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GabrielKP / enc

The encoders
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Encoding Models

A project reproducing endocing models published by LeBel et al. 2023.

documentation Code style: black

Report

We have documented the results of the project in our encoding report

Setup

# setup up conda environment and install git-annex
conda create -n enc python=3.9 conda-forge::git-annex
conda activate enc

# install dependencies
pip install -r requirements.txt

# install pre-commit
pre-commit install

# run pre-commit against all files once
pre-commit run --all-files

# Copy the config
cp config.example.yaml config.yaml

Download data

# download empty dataset (ideally not within this repository)
cd <separate-data-dir>
datalad clone https://github.com/OpenNeuroDatasets/ds003020.git
cd ds003020

# Edit config.yaml such that your data path points to the ds003020 repository

# Stories: https://www.nature.com/articles/s41597-023-02437-z/tables/1
datalad get derivative/preprocessed_data/UTS02/alternateithicatom.hf5
datalad get derivative/preprocessed_data/UTS02/souls.hf5
datalad get derivative/preprocessed_data/UTS02/avatar.hf5
datalad get derivative/preprocessed_data/UTS02/legacy.hf5
datalad get derivative/preprocessed_data/UTS02/odetostepfather.hf5
datalad get derivative/TextGrids/alternateithicatom.TextGrid
datalad get derivative/TextGrids/souls.TextGrid
datalad get derivative/TextGrids/avatar.TextGrid
datalad get derivative/TextGrids/legacy.TextGrid
datalad get derivative/TextGrids/odetostepfather.TextGrid
datalad get stimuli/alternateithicatom.wav
datalad get stimuli/souls.wav
datalad get stimuli/avatar.wav
datalad get stimuli/legacy.wav
datalad get stimuli/odetostepfather.wav
datalad get derivative/pycortex-db/UTS02/
datalad get derivative/english1000sm.hf5

Setup pycortex (for visualization)

  1. Find out the location of the pycortex config: In the ipython terminal:
import cortex
cortex.options.usercfg

  1. Open the config file (should be a */options.cfg)

  2. Modify the filestore entry to point towards ds003020/derivative/pycortex-db

  3. To use quickshow install inkscape: https://inkscape.org/release/inkscape-1.3.2/

  4. Make sure inkscape is available in the terminal. Instructions Mac

Team

License