Search found 20 matches

by sohaib786
Wed Mar 03, 2021 12:09 pm
Forum: Anatomically detailed models
Topic: Loading a morphology as a hoc file
Replies: 9
Views: 438

Re: Loading a morphology as a hoc file

Amazing. Thanks!
by sohaib786
Tue Mar 02, 2021 4:45 am
Forum: Anatomically detailed models
Topic: Loading a morphology as a hoc file
Replies: 9
Views: 438

Re: Loading a morphology as a hoc file

Does it contain a statment of the form begintemplate Foo Yes. Following are the starting statements begintemplate celltemplate public soma,dend,all,dends,basal,apcounter,apvec,nil,LOTlist,CClist,FocalList,Vvec,numdend,primedends//,FocalDends,NumberActiveDends objref all,dends,basal,apcounter,apvec,...
by sohaib786
Sun Feb 28, 2021 9:19 am
Forum: Anatomically detailed models
Topic: Loading a morphology as a hoc file
Replies: 9
Views: 438

Re: Loading a morphology as a hoc file

Thanks for your prompt responses. What do you get and how is it different from what you expected? I am expecting to load the morphology (similar to loading a swc file), check different parameters to make sure I can use it for my simulations. What I tried to do- 1) Double click and load the hoc file....
by sohaib786
Thu Feb 25, 2021 9:02 am
Forum: Anatomically detailed models
Topic: Loading a morphology as a hoc file
Replies: 9
Views: 438

Loading a morphology as a hoc file

Hi Ted I am trying to load a morphology as a hoc file in GUI instead of using the import3d<cell builder tool (because i don't have the swc file). When I do this, I don't get something similar to the cell builder tool. I double checked that using the model view option. Can you point where I am going ...
by sohaib786
Tue Oct 06, 2020 1:20 pm
Forum: UNIX/Linux
Topic: Installing on Ubuntu 20.04 (GUI not working)
Replies: 7
Views: 1516

Re: Installing on Ubuntu 20.04 (GUI not working)

The error which I posted is from 7.6.7.

Code: Select all

from neuron import h
is working. But the GUI doesn't pop up, but it gives the output which I shared in the first post.
by sohaib786
Sun Oct 04, 2020 1:55 pm
Forum: UNIX/Linux
Topic: Installing on Ubuntu 20.04 (GUI not working)
Replies: 7
Views: 1516

Re: Installing on Ubuntu 20.04 (GUI not working)

After using sudo pip3 install neuron, it did the installation(successfully) but didn't work. This is its location. It is still present. neuron in /usr/local/lib/python3.8/dist-packages (7.8.1.1) I then installed using tar.gz file of 7.6.7 version of nrn and iv, which I had downloaded some days back ...
by sohaib786
Sun Oct 04, 2020 8:22 am
Forum: UNIX/Linux
Topic: Installing on Ubuntu 20.04 (GUI not working)
Replies: 7
Views: 1516

Installing on Ubuntu 20.04 (GUI not working)

Hi, After installing the package I wanted to run the gui for which I wrote in the terminal- nrngui -python This gave the following error- Duke, Yale, and the BlueBrain Project -- Copyright 1984-2018 See http://neuron.yale.edu/neuron/credits /home/sohaib/neuron/nrn/x86_64/bin/nrniv: Couldn't find: st...
by sohaib786
Thu Mar 28, 2019 4:30 pm
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 12460

Re: Morphology and AP generation

Do you see a problem with iteration over segments when you just use Python from NEURON, without Jupyter? Had not tried before. However, upon checking, it works fine with just python. In both cases, i.e Loading with or without GUI doesn't affect it and works fine. Jupyter seems to create some troubl...
by sohaib786
Tue Mar 26, 2019 1:49 am
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 12460

Re: Morphology and AP generation

email that zip file
Thanks. Sure.
what version of
NEURON is being used by the notebook
Neuron Version : NEURON -- VERSION 7.5 master (6b4c19f) 2017-09-25
Anaconda: Version 5.2.0 , Build Channel- py36_3
by sohaib786
Mon Mar 25, 2019 4:53 am
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 12460

Re: Morphology and AP generation

You should get something like this I do get like this. But intriguingly, sometimes it doesn't print all of them. Also sometimes, when i load a file such as this. from neuron import h h.load_file('/home/sohaib/neuron/ASC Files/fmc3_1') h.load_file('/home/sohaib/neuron/ASC Files/fmc3_1') (fmc3_1 is a...
by sohaib786
Sun Mar 24, 2019 12:55 pm
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 12460

Re: Morphology and AP generation

Two things happen when this command is run. for sec in h.allsec(): for seg in sec: print(seg) It prints soma(0.5) dend[0](0.5) dend[1](0.5) dend[2](0.5) dend[3](0.5) so on and so forth But sometime it prints soma(0.5) dend[0](0.1) dend[0](0.3) dend[0](0.5) dend[0](0.9) dend[1](0.1) dend[1](0.3) dend...
by sohaib786
Sat Mar 23, 2019 1:30 pm
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 12460

Re: Morphology and AP generation

I tried doing a weighted compartment analysis. However, I checked some of the parameters of all the dendrites to get an idea and found this problem. I took a dendrite randomly and enquired into its segments and their morphological parameters. x = h.dend[2] for i in x.allseg(): print(i, i.area(), i.d...
by sohaib786
Fri Mar 22, 2019 6:19 am
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 12460

Re: Morphology and AP generation

That was really insightful. By Excitability, I meant that the cell may report a higher number of AP's by a reduction in the threshold, reduced spike interval, or increased amplitude of Vsoma. The reason for this view is because REM sleep deprivation has been hypothesized to increase cell excitabilit...
by sohaib786
Tue Mar 19, 2019 9:14 am
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 12460

Re: Morphology and AP generation

I am trying to study the effect of the altered structure on cell function caused due to REM sleep deprivation. I have morphology for both control and treatment group, and I am using biophysical properties of the control group. I am exciting a single dendrite at its midpoint and checking voltage at t...
by sohaib786
Tue Mar 12, 2019 2:29 am
Forum: NEURON + Python
Topic: BioPhysical properties of imported morphology in Python
Replies: 9
Views: 3060

Re: BioPhysical properties of imported morphology in Python

No it doesn't. It does seem to load the hoc file. I accessed details like h.soma.Ra which it reported the value I had put in earlier. I also ran a simulation placing an I clamp at a different dendritic positions and it generated spike perfectly. Read the Programmer's Reference documentation of load...