Nemo-TMS model generation failure

[kennelly25]

Hello all,
I have just recently been using NEURON and SimNIBS to model the affect of a TMS device on the brain, yet I am having a bizzare issue with generating a model in matlab, since I am able to successfully generate a model on an older computer, yet on my current computer (which I have tried to set up exactly as the old one) the model generation fails but NEURON launches and all other NEURON functionality is fine, yet there are a few files of code missing from the NEURON folder in the model generation. Could anyone help me?

[ted]

I am unaware that SimNIBS does anything with NEURON. Can you point me to a reference that says something about this?

Even so, given that the symptom is failure of SimNIBS, why not ask the developers/maintainers of SimNIBS for help, e.g. at the GitHub repo for SimNIBS?

[kennelly25]

Yes, here is the specific code and the second link is to the full tutorial for their combined use.
https://simnibs.github.io/simnibs/build ... aller.html
https://documentcloud.adobe.com/spodint ... cale=en-us

The reason that I suspect it to not be a simNIBS issue is because simNIBS only job is to generate a mesh file of the brain which is then paired with NEURON to simulate the model of a brain, and this generation is completely fine, the problem lies within the generation of the model files itself, which is done by a matlab program where after the generation is "completed" either there is an error message right where the program checks if there are any issues with NEURON or there is nothing but some files missing from the NEURON folder in the model itself that cause NEURON and Nemo-TMS to not work.

[ted]

The first URL points to stuff that doesn't mention NEURON at all.

The second points to something at documentcloud.adobe.com that returns a

URL provided is expired or invalid.

error message.

Is there a published article, even a pdf at bioRxiv, that says something about this?

[ted]

Ah, Shirinpour et al. 2021. Something Hananeia, Jedlicka et al. were working on.

What version of NEURON was running on the older computer, and what version is running on the new one?

a few files of code missing from the NEURON folder in the model generation

What files would those be? What error messages are generated, if any?

[kennelly25]

Both the old and new computer are running on the same version NEURON 8.2. https://github.com/OpitzLab/NeMo-TMS, this is a link to the github where the full tutorial pdf can be found and this should help give some context. The bugged Neuron folder is missing the files init_con.hoc, init_pp.hoc, init_rec.hoc, neuron_runthis.hoc, a few Dat files specific to the model generation, and finally save_rec.hoc

[ted]

None of those are distributed with NEURON itself. My guess is they're generated by other code that is part of SimNIBS. You need to ask the developers/maintainers of SimNIBS for help.