Sorry, but I have as much knowledge of Neurolucida and Mdplot as my stapler does.
On Nov 30, 2011, at 12:54 PM, Andrei de Oliveira wrote: > 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 > _______________________________________________ > 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
