Update README.md

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: [email protected]