Search found 5948 matches

by ted
Fri Sep 17, 2021 11:53 am
Forum: Anatomically detailed models
Topic: Error in loading morphology from swc file
Replies: 3
Views: 11

Re: Error in loading morphology from swc file

trying to run already existing code. While loading a morphology of a spiny projection neuron I get the following error Very strange. The Import3d GUI tool had no problem with this swc file under Linux Mint 20.1 (NEURON 8.0.0 HEAD (429d11ef) 2021-04-30 installed yesterday via pip3) or CentOS 7 with ...
by ted
Fri Sep 17, 2021 9:59 am
Forum: Anatomically detailed models
Topic: cable model with manual diameters and dynamics
Replies: 1
Views: 12

Re: cable model with manual diameters and dynamics

Can't answer your questions. The code excerpt contains no statement that creates a section or references the properties of a section or segment. There isn't even a reference to any NEURON-specific keyword (pi and names of common units like siemens and um don't count).
by ted
Fri Sep 17, 2021 9:50 am
Forum: NEURON + Python
Topic: undefined symbol: nrnpython_start
Replies: 8
Views: 99

Re: undefined symbol: nrnpython_start

After installing NEURON with pip3 install neuron I didn't add it to the path. At trying to compile mod files Ubuntu prompts me to install neuron-dev with sudo apt which was version 7.6.3. How (not) helpful. Under Linux Mint (a close cousin of Ubuntu), pip install of NEURON simply adds .local/bin to...
by ted
Wed Sep 15, 2021 2:16 pm
Forum: NEURON + Python
Topic: undefined symbol: nrnpython_start
Replies: 8
Views: 99

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: 8
Views: 99

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: 8
Views: 99

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: 44

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: 53

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: 7308

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: 152

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: 152

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: 138

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: 143

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: 369

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: 246

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...