www.neuron.yale.edu

* the setup works fine in regular neuron

Hi all, We are trying to use the updated vecStim mechanism to run simulations in CoreNEURON. Unfortunately the simulation fails with an error message saying that POINTER is not pointing to voltage or mechanism. We have localized the error to the pointer in the vecStim mechanism (since the error goes...

Hi, I get a segmentation error when running multiple version of the same simulations (with different parameters) in parallel on a super computer (Beskow; PDC; Royal Institutet of Technology; Stockholm). I only get the error when I use the tvec argument of the Vector.record() method: vdest.record(var...

I only have one NetCon per synapse so that would be adequate, yes. I'm also not pointing to the weight of the NetCon object but to the current of the synapse itself. e.g. from neuron import h def cell insert synapses (in some segments) insert spikeMonitor (in all sections) for sec in h.allsec(): for...

Well, probably not. I use "fake" as pointer target for segments not containing synapses.
That is they are pointed back to themselves...

Hi all, I have a model with a detailed morphology that I drive with synaptic input (of Exp2syn type). I would now like to visualize the synaptic activation in a animation/movie, i.e. map the synaptic current onto the morphology over time. Is there a best practice for this? I have made a clumsy quick...

I'm still puzzled about what it was you got from Ubuntu's Software Center; will look into this. I have now reinstalled NEURON using the .deb file. The reason why I thought I got it trough the Software Center the first time is because when clicking on the link to the deb package you are asked if you...

By any chance did you install one of these "Debian Science" packages--the "Debian Science packages for modeling of neural systems", or maybe "Simulator-independent specification of neuronal network models" ? I don't remember unfortunatelly. I will reinstall NEURON usin...

Are you sure you got it from Ubuntu's Software Center, or did you pick up a .deb file from http://www.neuron.yale.edu/neuron/download ? I'm not sure - I might have picked up a .deb file. I sure started at your official page anyhow. This is the information text about NEURON in software center: iclas...

I have now modified my first swc morphology so that the end point is defined as an end point istead of a dendrite: # Original file 050803d_finaltrace.swc edited by Duncan Donohue using StdSwc version 1.31 on 3/4/08. # Irregularities and fixes documented in 050803d_finaltrace.swc.std. See StdSwc1.31....

Thanks for taking time testing my swc morphologies! In each case, NEURON's Import3d tool reported problems, but it did the right thing. Here are the comments that hoc printed to the terminal: ... The comments is not the same as the ones I get when importing. I get the following message: Notice: ./mo...

If you only want the distance of the sections' 1 ends from the reference point, just use forall print secname(), " ", distance(1) and be done with it--no need to find the distance to the 0.5 location and then add L/2. Agreed, much better. d = |a - b| = sqrt( (xa-xb)^2 + (ya-yb)^2 + (za-zb...

Ok I think we are getting somewhere. In general the distance I would expect for an arbitrary single branch structure in absolute coordinates connected to the mid point of the soma (i.e. we only count the dendritic length) is: sum( norm( [x(i), y(i), z(i]) - [x(i-1), y(i-1), z(i-1)]) That is if we ha...

First of all, thank you for the fast reply - to have a living forum at disposal is fantastic! Do the new results make sense? It make perfect sence, thank you. An ambiguous statement... I realise I did not give enought detailes in the introduction of the question. I have not specified nseg so there i...

If all you need is distance from the soma, there is no need for SectionRef or all the elaborations discussed in that thread. Just set a reference point for distance measurements (decide whether it is to be the 0 or 1 end of soma, or maybe soma's midpoint), then use forall for (x,0) { rangevar(x) = ...