Search found 5945 matches

by ted
Wed Sep 15, 2021 2:16 pm
Forum: NEURON + Python
Topic: undefined symbol: nrnpython_start
Replies: 5
Views: 77

Re: undefined symbol: nrnpython_start

The output with a path with no spaces is the same as the one above Right, but did NEURON still crash? I just re-read your message from earlier today and realized the meaning of these sentences: I notice that the NEURON version is 7.6.3, even though on NEURON's website 8.0 is the latest version. If ...
by ted
Wed Sep 15, 2021 11:33 am
Forum: NEURON + Python
Topic: undefined symbol: nrnpython_start
Replies: 5
Views: 77

Re: undefined symbol: nrnpython_start

Thanks for your prompt response, but that's not "the entire message that NEURON prints to the terminal". The most important missing item is the first line, which reports details about the version of NEURON that you're using--just in case you're running into a bug that has already been fixe...
by ted
Tue Sep 14, 2021 11:37 am
Forum: NEURON + Python
Topic: undefined symbol: nrnpython_start
Replies: 5
Views: 77

Re: undefined symbol: nrnpython_start

Even if I have the mod files in the same level of the directory tree as the rest of the code . . . Please do this test. Create a new directory. Put your mod files in that directory. In that directory execute nrnivmodl Then in that same directory execute nrngui What is the entire message that NEURON...
by ted
Tue Sep 14, 2021 11:32 am
Forum: Anatomically detailed models
Topic: Importing Imaris files using import 3D tool
Replies: 2
Views: 36

Re: Importing Imaris files using import 3D tool

I tried to look for a way to convert the Imaris files to SWC but could not find any good options. Import3d's algorithms require an input file that contains morphometric data, specifically measurements of diameters at particular locations in space, structured in a way that identifies neurites and br...
by ted
Fri Sep 10, 2021 10:58 am
Forum: Other questions
Topic: List of all currents that comprise segment membrane current
Replies: 1
Views: 50

Re: List of all currents that comprise segment membrane current

I cannot seem to get the sum of the ionic currents for each segment to equal the segment's i_membrane_
How big is the discrepancy? If you are using fixed time step, does the discrepancy become smaller if you switch to adaptive integration?
by ted
Wed Sep 08, 2021 12:32 am
Forum: Getting started
Topic: how to display 3d coordinates of a segment
Replies: 9
Views: 7303

Re: how to display 3d coordinates of a segment

One question.

Does your method return the same values as those produced by interpxyz?
by ted
Wed Aug 25, 2021 12:02 pm
Forum: Other questions
Topic: Implementing extracellular potential from sinusoidal sources
Replies: 5
Views: 138

Re: Implementing extracellular potential from sinusoidal sources

they assign sinusoidal time-series to some variables, but these are nowhere connected to previously calculated potentials Presumably you want to understand how extracellular stimulation is implemented. First read the Programmer's Reference documentation of extracellular. Note that (1) extracellular...
by ted
Wed Aug 25, 2021 10:56 am
Forum: Other questions
Topic: Implementing extracellular potential from sinusoidal sources
Replies: 5
Views: 138

Re: Implementing extracellular potential from sinusoidal sources

Name of the file that contains "Full model code:" ?
by ted
Thu Aug 12, 2021 12:08 pm
Forum: NEURON + Python
Topic: Import3d tool via Jupyter
Replies: 2
Views: 132

Re: Import3d tool via Jupyter

Easy workaround: launch Python, import h and gui, then use the NEURON Main Menu toolbar to access the Import3d tool to your heart's content. From the CellBuilder export either a hoc file that you can use to create a top-level instance of your cell model, or a hoc file that defines new cell class tha...
by ted
Thu Jul 22, 2021 1:41 pm
Forum: NEURON + Python
Topic: Exporting .ses from Linear Circuit Builder
Replies: 1
Views: 127

Re: Exporting .ses from Linear Circuit Builder

ckelley was actually trying to use the Linear Circuit Builder to export a template (class definition in hoc) for a class that, when instantiated, would add to NEURON the equations that describe a circuit. That's different from saving a session file--a session file contains code that recreates one or...
by ted
Sat Jul 17, 2021 3:29 pm
Forum: Reaction-diffusion in NEURON
Topic: Pass ._ref_concentration to pc.source_var()?
Replies: 6
Views: 341

Re: Pass ._ref_concentration to pc.source_var()?

Ma et al. 2013 Presumably you're referring to Tang et al. 2013 in PLoS One, DOI: 10.1371/journal.pone.0080324. Since you're already using rxd, it will be most natural to follow my second suggestion rxd-implemented mechanism in the astrocyte(s) that generates an efflux of the released substance and ...
by ted
Sat Jul 17, 2021 12:56 am
Forum: Other questions
Topic: calculate IPSP by IPSC
Replies: 3
Views: 242

Re: calculate IPSP by IPSC

Something to think about before you go any further: D_Cl is 2 um2/ms. That means radial concentration gradients vanish rapidly in neurites with diameters on the order of 5 um or smaller. Much faster than the time course of GABA-A synaptic conductance change or transmembrane current. This means chlor...
by ted
Fri Jul 16, 2021 11:40 pm
Forum: Other questions
Topic: Rectifying gap junctions
Replies: 1
Views: 110

Re: Rectifying gap junctions

Yes.
by ted
Fri Jul 16, 2021 1:16 pm
Forum: Reaction-diffusion in NEURON
Topic: Pass ._ref_concentration to pc.source_var()?
Replies: 6
Views: 341

Re: Pass ._ref_concentration to pc.source_var()?

What are you trying to represent? Calcium-dependent release of neurotransmitters or other substances from astrocytes? Effects on neighboring neurons could be accomplished with a POINTER in an NMODL file for a density or point process mechanism in the affected neuron sections. Another way would be to...
by ted
Fri Jul 16, 2021 10:59 am
Forum: Other questions
Topic: calculate IPSP by IPSC
Replies: 3
Views: 242

Re: calculate IPSP by IPSC

It's feasible but if you want more specific help, you'll need to provide some information about the model that you currently have. Is it a conceptual model (hypothesis) or have you actually implemented a computational model? If it is a computational model, what is your implementation (source code) o...