diff --git a/README.md b/README.md index bb6a93c..aa2117a 100644 --- a/README.md +++ b/README.md @@ -2,24 +2,38 @@ 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 + +**Measuring brain beats: cardiac-aligned fast fMRI signals.** +Dora Hermes, Hua Wu, Adam Kerr, Brian Wandell, *Human Brain Mapping 2022* + +Please cite this work when using the code. ## Download data - Data related to this manuscript are located on OpenNeuro: -doi:10.18112/openneuro.ds004213.v1.0.0 +Data related to this manuscript are located on [OpenNeuro](https://openneuro.org/datasets/ds004213). -Download data and save them in the /local/BrainBeat folder in this repository. +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 +Run: `main_createFigures.m` + +Figures will be saved in: `/BrainBeat/local/BrainBeat/derivatives/figures/` + +## Dependencies + +General toolboxes +- [vistasoft](https://github.com/vistalab/vistasoft) +- [bids-matlab](https://github.com/bids-standard/bids-matlab) +- [spm12](https://github.com/spm/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 -Figures will be saved in: -/BrainBeat/local/BrainBeat/derivatives/figures +## Notes on data and BIDS formatting -## Notes on BIDS formatting +Anatomical MRI images were de-identified using the [mri_reface](https://www.nitrc.org/projects/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. @@ -30,17 +44,6 @@ Physio data include PPG, RESP in all subjects and cardiac ECG measurements in a - 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. -## Dependencies - -General toolboxes -- vistasoft: https://github.com/vistalab/vistasoft -- bids-matlab is located in utilities/external for reading tsv and json files (source: https://github.com/bids-standard/bids-matlab) -- spm12: https://github.com/spm/spm12 (addpath to this and run spm('Defaults','fmri')) - -Matlab toolboxes: -- signal processing toolbox -- statistics toolbox -- image processing toolbox ## Contact Dora Hermes: dorahermes@gmail.com