Question for the dipole moment location

[fatelist82]

Dear representative,

Hello. I attempted to replicate findings from another group (https://github.com/jessierademacher/Ketamine_E-I/tree/main/05_Computational_Modeling/Ketamine_PV_10). My goal was to adapt their script for use with a new condition of disease models. The issue is that when estimating dipole location, I could estimate the spikes ("SPIKES" in the code), but not the moment dipole location ("DIPOLEMOMENT"). I instead had a gid (blank in the code).

My specs are as follows:
Python: 3.10
Neuron: 8.2.7
NFPy: 2.3.6
The code I am working on is saved here: https://github.com/fatelist82/troubleshooting/blob/main/circuit.py

I upgraded the Neuron package to version 9, but the issue persists. Any advice would be greatly appreciated.

Thank You
Sincerely,
Yoojin Lee

[nrnhines]

Are you able to successfully run the Ketamine github repository model on your system?

I notice in the Ketamine github repository, one of the python module requirements is NEURON==7.8.0.119 but that cannot be satisfied for Python 3.10.14

I also cannot satisfy that exactly with python 3.9.21 although I can install NEURON==7.8.2

When I fell back to python 3.7.17, I was able to satisfy that requirement.

$ pyenv shell 3.7.17
$ python -m venv env
$ source env/bin/activate
$ python -m pip install --upgrade pip
(env) hines@hines-ThinkStation-P5:~/tmp$ python -m pip install 'NEURON==7.8.0.119'
...
Installing collected packages: numpy, NEURON
Successfully installed NEURON-7.8.0.119 numpy-1.21.6

I did not take the trouble to clone the Ketamine github repository and see if pip install -r 05_Computational_Modeling/requirements.txt would succeed. I do not know how to run that complicated model or whether I can get results in a reasonable time.

Starting out, I have no idea what you operationally mean by

I could estimate the spikes ("SPIKES" in the code), but not the moment dipole location ("DIPOLEMOMENT"). I instead had a gid (blank in the code).

Are you trying to update a fork of https://github.com/jessierademacher/Ketamine_E-I/tree/main/05_Computational_Modeling/Ketamine_PV_10 so that it runs with Python-3.10 and a modern NEURON?