Overview

This repository hosts the example notebooks that are included as a companion to the paper Kumar et al. (2020) BrainIAK: Brain Imaging and Analysis Kit. Instructions for running each analysis (including links to the relevant datasets and setup instructions) are included as part of each notebook.

Contents

The following notebooks are included in the repository (section numbers from the paper are noted in parentheses):

1. Intersubject Correlation (ISC; Section 2.1)
2. Shared Response Model (SRM; Section 2.2)
3. Full Correlation Matrix Analysis (FCMA; Section 2.3)
4. Bayesian Representational Similarity Analysis (BRSA; Section 2.4)
5. Event Segmentation (Section 2.5)
6. Topographic Factor Analysis (TFA; Section 2.6)
7. Inverted Encoding Model (IEM; Section 2.7)
8. Simulating Realistic fMRI Data (fmrisim; Section 2.8)
9. Matrix-Normal Models (Section 2.9.2)
10. Real-Time fMRI Analysis (Section 3)

Installation

Step 1. You need to install BrainIAK and related software to run these example notebooks. To install the software and configure an environment to run Jupyter notebooks, we have provided a variety of installation options as part of the BrainIAK tutorials: https://brainiak.org/tutorials.

Step 2. Once you complete installation in Step 1, you are ready to use the example notebooks in this repository (after you complete the steps below) and the associated data needed to run them.

Download Example Notebooks

To download these example notebooks, execute this command on your terminal:

git clone https://github.com/brainiak/brainiak-aperture.git

Data

The notebooks include instructions for downloading and using data. All the data used is publicly available.

The following example notebooks require a different installation sequence.

1. The TFA notebook comes with its own Docker container, that includes all data and software required to run the notebook. You can follow the installation instructions in the notebook to run it.

2. The Real-Time fMRI Analysis notebook requires installing a web server, the instructions for which may be found here.

License

Like BrainIAK itself, these example are open-sourced and can be freely used, modified, and shared. They are licensed under the Apache License, Version 2.0.