README.md

q1k_eeget_init

Initialization code for the EEG/ET data from the Q1K project.

clone stuff

git clone https://github.com/lina-usc/q1k_eeget_init.git

do the installs, etc...

cd q1k_eeget_init
python3 -m venv env
source env/bin/activate
python -m pip install --upgrade pip
pip install mne
pip install -r ./q1k_eeget_init/requirements.txt
pip install -e .

download the raw session files from the remote cluster...

On a local computer navigate to the project path and download the raw session files to the sourcefiles folder

For example if the "q1k" folder is in your home directory:

cd ~/q1k/pilot/q1k-external-pilot
scp -r <username>@narval.computecanada.ca:/project/def-emayada/q1k/pilot/q1k-external-pilot/sourcefiles/012_1 sourcefiles

perform the init procedure...

open the q1k_eeget_init.ipynb in VSCode and follow the instructions..

upload the BIDS raw data file to the remote cluster for pylossless processing...

If it is the first task of the session being processed upload the entire folder... e.g.

scp -r ~/q1k/pilot/q1k-external-pilot/sub-012 <username>@narval.computecanada.ca:/project/def-emayada/q1k/pilot/q1k-external-pilot

If the session already has a folder on the remote cluster just upload the specific files... e.g.

scp -r ~/q1k/pilot/q1k-external-pilot/sub-012/ses-01/eeg/*_task-vp_* <username>@narval.computecanada.ca:/project/def-emayada/q1k/pilot/q1k-external-pilot/sub-012/ses-01/eeg
scp -r ~/q1k/pilot/q1k-external-pilot/sub-012/ses-01/*_scans.tsv <username>@narval.computecanada.ca:/project/def-emayada/q1k/pilot/q1k-external-pilot/sub-012/ses-01

... then running the pylossless pipeline on the raw BIDS session is handled by the q1k_pylossless package at...