Search found 12 matches

by edaneshi
Tue Feb 13, 2018 3:01 am
Forum: NEURON + Python
Topic: Updating extracellular values for all segments!
Replies: 7
Views: 2047

Re: Updating extracellular values for all segments!

That's true. Thank you for your comment and help Dr. Carnevale.
by edaneshi
Mon Feb 12, 2018 1:41 pm
Forum: NEURON + Python
Topic: Updating extracellular values for all segments!
Replies: 7
Views: 2047

Re: Updating extracellular values for all segments!

Thank you Dr. Hines,

It works perfectly now! Thank you for your time and help!

Side note to other Neuron users: You may need to use "mknrndll" tool to recompile some of your mod files before you can run your models with the new version of Neruon!
by edaneshi
Sun Feb 11, 2018 9:00 pm
Forum: NEURON + Python
Topic: Updating extracellular values for all segments!
Replies: 7
Views: 2047

Re: Updating extracellular values for all segments!

Great! Thank you Dr. Hines for the fix.
Just a novice question. How should I update this NEURON file on a MAC? Should I uninstall Neuron and reinstall it with the MAC installer tool?
Is the NEURON installer package also updated?

Thank you!
by edaneshi
Sat Feb 10, 2018 7:21 pm
Forum: NEURON + Python
Topic: Updating extracellular values for all segments!
Replies: 7
Views: 2047

Re: Updating extracellular values for all segments!

I should also mention that I could set the xraxial values for each segment individually in a for loop: h.finitialize() for seg in Soma: seg.xraxial[0]=100 print(seg.xraxial[0], seg.xraxial[1], seg.diam) h.psection(sec=Soma) and I get the following results: 100.0 1000000000.0 500.0 100.0 1000000000.0...
by edaneshi
Sat Feb 10, 2018 6:52 pm
Forum: NEURON + Python
Topic: Updating extracellular values for all segments!
Replies: 7
Views: 2047

Updating extracellular values for all segments!

Dear Ted, I created a section in Python with 7 segments and inserted an extracellular mechanism. Soma=h.Section() Soma.nseg=7 Soma.insert('extracellular') Soma.xraxial[0]=100 Soma.xg[0]=1e10 Soma.xc[0]=0 However, when I print xraxial values for each segment, I see that only one segment's xraxial val...
by edaneshi
Sun Nov 06, 2016 6:04 pm
Forum: Getting started
Topic: How to make multiple segments with different length?
Replies: 5
Views: 6311

Re: How to make multiple segments with different length?

Dear Ted, Thank you for taking the time and helping me. Don't. Enforce a nonzero minimum length. So, let's assume that I have a long axon and I have a section (Length=L) in somewhere in the middle of my axonal model that I want to split it into two smaller sections. 1- All properties of these two se...
by edaneshi
Sat Nov 05, 2016 8:20 pm
Forum: Getting started
Topic: How to make multiple segments with different length?
Replies: 5
Views: 6311

Re: How to make multiple segments with different length?

Dear Ted, Thanks for your reply and help. I really appreciate it. However, I have a question regarding splitting my section into different sections. In my application, my initial intent was to change the diameter (and some other range variables) of part of a section(s) in my axonal model based on my...
by edaneshi
Fri Nov 04, 2016 7:18 pm
Forum: Getting started
Topic: How to make multiple segments with different length?
Replies: 5
Views: 6311

How to make multiple segments with different length?

Dear Ted, I was wondering if it is possible to have a section with multiple segments such that the length of each segment is not equal to the other segments's length? For example, let's assume that I have an internode section in my neuron model. Its length is 100um. I would like to have 5 segments. ...
by edaneshi
Wed Oct 21, 2015 2:18 pm
Forum: Getting started
Topic: what is the minimum value that can be assigned to a section
Replies: 3
Views: 5328

Re: what is the minimum value that can be assigned to a sect

Dear Dr. Carnevale, Thank you very much for your reply. Here I explain my rational for using this method and I would appreciate it if you could let me know which part is wrong: Each section is a cylinder in my model. As far as I know, the surface area in terminal nodes (x=0,1) is zero. Therefore, th...
by edaneshi
Tue Oct 20, 2015 10:01 pm
Forum: Getting started
Topic: what is the minimum value that can be assigned to a section
Replies: 3
Views: 5328

what is the minimum value that can be assigned to a section

Dears, I was wondering what is the minimum value that can be assigned to a section in NEURON without inducing computational problems? I want to model a kind of injury in neurons. I have a model of an axon with three (types) sections in internodal regions like this: Type 1 : A section with user-defin...
by edaneshi
Wed Aug 20, 2014 11:01 pm
Forum: Getting started
Topic: Recording Ionic concentrations
Replies: 1
Views: 2094

Recording Ionic concentrations

Dear Ted, I have a model of an axon with some membrane mechanisms (NMODL files of Fast K, Na and ...) added to that. In every NMODL file, I use "USEION x READ xi,xo,enx WRITE ix " to actually force NEURON keep track of ionic concentrations (xi,xo). These mechanisms are added to different sections of...
by edaneshi
Mon Aug 11, 2014 5:11 pm
Forum: Getting started
Topic: Recording membrane voltage along an axon
Replies: 1
Views: 1845

Recording membrane voltage along an axon

Dear Ted, I have made a simple model of an axon with 21 nodes. I use Clamp() to stimulate the first node of my axon. All nodes (and the same idea for internode) have similar properties (Passive + HH mechanisms). I recorded membrane voltage at all nodes (node[1].v(0.5),node[2].v(0.5),...). Surprising...