Search found 77 matches

by shyam_u2
Tue Jul 09, 2019 4:32 pm
Forum: Anatomically detailed models
Topic: Morphology import error
Replies: 4
Views: 634

Re: Morphology import error

Thanks so much for taking the time to explain me the problem. The morphology as viewed using Neurolucida/HBP Neuron Morphology viewer looks good without any issues. I don't see any point which is not connected to the parent. Only when I import it in NEURON, there are a few points without any parent....
by shyam_u2
Tue Jul 02, 2019 10:07 am
Forum: Anatomically detailed models
Topic: Morphology import error
Replies: 4
Views: 634

Morphology import error

I am trying to import a morphology (from an .swc file) through cell builder. NEURON says that there are file translation problems. The terminal emits an error message saying that there is more than one tree. Any information on this appreciated.

Thanks in advance
by shyam_u2
Mon Aug 06, 2018 7:00 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Inconsistent units
Replies: 3
Views: 1129

Re: Inconsistent units

The previous primary expression with units: 1 kg/m3-sec is missing a conversion factor and should read:
(6.02217e+026)*() at line 54 in file updateo2o.mod
by shyam_u2
Sun Aug 05, 2018 5:55 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Inconsistent units
Replies: 3
Views: 1129

Inconsistent units

Hi all, I have this mod mechanism to compute local oxygen concentration from bath oxygen concentration and from the activity of Nakpumps in neuron and glia. The mod file compiles without any error. However, running this script with modlunit returns a conversion error which I couldn't understand. Any...
by shyam_u2
Tue Jun 06, 2017 3:10 pm
Forum: Anatomically detailed models
Topic: Mapping of hoc toploogy and 3D morphology
Replies: 1
Views: 5428

Mapping of hoc toploogy and 3D morphology

I recently exported a .asc file and created a hoc template. Everything works well, thanks to this forum and the well documented procedures on how to use import3D. I am recording transmembrane currents from certain compartments/segments. I have the morphology plotted using the trees toolbox. I need t...
by shyam_u2
Thu Mar 02, 2017 5:15 pm
Forum: Parallel NEURON
Topic: Display time as the simulation progresses
Replies: 1
Views: 4905

Display time as the simulation progresses

I am running a network model in using Parallel NEURON. I want to display the following while the model is running: The "biological" millisecond and the real time taken (in seconds) to run for that particular millisecond, FOR EACH HOST. For example, if running on 3 hosts, "running millisecond 1 in ho...
by shyam_u2
Thu Feb 02, 2017 6:36 pm
Forum: NEURON + Python
Topic: Python to hoc
Replies: 2
Views: 8990

Python to hoc

Can some one tell me the hoc version of this python code ?

Code: Select all

		self.Adend1.connect(self.soma,   0.5, 0)
Thanks in advance,
S
by shyam_u2
Tue Sep 20, 2016 5:03 pm
Forum: Other questions
Topic: Slow spillover component
Replies: 2
Views: 4500

Slow spillover component

I trying to modify Exp2Syn.mod to include a second, slow decay constant, tau3, that contributes to 10% of peak amplitude. How do I change the existing Exp2Syn.mod to model the slow decay constant ? COMMENT 2 Two state kinetic scheme synapse described by rise time tau1, 3 and decay time constant tau2...
by shyam_u2
Wed Jul 20, 2016 12:41 pm
Forum: Other questions
Topic: Mknrndll help
Replies: 2
Views: 4137

Re: Mknrndll help

Great.. It works. Thanks very much
by shyam_u2
Mon Jul 18, 2016 3:59 pm
Forum: Other questions
Topic: Mknrndll help
Replies: 2
Views: 4137

Mknrndll help

I am new to using NEURON on Windows..

I installed NEURON on my Windows Desktop. When I typed mknrndll (after cding to the folder where my mod files are) it doesn't recognize the command. It says "mknrndll is not recognized as an internal or external command". Can someone help ?


Thanks,
by shyam_u2
Wed Jun 15, 2016 2:18 am
Forum: Other questions
Topic: Segmentation violation error
Replies: 1
Views: 2873

Segmentation violation error

Hello, I am trying to run my single cell multi-compartmental model. The problem is, when I change the temperature of my model (even by 1 degree either by increasing or decreasing ) I get this strange segmentation violation error. /Applications/NEURON-7.3/nrn/x86_64/bin/nrniv: Segmentation violation ...
by shyam_u2
Tue Nov 05, 2013 1:52 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Problem with saturating synapse model
Replies: 8
Views: 4413

Re: Problem with saturating synapse model

While a fix for this is being developed (allow specification of the self-event that is to be moved?), the interim workaround is to limit each instance of the saturating synapse mechanism AMPA_S to a single input stream per instance--that is, one NetCon per AMPA_S instance.
Is this bug fixed ?
by shyam_u2
Thu Aug 22, 2013 2:33 am
Forum: Anatomically detailed models
Topic: compute nseg
Replies: 1
Views: 5624

compute nseg

I don't understand the following line from fixnseg.hoc nseg = int((L/(d_lambda*lambda_f(freq))+0.9)/2)*2 + 1 I want to set the distance between adjacent nodes to 10% of AC length constant at 100 Hz. For a compartment of length 60 um, diam 3 um, Ra 100 um and cm =1uf/cm2,I get the distance between ad...
by shyam_u2
Sun Aug 18, 2013 9:32 pm
Forum: Anatomically detailed models
Topic: Axial currents between two compartments
Replies: 3
Views: 6598

Re: Axial currents between two compartments

The documentation of 'ri' says that it returns the resistance (in megohms) between the center of the segment containing x and its parent segment. First of all, I don't understand how NEURON computes the parent segment of a section. How could the resistance at the point of connect between soma and de...
by shyam_u2
Fri Aug 16, 2013 3:49 am
Forum: Anatomically detailed models
Topic: Axial currents between two compartments
Replies: 3
Views: 6598

Axial currents between two compartments

Consider we have two sections soma and dend and connect them in the following way: connect dend(0),soma(0).
If I print the axial resistance (ri) at soma(0) and dend(0) it says 1e30. Does it mean that there is no flow of current between these points ?