BrainBeat

This repository contains functions to do the analyses and generate figures from the manuscript titled:

Measuring brain beats: cardiac-aligned fast fMRI signals. Dora Hermes, Hua Wu, Adam Kerr, Brian Wandell, Human Brain Mapping 2022 https://doi.org/10.1002/hbm.26128

Please cite this work when using the code.

Download data

Data related to this manuscript are located on OpenNeuro.

Download data and save them in the /local/BrainBeat/ folder in this repository.

Recreate figures from the manuscript

Add appropriate paths (see notes on dependencies below) Run: main_createFigures.m

Figures will be saved in: /BrainBeat/local/BrainBeat/derivatives/figures/

Dependencies

General toolboxes

• vistasoft
• bids-matlab
• spm12, never use genpath when adding SPM in your matlab path, always addpath to the main SMP folder and run spm('Defaults','fmri'))

Matlab toolboxes:

• signal processing toolbox
• statistics toolbox
• image processing toolbox

Notes on data and BIDS formatting

Anatomical MRI images were de-identified using the mri_reface function from Christopher Schwarz.

Slice timing

The _bold.json file contains a field with the SliceTiming. This is essential to get the timing accuracy for every slice.

Physio data

Physio data include PPG, RESP in all subjects and cardiac ECG measurements in a few subjects. Sampling frequencies differ across subjects and these data have to be stored in different .tsv.gz files in the BIDS format.

• PPG physio files have to have the same name as the recording plus a _recording-PPG label.
• RESP physio files have to have the same name as the recording plus a _recording-RESP label.
• ECG physio files have to have the same name as the recording plus a _recording-ECG label.

Contact

Dora Hermes: dorahermes@gmail.com