Search found 38 matches

by Qroid_montreal
Thu Jul 25, 2013 12:02 pm
Forum: Other questions
Topic: Modeling a neuron in a spatially smooth Ve
Replies: 5
Views: 2384

Re: Modeling a neuron in a spatially smooth Ve

Am I incorrect in thinking that Vi remains at -70 mV (relative to ground)? Is Vi also changed by the addition of the battery, such that now Vi = (-70 + 1500) mV = 1430 mV? If that's the case then Vm = (1430 - 1500) mV = -70 mV. This would mean that the battery doesn't change Vm. Is that right? Thanks.
by Qroid_montreal
Thu Jul 25, 2013 11:22 am
Forum: Other questions
Topic: Modeling a neuron in a spatially smooth Ve
Replies: 5
Views: 2384

Re: Modeling a neuron in a spatially smooth Ve

Embarrassed how rusty I am at this... Let's see what I can do. In the first situation, Vo = 0 mV, Vm = -70 mV. So Vi = Vm+Vo = -70 mV. In the second situation, the voltage difference between Vi and ground remains the same (Vi=-70 mV). Vo has been changed by the battery, so Vo = 1.5 V. The new membra...
by Qroid_montreal
Tue Jul 23, 2013 4:20 pm
Forum: Other questions
Topic: Modeling a neuron in a spatially smooth Ve
Replies: 5
Views: 2384

Modeling a neuron in a spatially smooth Ve

Hello, I'm a grad student trying to model the effects of spatially-distributed, time-varying charges on an action potential. To do this, I'm simulating the Mainen and Sejnowski layer V pyramidal neuron ( http://senselab.med.yale.edu/modeldb/showmodel.asp?model=2488 ) and changing the conductance in ...
by Qroid_montreal
Thu Aug 30, 2012 11:27 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Modeling dynamic extracellular fields
Replies: 19
Views: 9755

Re: Modeling dynamic extracellular fields

I made a toy model and confirmed that the stimulus is being read correctly. Both print statements and the List of stimulus vectors show the stimulus data. A print statement inside advance such as this: proc advance() { access SectionName print e_extracellular(.5) fadvance() } shows that only the las...
by Qroid_montreal
Tue Aug 21, 2012 5:44 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Modeling dynamic extracellular fields
Replies: 19
Views: 9755

Re: Modeling dynamic extracellular fields

Hi Ted. As always, thanks for your thoughtful reply. I'm coming back to this problem after a few months away. Briefly, I'm reading in data from an external file and playing it to e_extracellular in each segment. My problem is that while the whole file is being read, only the last line is being used ...
by Qroid_montreal
Fri Apr 20, 2012 5:26 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Modeling dynamic extracellular fields
Replies: 19
Views: 9755

Re: Modeling dynamic extracellular fields

Thanks again for the help. I'm encountering this problem. I'm using Matlab to generate extracellular potential traces as a function of xyz location and time. The extracellular potential for the center of each segment is then saved in a text file, and the data from this text file is then read with Ve...
by Qroid_montreal
Fri Apr 20, 2012 11:53 am
Forum: Getting started
Topic: Using a variable to set vector size - problem
Replies: 4
Views: 1864

Re: Using a variable to set vector size - problem

ted wrote:At the oc> prompt, type this
NtimeSteps-359
then press the "Enter" key.
What do you see?
-5.6843419e-14

Ah, I see. And Vector.resize(n) floors n, right? If so, is it generally a good technique to use n+0.5 when resizing?
by Qroid_montreal
Fri Apr 20, 2012 11:05 am
Forum: Getting started
Topic: Using a variable to set vector size - problem
Replies: 4
Views: 1864

Using a variable to set vector size - problem

I'm encountering the following problem when using a variable to resize a vector. Briefly I use scanvar() to read in a value, then use this to calculate NtimeSteps. As you can see, NtimeSteps is initially 359, but tmpvec.resize(NtimeSteps) results in a vector with 358 elements. When I set NtimeSteps ...
by Qroid_montreal
Wed Apr 18, 2012 1:21 pm
Forum: Other questions
Topic: Extracellular stimulation of cutaneus afferents
Replies: 7
Views: 3228

Re: Extracellular stimulation of cutaneus afferents

Say I want to store e_extracellular(0.5) for each section at each time point in another variable for later analysis, how would I do this? I'm confused how to access and store variables (range or otherwise) as the simulation runs. As always, many thanks.
by Qroid_montreal
Tue Apr 17, 2012 6:31 pm
Forum: Other questions
Topic: Extracellular stimulation of cutaneus afferents
Replies: 7
Views: 3228

Re: Extracellular stimulation of cutaneus afferents

ted wrote: Have you verified that they play their values into the corresponding instances of e_extracellular in the course of a simulation?
What are the general ways to do this? If I'm playing a vector to e_extracellular, how would I access e_extracellular(t) for each section and each time point?
by Qroid_montreal
Thu Apr 12, 2012 2:54 pm
Forum: Getting started
Topic: Multiple hoc files, single model
Replies: 1
Views: 1546

Multiple hoc files, single model

Beyond conceptual clarity, is there a motivation to split hoc code into multiple hoc files? For example, could all the hoc files found in the example here (http://www.neuron.yale.edu/phpBB/viewto ... f=28&t=168) be combined without affecting the implementation of the model?
by Qroid_montreal
Thu Apr 12, 2012 12:00 pm
Forum: Other questions
Topic: "Extracellular stimulation and recording" - question
Replies: 1
Views: 1931

"Extracellular stimulation and recording" - question

I have a question about the Extracellular Stimulation and Recording post in the Hot Tips forum (https://www.neuron.yale.edu/phpBB/viewtopic.php?f=28&t=168). The post says that there are two approaches to extracellular stimulation. One is to introduce into the cable equation a current term that's equ...
by Qroid_montreal
Wed Apr 11, 2012 6:03 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Modeling dynamic extracellular fields
Replies: 19
Views: 9755

Re: Modeling dynamic extracellular fields

Thanks so much. NEURON is a fantastic tool, and a big part of that is how helpful (and patient) this forum is. Thanks again. I'll let you know how it goes.
by Qroid_montreal
Tue Apr 10, 2012 5:54 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Modeling dynamic extracellular fields
Replies: 19
Views: 9755

Re: Modeling dynamic extracellular fields

Back to your original question: all you have to do to simulate the effect of an extracellular field on a NEURON model is to insert the extracellular mechanism into the model's sections, then drive each segment's e_extracellular with a signal that corresponds to the time course of extracellular pote...
by Qroid_montreal
Tue Apr 10, 2012 12:40 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Modeling dynamic extracellular fields
Replies: 19
Views: 9755

Re: Modeling dynamic extracellular fields

In your example, is Vm=0 precisely because there's no current flowing across the membrane? So there's no voltage drop because V=IR=0 - is that right?

Thanks a lot. The approach in the link looks very explicit. I'm working on that now.