Search found 52 matches

by csh
Fri Dec 14, 2007 3:08 pm
Forum: Anatomically detailed models
Topic: current is zero in some segments
Replies: 14
Views: 6394

So, then I should also use the axial resistance in the middle as well? The specific axial resistance Ra is a section variable that is constant throughout a section. There is a helper function called ri(x) that makes it easier to calculate the axial resistance between two adjacent nodes ( http://www...
by csh
Fri Dec 14, 2007 2:47 pm
Forum: Anatomically detailed models
Topic: current is zero in some segments
Replies: 14
Views: 6394

From reading the User's Forum posts, I thought the correct way to calculate currents was to measure voltages at each end of a segment and use the axial resistance in that segment. Is that incorrect? If you literally mean the beginning and end of one and the same segment, this is wrong, because volt...
by csh
Fri Dec 14, 2007 1:24 pm
Forum: Anatomically detailed models
Topic: current is zero in some segments
Replies: 14
Views: 6394

steps_per_ms = 1 dt = 1e-2 This will result in a very low resolution of your plots. Try dt = 1e-2 steps_per_ms = 1/dt to plot 1 point per time step. ra = 100 hoc is case-sensitive. Axial resistance is R a . rm = 30000 rm is not a valid hoc keyword. If you use the pas mechanism for passive (leak) co...
by csh
Tue Dec 11, 2007 7:13 am
Forum: Getting started
Topic: conductance distribution
Replies: 3
Views: 2576

Re: conductance distribution

create A A {L=100 diam=20 nseg=7} By specifying nseg =7, section A will have exactly 7 segments, no more and no less. Each of these segments will have one node at its midpoint "at which the voltage of the segment is defined", to cite from chapter 5 of the NEURON book. Although there are also termin...
by csh
Fri Oct 05, 2007 12:28 pm
Forum: Getting started
Topic: Classical Cable Theory
Replies: 3
Views: 7492

Re: Classical Cable Theory

I have a question on defining electrotonic distance in the classical cable theory and in NEURON. An excellent introduction to cable theory is given in chapter 4 of Johnston & Wu, "Foundations of Cellular Neuropysiology", MIT Press, Cambridge, 1995. All your questions are answered within a few pages...
by csh
Wed Aug 29, 2007 5:41 am
Forum: Other questions
Topic: If statement, throw an error
Replies: 5
Views: 4025

With regard to the opening post, I find it strange that we don't see, "I won't print because of the assignment" on the command line because the variable test is successfully assigned. The assignment operator (=) returns the result of the assignment in hoc, C and C++ so that you can use chainings su...
by csh
Tue Apr 10, 2007 6:01 am
Forum: UNIX/Linux
Topic: Compiling NEURON/interviews in UBUNTU
Replies: 7
Views: 11628

sudo apt-get install gnome-devel (if you use gnome. with kde: kde-devel). If this doesn't help use as well: sudo apt-get install x-dev That should work! happy hacking, Philipp I recently ran into the same problems in Ubuntu (feisty). Although I thought I had installed every single x-development pac...
by csh
Tue Jan 30, 2007 3:54 am
Forum: The GUI
Topic: How to record data from the graph to text file ??
Replies: 7
Views: 11190

Re: How to record data from the graph to text file ??

I was examining the electrotonic properties, especially "V(measure)/V(inject) ", of a model cell with the Impedance tool and I could see the results in "LogAvsX[0]" window. However, I couldn't find the way to record all results to the text file for further analysis. Is there any way to do so? A get...
by csh
Fri Jan 26, 2007 12:42 pm
Forum: Getting started
Topic: some calclulation
Replies: 4
Views: 3515

ted wrote:What is an ADP?
An Afterdepolarization, I assumed.
by csh
Fri Jan 26, 2007 8:20 am
Forum: Getting started
Topic: some calclulation
Replies: 4
Views: 3515

Re: some calclulation

Is there any way to calculate the area under the curve of an ADP using NEURON? You could record voltage into a Vector during simulation, subtract the baseline, and then calculate the integral using integral record is described here: http://www.neuron.yale.edu/neuron/static/docs/help/neuron/general/...
by csh
Fri Jan 26, 2007 2:44 am
Forum: UNIX/Linux
Topic: Running NEURON on AIX 5.1/PowerPC
Replies: 2
Views: 3305

If anyone encounters similar problems, here is a short follow-up: Michael Hines helped me sort out this problem. I had to explicitly disable shared libraries during configure, so here is what I did: ./configure --prefix='pwd' --disable-shared --without-x --without-nrnjava As far as I tested it, ever...
by csh
Thu Jan 25, 2007 10:58 am
Forum: UNIX/Linux
Topic: Running NEURON on AIX 5.1/PowerPC
Replies: 2
Views: 3305

Running NEURON on AIX 5.1/PowerPC

Hi, has anyone ever tried to run NEURON on AIX (more specifically, AIX 5L 5.1)? I can configure and make NEURON 6.0.821, however, when I try to run it, I get a Segmentation fault(coredump) right away (both with ./nrniv and ./special). I have configured as follows: ./configure --without-x --without-m...
by csh
Thu Jan 18, 2007 11:32 am
Forum: Adding new mechanisms and functions to NEURON
Topic: AMPA, NMDA, GAMBAa NOT COMPÄ°LE CVODE ERROR
Replies: 3
Views: 4522

Re: AMPA, NMDA, GAMBAa NOT COMPÄ°LE CVODE ERROR

hi, all friends i download mr. Alain Destexhe's publication's demo file BAKCP.zip but i can't compile with NEURON 5.9 and i have errors folowing error code in NEURON 5.9 best regard I'm searching for the same file, anybody has the link? Direct link to the file: http://cns.iaf.cnrs-gif.fr/files/BACK...
by csh
Thu Jan 04, 2007 7:13 am
Forum: Other questions
Topic: Missing variable in Imp1
Replies: 1
Views: 2533

Missing variable in Imp1

Hi, while using the "Imp1" wrapper class defined in share/lib/hoc/impedanc.hoc, I found that extended was used in Imp1.compute() without having been declared. Adding it to the public member list and initializing it to 0 in init() made the class work fine. Did I make a mistake while using the class o...
by csh
Fri Sep 29, 2006 10:24 am
Forum: Anatomically detailed models
Topic: collapse a dendritic tree
Replies: 17
Views: 14972

First of all, Michael Hines' solution of introducing a Vector seems a lot more elegant than mine, because appending elements will update the Vector's size and n_comp automatically. I have therefore changed my code accordingly: // Modified 09/28/06, CSH------------------------------------------------...