Search found 43 matches

by fabien tell
Tue Aug 28, 2018 10:51 am
Forum: Anatomically detailed models
Topic: how to calculate section area
Replies: 5
Views: 502

Re: how to calculate section area

Hello again, I have a soma : L= 31 diam = 10 So according to I learned at school, the surface of a cylinder S= PI*diam*L (if we neglect the disk surfaces). With neuron I got : oc>soma {print L} 31 oc>soma {print diam} 10 oc>soma {print area(0.5)} 324.63124 By hand I got 3.14*10*31 = 31.4*31= 973.4 W...
by fabien tell
Mon Aug 27, 2018 11:25 am
Forum: Anatomically detailed models
Topic: how to calculate section area
Replies: 5
Views: 502

Re: how to calculate section area

Hello Ted,

Actually you're right; it works as it should. I mixed up with section names. Sorry for bothering....

Acting fast is sometimes the enemy of thinking !!!!

Thanks a lot
by fabien tell
Mon Aug 27, 2018 5:29 am
Forum: Anatomically detailed models
Topic: how to calculate section area
Replies: 5
Views: 502

how to calculate section area

Hello, I'd like to calculate areas of different sections. I've read the documentation and searched through the forum but it remains unclear to me. How do I use the the area () command ? I loaded a hoc file with full morphology then I tried this : soma { surface= area(0.5) print surface } axon { surf...
by fabien tell
Thu Aug 09, 2018 4:33 am
Forum: UNIX/Linux
Topic: upgrade problem in Ubuntu [SOLVED]
Replies: 3
Views: 830

Re: upgrade problem in Ubuntu [SOLVED]

Hello,

I found the solution by reading this excellent forum :

viewtopic.php?f=6&t=2636

It does work on ubuntu 18.0

Thanks again

Fabien
by fabien tell
Wed Aug 08, 2018 10:27 am
Forum: UNIX/Linux
Topic: upgrade problem in Ubuntu [SOLVED]
Replies: 3
Views: 830

Re: upgrade problem in Ubuntu

Hello Ted, Hope you're well. I used the deb file: nrn-7.5x86_64.deb. I did not get an error at this stage. It happens with any version (or flavour) of Ubuntu . If I try to install an old version (7.4 or before) I got an error on Ubuntu 18 (missing dependencies) but it works on previous release of Ub...
by fabien tell
Wed Aug 08, 2018 5:34 am
Forum: UNIX/Linux
Topic: upgrade problem in Ubuntu [SOLVED]
Replies: 3
Views: 830

upgrade problem in Ubuntu [SOLVED]

Hello, I tried to upgrade Neuron from 7.4 to the newest version under Ubuntu (14.10 or 18.10). The program installs without problem bu not my old programs don't work anymore I got error mistake when launching them : 64-linux_gnu_ld :cannot find -lncurses and so the libnrnlech.la file failed Did some...
by fabien tell
Fri May 04, 2018 11:21 am
Forum: Adding new mechanisms and functions to NEURON
Topic: firing frequency
Replies: 3
Views: 535

Re: firing frequency

Hello Ted, Thanks a lot. I'll try on monday. I should expect to get 7 time intervals on the screen, right ? Then if I need to send them into a file, I should proceed in the same way (using the right command of course). To get the average ISI,I only need to sum all the values and divide them by nbspi...
by fabien tell
Fri May 04, 2018 8:07 am
Forum: Adding new mechanisms and functions to NEURON
Topic: firing frequency
Replies: 3
Views: 535

firing frequency

Hello Ted, I know that this topic has already been addressed in the forum but despite many trials I couldn’t make it to work properly. So I have to "abdicate". I wrote the code thereafter. I got the correct number of spikes but I did not understant how to extract the timing from the netcon vector an...
by fabien tell
Wed Jan 31, 2018 9:39 am
Forum: Getting started
Topic: How to load and replace hoc files within a loop
Replies: 4
Views: 590

Re: How to load and replace hoc files within a loop

Thanks again Ted

Have a good day.

Fabien
by fabien tell
Wed Jan 31, 2018 5:45 am
Forum: Getting started
Topic: How to load and replace hoc files within a loop
Replies: 4
Views: 590

Re: How to load and replace hoc files within a loop

Thanks a lot Ted. I understand the idea. However, I thought it was possible to "destroy" the hoc file containing the topology of the cell (or any hoc file containing the biophysic) after a run by calling (loading) new hoc files (or by inserting a special instruction ?). You mean that if I intend to ...
by fabien tell
Mon Jan 29, 2018 10:12 am
Forum: Getting started
Topic: How to load and replace hoc files within a loop
Replies: 4
Views: 590

How to load and replace hoc files within a loop

Hello Ted, Hope everything is fine with you. I'm currently working using different morphological files (hoc files obtained form cell builder) from neurons to analyse the impact of morphology on cell firing. Each file contains a detailed morphology with similar topology by different length or diamete...
by fabien tell
Thu Feb 23, 2017 1:37 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: saving vectors to file
Replies: 7
Views: 5833

Re: saving vectors to file

Thanks again Ted, That's what I thought for the init and run button. You wrote Changing a section's nseg may destroy existing nodes and create new ones. That will break vector recording of range variables from the nodes that no longer exist, and of course nothing will be recorded from the new nodes ...
by fabien tell
Thu Feb 23, 2017 12:02 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: saving vectors to file
Replies: 7
Views: 5833

Re: saving vectors to file

Thanks you Ted, I managed to make it work. Th only minor problem I have is that I have to launch the simulation with init and run button, otherwise the file is empty.For example, I used to reinitialize the number of segments every time I altered geometry with a basic procedure proc geom_nseg() { for...
by fabien tell
Mon Feb 20, 2017 2:03 am
Forum: Adding new mechanisms and functions to NEURON
Topic: saving vectors to file
Replies: 7
Views: 5833

Re: saving vectors to file

Dear Ted, Thanks a lot for you prompt answer. If I understand well, I could use the same procedure to fill a file with three or more vectors assuming that I take into account the length problem you mentioned. For example, I could record in the same file the time, the action potential v trace , its f...