www.neuron.yale.edu

Thanks again Ted

Have a good day.

Fabien

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 ...

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...

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 ...

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...

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...

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 : "...

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...

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...

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(...

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...

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...

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"...

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...

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