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Hello, 1. I've made a multi-compartmental single-cell model neuron that runs without error with multisplit over 6 processors (on a single Microsoft Windows/Intel computer). 2. I've added many (e.g. 2000) Exp2Syn point processes to this single cell, distributed across most of the segments, with each ...

That's why I suggested the CVode class's record() method. http://www.neuron.yale.edu/neuron/static/docs/help/neuron/neuron/classes/cvode.html#record cvode.record(&rangevar, yvec, tvec, 1) captures rangevar not at the "integration" times, but at the times specified by tvec. It does thi...

when the experimental sampling rate doesn't match the simulation time steps (or adaptive time is used): how does one best calculate the error between these time-series (or in the freq domain)? Resample the original data at appropriate intervals. The Vector class's interpolate uses linear interpolat...

Gotcha, thanks. calculate error measures and add them up I get this conceptually, it's the implementation that poses questions for me. For example, when the experimental sampling rate doesn't match the simulation time steps (or adaptive time is used): how does one best calculate the error between th...

Thank you Ted for your quick response. It confirms to me that I can (almost) do what I want, and that's good news :), but also that I'd need to implement my own "error calculation" (objective) functions for each of the measures of interest, and then combine these. As a result, your post ha...

Hello, I've been using the MRF with multiple "Run Fitness" generators. However, now I would like to simultaneously optimize multiple quantities derived from a single simulation run. I'd like to avoid running the simulation more than once for a given set of parameter values. For context: I'...

Reconstructions saved in the ASC format from the most recent version of Neurolucida (v10) seem to identify the soma contours with the header "Cell Body", whereas the previous version (v9) used the "CellBody" header. There may be other changes as well - I've requested clarificatio...

I've recently started using TextPad on Windows as an editor for hoc, ses, and mode files; there is a free trial version. This editor has tabs for multiple open documents, and also allows side-by-side or top-and-bottom panes for viewing two files simultaneously. There is a built-in file comparison fu...

I believe we've identified sources of some, maybe all, the problems I've encountered. I've succeeded in generating a .hoc file containing the morphology reconstructed in Neurolucida, with minor differences. Some errors remain during the conversion process, but I believe they can be ignored. I believ...

Well, you already fixed one problem by doing the following: Update: Within Neurolucida, I modified the reconstruction such that the soma contours were marked as "Cell Body". While this does not change the geometry of the soma in the reconstruction, it seems to have provided enough identif...

My soma reconstruction in NL consists of 19 contours, each in a single z-plane. The generated .hoc for the 3D geometry specification creates 19 sections (soma[0] to soma[18]). Looking at the pt3dadd() calls for these sections, I see the that all points in a single section are at a single z-value, w...

(Ted, while I was composing this message, you replied to the thread) Update: Within Neurolucida, I modified the reconstruction such that the soma contours were marked as "Cell Body". While this does not change the geometry of the soma in the reconstruction, it seems to have provided enough...

Hi Ted, I'm still trying to get this (Neurolucida to NEURON) to work, but not much luck yet. I'll go back and try to debug from a very simple NL model. I've been using Import3D with a v3 NL .asc file. Most of the "problem points" seem to be at the soma, and in particular where each z-level...

I've completed a detailed reconstruction of a neuron using Neurolucida software. What are current best practices / instructions / gotchas for bringing this morphology into NEURON for simulations? The soma was reconstructed using NL's "contour" mode, i.e. as a sequence of closed polygons, e...

Thank you, in this new version the dialogs open on my main screen - works great.