira* MSc Student (Physiology) Laboratório de Neurobiologia II Instituto de Biofísica Carlos Chagas Filho Universidade Federal do Rio de Janeiro - UFRJ Cidade Universitária, Ilha do Fundão, RJ Phone: 55 - 21 - 2562-6514
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