Whole-Project Neuralynx to NWB Converter

This is a work in progress script to automate conversion for the “vStr_phase_stim” project by Manish Mohapatra of Dartmouth College. It is best used from the live HEAD as it is subject to active development.

Installation

Fetch the newest version git and install it using setuptools (this will also allow you to use changes you manually make to the repository files):

git clone git@github.com:TheChymera/neuralynx_nwb.git
cd neuralynx_nwb
echo "export PATH=\$HOME/.local/bin/:\$PATH" >> ~/.bashrc
source ~/.bashrc
python setup.py develop --user

If you are getting a Permission denied (publickey) error upon trying to clone, you can either:

• Add an SSH key to your GitHub account.
• Pull via the HTTPS link git clone https://github.com/TheChymera/neuralynx_nwb.git.

Usage

The fundamental usage of the data conversion (assuming data is located under the default path) can be initiated via:

python -c 'import convert; convert.reposit_data(debug=True)'

Data

The conversion tool currently uses the vStr_phase_stim data, which (unless another path is given via the data_path parameter) should be located under an eponymous directory inside ~/.local/share/datalad/, i.e. ~/.local/share/datalad/vStr_phase_stim. If the data collecition is too large for the user home directory, or is shared with other users on the machine, it can be located under a different partition (e.g. /mnt/data/datalad) and a symlink can be created for ~/.local/share/datalad/ to point to that location. The example command for these paths would be:

ln -s /mnt/data/datalad ~/.local/share/datalad