don-tpanic / brain_data

Source code for brain data processing and analysis in paper <A controller-peripheral architecture and costly energy principle for learning>

A controller-peripheral architecture and costly energy principle for learning

Description

This is a complementary repo to which focuses on fMRI BOLD data processing and analysis in this research paper.

Structure and main components

This repo can be roughly divided into two parts: fMRI data processing and fMRI data analysis.
For fMRI data processing,

1. bids.py organises raw fMRI datasets into the standard Brain Imaging Data Structure (BIDS).
2. glm.py fits Generalised Linear Models (GLMs) on preprocessed fMRI BOLD data and extracts beta weights for actual analysis.

For fMRI data analysis,

1. roi_rsa.py runs a similar representational similarity analysis in Mack et al., 2016
2. pca.py runs a similar analysis in Mack et al., 2020
3. pca_3runs.py runs a similar analysis in Ahlheim et al., 2018
4. decoding.py runs a similar neural decoding analysis in Braunlich & Love, 2019

Environment setup

1. Create a docker file using neurodocker

neurodocker generate docker \
--pkg-manager apt \
--base-image neurodebian:stretch-non-free \
--arg DEBIAN_FRONTEND=noninteractive \
--install convert3d fsl ants gcc g++ graphviz tree \
        git-annex-standalone vim emacs-nox nano less ncdu \
        tig git-annex-remote-rclone octave netbase \
--spm12 version=r7771 \
--miniconda \
version=latest \
conda_install="python=3.8 pytest jupyter jupyterlab jupyter_contrib_nbextensions
                traits pandas matplotlib scikit-learn scikit-image seaborn nbformat
                nb_conda" \
pip_install="https://github.com/nipy/nipype/tarball/master
                https://github.com/INCF/pybids/tarball/master
                nilearn nipy duecredit nbval" \
> nipype.Dockerfile

2. Build an image based on the dockerfile (make sure the directory where the Dockerfile is is empty). . means using the current directory.

docker build --tag nipype .

3. Start an iterative session inside the image, changes will be removed after exiting.

docker run -it --rm nipype

4. Mount a local directory inside the above container’s diretory. Changes made inside the container will change the local container.
   

docker run -it --rm -v /home/ken/projects/brain_data/:/home/ken/projects/brain_data/ nipype

Attribution

@article {Luo2023.01.16.524194,
    author = {Xiaoliang Luo and Robert M. Mok and Brett D. Roads and Bradley C. Love},
    title = {A controller-peripheral architecture and costly energy principle for learning},
    elocation-id = {2023.01.16.524194},
    year = {2023},
    doi = {10.1101/2023.01.16.524194},
    publisher = {Cold Spring Harbor Laboratory},
}