Search found 43 matches

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: 7448

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: 7057

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: 7057

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: 7057

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: 7057

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: 7057

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: 9038

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: 9038

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: 9038

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: 9038

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: 9038

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: 6118

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...
by fabien tell
Mon Mar 14, 2016 1:46 pm
Forum: Anatomically detailed models
Topic: setting non uniform conductances in a section
Replies: 6
Views: 6118

Re: setting non uniform conductances in a section

Hello Ted, You're right. I tried to specific non uniformity in several section in my hoc code but it does work only for the first one. For the second section I get a median conductance of 1500 !!! create dend1 create DSI dend1 : I don't have to write "access" do I ? {nseg=9 L=40 diam=2 Ra = 150.0 cm...
by fabien tell
Mon Mar 14, 2016 11:14 am
Forum: Anatomically detailed models
Topic: setting non uniform conductances in a section
Replies: 6
Views: 6118

Re: setting non uniform conductances in a section

Hello again, By the time I posted the previous message I tried this and it seems to be working well : create DSI access DSI DSI { nseg=9 L=50 diam=1.5 Ra=150 cm=1 insert Na12 ena=60 } forsec "DSI" for (x,0) {gbar_Na12(x)=(950*x)} /* in fact "x" is is the "length" (the position?) of a negative seg (0...
by fabien tell
Mon Mar 14, 2016 9:06 am
Forum: Anatomically detailed models
Topic: setting non uniform conductances in a section
Replies: 6
Views: 6118

setting non uniform conductances in a section

Hello, I'm trying to set an non uniform conductance in a section. I read the "Specifying parameterized variation of biophysical properties" tutorial but I did not want to use the cell builder system. I need to put a statement in my hoc files. As suggested in the tutorial, I've tried the following bu...