www.neuron.yale.edu

Hi all,
my name is Marco Pirini and I'm a new Neuron user at Duke University. I'm working with the precompiled 5.9 version of Neuron on Windows XP.
I should implement a unique model with several neurons; some of them requires a 2-layer (default) extracellular mechanism, other require only 1 layer extracellular mechanism. How could it be possible to have these different configurations in the same .mod file?
I've tried the following things:

- to look for infomation on the Extracellular page in the on-line help documentation, where it's suggested to change the line:

#define EXTRACELLULAR 2

in nrn/src/nrnoc/options.h and to recompile:

recompile both nrnoc and nrniv

what does this last statement mean?

- anyway, the previous method should't solve my problem, since I need to have two different extracellular mechanisms in the same .mod file. So, I'm thinking to find the source file for the extracellular mechanism and, saving and compiling it with a different name, changing it accordingly to the number of layers I need. In this manner, I could have as many extracellular mechanism as I want. The question is: where could I find the source code? I can't find the file:

$NEURONHOME/src/nrnoc/extcell.c

indicated by on-line guide.

Could anyone please help me?
Thanks, have a nice day

There is no need to recompile. As you said, in the standard distribution of NEURON, the
extracellular mechanism has two layers--see
http://www.neuron.yale.edu/neuron/stati ... racellular
--but the default values of all of its parameters are such that neither layer has any effect.
If your model has some sections where only the innermost layer should have an effect,
then change only the inner layer's parameters; these are called xc, xg, and raxial
(synonyms for xc[0], xg[0], and raxial[0]). For those sections in which you want both
layers to have an effect, then change not only xc, xg, and raxial, but also xc[1], xg[1],
and raxial[1].

The only problem here is that e_extracellular is actually in the second layer, in series with
xg[1]. If you want e_extracellular to lie outside of the second layer, nrnoc and nrniv must
be recompiled after setting
#define EXTRACELLULAR 3
in nrn/src/nrnoc/options.h. However, to recompile for MSWin you will need to have a full
cygwin installation. From your message I gather that you are not already a cygwin
maven. If you really need 3 layers, let me know.