Search found 95 matches

by neuromau
Sat Jul 28, 2018 8:55 am
Forum: OS X
Topic: Precompiled NEURON 7.5 install on Sierra - not quite successful
Replies: 2
Views: 635

Precompiled NEURON 7.5 install on Sierra - not quite successful

Hello, after installing the precompiled NEURON 7.5 app on Mac 10.12.6 Sierra, it looks like installed but the programs don't launch. If I click the nrngui or neurondemo icon in the Applications / NEURON folder, no GUI loads. Only a bash shell loads and just says "-e" and nothing else, and it seems t...
by neuromau
Fri Jul 28, 2017 8:22 am
Forum: Anatomically detailed models
Topic: Using Import3D on Mac
Replies: 4
Views: 5506

Re: Using Import3D on Mac

Ah, of course! I am working with a different model in my Mac, one that does have a "spines" mod file. I should have realized that right away! Thank you, I'll rename that suffix in the file.
by neuromau
Thu Jul 27, 2017 12:20 pm
Forum: Anatomically detailed models
Topic: Using Import3D on Mac
Replies: 4
Views: 5506

Re: Using Import3D on Mac

I checked the alpha folder and found an installer from July 4, so installed that instead (other version I installed was listed as the most recent general release for Mac on the downloads page). I still get the same error although on a different line number now: oc>/Applications/NEURON-7.5/nrn/x86_64...
by neuromau
Thu Jul 27, 2017 9:46 am
Forum: Anatomically detailed models
Topic: Using Import3D on Mac
Replies: 4
Views: 5506

Using Import3D on Mac

I am having an issue using Import3D on Mac OS. I just uninstalled and reinstalled NEURON to be sure, and it is still happening. It claims a syntax error (but I didn't see what was erroneous-looking in the read_nlcda3.hoc file near line 1018). $ nrngui NEURON -- VERSION 7.4 (1380:90539e842093) 90539e...
by neuromau
Thu Jun 15, 2017 1:29 pm
Forum: Specific models
Topic: Bezaire/Raikov/Soltesz CA1 network model
Replies: 0
Views: 13300

Bezaire/Raikov/Soltesz CA1 network model

This is a placeholder thread for discussing the model used in Bezaire et al, eLife 2016. The model code is available in ModelDB at: https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=187604 . The development code will also soon be available on Open Source Brain at: http://opensourcebrain.o...
by neuromau
Thu Aug 25, 2016 9:55 am
Forum: NEURON + Python
Topic: Using pc.broadcast with python
Replies: 2
Views: 9073

Re: Using pc.broadcast with python

Ah, thank you Michael!
by neuromau
Tue Aug 16, 2016 2:18 pm
Forum: NEURON + Python
Topic: Using pc.broadcast with python
Replies: 2
Views: 9073

Using pc.broadcast with python

I am having trouble using the pc.broadcast() function correctly in Python. Here is my file mwe.py: from mpi4py import MPI from neuron import h MyString = "oldName" print "The original string is: " + MyString pc = h.ParallelContext() pc.barrier() if int(pc.id()) == 0: MyString="newNameTest" print "Ho...
by neuromau
Tue Aug 16, 2016 12:53 pm
Forum: NEURON + Python
Topic: Nice tutorials, one minor question
Replies: 1
Views: 8610

Nice tutorials, one minor question

I enjoyed going through the very clear and through neuron+python tutorials. I think there is one line that needs to be updated, or (more likely) it was some sort of user error on my part, being new to python. It is the ball-and-stick network tutorial at: http://neuron.yale.edu/neuron/static/docs/neu...
by neuromau
Mon Jun 06, 2016 11:01 pm
Forum: SimTracker
Topic: Welcome to the SimTracker Forum!
Replies: 1
Views: 17842

Welcome to the SimTracker Forum!

Welcome to the SimTracker Forum! This forum area is your place to receive support about the SimTracker tool ( http://mariannebezaire.com/simtracker/ ) as well as the associated NEURON code template ( https://senselab.med.yale.edu/ModelDB/showModel.cshtml?model=187604 ). Feel free to ask questions, r...
by neuromau
Fri Nov 20, 2015 11:40 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Set pointer when using mod file that defines pointer
Replies: 1
Views: 5146

Set pointer when using mod file that defines pointer

This is just an FYI - my code was erroring out during a call to fcurrent() (as part of the call from finitialize() during the init procedure). It was reporting a segmentation violation and it took me awhile to realize it was due to the use of a mechanism (mod file) that defined and used a couple of ...
by neuromau
Tue Sep 22, 2015 10:26 am
Forum: OS X
Topic: NEURON and MATLAB on Mac
Replies: 2
Views: 5213

Re: NEURON and MATLAB on Mac

The NEURONHOME environment variable is incorrect. If it exists at all, it should be /Applications/NEURON-7.4/nrn/share/nrn That was it, everything works fine after setting NEURONHOME correctly! At any rate, without that variable, what is the result, after a launch, of the hoc function print neuronh...
by neuromau
Thu Sep 17, 2015 12:25 pm
Forum: OS X
Topic: NEURON and MATLAB on Mac
Replies: 2
Views: 5213

NEURON and MATLAB on Mac

Hello, I have just started using a Mac with Yosemite 10.10.5, but I am having a little NEURON trouble (or maybe it's actually MATLAB trouble?). I installed NEURON 7.4 and it is working fine. But then when I try to run it from MATLAB 2015a using a system call (which I can do just fine in Linux or Win...
by neuromau
Sun Sep 21, 2014 7:22 pm
Forum: Anatomically detailed models
Topic: Computing impedance after running define_shape
Replies: 2
Views: 5689

Re: Computing impedance after running define_shape

I'm on Windows 8 using: NEURON -- VERSION 7.3 ansi (1078:2b0c984183df) 2014-04-04 For this code example: 1. Yes, the error goes away when I insert pas into a section. 2. Good call, in my regular code I remembered to initialize, but I had inadvertently removed it from this code. My full code (with al...
by neuromau
Fri Sep 19, 2014 4:57 pm
Forum: Anatomically detailed models
Topic: Computing impedance after running define_shape
Replies: 2
Views: 5689

Computing impedance after running define_shape

I want to run the compute function of the impedance mechanism after running define_shape(). However, it leads to the following error: Fatal Complex arithmetic error. Attempted division by zero. If I use the compute function prior to running define_shape(), it works just fine. I'm not sure why it doe...
by neuromau
Tue Jun 24, 2014 4:37 pm
Forum: Other questions
Topic: When using a model with a custom init procedure...
Replies: 0
Views: 1003

When using a model with a custom init procedure...

When using a model with a custom init procedure, check to make sure the initialization was done correctly. This means, compare the functions called by the custom init procedure with those called in the regular init procedure as shown in Chapter 8.3 of The NEURON Book, to make sure no necessary funct...