Demo

This deom will run the docker image of bidsMReye on the fmriprep preprocessed data of the SPM MOAE dataset (that you can find on the open science framework).

For Linux or MacOS you can use make to get the data of the demo.

make tests/data/moae_fmriprep

For Windows you will have to download the data manually.

• data

  • URL: https://osf.io/vufjs/download

  • destination folder: tests/data/moae_fmriprep

The directory where you want to run the demo should look like this:

└── tests
    └── data
        └── moae_fmriprep
             ├── logs
             └── sub-01
                 ├── anat
                 ├── figures
                 └── func

Preparing the data

Extracts the timeseries from the eye mask in the preprocessed fMRI images.

docker run --rm -it \
      --user "$(id -u):$(id -g)" \
      -v $PWD/tests/data/moae_fmriprep:/home/neuro/data \
      -v $PWD/outputs/moae_fmriprep/derivatives:/home/neuro/outputs/ \
            cpplab/bidsmreye:latest \
            /home/neuro/data/ \
            /home/neuro/outputs/ \
            participant \
            --action prepare

Computing the eye movements

This step will use the extracted timeseries to predict the eye movements using the default pre-trained model of deepmreye.

docker run --rm -it \
      --user "$(id -u):$(id -g)" \
      -v $PWD/tests/data/moae_fmriprep:/home/neuro/data \
      -v $PWD/outputs/moae_fmriprep/derivatives:/home/neuro/outputs/ \
            cpplab/bidsmreye:latest \
            /home/neuro/data/ \
            /home/neuro/outputs/ \
            participant \
            --action generalize