Getting PEPPER set up - Githubissues

To start running PEPPER, clone and switch to the dev branch which includes our most relevant work:

git clone https://github.com/NDCLab/pepper-pipeline.git
cd pepper-pipeline 
git fetch
git checkout dev

Afterward, you can set up the "docker" container which allows for quick environment set-up to reliably run the pipeline. Detailed instructions here.

By default the repo does not contain a large EEG BIDS data set, but for a sample run, we can use the data located in the test folder. The "load_data" section of the "input_config.json" file can be set up like so to access this sample data located in scripts/tests/test_bids_data.

"load_data": {
        "root": "scripts/tests/test_bids_data",
        "output_root": "CMI",
        "subjects": ["*"],
        "tasks": ["*"],
        "exceptions": {
            "subjects": "",
            "tasks": "",
            "runs": ""
        },
        "channel_type": "eeg",
        "exit_on_error": false,
        "overwrite": true,
        "parallel_runs": 1
    },

NDCLab / pepper-pipeline

Getting PEPPER set up #428