Search found 17 matches

by rlindroos
Thu Feb 14, 2019 6:52 am
Forum: NEURON + Python
Topic: Driving synaptic event using vecStim
Replies: 21
Views: 9620

Re: Driving synaptic event using vecStim

* the setup works fine in regular neuron
by rlindroos
Thu Feb 14, 2019 4:45 am
Forum: NEURON + Python
Topic: Driving synaptic event using vecStim
Replies: 21
Views: 9620

Re: Driving synaptic event using vecStim

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...
by rlindroos
Mon Nov 12, 2018 10:43 am
Forum: Parallel NEURON
Topic: segmentation fault when recording specific time points into h.Vector
Replies: 1
Views: 1144

segmentation fault when recording specific time points into h.Vector

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...
by rlindroos
Wed Aug 22, 2018 2:17 am
Forum: NEURON + Python
Topic: Animation of synapse activation
Replies: 4
Views: 2200

Re: Animation of synapse activation

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...
by rlindroos
Tue Aug 21, 2018 12:33 pm
Forum: NEURON + Python
Topic: Animation of synapse activation
Replies: 4
Views: 2200

Re: Animation of synapse activation

Well, probably not. I use "fake" as pointer target for segments not containing synapses.
That is they are pointed back to themselves...
by rlindroos
Fri Aug 17, 2018 7:31 am
Forum: NEURON + Python
Topic: Animation of synapse activation
Replies: 4
Views: 2200

Animation of synapse activation

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...
by rlindroos
Tue Jan 21, 2014 7:25 am
Forum: Getting started
Topic: the distance() function
Replies: 18
Views: 9925

Re: the distance() function

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 rlindroos
Tue Jan 21, 2014 6:44 am
Forum: Getting started
Topic: the distance() function
Replies: 18
Views: 9925

Re: the distance() function

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 using the link you posted above an...
by rlindroos
Mon Jan 20, 2014 11:39 am
Forum: Getting started
Topic: the distance() function
Replies: 18
Views: 9925

Re: the distance() function

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...
by rlindroos
Mon Jan 20, 2014 11:10 am
Forum: Getting started
Topic: the distance() function
Replies: 18
Views: 9925

Re: the distance() function

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....
by rlindroos
Mon Jan 20, 2014 7:18 am
Forum: Getting started
Topic: the distance() function
Replies: 18
Views: 9925

Re: the distance() function

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...
by rlindroos
Fri Jan 10, 2014 12:26 pm
Forum: Getting started
Topic: the distance() function
Replies: 18
Views: 9925

Re: the distance() function

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)^2 ). Her...
by rlindroos
Fri Jan 10, 2014 7:03 am
Forum: Getting started
Topic: the distance() function
Replies: 18
Views: 9925

Re: the distance() function

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...
by rlindroos
Thu Jan 09, 2014 10:14 am
Forum: Getting started
Topic: the distance() function
Replies: 18
Views: 9925

Re: the distance() function

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...
by rlindroos
Wed Jan 08, 2014 5:16 am
Forum: Getting started
Topic: copy and use object reference (SectionRef) in function
Replies: 3
Views: 2219

Re: copy and use object reference (SectionRef) in function

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) = ...