Search found 6305 matches
- Wed Jul 26, 2023 9:10 pm
- Forum: NetPyNE
- Topic: non-uniform distribution of ion channel
- Replies: 1
- Views: 17061
Re: non-uniform distribution of ion channel
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...
- Wed Jul 26, 2023 8:50 pm
- Forum: MSWin
- Topic: Python cannot import neuron library on Windows install
- Replies: 7
- Views: 18598
Re: Python cannot import neuron library on Windows install
Uninstall NEURON, then reinstall it.
- Mon Jul 24, 2023 11:01 am
- Forum: Anatomically detailed models
- Topic: Setting RMP according to experimental measurements.
- Replies: 5
- Views: 18573
Re: Setting RMP according to experimental measurements.
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...
- Fri Jul 21, 2023 4:16 pm
- Forum: Anatomically detailed models
- Topic: Setting RMP according to experimental measurements.
- Replies: 5
- Views: 18573
Re: Setting RMP according to experimental measurements.
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?
- Fri Jul 21, 2023 11:26 am
- Forum: Anatomically detailed models
- Topic: Setting RMP according to experimental measurements.
- Replies: 5
- Views: 18573
Re: Setting RMP according to experimental measurements.
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...
- Fri Jul 21, 2023 11:05 am
- Forum: Other questions
- Topic: Code: Getting Value of Voltage at end of current pulse
- Replies: 3
- Views: 16265
Re: Code: Getting Value of Voltage at end of current pulse
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 ...
- Wed Jul 19, 2023 1:03 pm
- Forum: Other questions
- Topic: Code: Getting Value of Voltage at end of current pulse
- Replies: 3
- Views: 16265
Re: Code: Getting Value of Voltage at end of current pulse
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?...
- Tue Jul 18, 2023 1:06 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Extracellular Mechanism and Hodgkin-Huxley
- Replies: 10
- Views: 26329
Re: Extracellular Mechanism and Hodgkin-Huxley
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...
- Thu Jul 13, 2023 1:16 pm
- Forum: Other questions
- Topic: ImportError when importing the unit 'nA' from neuron.units
- Replies: 1
- Views: 15248
Re: ImportError when importing the unit 'nA' from neuron.units
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
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
- Wed Jul 12, 2023 3:49 pm
- Forum: MSWin
- Topic: Nemo-TMS model generation failure
- Replies: 6
- Views: 18203
Re: Nemo-TMS model generation failure
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.
- Wed Jul 12, 2023 12:23 am
- Forum: MSWin
- Topic: Nemo-TMS model generation failure
- Replies: 6
- Views: 18203
Re: Nemo-TMS model generation failure
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...
- Wed Jul 12, 2023 12:14 am
- Forum: MSWin
- Topic: Nemo-TMS model generation failure
- Replies: 6
- Views: 18203
Re: Nemo-TMS model generation failure
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
Is there a published article, even a pdf at bioRxiv, that says something about this?
The second points to something at documentcloud.adobe.com that returns a
error message.URL provided is expired or invalid.
Is there a published article, even a pdf at bioRxiv, that says something about this?
- Tue Jul 11, 2023 6:48 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Extracellular Mechanism and Hodgkin-Huxley
- Replies: 10
- Views: 26329
Re: Extracellular Mechanism and Hodgkin-Huxley
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...
- Tue Jul 11, 2023 5:38 pm
- Forum: MSWin
- Topic: Nemo-TMS model generation failure
- Replies: 6
- Views: 18203
Re: Nemo-TMS model generation failure
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?
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?
- Mon Jul 10, 2023 1:59 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Extracellular Mechanism and Hodgkin-Huxley
- Replies: 10
- Views: 26329
Re: Extracellular Mechanism and Hodgkin-Huxley
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...