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Broken Voltage Grapher

Posted: Wed Dec 05, 2018 1:17 am
by DavidSwygart
Hello, I am new to NEURON and am having problems using the GUI to plot voltage. I have created a script (SWC_read.hoc) to load SWC morphology data and add synapses at specific locations and also record voltage from output synapse locations. As I go along, I have been using the GUI to run the simulation (Tools>RunControl) and plot voltage (Graph>Voltage axis), to ensure that my code is working like I think it should. Everything seemed to be working until I specified Ra. Now when I try to run the simulation, the graph does not plot anything but just creates a leftward diagonal line (see picture). The value for which I specify Ra doesn't seem to matter. Does anyone have any idea what might be going on?

Code: Select all

// Create Cell
objectvar bpc
objectvar Vout
bpc = new cellfromSWC("imageStack_GapsFilled.swc","RibbonIndices.txt","InhibitoryIndices.txt")

// Set Biophysics
forall insert pas
	forall g_pas = 0.000041668
	forall e_pas = -41
forall Ra = 24.5
forall Cm = 1.1
With Ra specified

With "forall Ra = 24.5" commented out

Re: Broken Voltage Grapher

Posted: Wed Dec 05, 2018 10:14 am
by ted
Diagnosing the problem will require being able to reproduce it. Zip up the files necessary to reproduce it
(see viewtopic.php?f=28&t=1048)
and email the zip file to
ted dot carnevale at yale dot edu
and I'll let you know what I find out.

Re: Broken Voltage Grapher

Posted: Wed Dec 05, 2018 12:33 pm
by DavidSwygart
Hello, thanks for your quick response. I have sent the code that I have been having trouble with. I now notice that when I reduce nseg to a lower value, the grapher doesn't work even without specifying Ra. So, I am very confused as to what is going on.

Re: Broken Voltage Grapher

Posted: Tue Dec 18, 2018 3:10 pm
by DavidSwygart
Just an update for anyone reading this. I was creating a cell using custom code that read data from an SWC file. I switched to importing the SWC information using the import3D tool and everything is working now.