Installation guide

This install setup is tested for Linux (Ubuntu) with a GPU.

It is recommended to create an anaconda environment and install all sources there. For this, please go to anaconda and install. After you’re done with installing anaconda, please setup the environment for the eeg-to-fmri package with:

source $PATH_TO_ANACONDA/bin/activate
conda create -n eeg_fmri python=3.8
source $PATH_TO_ANACONDA/etc/profile.d/conda.sh
conda activate eeg_fmri

If you installed anaconda at /home/you/anaconda3 then that is your $PATH_TO_ANACONDA variable.

Following, let us setup cuda and cudnn. Download cudnn:

wget https://developer.download.nvidia.com/compute/redist/cudnn/v8.0.1/cudnn-11.0-linux-x64-v8.0.1.13.tgz

Install cudatoolkit==11.2 available at conda-forge:

conda install -c conda-forge cudatoolkit==11.2

And setup cudnn:

tar -xzvf cudnn-11.2-linux-x64-v8.1.1.33.tgz
mv cuda/include/cudnn*.h $CONDA_PREFIX/include/
mv cuda/lib64/libcudnn* $CONDA_PREFIX/lib/
rm -r cuda
chmod a+r $CONDA_PREFIX/include/cudnn*.h $CONDA_PREFIX/lib/libcudnn*
mkdir -p $CONDA_PREFIX/etc/conda/activate.d
echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CONDA_PREFIX/lib/' > $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh

Now, you can finally install the eeg-to-fmri package:

pip install --upgrade eeg-to-fmri

Some additional steps are needed to ensure the package runs accordingly. You need to specify the path for your datasets. For instance, I have my datasets at /home/david/datasets/, then the environment variable for the datasets should be EEG_FMRI_DATASETS=/home/david/datasets/. Since this variable only needs to be active, when running the eeg-to-fmri code, please put it in the activate folder, so everytime you activate the environemnt the variable exists.

echo 'export EEG_FMRI_DATASETS=/path/to/datasets/' >> $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh