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