Search found 17 matches

by luciana
Mon Mar 05, 2018 6:15 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Three questions on extracellular stimulation and recording
Replies: 7
Views: 8036

Re: Three questions on extracellular stimulation and recording

Hi everyone,

I would like to know what is the main difference between NEURON xtra mechanism and LFPy (https://lfpy.github.io) in the calculation of extracellular potential in a particular spatial location (x,y,z) ?

Thank you very much

Luciana.
by luciana
Thu Apr 27, 2017 10:13 am
Forum: Other questions
Topic: vext in extracellular mechanism
Replies: 7
Views: 6023

Re: vext in extracellular mechanism

Thank you very much Ted. I will send you the hoc,mod and ses files to your e-mail.
by luciana
Tue Apr 18, 2017 3:08 pm
Forum: Other questions
Topic: vext in extracellular mechanism
Replies: 7
Views: 6023

Re: vext in extracellular mechanism

Hi everyone, I have another question related to Vext in extracellular mechanism. I want to adjust the amplitude of the extracellular action potential simulated to our experimental data. I thought for that purpose I should change xg parameter (conductivity in extracellular layer) and the waveform of ...
by luciana
Tue Sep 20, 2016 5:09 pm
Forum: Other questions
Topic: action potential initiation site
Replies: 19
Views: 15413

Re: action potential initiation site

Oh, I forgot answer your other question.
ted wrote: Before discussing the effects of changing soma diameter, let me ask one question: what were the values of nseg in your model?
nseg = 1 for both compartments (soma and axon).
by luciana
Tue Sep 20, 2016 4:26 pm
Forum: Other questions
Topic: action potential initiation site
Replies: 19
Views: 15413

Re: action potential initiation site

I'm sorry my english is not very good. Let's start again. What happens if you make soma.diam even larger? Does the range of stimulus amplitudes that make the axon fire first become wider or narrower? When I increase the diameter of the soma (soma.diam), the range of stimulus amplitudes that make the...
by luciana
Tue Sep 13, 2016 1:27 pm
Forum: Other questions
Topic: action potential initiation site
Replies: 19
Views: 15413

Re: action potential initiation site

What happens if you make soma.diam even larger? Does the range of stimulus amplitudes that make the axon fire first become wider or narrower Ted, if soma.diam become even larger, I can't find any stimulus amplitude that make the axon fire first. I pass from soma firing first to none fire state. How...
by luciana
Mon Sep 12, 2016 6:58 pm
Forum: Other questions
Topic: action potential initiation site
Replies: 19
Views: 15413

Re: action potential initiation site

What happens to the soma+axon model if you reduce the stimulus current amplitude? The time between the stimulus and the action potential is bigger with lower current amplitudes. In some point the current in not suffiecient to generate the action potential. amplitud = 0.1 nA, soma and axon both fire...
by luciana
Mon Sep 12, 2016 3:03 pm
Forum: Other questions
Topic: action potential initiation site
Replies: 19
Views: 15413

Re: action potential initiation site

Dear Ted, I modeled this simple example that you proposed. Imagine a cell with a spherical soma. A dendrite is attached to one side of the soma, and an axon is attached to the other side. The geometry of the cell is: soma L = diam = 10 um dend L = 500 um, diam = 2 um axon L = 500 um, diam = 1 um Ra ...
by luciana
Wed Jun 08, 2016 4:51 pm
Forum: Getting started
Topic: load several geomtery file
Replies: 14
Views: 16517

Re: load several geomtery file

Hi Ted!
Thanks for your answer. What you say, make me sense.
But, I have figured out it this way:
In the shell script:

Code: Select all

repeat
   run a simulation with a new condition
   read LINE of the output file
   echo $LINE >> textfile.txt
until done
Ah! and thank you for the reference,
Luciana.
by luciana
Mon Jun 06, 2016 10:34 pm
Forum: Getting started
Topic: Idraw files
Replies: 3
Views: 6552

Re: Idraw files

Thank you Ted! Idraw seems work nice for me! I will use it. When I have to mix NEURON's figures with python's plots, I will save the NEURON's figures using: Window/Print & File Window Manager, Print/PostScript and then open them with Illustrator and make the merge with Python's plots (.pdf, .jpg, etc)
by luciana
Mon Jun 06, 2016 10:23 pm
Forum: Getting started
Topic: load several geomtery file
Replies: 14
Views: 16517

Re: load several geomtery file

Hello, I have wrote a shell script that calls NEURON many times, each time with a different argument that makes NEURON load a different c*.hoc file. Inside the loop (in the batch file) I have: nrngui -c "zzz=$file" test.hoc and like Ted wrote above, the hoc program create a file name that is passed ...
by luciana
Fri Jun 03, 2016 5:26 pm
Forum: Getting started
Topic: Idraw files
Replies: 3
Views: 6552

Idraw files

Hi! I want to print several graphs and until now I have used idraw for merging the figures and then print them. I have done this clicking Window/Print & File Window Manager, make the selection and then Print/Idraw then I open the file writing >idraw filename and clicking on File/Import Graphic... I ...
by luciana
Mon Jan 12, 2015 2:48 pm
Forum: Anatomically detailed models
Topic: Importing 3D data: number of sections
Replies: 1
Views: 6511

Importing 3D data: number of sections

Hello! I imported a neurolucida file (.asc) to NEURON. The dendritic tree was pooled into 56 sections, but I would prefer more sections containing less vectors (hopefully around 100) in order to be able to discriminate within branches. More specifically, I would like to insert different conductances...
by luciana
Wed Mar 12, 2014 1:19 pm
Forum: OS X
Topic: NEURON in Mac OsX 10.9.2
Replies: 11
Views: 11226

Re: NEURON in Mac OsX 10.9.2

It works!!! installing XQuartz 2.7.5 the message desappears and NEURON run perfectly.
Thank you very much I'm so happy
by luciana
Tue Mar 11, 2014 6:48 pm
Forum: OS X
Topic: NEURON in Mac OsX 10.9.2
Replies: 11
Views: 11226

Re: NEURON in Mac OsX 10.9.2

I have removed the NEURON application and installed it again (the same one). And appears something new!: -e dyld: Library not loaded: /opt/X11/lib/libX11.6.dylib Referenced from: /Applications/NEURON-7.3/nrn/x86_64/bin/nrniv Reason: image not found ./nrngui.sh: line 25: 1312 Trace/BPT trap: 5 ${NRNG...