That's OK, Donna. I'll try something else in NL. Thanks a lot anyway!
2011/12/1 Donna Dierker <[email protected]> > 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 > -- *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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