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by vladimirov
Mon Jul 14, 2014 5:06 pm
Forum: Modeling networks
Topic: Resetting NetStim rate immediately
Replies: 4
Views: 6533

Re: Resetting NetStim rate immediately

Thanks for your response, Ted. These solutions with artificial spiking cells seem very counter-intuitive (to me). I think I should probably switch to single-compartment HH models, where injected current can immediately change the spiking rate of a cell. Thanks!
by vladimirov
Sat Jul 12, 2014 12:04 am
Forum: Modeling networks
Topic: Resetting NetStim rate immediately
Replies: 4
Views: 6533

Re: Resetting NetStim rate immediately

:-(
The stimulus V is supposed to change continuously during simulation. If I switch conductance-based cell models instead of artificial spiking cells, would there be any way to instantly convert V->F (stimulus to firing rate)?
by vladimirov
Fri Jul 11, 2014 3:25 pm
Forum: Modeling networks
Topic: Resetting NetStim rate immediately
Replies: 4
Views: 6533

Resetting NetStim rate immediately

Hi, folks I am using NetStim() instances to drive activity my IntFire4 neurons with a stimulus V of varying magnitude. The stimulus can change quickly (about every 50 ms), so I am trying to implement variation in spiking rate using NetStim() instances. So, in the beginning of simulation each cell in...
by vladimirov
Tue Jul 24, 2012 2:12 pm
Forum: Getting started
Topic: Sampling a vector with variable time step
Replies: 2
Views: 1242

Re: Sampling a vector with variable time step

Solved the problem, thank you!
by vladimirov
Tue Jul 24, 2012 10:43 am
Forum: Getting started
Topic: Sampling a vector with variable time step
Replies: 2
Views: 1242

Sampling a vector with variable time step

Hello, Can someone give me an advice how to sample a vector f(t) (voltage), which is drawn by NEURON GUI with variable time step? I basically need values of f(t) at equally spaced time points ti for a usual FFT. I tried to export it (pick Vector->save to file) and perform interpolation, so that f(t)...
by vladimirov
Mon Jul 09, 2012 6:32 pm
Forum: NEURON hacks
Topic: Calculating LFP from multicompartment neuron
Replies: 6
Views: 11570

Re: Calculating LFP from multicompartment neuron

Got it, I did not insert the pointers. Now it seems to work. Thanks!
by vladimirov
Mon Jul 09, 2012 4:39 pm
Forum: NEURON hacks
Topic: Calculating LFP from multicompartment neuron
Replies: 6
Views: 11570

Re: Calculating LFP from multicompartment neuron

Ted, I am going through your example code Extracellular stimulation and recording . When I insert xtra mechanism into a minimal hh model, such as create soma soma { insert hh insert pas insert xtra } access soma I get the following error, when I press Run: nrniv: Segmentation violation near line 20 ...
by vladimirov
Mon Jul 09, 2012 10:10 am
Forum: NEURON hacks
Topic: Calculating LFP from multicompartment neuron
Replies: 6
Views: 11570

Re: Calculating LFP from multicompartment neuron

Many thanks, Ted. Your response is solving the question in full, as always!
by vladimirov
Fri Jul 06, 2012 4:17 pm
Forum: NEURON hacks
Topic: Calculating LFP from multicompartment neuron
Replies: 6
Views: 11570

Calculating LFP from multicompartment neuron

Hello, Could anyone give a hint how to efficiently calculate LFP of a multicompartment cell? I know the basic theory, the line source model - take all transmembrane currents and sum them with weights inversely proportional to the distance from electrode. How to implement this in NEURON in a neat way...
by vladimirov
Fri May 11, 2012 4:48 pm
Forum: NEURON + Python
Topic: Model (hoc file), plotting output in Python
Replies: 15
Views: 9089

Re: Model (hoc file), plotting output in Python

From my user's perspective, I am going to stay mainly in hoc because, as Ted pointed out, native NEURON GUI is richer and more versatile than python substitutes I found so far. But I don't see any convenient way to generate publishing-quality plots using NEURON GUI, except pick vector->save in txt f...
by vladimirov
Thu May 10, 2012 10:18 pm
Forum: NEURON + Python
Topic: Model (hoc file), plotting output in Python
Replies: 15
Views: 9089

Re: Model (hoc file), plotting output in Python

Thank you, Uri. I will try your long-term advice and get rid of hoc GUI but retain the hoc computational part.
by vladimirov
Thu May 10, 2012 2:55 pm
Forum: NEURON + Python
Topic: Model (hoc file), plotting output in Python
Replies: 15
Views: 9089

Model (hoc file), plotting output in Python

Hi, Could you please give a hint on how to run existing hoc file which includes some GUI (ses-file) by using Python? I have PyNEURON installed and run my hoc file with from neuron import * h('load_file("mosinit.hoc")') I get the following errors: In [6]: h('load_file("mosinit.hoc")') NEURON: Couldn'...
by vladimirov
Wed May 09, 2012 1:49 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: STDP
Replies: 9
Views: 5579

Re: STDP

How to fish
...
I was tinkering around this example for couple of hours trying to understand why it does not work out for me (no synapse potentiation occurs). Finally I found the reason: in provided stdp.mod file, both potentiation (p) and depression (d) parameters were set to zero :)))
by vladimirov
Wed May 02, 2012 11:31 am
Forum: Getting started
Topic: Fitting time constants for EPSPs
Replies: 6
Views: 7958

Re: Fitting time constants for EPSPs

Many thanks, Ted, I appreciate your feedback!
by vladimirov
Tue May 01, 2012 1:59 pm
Forum: Getting started
Topic: Fitting time constants for EPSPs
Replies: 6
Views: 7958

Re: Fitting time constants for EPSPs

Hi, Ted, Thanks a lot for the explanations. Here are the answers to your questions: 1) I think the difference is because membrane is a capacitor and its (somatic) time constant can be quite long. So once the current is injected by IPSC, it can take a while to equilibrate the membrane potential, henc...