Search found 42 matches

by bsuter
Thu Jul 30, 2020 2:49 pm
Forum: General questions and discussions about computational neuroscience
Topic: What does SWC stand for?
Replies: 5
Views: 13668

Re: What does SWC stand for?

Hi Ted, The neuromorpho FAQ that you linked below cites "Cannon 1998" for the SWC format. That seems to be this paper, which includes at least the presumed "W", aka Wheal. Whether Cannon or Cole (or both) are the "C" remains a mystery for now ... Cannon RC, Turner DA, Pyapali GK, and Wheal HV. An on...
by bsuter
Sun Jul 14, 2019 4:50 pm
Forum: Anatomically detailed models
Topic: Neurolucida to NEURON best practices?
Replies: 26
Views: 28515

Re: Neurolucida to NEURON best practices?

Dear Ted, have you had a chance to look at our files? Or do you know if Michael has ever implemented the fix (for contour-stack somas) that was discussed above (but several years ago)? We have a large number of reconstructions suffering from this issue, and are stuck until we find a solution. I've c...
by bsuter
Thu Jul 11, 2019 11:37 am
Forum: Anatomically detailed models
Topic: Neurolucida to NEURON best practices?
Replies: 26
Views: 28515

Re: Neurolucida to NEURON best practices?

Dear Ted, I have sent you the requested files by email.
by bsuter
Tue Jul 09, 2019 6:43 am
Forum: Anatomically detailed models
Topic: Neurolucida to NEURON best practices?
Replies: 26
Views: 28515

Re: Neurolucida to NEURON best practices?

A few years back here in this thread we figured out that your nice 'proc somastack_process' code for importing a cell body modeled as a z-stack of xy-contours was not being used by Import3D. Instead, older code (import3d_gui.hoc::contourstack2centroid) was generating a 3D mesh. At the time, Michael ...
by bsuter
Wed Sep 30, 2015 2:55 am
Forum: Other questions
Topic: Making system calls on Windows
Replies: 4
Views: 2129

Re: Making system calls on Windows

I'd suggest moving to 7.4. Will doing so solve my current problem, namely that system() doesn't see (some?) binaries on my Windows path? Maybe, maybe not. What it will do is help you avoid working hard to get something going under cygwin, only to have to abandon that solution when you eventually up...
by bsuter
Tue Sep 29, 2015 12:24 am
Forum: Other questions
Topic: Making system calls on Windows
Replies: 4
Views: 2129

Re: Making system calls on Windows

Unless you have a very specific reason for sticking with 7.2 Is 7.4 fully backwards compatible with models made under 7.2? I plan to use 7.4 for new models. I'm currently revisiting a model made under 7.2 looking to obtain a quick answer to a few minor changes in parameters, so I'd hoped to achieve...
by bsuter
Mon Sep 28, 2015 1:59 pm
Forum: Other questions
Topic: Making system calls on Windows
Replies: 4
Views: 2129

Making system calls on Windows

My goal: write a hoc convenience function for saving data from a simulation run to disk as multiple files and then archiving these files into a single .zip file. My initial approach (using a simplified test case): system("7z a testfile.zip sv.dat") My problem: when I call system("stringcommand"), I ...
by bsuter
Fri Mar 08, 2013 11:07 pm
Forum: Anatomically detailed models
Topic: Neurolucida to NEURON best practices?
Replies: 26
Views: 28515

Re: Neurolucida to NEURON best practices?

Thanks Ted - the way you described is indeed how I've been measuring section area. Perhaps I misunderstood Hines' post - I took him to be saying that the "somastack_process" procedure (or possibly some other procedure) report the area of the soma after remodeling it based on the principle axis deriv...
by bsuter
Thu Mar 07, 2013 4:05 pm
Forum: Other questions
Topic: CVode warnings: what's the cause and how can I turn them off
Replies: 3
Views: 2938

Re: CVode warnings: what's the cause and how can I turn them

Posting an update and solution in case someone else runs into similar errors. Michael Hines and Michele Migliore both helped in diagnosing the cause of the problem and proposing solutions. 1. Quick answer: A time constant in one of my mechanisms (h.mod) came so close to zero that cvode required a ve...
by bsuter
Thu Mar 07, 2013 3:11 pm
Forum: Anatomically detailed models
Topic: Neurolucida to NEURON best practices?
Replies: 26
Views: 28515

Re: Neurolucida to NEURON best practices?

Thank you very much for your help and explanation. I'm using v7.2, but have used v7.1 in the past with the same experience. I'm happy to hear about your ongoing improvements / expansions. It does print an accurate area Could you please elaborate? As you suggest, I'm interested to "compare to the are...
by bsuter
Mon Mar 04, 2013 5:18 am
Forum: Anatomically detailed models
Topic: Neurolucida to NEURON best practices?
Replies: 26
Views: 28515

Re: Neurolucida to NEURON best practices?

In its present implementation, Import3D should be able to handle somas whose morphometric data were obtained in any of these three different ways: 1. as a sequence of x,y,z,diam measurements, i.e. like any other neurite. 2. by tracing an outline of the perimeter of the soma at one z level. In this ...
by bsuter
Wed Feb 13, 2013 4:32 pm
Forum: Other questions
Topic: CVode warnings: what's the cause and how can I turn them off
Replies: 3
Views: 2938

CVode warnings: what's the cause and how can I turn them off

Hello, During my simulations a very large number of warnings appear in the console. The warnings seem to occur around the times when action potentials occur in my simulation, which is also when the adaptive integration method uses short time steps. The warnings always look like this: CVode-- Warning...
by bsuter
Thu Feb 07, 2013 3:41 am
Forum: Parallel NEURON
Topic: Multisplit single cell with many synapses
Replies: 4
Views: 3487

Re: Multisplit single cell with many synapses

Thank you for the paper references. I still don't understand what determines the actual minimal NetCon.delay for a given multisplit model, but I've done some empirical tests and was able to adjust my model parameters to run parallelized (multisplit, 6 threads, cache efficient) without errors. In the...
by bsuter
Mon Feb 04, 2013 2:52 pm
Forum: Anatomically detailed models
Topic: Correction to the Shape documentation?
Replies: 0
Views: 1750

Correction to the Shape documentation?

I believe there is an error in the online documentation for the nearest method of the Shape class: http://www.neuron.yale.edu/neuron/static/docs/help/neuron/neuron/classes/shape.html#nearest The nearest arc position of the selected section as well as the section is available from push_section . I be...
by bsuter
Mon Feb 04, 2013 12:49 pm
Forum: Parallel NEURON
Topic: Multisplit single cell with many synapses
Replies: 4
Views: 3487

Re: Multisplit single cell with many synapses

Hi Ted, I called it an error because in addition to that message, the simulation does not run: oc>run() nrniv: usable mindelay is 0 (or less than dt for fixed step method) near line 439 run() ^ finitialize(-79.8 ) init( ) stdinit( ) run( ) That's not an error, it's just an automatically generated st...