Search found 27 matches

by Sherif
Mon Mar 05, 2012 6:56 pm
Forum: Other questions
Topic: Finding a netcon through its target
Replies: 1
Views: 837

Finding a netcon through its target

Hi, I was given a model cell that has synapses (Exp2Syn type) and I want to calculate the synaptic conductance over that model cell. To do that, my strategy was the following: 1- for each section in the cell, find the pointprocesses of the Exp2Syn type 2- iterate over these PPs to: 2-1- find the net...
by Sherif
Mon Oct 24, 2011 4:19 pm
Forum: Other questions
Topic: Transfer impedance gives infinity?
Replies: 2
Views: 1645

Transfer impedance gives infinity?

Hi all, I have a model whose topology is a ball (soma) and several sticks (dendrites). I use the impedance class in order to calculate the electrotonic distance of each dendritic segment from the soma using the following code: finitialize(-65) zz = new Impedance() soma { zz.loc(0.5) } zz.compute($1,...
by Sherif
Tue Aug 23, 2011 12:51 am
Forum: Other questions
Topic: Recording soma potential in multiple cells using Cvode.recor
Replies: 3
Views: 1992

Re: Recording soma potential in multiple cells using Cvode.r

That's really a nice structure. The use of obfunc in conjunction with object lists handeled the vectors in a really easy way. Thanks, Ted!!!!
by Sherif
Fri Aug 19, 2011 7:21 pm
Forum: Other questions
Topic: Recording soma potential in multiple cells using Cvode.recor
Replies: 3
Views: 1992

Recording soma potential in multiple cells using Cvode.recor

Hi, I have a list of cell objects and want to record the somatic potential of each cell in the list. I wrote the following code to insert an IClamp in each cell and record Vsoma and injected current for further processing. However, I get a syntax error that I couldn''t figure out. Your help will be ...
by Sherif
Mon Jun 27, 2011 12:15 pm
Forum: Other questions
Topic: Input impedance
Replies: 5
Views: 2266

Re: Input impedance

Hi All,

Ted was able to fix the problem. The fix was placing an finitialize(-65) statement at the beginning of the Compute_Zin() procedure. This statrement was necessary for initializing the gating states properly.
by Sherif
Thu Jun 23, 2011 7:01 pm
Forum: Anatomically detailed models
Topic: Neurolucida to NEURON best practices?
Replies: 26
Views: 24444

Re: Neurolucida to NEURON best practices?

My question is relevant to this topic so I am posting my question here. We have been running into trouble viewing the soma of our 3D imported neuron created in Neurolucida into NEURON. Following the previous posts in this forum, we set all the soma contours to cell body as well as organizing them in...
by Sherif
Mon Jun 20, 2011 1:30 pm
Forum: Other questions
Topic: Input impedance
Replies: 5
Views: 2266

Re: Input impedance

psection() works fine before or after calling the impedance calculations. Also, finitialize(-65) works fine (prints 1 on the command line) with no error messages before or after the impedance calculations.
by Sherif
Thu Jun 16, 2011 5:41 pm
Forum: Other questions
Topic: Input impedance
Replies: 5
Views: 2266

Input impedance

Hi all, I used the following function to measure the input impedance of a neuron model; however, when I printed the variable Zin I got "nan". Any advice on what could be the reason for that? proc Compute_Zin() { localobj z z = new Impedance() soma { z.loc(0.5) } z.compute(1, 1) Zin = 0 soma { Zin = ...
by Sherif
Tue Oct 26, 2010 12:18 pm
Forum: Modeling networks
Topic: Saving the data of a spikeplot figure to external file
Replies: 1
Views: 1924

Saving the data of a spikeplot figure to external file

Hi, I have a network of 50 cells whose output is displayed as a raster of spikes in a Spikeplot graph. I want to save these data to an external .dat file. I found that when I use the "pick vector" tool it selects only the raster of one cell, not all cells. Is there a way to save these data for all c...
by Sherif
Wed Oct 08, 2008 3:57 pm
Forum: Anatomically detailed models
Topic: Problem in importing 3D data to Neuron
Replies: 2
Views: 2686

Problem in importing 3D data to Neuron

Hi, I am trying to import a 3D reconstructed morphology (.asc file) of a neuron using the 3D import tool in Neuron. After importing the file I got a message from Neuron on possible roon-branch errors in which it suggests connecting some branches to nearest soma. I looked at the values of these offse...
by Sherif
Mon Jun 16, 2008 11:33 am
Forum: Other questions
Topic: Accessing pointprocesses present in a section
Replies: 5
Views: 3371

Re: Accessing pointprocesses present in a section

Hi Ted, Wow. This is exactly what I wanted. Thanks Ted very much. It was not clear, at least for me, from the description of MechanismType Class that the created list will have the mechanisms available at the currently accessed section. I thought it will have the mechanisms available in all sections...
by Sherif
Fri Jun 13, 2008 4:08 pm
Forum: Other questions
Topic: Accessing pointprocesses present in a section
Replies: 5
Views: 3371

Accessing pointprocesses present in a section

Hi, I would appreciate your advice on how to access/modify the settings of a pointprocess object such as an Exp2Syn present in a section. In simple terms, I have a neuron model with many sections. Some of these sections have synapses (Exp2Syn), while others do not. I am iterating over the sections (...
by Sherif
Thu Mar 13, 2008 3:22 pm
Forum: Other questions
Topic: section stack overflow
Replies: 3
Views: 4028

Hello, I got the same error message "section stack overflow" and found where the recursive call of a function took place. Is there a way to increase the stack size over the 20 limit at least for now? I am in the middle of a project and rather to use the same code before going back and modify it. Tha...
by Sherif
Thu Mar 13, 2008 11:39 am
Forum: Other questions
Topic: Sectionlist as a vector of strings
Replies: 3
Views: 2615

Many thanks Ted.

One thing to confirm. When I say

Code: Select all

forsec "den" { .... }
the loop will iterate over sections whose names start with "den" according to their creation order not alphabetical order?
by Sherif
Wed Mar 12, 2008 1:06 am
Forum: Other questions
Topic: Sectionlist as a vector of strings
Replies: 3
Views: 2615

Sectionlist as a vector of strings

Hello, I have a sectionlist that has the names of more than 50 sections of my model. I want to iterate over the first 10 sections and run Statement 1, and the second 10 sections and run Statement 2, and so on. In other words, I want to know a way of using the sectionlist as a vector of strings that ...