www.neuron.yale.edu

I will need to be able to reproduce the problem. Please zip up the source code and email it to
ted dot carnevale at yale dot edu
and I will tell you what I find out.

As I recall, the original implementation by McIntyre & Grill didn't actually perturb extracellular potential. Instead, they used the "activating function" approach in which the effect of extracellular stimululation on the axon is represented by injecting a current into each compartment...

I hope you get an "out of range" error when the stimulus is 100 V. If you do this to living tissue, you'll fry something.

Bolus is a time honored term for qualitative description of the time course of injecting a drug, but not so for electrical stimulation, which has its own well established vocabulary. For the sake of clarity and mutual understanding, let's stick with the latter: one speaks of pulses or other waveform...

The ses file recreates the CellBuilder tool. The hoc file creates the model cell. If you have gone to the effort of using a CellBuilder to create a model specification, it's a good idea to save it to a ses file in case you want to change something later on (like disretization method, biophysical pro...

What do you mean by "a singular point"?
What does "our wave form as a bolus" mean?

Having read my previous post, someone might well ask "OK, Mr. Wizard, I have all the source code. How do I proceed?" First execute nrnivmodl to compile the mod files. Next create your own rig.ses file. 1. Execute nrngui 2. In the NEURON Main Menu toolbar click on Build/single compartment 3...

Good questions. Also good to see that you're resolving documentation ambiguities by testing to see what syntax works and what doesn't. You might find it helpful to read chapter 9 of The NEURON Book. If you don't have the book, get this draft instead https://www.neuron.yale.edu/ftp/ted/book/revisions...

Here's the code that I used. The main file is called test.hoc. It starts with // model of monopolar extracellular stimulation of an axon // stimulus is a 100 us current pulse that drives extracellular potential load_file("nrngui.hoc") ///// create model cell load_file("axon.hoc")...

I can't say I have ever seen a units declaration in the form sec_to_ms = (s) -> (ms) but then I haven't seen all NMODL code that has ever been written. Who knows, this might be the wave of the future. If a point process generates a current, that current must be in nanoamps. If a density (aka distrib...

Thank you. I'll review it and reply accordingly. In the meantime I decided to run a test of my own, using a simple model: cylindrical axon geometry: diam 1 um, length 1000 um, 0 end at 0,0,0, 1 end at 1000, 0, 0 (all units in um) biophysics: hh membrane at standard operating temperature (6.3 deg C),...

You could just zip up all the source files that are needed to reproduce your results (hoc, mod, ses, swc, txt, dat--but also see viewtopic.php?t=1048) and email them to ted dot carnevale at yale dot edu

First, some important questions: What is your operational definition of "activating potential" (by what experimental procedure did you determine its numerical value)? Can you present a table of your results? An extracellular potential was applied to the axon. How? Specifically: What was yo...

Your "3D mesh" defines a "stimulated volume" in space. Your first task is to decide the location and orientation of your model cell in that volume. That's something that you and your PI must do. Next, for each segment in your model, you have to do two things: (1) determine the co...

Apologies for the double post, tried to edit and messed it up. OK, double post is now gone. BTW I'm an expert on messing up edits of posts. By "put in an electrode", I meant apply an extracellular stimulus. Got it. The reason for trying to get a different segment division of the model due...