Search found 46 matches

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: 7995

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: 7995

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: 7995

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...
by fabien tell
Sun Feb 19, 2017 11:09 am
Forum: Adding new mechanisms and functions to NEURON
Topic: saving vectors to file
Replies: 7
Views: 7995

saving vectors to file

Hello, I need to automatically (through a Gui) save results of simulation. In this case, I need to save as a text file , a vector which is teh second derivative of an action potential against the time. I wrote this code which is launched after a compete run : // create objects to put Vectors : "spik...
by fabien tell
Mon Jun 13, 2016 11:02 am
Forum: Anatomically detailed models
Topic: tapered dendrites
Replies: 7
Views: 7636

Re: tapered dendrites

Hello Ted, Thanks again for you help. I read the suggested section and I read again the Book. I'd be a liar if I said that I understood everything well. It would take a bit of time to digest it. Anyway, I think I got the "potential artefact topic" explained in 5.5.3 section of the Book. In my model ...
by fabien tell
Fri Jun 10, 2016 2:52 am
Forum: Anatomically detailed models
Topic: tapered dendrites
Replies: 7
Views: 7636

Re: tapered dendrites

Hello Ted, Thanks for the advice. To check for correctness , I examined the shape plot at various magnification to see tapered dendrites and if it updates correctly; It seem to be Ok. I may also write diameters for some sections at the end of a run to be sure. Something I don't fully understand is w...
by fabien tell
Thu Jun 09, 2016 4:53 am
Forum: Anatomically detailed models
Topic: tapered dendrites
Replies: 7
Views: 7636

Re: tapered dendrites

Hello again, I just rewrote the code as suggested : proc celldef() { topol() subsets() geom() biophys() geom_nseg() diam_seg() } // I declared a new procedure called diam_seg create soma, dend1[3], dend1_1[3], dend2[5], SDI, SIprox, SIdistal create axon proc topol() { local i connect dend1(0), soma(...
by fabien tell
Thu Jun 09, 2016 3:30 am
Forum: Anatomically detailed models
Topic: tapered dendrites
Replies: 7
Views: 7636

Re: tapered dendrites

Hello Ted, Thanks a lot. To be sure I understood it well: I build the neuron's topology with the cell builder which is supposed to use 3D coordinates : proc celldef() { topol() subsets() geom() biophys() geom_nseg() } create soma, dend1[3], dend1_1[3], dend2[5], SDI, SIprox, SIdistal create axon pro...
by fabien tell
Wed Jun 08, 2016 11:43 am
Forum: Anatomically detailed models
Topic: tapered dendrites
Replies: 7
Views: 7636

tapered dendrites

Hello, I build a model by using the cell builder to generate the hoc code. I then altered it to get tapered dendrites but it does'nt seem to work. I did not get any errors and the model is running but when I check the geometry with the shape plot (show diam) tool ,; dendrites are not tapered. Here i...
by fabien tell
Fri Apr 01, 2016 3:04 am
Forum: Adding new mechanisms and functions to NEURON
Topic: recording the second derivative of an action potential
Replies: 13
Views: 9611

Re: recording the second derivative of an action potential

Thanks again TED, Actually, it's even easier if I simplify the code objref d2, g2 // d2 will contain derivative of i_cap, g2 will plot that vs. i_cap d2 = new Vector() // objref nil proc postprocess() { d2.deriv(icvec, dt) //if (g2==nil) { g2 = new Graph(0) //} else { //g2.exec_menu("Erase") // } d2...
by fabien tell
Tue Mar 29, 2016 11:05 am
Forum: Adding new mechanisms and functions to NEURON
Topic: recording the second derivative of an action potential
Replies: 13
Views: 9611

Re: recording the second derivative of an action potential

Hello Ted, I tried your solution. It works well. The only problem is that when I run "myrun ()" a second graph (the graph with the second derivative) is put on the screen with the same trace than the first one (which is blank before my run) then if I changed some parameters and do run plus my run th...
by fabien tell
Sat Mar 26, 2016 3:17 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: recording the second derivative of an action potential
Replies: 13
Views: 9611

Re: recording the second derivative of an action potential

Thanks a lot Ted,


I 'll try it after the long week end and I will post the (commented) code for others.

Have a good Easter day. Go easy on chocolate !!!

Regards

fabien
by fabien tell
Sat Mar 26, 2016 7:24 am
Forum: Adding new mechanisms and functions to NEURON
Topic: recording the second derivative of an action potential
Replies: 13
Views: 9611

Re: recording the second derivative of an action potential

Thanks again Ted, I therefore wrote this : load_file("nrngui.hoc") tstop=50 dt=0.025 celsius=32 v_init=-55 finitialize(v_init) create soma soma { nseg=1 L=35 diam=15 Ra = 150.0 cm=1 insert pasnts insert kdrDA gbar_kdrDA=100 insert Na12 Vmid_ac_Na12 = -35 gbar_Na12=250 insert ka gbar_ka=2 ena=60 ek=-...
by fabien tell
Fri Mar 25, 2016 6:08 am
Forum: Adding new mechanisms and functions to NEURON
Topic: recording the second derivative of an action potential
Replies: 13
Views: 9611

Re: recording the second derivative of an action potential

Hello, I've been trying to obtain the derivative of v at soma uisng the vectors but something is wrong since the terminal "tells" me that it is not possible to obtain a derivative with less than two points which is true. create soma soma { nseg=1 L=35 diam=15 Ra = 150.0 cm=1 insert pasnts insert kdr...
by fabien tell
Mon Mar 14, 2016 4:39 pm
Forum: Anatomically detailed models
Topic: setting non uniform conductances in a section
Replies: 6
Views: 6574

Re: setting non uniform conductances in a section

Thanks again Ted, I know that the colon is not a comment delimiter. It was just to highlight my question. Thank you for explaining to me the last point about the hoc code generated by the cell builder. I'll try it. And you're right (as usual), as a recorder player I didn’t learn everything from scra...