Search found 25 matches

by mzenker
Mon Oct 08, 2018 8:44 am
Forum: Getting started
Topic: The math behind extracellular mechanisms
Replies: 21
Views: 16991

Re: The math behind extracellular mechanisms

Hi, this is an old thread, but the subject isn't... ;) Proceeding from the outside in, the potentials at the ith nodes are vext[1]_i, vext_i, and v_i + vext_i. (...) - v_i * cm*D + vext_i * (cm + xc)*D - vext[1]_i * xc*D = vext_i-1 * (1/xraxial_i) - vext_i * ((1/xraxial_i) + (1/xraxial_i+1)) + vext_...
by mzenker
Tue Oct 02, 2018 9:21 am
Forum: Anatomically detailed models
Topic: Extracellular Fields
Replies: 29
Views: 24878

Re: Extracellular Fields

Hi Ted, thank you for clarifying this! I will reconsider the other approach, but I will probably stay with this one, because * it is rather simple to implement, * it works for me so far, * my model is rather small (~950 sections at the moment - I imagine that networks of neurons have much more secti...
by mzenker
Mon Oct 01, 2018 4:18 am
Forum: Anatomically detailed models
Topic: Extracellular Fields
Replies: 29
Views: 24878

Re: Extracellular Fields

Hi Ted,

the file is in the zip archive here: http://www.neuron.yale.edu/ftp/ted/neuron/ecstim.zip
The code is shown and described in the 7th post in this thread (I cannot make an exact URL here since it has no subject).

Thank you,
Matthias
by mzenker
Thu Sep 27, 2018 5:59 am
Forum: Anatomically detailed models
Topic: Extracellular Fields
Replies: 29
Views: 24878

Re: Extracellular Fields

Hi, I have found the information in this thread very useful to set up a model with extracellular stimulation by a potential. Now I have a simple (?) question. In the setstim() procedure, there is a vector list veclist which is filled with the stimulus vectors. Apparently this list is just filled and...
by mzenker
Tue Sep 25, 2018 6:56 am
Forum: Anatomically detailed models
Topic: Extracellular Fields
Replies: 29
Views: 24878

Re:

For people reading this thread: The topic referenced by Ted in the 3rd post is now under viewtopic.php?t=168.

Matthias
by mzenker
Mon Sep 24, 2018 7:47 am
Forum: Getting started
Topic: Single node with McIntyre equations fires without stimulus
Replies: 9
Views: 2324

Re: Single node with McIntyre equations fires without stimulus

Hi Ted, thank you for yet another informative message and pedagogical challenge! ;) I am not sure if this was to be expected, however... If we could predict everything, there would be no need to do any experiments of any kind (including experiments on computational models). Agreed. However, it is us...
by mzenker
Fri Sep 21, 2018 6:02 am
Forum: Getting started
Topic: Single node with McIntyre equations fires without stimulus
Replies: 9
Views: 2324

Re: Single node with McIntyre equations fires without stimulus

Hi Ted, thank you very much for your helpful message. I have learned more about NEURON and about my case. I have done what you suggested. I have created a file changeparams.hoc containing the following code: node[0] { xraxial[0]=1e9 Ra = 1e9 //Ra=rhoa/10000 } MYSA[0] { xraxial[0]=1e9 Ra = 1e9 //Ra=r...
by mzenker
Thu Sep 20, 2018 4:15 am
Forum: Getting started
Topic: Single node with McIntyre equations fires without stimulus
Replies: 9
Views: 2324

Re: Single node with McIntyre equations fires without stimulus

Hi Ted, thank you for your message. Perhaps I was not clear enough in my description of what I have done. I have downloaded the McIntyre et al. source code from the ModelDB and run it with NEURON. If I don't change anything in the model, I see zero activity, i.e. a flat line at -80 mV when the stimu...
by mzenker
Wed Sep 19, 2018 7:34 am
Forum: Getting started
Topic: Single node with McIntyre equations fires without stimulus
Replies: 9
Views: 2324

Re: Single node with McIntyre equations fires without stimulus

Hi Ted, thank you for your answer. I have now checked again that the Parameters are the same - as far as I use the McIntyre model, i.e. as far as the node and the axnode mechanism is concerned. Of course the model by McIntyre et al. is more complex, as it contains many nodes and also explicitly mode...
by mzenker
Mon Sep 17, 2018 11:30 am
Forum: Getting started
Topic: Single node with McIntyre equations fires without stimulus
Replies: 9
Views: 2324

Single node with McIntyre equations fires without stimulus

Hi, I am new to NEURON and want to reproduce a model found in a paper by Mercadal et al (2017) http://stacks.iop.org/0031-9155/62/i=20/a=8060 . They say they use a model for a myelinated axon where the behaviour of the nodes is described by the equations by McIntyre (2002). I have found the correspo...