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fMRI Decoding

Code for the article "Comprehensive decoding mental processes from Web repositories of functional brain images", published in Nature Scientific Reports 2022.

Installation

  • Setup a virtual environment (conda, virtualenv, pyenv, ..) and install requirements 
    virtualenv venv -p python3.6
. venv/bin/activate
pip install -r requirements.txt
  • If you have Neurovault already downloaded on your machine, create a symlink in the Data/ folder 
    sudo ln -s /path/to/already/downloaded/neurovault Data/neurovault
    Note: For Parietal users, Neurovault is already downloaded at /storage/store2/data/neurovault on Drago.
  • Add folder path to the PYTHONPATH 
    export PYTHONPATH="$(pwd):$PYTHONPATH"

Experiments

All scripts to perform the experiments are stored in the Experiments/ folder. In particular:

  • the a_preparation_pipeline script performs all preprocessing for images and labels
  • the b_decoding_experiment script performs training (from the output of the previous scripts)
  • the c_plot_perf_and_models generate some figures of the paper

For explanations on each argument, you can call python {a_preparation_pipeline.py|b_decoding_experiment.py|c_plot_perf_and_models.py} --help