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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, P...

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...

Dear Ted, I have sent you the requested files by email.

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 ...

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...

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...

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("stri...

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 ...

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...

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 th...

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 ...

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...

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...

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...

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...