README.md

fmralign-tutorials

A collection of tutorials for functional alignment methods in fMRI data. This repository does not include implementations of these methods; for this, we recommend BrainIAK, fmralign, or pyMVPA.

Local Installation

To access this material locally, you can download this repository and install the requirements using pip. We recommend that you install these requirements within a virtual environment; for example, the following commands will create a conda environment and install all necessary packages:

git clone https://github.com/neurodatascience/fmralign-tutorials
cd fmralign-tutorials
conda create --name fmralign-tutorials python=3.6
source activate fmralign-tutorials
pip install -r requirements.txt

You can render the tutorials using Jupytext, which provides a convenient means to sync the user-friendly notebook interface with a git-friendly MyST markup.

For example, for the 03-procrustes tutorial, simply run:

jupytext 03-procrustes.md --to notebook
jupytext --set-formats md:myst, ipynb 03-procrustes.md
jupytext --sync 03-procrustes.md 03-procrustes.ipynb

You can then launch the notebook using:

jupyter notebook 03-procrustes.ipynb

All changes you make there will be automatically updated in the associated MyST file.