Search found 21 matches

by regger
Fri Oct 17, 2014 12:06 pm
Forum: Other questions
Topic: What kind of unit is ohm-cm ?
Replies: 6
Views: 3417

Re: What kind of unit is ohm-cm ?

It's ohm*cm. You get the total resistance of a piece of wire of length L and cross-sectional area A by

R total = Ra * L / A

Since R total is of dimension [resistance], Ra must have dimension [resistance * length].

hope this helps,
Robert
by regger
Fri Oct 10, 2014 6:03 am
Forum: NEURON + Python
Topic: Simple function to add synapses
Replies: 8
Views: 4535

Re: Simple function to add synapses

If you want to deliver events to a NetCon at specified times, the correct way to do this is using a VecStim as the source. You can find a good explanation by ted about how to use it here . (N.B.: A NetStim delivers a spike train at regular intervals or stochastically with a mean rate, but is not rea...
by regger
Thu Oct 02, 2014 5:22 am
Forum: NEURON + Python
Topic: Accessing synapses on a section
Replies: 3
Views: 1809

Re: Accessing synapses on a section

I don't know about accessing synapses through sections, but the other way around is certainly possible. Use a PointProcess's get_loc() method, which pushes the section the PointProcess is attached to onto the section stack and returns the relative position (x) along that section. Using the section's...
by regger
Mon Jul 21, 2014 1:47 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: NET_RECEIVE is not called when expected
Replies: 8
Views: 3055

Re: NET_RECEIVE is not called when expected

Thank you Ted! That was a bit surprising since some object types persist even if they are not given a reference (Section, for example). Actually, that's expected python behavior. The section is an exception, and if you don't assign it to a reference, it will be difficult to get a handle on this sec...
by regger
Thu Jul 17, 2014 6:12 am
Forum: Other questions
Topic: Import SWC file from NeuroMorpho -> Export as HOC file
Replies: 9
Views: 3445

Re: Import SWC file from NeuroMorpho -> Export as HOC file

Thanks, to understand it fully, this means, that, if I would add by pt3dadd() points to a section, i implicit define an order of the points along the section, right? Best, Stephan Correct. The first point in a section added by pt3dadd() corresponds to x=0 of the branch (loosely speaking, also of th...
by regger
Wed Jul 16, 2014 11:09 am
Forum: Other questions
Topic: Import SWC file from NeuroMorpho -> Export as HOC file
Replies: 9
Views: 3445

Re: Import SWC file from NeuroMorpho -> Export as HOC file

Hi Stephan, check out the part of the NEURON documentation about n3d() , x3d(i), y3D(i) and z3d(i)... sounds like that's what you're looking for. These functions return the x/y/z coordinate of the ith point along the currently accessed section - so x=0 would be i=0, and x=1 would be i=n3d()-1. cheer...
by regger
Thu Jun 26, 2014 10:36 am
Forum: Adding new mechanisms and functions to NEURON
Topic: add/omit a synapse for different iterations
Replies: 3
Views: 1853

Re: add/omit a synapse for different iterations

The usual way to set up and control synapses in NEURON is using the NetCon class. This offers some very convenient interfaces to what you usually need to set up and control connections: 1. the source - either an analog signal, such as the voltage in an axon terminal, or a "digital" spike source, suc...
by regger
Mon Mar 03, 2014 2:40 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: setting seed in a Distributed Mechanism
Replies: 1
Views: 1353

Re: setting seed in a Distributed Mechanism

Hi, I tried to do the same thing at some point and I think I did it with help of the init block and declaring a RANGE variable that was then used to call set_seed(RANGE var) from the init block of the mechanism. Don't remember exactly though. Also, I think I remember there was only one scop RNG inst...
by regger
Mon Feb 17, 2014 7:42 am
Forum: NEURON + Python
Topic: Obtaining a segmentation fault using neuron
Replies: 11
Views: 5056

Re: Obtaining a segmentation fault using neuron

Dear Robert, When you say the "code works fine for me" you mean you obtain the same kind of error, don't you? No. I mean it works and I don't get an error. I do get the same error as you when I execute your statements afterwards. However, I don't get the autocomplete option for h.newSec in ipython....
by regger
Wed Feb 12, 2014 7:29 am
Forum: NEURON + Python
Topic: Obtaining a segmentation fault using neuron
Replies: 11
Views: 5056

Re: Obtaining a segmentation fault using neuron

Hi Romain, yes I tried the code I posted and it works fine for me. On the other hand, I can't reproduce the autocomplete thing at the iptyhon console. You would have to post the whole code you were using. But it's probably related to the other problem. It seems like the python object newSec does not...
by regger
Tue Feb 11, 2014 8:04 am
Forum: NEURON + Python
Topic: Obtaining a segmentation fault using neuron
Replies: 11
Views: 5056

Re: Obtaining a segmentation fault using neuron

NEURON can crash with a segfault because it's written in C, you're just using a python wrapper. So behind the scenes, there's still a lot of pointers hanging around, and you may or may not have done something there... Anyways, to subclass the neuron section, you should initialize the nrn.Section obj...
by regger
Mon Aug 05, 2013 8:53 am
Forum: Other questions
Topic: Bad_alloc error
Replies: 3
Views: 3627

Re: Bad_alloc error

My guess would be you don't have enough RAM to record all the data for such a long time. Simplest solution would be to try running it on a machine with more RAM. If that's not an option, you should look into pausing the simulation at certain intervals, writing all the information to disk, clearing a...
by regger
Mon Aug 05, 2013 6:11 am
Forum: Other questions
Topic: Bad_alloc error
Replies: 3
Views: 3627

Re: Bad_alloc error

That's actually a pretty generic error message raised typically when a program fails to dynamically allocate memory during runtime. You say it's a large scale model - do you record a lot of variables from all neurons? If yes, does it run ok for a shorter amount of time? Have you tried running it on ...
by regger
Fri Jul 05, 2013 6:05 am
Forum: Other questions
Topic: Usage of Celsius
Replies: 2
Views: 1452

Re: Usage of Celsius

As far as I'm aware, celsius is a global variable in hoc, meaning it has the same value everywhere in your NEURON session. If you want to assign different temperatures to different populations, you could declare a RANGE variable 'local_temperature' in all your NMODL files that are affected by temper...
by regger
Mon Nov 12, 2012 2:58 pm
Forum: Getting started
Topic: Recording range variable in Vector
Replies: 5
Views: 3020

Re: Recording range variable in Vector

Thank you for following up on this so quickly.
Your explanation makes sense. Crucial point that's definitely worth remembering for other mechanisms.

All the best,

Robert