Search found 18 matches

by Kim Ha
Tue Sep 17, 2013 9:56 am
Forum: Getting started
Topic: Creating asymmetry in a model
Replies: 1
Views: 1127

Creating asymmetry in a model

Ted Thanks for your help in automating the process. Now I am stuck at created asymmetry in my model. I have tried to reproduce " Neurokinematic modeling of complex swimming patterns of the larval zebrafish" from Scott A. Hill I could did it pretty well. Just for information I used NetStim (Artificia...
by Kim Ha
Thu Aug 08, 2013 6:02 am
Forum: Getting started
Topic: Neuron for Mac version 10.8.4
Replies: 4
Views: 1822

Re: Neuron for Mac version 10.8.4

Ted and Hines,
The dmg file I am using is nrn-7.3.x86_64-apple-OSX10.7.dmg.
by Kim Ha
Wed Jul 24, 2013 7:35 pm
Forum: Getting started
Topic: Neuron for Mac version 10.8.4
Replies: 4
Views: 1822

Neuron for Mac version 10.8.4

Hi Ted, I try to set up Neuron for my new Macbook. The following appear in neuron command window Last login: Thu Jul 25 06:30:43 on ttys000 wirelessprvnat-172-16-214-72:~ hapham$ cd ; clear; cp .nrn_as2sh /tmp/nrn_as2sh$$; sh /tmp/nrn_as2sh$$;rm -f /tmp/nrn_as2sh$$ ; exit -e NEURON -- Release 7.3 (8...
by Kim Ha
Wed Jul 24, 2013 12:34 pm
Forum: Getting started
Topic: parameter values and the resulting equations
Replies: 1
Views: 1267

parameter values and the resulting equations

I have a question about the resistance of neuron membrane. According to the cable equation:
rm = R/(2pia)
cm = C2pia
where a is the axon radius, when I change 'a' in the model, will rm and cm change automatically with 'a' by the above equation in Neuron?
by Kim Ha
Mon Jul 22, 2013 7:22 pm
Forum: Getting started
Topic: Changing the properties of cells
Replies: 1
Views: 1103

Changing the properties of cells

Hi Ted, To change Ra of all cells in my model, I excute the following code: for i=0, cells.count()-1 { Ra = 100 } However the spike train does not change (note that when I open the hoc file by txt, change the value there and save, the spike train changes). Can you show me my problem? To change the p...
by Kim Ha
Sat Jul 20, 2013 12:28 pm
Forum: Getting started
Topic: Input a vector to neuron
Replies: 7
Views: 4250

Re: Input a vector to neuron

Ted, For the first test, the following appears: NEURON -- Release 7.3 (849:5be3d097b917) 2013-04-11 Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013 See http://www.neuron.yale.edu/neuron/credits /cygdrive/c/Windows/system32 0 oc> For the second test, the command window prints the followi...
by Kim Ha
Wed Jul 17, 2013 8:54 pm
Forum: Getting started
Topic: Cannot see all cell names in NetGUI window
Replies: 1
Views: 1300

Cannot see all cell names in NetGUI window

Hi Ted, I am building a model of 61 cells. After finishing cell builder, I open Network Builder window. However, I am not able to see all my cell names in that window and cannot scroll up and down the page. I also try several things like view=plot or zoom in and out , but they do not help. Can you s...
by Kim Ha
Wed Jul 17, 2013 10:52 am
Forum: Getting started
Topic: Input a vector to neuron
Replies: 7
Views: 4250

Re: Input a vector to neuron

Ted, I have tried saving all files in a folder. In my init_fishmodel.hoc I have: load_file("nrngui.hoc") load_file("fishmodel.hoc") load_file("initrun_fishmodel.hoc") load_file("wtdel.hoc") But the program cannot find fishmodel.hoc, initrun_fishmodel.hoc and wtdel.hoc. Therefore, I have to wirte the...
by Kim Ha
Tue Jul 16, 2013 7:56 pm
Forum: Getting started
Topic: Fitting experimental model and simulation model
Replies: 1
Views: 1095

Fitting experimental model and simulation model

Hi Ted, I have built a network model of fish. The spike train obtained by this model was then analyzied and compared with the real fish. At first, the artifitial model and the real one did not fit each other. Then I tried to change some parameters, such as: synaptic weight, delay time, length, resis...
by Kim Ha
Tue Jul 16, 2013 2:10 pm
Forum: Getting started
Topic: Input a vector to neuron
Replies: 7
Views: 4250

Re: Input a vector to neuron

Thank you for your instruction. I got your idea. Actually, I was working on the same thing as yours. I save delay and weigh to two text files and then scan them to neuron files. The code looks like the following: //Note to open ha.dat file need to change the directory to the position we save the fil...
by Kim Ha
Mon Jul 08, 2013 7:23 pm
Forum: Getting started
Topic: Input a vector to neuron
Replies: 7
Views: 4250

Input a vector to neuron

Hi Ted, 1. I am trying to input a vector which has two column, one is synaptic weight and one is delay time, to Neuron. This vector is created by Matlab and is saved as .txt file. However, I am not able to open it in Neuron. I also find that the vector with one column can be openned. What should I d...
by Kim Ha
Mon Jul 08, 2013 12:07 am
Forum: Getting started
Topic: How to export the spike train data from .ses file to matlab
Replies: 10
Views: 6590

Re: How to export the spike train data from .ses file to mat

Hi Ted,
Yes I am able to save all spike times to a file now.
by Kim Ha
Fri Jul 05, 2013 1:51 am
Forum: Getting started
Topic: How to export the spike train data from .ses file to matlab
Replies: 10
Views: 6590

Re: How to export the spike train data from .ses file to mat

Hi Ted, I have rechecked my code and found many silly mistakes. I have fixed my code: oc>objref f2 oc>for i=0, 4 { oc>sprint(name, "%d", idvec.x[i]) oc>f2 = new File("name") oc>f2.wopen("name") oc>for j=0, tvec.size()-1 { oc>f2.printf("%f\n", tvec.x[j]) > oc>} > oc>f2.close() > oc>} oc>run() However...
by Kim Ha
Wed Jul 03, 2013 8:04 pm
Forum: Getting started
Topic: How to export the spike train data from .ses file to matlab
Replies: 10
Views: 6590

Re: How to export the spike train data from .ses file to mat

Hi Ted, I got your idea. Instead of saving the spike trains of all cells in a same file, I now want to save them separately. For example, "cell1.txt" contains the spike train of the cell 1 only and "cell2.txt" contains the spike train of cell 2 only and so on. Therefore, I use string to name the fil...
by Kim Ha
Tue Jul 02, 2013 2:53 pm
Forum: Getting started
Topic: How to export the spike train data from .ses file to matlab
Replies: 10
Views: 6590

Re: How to export the spike train data from .ses file to mat

Hi Ted, Your instruction is quite clear. I got the code worked but not automatically. I execute the following code to export the data to a file: oc>objref f1 oc>f1 = new File("cell3.txt") oc>f1.wopen("cell3.txt") 1 oc>for i=0, tvec.size-1 nil { > oc>f1.printf("%f\t%d\g", tvec.x[i], idvec.x[i]) > oc>...