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Hello, I am importing a 3d morphology using the Import 3D tool. When I import I get an error: Main branch starting at line 657 is outside the soma bounding boxes Making a logical connection to center of nearest soma I then get a "Possible root branch errors" dialog box that says" Defa...

Oh, and is there also a way to put a label by the dot that says the location such as "dend[49](0.64)"

Thanks!

I am placing synapses on a realistic dendritic morphology via .hoc code for example: objref syn1 access dend[49] syn1 = new AlphaSynapse(.928571) // place a synapse //syn1 = new AlphaSynapse(0.642857) syn1.get_loc() syn1.onset = 1 // ms syn1.tau = 5 // ms syn1.gmax = .001 // uS syn1.e = 0 // mV Then...

Hi Ted, Sorry to rehash this again, but I think the max mechanism you posted on this thread on Sep 3 to find the maximum epsp isn't quite right. I didn't notice it before due to a bug I had in my code. I think the mechanism is finding the epsp amplitude at all segments of the dendritic tree at the l...

I am attempting to build a model via the gui. I would like to use the ion channels from the Mainen and Sejnowski (1996) paper (called patdemo on modelDB). I can see the ion channel mechanisms in the 'Specify Strategy' under Biophysics in the Cell Builder. As an example, when I choose to insert na (b...

I have a cell with 68 sections: a soma section and dend sections 0 though 66. I want to plot a voltage trace at various places in the dendrites. When I open 'plot what' in the graph menu in order to choose the sections I want to see only a few sections show up in the menu: dend[0]. dend[1]. dend[2]....

I am wondering if there is anyway to reopen a cell builder to an already built cell. For example, say "you" build a cell and run it. You are tweaking the parameters in the cell and rerunning to see what the effects are on the cell. Then you accidently close the cell builder and want to reo...

Also I would like to put the maximum epsp amplitudes in a vector so that I can take the .max and .min of the vector in order to automatically set the scale of my ShapePlot. I think I need something like the following but I can't quite get it right: //put the max amplitute epsp of every segment and s...

Hi Ted, I am trying to get the hoc commands working to plot the max mechanism using the PlotShape commands. Currently I have: objref sh sh = new PlotShape() sh.variable("max") sh.scale(some number, other number) This brings up a ShapePlot with the appropriate variable (max). However, the c...

Ted, I finally get it! I neglected to mention that all this time I had been repeatedly reading the Programmers Reference I just didn't understand it. Here is a summary of the distance function that is a bit more clear for me-- perhaps it will help someone else that maybe as confused as I was: Two st...

With regard to distance(), I was trying to play with a simple model to figure out what is going on: create axon access axon {nseg = 5 L=1000} for (x) print x, distance(0,x) Here the output is: 0 0 0.1 0.1 0.3 0.3 0.5 0.5 0.7 0.7 0.9 0.9 1 1 When I do for (x) print x, distance(1,x) The output is 0 10...

Sorry Ted, I don't quite get it--sorry to be so slow on the uptake. Are you saying that I can run your original code but then add a 'forall insert max' at the bottom (after compiling the max.mod file) and then a set of graphing commands? Or am I supposed to use the code I altered (which also errored...

Thank you, this was very helpful to get me started. I do have a couple more questions. I succeeded in getting your code working on my own morphologies. However I am trying to tweak the code to do something similar and I realize I don't understand some things. The code you provided creates a plot of ...

Hi Ted,

I would like to plot a graph much like figure 4D in your paper "Transfer impedance and synaptic integration". I can't find that code on modelDB. Is there a way I can get a hold of it, or do you know of another code that does similar things I can take a look at?

Thanks!
Corinne

I would like to resurrect this thread with a closely related question. In the Mainen & Sejnowski model, I was curious if the spiking behavior would be similar if I scaled up the size of the small L3 Aspiny neuron (lcAS3.hoc in the demofig1.hoc code), so that its surface area was equal to that of...