Search found 5728 matches

by ted
Thu Feb 13, 2020 2:07 pm
Forum: Anatomically detailed models
Topic: Neuron transforms soma that is loaded from .swc. What is the rule for it?
Replies: 4
Views: 653

Re: Neuron transforms soma that is loaded from .swc. What is the rule for it?

My question. How I can make this output to be? (as it's supposed to be) Here's the answer: throw away the Python and hoc code that you are using. The SWC data describes a shape that consists of a soma and an axon. The hoc template is very strange, not remotely relevant to the SWC data, and unnecess...
by ted
Mon Feb 10, 2020 12:57 pm
Forum: Anatomically detailed models
Topic: Neuron transforms soma that is loaded from .swc. What is the rule for it?
Replies: 4
Views: 653

Re: Neuron transforms soma that is loaded from .swc. What is the rule for it?

The first line of data in your SWC file # index type X Y Z radius parent 1 1 0.000000 0.000000 0.000000 5.442800 -1 is what we call, for lack of a better term, a "one point specification of a soma." There has never been an "official" definition of the SWC format, so it's hard to be dogmatic about th...
by ted
Sat Feb 08, 2020 11:58 am
Forum: Getting started
Topic: finitialize() not working?
Replies: 2
Views: 417

Re: finitialize() not working?

Much of NEURON's standard run system is implemented in nrn/share/nrn/lib/hoc/stdrun.hoc h.run() executes the code in a procedure called run() that is defined in stdrun.hoc. Here is the chain of (most of the) procedures that are executed when you call h.run(). All of these are defined in stdrun.hoc: ...
by ted
Fri Jan 31, 2020 12:17 pm
Forum: Modeling networks
Topic: How to add miniature current in cortical network
Replies: 1
Views: 413

Re: How to add miniature current in cortical network

The easiest way might be to use IClamps to inject depolarizing current pulses into one or more of your model's cells. Or if your model has some excitatory synapses, you might drive one or more of those synapses with one event or a short burst of events produced by a NetStim. See the Programmer's Ref...
by ted
Fri Jan 31, 2020 12:12 pm
Forum: NEURON + Python
Topic: For loop over section's segments in Python and HOC returns different values
Replies: 4
Views: 477

Re: For loop over section's segments in Python and HOC returns different values

Changing parameters on a density mechanism at the 1 location will set them at the last node of positive area (since density mechanisms cannot exist at points). As a consequence, using for(x) instead of for(x, 0) to loop over segments to setup a conductance gradient within a section (e.g. gmax varyi...
by ted
Wed Jan 29, 2020 11:08 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Interfacing NEURON with other software on runtime
Replies: 4
Views: 500

Re: Interfacing NEURON with other software on runtime

It would have been my pleasure to have written the post that got your thanks, but it was Robert McDougal who wrote that clear and very effective reply to your question. Thank you, Robert! That should go in the FAQ list, or perhaps better, in the Forum's own Hot tips area.
by ted
Tue Jan 28, 2020 12:43 pm
Forum: NEURON hacks
Topic: How to connect multiple compartments of an axon using a for loop?
Replies: 3
Views: 470

Re: How to connect multiple compartments of an axon using a for loop?

For some reason, it isn't showing here that there is an i in square brackets next to the axon_1(0). Why don't you use the Forum's markup features? Those little buttons above the big edit field include one that is used to wrap blocks of code. Maybe read about this in the Forum's FAQ list, under "For...
by ted
Tue Jan 28, 2020 12:39 pm
Forum: NEURON hacks
Topic: How to connect multiple compartments of an axon using a for loop?
Replies: 3
Views: 470

Re: How to connect multiple compartments of an axon using a for loop?

Could anyone help me debug this part of my code?
Do you think the task might be simpler if you used a million "compartments" (sections, actually)? Or maybe it would be easier to figure out what went wrong if you tried just 3.
by ted
Tue Jan 28, 2020 12:35 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Modeling leaky integrate-and-fire neuron including Hodgkin–Huxley-like currents
Replies: 1
Views: 382

Re: Modeling leaky integrate-and-fire neuron including Hodgkin–Huxley-like currents

1. Is my implementation correct? How will you discover whether it works properly? Did Esser et al. publish a figure that shows how one of their model cells responds to injected current or synaptic activation? Or is such a figure in their previous paper that they cited as the basis for this model? I...
by ted
Tue Jan 28, 2020 11:15 am
Forum: NEURON + Python
Topic: Rset or reboot neuron without exist in python
Replies: 6
Views: 1347

Re: Rset or reboot neuron without exist in python

So is there a method to fully reset the simulator? Yes. It's called finitialize(), and it takes care of everything that is built into NEURON. But if you write some code that adds new state variables, it's up to you to make sure that those new state variables are properly initialized. See my previou...
by ted
Fri Jan 24, 2020 11:34 am
Forum: Parallel NEURON
Topic: multiple signals to a single POINT_PROCESS and thread safety of a POINTER.
Replies: 1
Views: 417

Re: multiple signals to a single POINT_PROCESS and thread safety of a POINTER.

How about approching the problem in a way that completely eliminates the need for pointers? The strategy depends on whether dopaminergic modulation of plasticity is stream-specific (selectively affects individual synapses) or not stream-specific (e.g. mediated by an intracellular second messenger th...
by ted
Tue Jan 14, 2020 9:17 pm
Forum: Modeling networks
Topic: design afferent stimulus events with phasic bursts
Replies: 3
Views: 1352

Re: design afferent stimulus events with phasic bursts

. . . if I need to deliver . . .
So? Have you tried to do it? How do you know there is a problem if you haven't tried it?
by ted
Tue Jan 14, 2020 11:45 am
Forum: Modeling networks
Topic: design afferent stimulus events with phasic bursts
Replies: 3
Views: 1352

Re: design afferent stimulus events with phasic bursts

If for each burst with specific intra-burst freq, I design a netstim() for it, that would be ending up with too many netstim() Really? What operating system are you using, and how much memory does it have? Assuming your code allows you to specify how many cells the network has, what is the largest ...
by ted
Mon Jan 13, 2020 1:00 pm
Forum: NEURON + Python
Topic: Finding middle of a section
Replies: 4
Views: 450

Re: Finding middle of a section

h.define_shape() does not create new points for sections whose morphology was defined by calling the pt3dadd method. True. My mistake. The way to discover the xyz locations of segment centers is to treat a section's pt3d data as piecewise linear functions of path length from the section's 0 end, an...
by ted
Mon Jan 13, 2020 11:40 am
Forum: NEURON + Python
Topic: Finding middle of a section
Replies: 4
Views: 450

Re: Finding middle of a section

I am currently working on an algorithm for finding the min. current needed to produce an action potential using extracellular stimulation and the MRG axon You say nothing about the geometry of the stimulating electrode(s) (point electrodes vs. electrodes with finite surface area, monopolar vs. bipo...