www.neuron.yale.edu

In order to diagnose a problem, you must first localize its source. removing things bit by bit (back to the working version) will take years... Then go back to the working version--you did save that, right?--and add complications and refinements one at a time, in small increments, testing at every s...

nrniv: undefined variable soma in hucre.ses near line 14 } ^ xopen("hucre.ses" ) If you are working with the CellBuilder, and not using the Network Builder, then the problem may just be that the CellBuilder's "Continuous Create" was not on. Open up just the CellBuilder's session...

As long as we are using spherical electrodes calculation of transfer resistance is easy and the xtra mechanism can be used unmodified. However, if we are using cylindrical pippets as electrodes, calculating resistance is a bit more tricky. One method to overcome this problem is to find as expressio...

That's very odd. Your hoc and ses files worked fine (reconstituted the model correctly) before you changed the NMODL code? If so, this nrniv: gNabar_NaP not in this property suggests that the NaP mechanism's NEURON block no longer declares gNabar. Does the last two messages come from the same source...

[So, as long as I confine myself to field geometries (hence electrode placement) which are symmetric with respect to the centriod of the sphere I am safe. At the risk of seeming pedantic, and mostly for the potential benefit of others who may read these exchanges, could you be more explicit about w...

If Ra is predefined then probably it is a good idea to change the example program to reflect this. Ra is not predefined. It is a keyword, which means only that it has a specific meaning and should not be usurped for some other purpose. The example you cite in the Programmer's Reference uses Ra corr...

That's odd indeed. Looking down the z or y axis, you see a circle, but looking down the x axis it's only a dot, and rotating that just slightly turns it into a thin ellipse. A bug in the rendering of shape plots? As to what you may be missing, there are three or four items, but the appearance of the...

Be sure to read these papers, which discuss various artifacts that frequenly affect morphometric data and can have serious adverse effects on simulation results: Kaspirzhny AV, Gogan P, Horcholle-Bossavit G, Tyc-Dumont S. Neuronal morphology data bases: morphological noise and assesment of data qual...

Rather than give you a fish, here's how to fish. If you can't just look at the code and quickly see what's wrong, try one of these strategies: 1. Insert print statements and see if the error message appears before or after the message is printed. This only works for run-time errors; it will not work...

One or more of the mechanisms is incorrect. Suggestions: 1. Be sure to read about similar mechanisms in chapter 9 of The NEURON Book, or at least the "enhanced preprint" of Hines, M.L. and Carnevale, N.T. Expanding NEURON's repertoire of mechanisms with NMODL. Neural Computation 12:995-100...

Here are the most important chapters for what you want to know. Chapter 10 and 11 of The NEURON Book contain information that you will need to know to model networks. But before you read it, you should be familiar with the contents of chapters 5 and 6 (modeling individual cells). If you need to lear...

Excellent. The book is more up-to-date than that old article on the WWW site.

You can use a Point Process Manager to manage an ExpSyn or Exp2Syn, but you will need to write some hoc code to send events to the synaptic mechanism. Example: suppose the Point Process Manager tells you that your Exp2Syn is called Exp2Syn[0]. Then you need some code that creates a NetStim, and a Ne...

Use an IClamp. Read about Point Processes in chapter 5 of The NEURON Book, or at
least read
Hines, M.L. and Carnevale, N.T.
The NEURON simulation environment.
Neural Computation 9:1179-1209, 1997
which you will find here
http://www.neuron.yale.edu/neuron/bib/nrnpubs.html

Zip up the hoc, ses, and mod files necessary to reproduce the problem
and send them to me
ted dot carnevale at yale dot edu
and I'll try to diagnose it and tell you how to fix it.