www.neuron.yale.edu

Exactly the same way you'd access any range variable. In hoc secname paramname(x) = somevalue where secname is the name of a section paramname is the name of the range variable you want to access x is normalized distance from the 0 end of the section to any point inside the segment of interest and s...

Uninstall NEURON, then reinstall it.

If a model cell is not spontanously active (not firing spikes or having spontaneous subthreshold fluctuations of membrane potential), then 1. If the model cell's concentrations and reversal potentials are all constant, it is fairly straightforward and easy to ensure that the model will have whatever...

Do these model cells have any mechanisms that affect concentrations of ions or second messengers? Examine the NEURON blocks of the mod files. Do you see any USEION statements that WRITE a concentration?

NEURON allows users to include so much complexity into their models that there's no single initialization strategy that works (let alone "works best") for all models. Particularly difficult are models that 1. have one or more state variables (other than membrane potential) with slow dynami...

Sometimes the best way to understand documentation, and avoid analysis paralysis, is to run your own tests. In this case, actually use Vector.record to capture your variable(s) of interest. Also record t. What did you discover? Now let me ask you another question: if you only want to know the value ...

from the programmer's reference Vector.record() notes, it seems to me that the vector does not record all the voltages from the stream of voltages. Hmm, if the documentation of Vector.record is that vague, we need to fix it. Can you point to (or quote) the particular part that led to your question?...

https://www.neuron.yale.edu/ftp/ted/neuron/stimsphere.zip contains source code for demonstrations of extracellular stimulation of a spherical cell with HH membrane properties in an electric field that induces a linear extracellular potential gradient parallel to the x axis. One implementation is en...

Yes, nA is not defined in neuron.units, and merely adding
nA = 1
to the list of "NEURON's default units" in the units.py file fixes the problem.

On my machine, units.py is in ~/.local/lib/python3.8/site-packages/neuron

None of those are distributed with NEURON itself. My guess is they're generated by other code that is part of SimNIBS. You need to ask the developers/maintainers of SimNIBS for help.

Ah, Shirinpour et al. 2021. Something Hananeia, Jedlicka et al. were working on. What version of NEURON was running on the older computer, and what version is running on the new one? a few files of code missing from the NEURON folder in the model generation What files would those be? What error mess...

The first URL points to stuff that doesn't mention NEURON at all.

The second points to something at documentcloud.adobe.com that returns a

URL provided is expired or invalid.

error message.

Is there a published article, even a pdf at bioRxiv, that says something about this?

2kV/m E-field magnitude For a model of a 5 um diam spherical cell with hh membrane properties, I'm getting 3.14522 kV/m; for a 10 um diam cell it's half as much (as expected). With extracellular potential gradient 0, rheobase to 4.5 places is 0.0017373 nA, and comparing the resulting trace with the...

I am unaware that SimNIBS does anything with NEURON. Can you point me to a reference that says something about this?

Even so, given that the symptom is failure of SimNIBS, why not ask the developers/maintainers of SimNIBS for help, e.g. at the GitHub repo for SimNIBS?

why does the transmembrane voltage even react if I play a non-zero amplitude pulse through e_extracellular, but never do anything with it? Good question. I bet you can figure this out for yourself with a toy example. Consider a model that consists of two adjacent segments. Draw the equivalent circu...