Search found 17 matches

by Christine Chung
Fri May 07, 2021 1:54 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Questions about the extracellular mechanism and the syntax of NMODL
Replies: 4
Views: 361

Re: Questions about the extracellular mechanism and the syntax of NMODL

Thank you for your reply, but I'm still confused even after reading the comments. I am trying to initially compute the potential of the neuron segments by COMSOL and then insert the data I produced into this code. Then in what variable (ex_xtra or er_xtra), should I insert the data of potential I've...
by Christine Chung
Mon May 03, 2021 5:43 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Questions about the extracellular mechanism and the syntax of NMODL
Replies: 4
Views: 361

Questions about the extracellular mechanism and the syntax of NMODL

Hello, I'm trying to interpret hoc and NMODL files and have questions about some codes. The sentences below are the codes that I want to ask. This code came from https://senselab.med.yale.edu/modeldb/showmodel.cshtml?model=144589#tabs-1 ModelDB: Modulation of hippocampal rhythms by electric fields a...
by Christine Chung
Mon Jan 18, 2021 3:15 am
Forum: Anatomically detailed models
Topic: The effect of changed dt and steps_per_ms
Replies: 3
Views: 389

Re: The effect of changed dt and steps_per_ms

Thanks for your kind explanation. Also, I read the article you recommended. However, I still have a question. As you mentioned, The error of of the approximate solution is generally reduced if time and space are chopped into smaller pieces. ... f the spatial or temporal discretization is too fine, r...
by Christine Chung
Wed Jan 13, 2021 2:45 am
Forum: Anatomically detailed models
Topic: The effect of changed dt and steps_per_ms
Replies: 3
Views: 389

The effect of changed dt and steps_per_ms

Hello, I'm a graduate student who studied with NEURON. I conducted extracellular stimulation to anatomically realistic models via the code written by Ted, and investigated electric field thresholds (through apc.n, I checked somatic membrane polarized over 0 or not). However, there was difference in ...
by Christine Chung
Tue Dec 17, 2019 8:31 pm
Forum: Anatomically detailed models
Topic: Is there any way to bifurcate axon?
Replies: 3
Views: 1108

Re: Is there any way to bifurcate axon?

Sorry for URL.
Model accession : 2488

https://senselab.med.yale.edu/ModelDB/s ... ls/#tabs-1
This is working URL.

Thank you
by Christine Chung
Tue Dec 17, 2019 12:02 am
Forum: Anatomically detailed models
Topic: Is there any way to bifurcate axon?
Replies: 3
Views: 1108

Is there any way to bifurcate axon?

Hello,
I'm using 'Z. F. Mainen and T. J. Sejnowski (1996)'s model'
https://senselab.med.yale.edu/ModelDB/s ... ls/#tabs-1
I want to bifurcate axon and modify the angle at branching point.

Is there way to do it in GUI tools? or modify the 3D coordinate?

Thank you in advance.
by Christine Chung
Fri Aug 09, 2019 1:48 am
Forum: Anatomically detailed models
Topic: How does 'Z. F. Mainen and T. J. Sejnowski (1996)' model work?
Replies: 2
Views: 1556

Re: How does 'Z. F. Mainen and T. J. Sejnowski (1996)' model work?

Thanks for providing information.
I changed diameter by using pt3dchange. Thanks!
by Christine Chung
Thu Aug 08, 2019 7:51 am
Forum: Anatomically detailed models
Topic: How does 'Z. F. Mainen and T. J. Sejnowski (1996)' model work?
Replies: 2
Views: 1556

How does 'Z. F. Mainen and T. J. Sejnowski (1996)' model work?

Hello, I'm beginner and trying to modify morphology of detailed models. I have question how this codes works. Z. F. Mainen and T. J. Sejnowski (1996)'s model https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=2488&file=/cells/#tabs-1 This is L5 pyramidal neuron: (since it is too long t...
by Christine Chung
Wed Jul 24, 2019 2:17 am
Forum: Getting started
Topic: Find threshold with APCount
Replies: 4
Views: 2086

Re: Find threshold with APCount

Thanks for your answer!
I learned a lot. And all things worked :)
by Christine Chung
Tue Jul 23, 2019 2:59 am
Forum: Getting started
Topic: Find threshold with APCount
Replies: 4
Views: 2086

Re: Find threshold with APCount

Thanks for your kind explanation, Ted. I monitored apc.n by increasing stimulation amplitude to find out the point where apc.n >0 (threshold). And I want to see apc.n of soma, dendrites and axon. I read NEURON book ch.4 and 5. Thanks for your suggestion. But still, there is a problem. I used apc = n...
by Christine Chung
Sun Jul 21, 2019 10:09 pm
Forum: Getting started
Topic: Find threshold with APCount
Replies: 4
Views: 2086

Find threshold with APCount

Hi, I have some questions about APCount. 1. I read explanation about APCount at programmer's reference. apc = h.APCount(section(x)) Here, section(x) should be written only number? For eaxmple, I write apc=h.APCount(0.5) for see threshold of soma. Can I use section name? 2. If not, How can I know the...
by Christine Chung
Thu May 23, 2019 11:48 pm
Forum: Other questions
Topic: how to deal with "subscript out of range error" in printing out coordinate.
Replies: 11
Views: 3341

Re: how to deal with "subscript out of range error" in printing out coordinate.

umm.. I found the error! exactly In code, without any function I made or loop, I put only forall {printf("%s: %d \n", secname(), n3d())} Then, the result looks axon did not have its coordination. loading membrane mechanisms from nrnmech.dll Additional mechanisms from files ca.mod cad.mod k...
by Christine Chung
Tue May 21, 2019 2:39 am
Forum: Other questions
Topic: how to deal with "subscript out of range error" in printing out coordinate.
Replies: 11
Views: 3341

Re: how to deal with "subscript out of range error" in printing out coordinate.

oh, I didn't copy all the result. The error was still happened.
And I found out that when I print secname and nn in front of for loop,

Code: Select all

printf("%s: %d \n", secname(), nn)
The axon part's outcome is zero.
by Christine Chung
Wed May 15, 2019 6:51 am
Forum: Other questions
Topic: how to deal with "subscript out of range error" in printing out coordinate.
Replies: 11
Views: 3341

Re: how to deal with "subscript out of range error" in printing out coordinate.

This is code which I put what you said-1.2. for ii = 1, nseg { print ii xr = range.x[ii] printf("one") center_pt.x[0] = xint.x[ii] printf("two") center_pt.x[1] = yint.x[ii] printf("three") center_pt.x[2] = zint.x[ii] printf("four") printf ("\n") //pr...
by Christine Chung
Tue May 14, 2019 1:29 am
Forum: Other questions
Topic: how to deal with "subscript out of range error" in printing out coordinate.
Replies: 11
Views: 3341

Re: how to deal with "subscript out of range error" in printing out coordinate.

I got your point. Now I tried to print in a for loop like this. for ii = 1, nseg { xr = range.x[ii] printf("one") print ii center_pt.x[0] = xint.x[ii] printf("two") print ii center_pt.x[1] = yint.x[ii] printf("three") print ii center_pt.x[2] = zint.x[ii] printf("fo...