Reliability and validity of brain-gastric phase synchronization

Python implementation of the analysis from Levakov et al. 2023 paper, "Reliability and validity of brain-gastric phase synchronization".

Getting started

First make sure you have the following prerequisites:

• Python 3.7+
• FSL
• Docker
• Python packages: numpy, scipy, nibabel, pandas, matplotlib, scikit-learn, nilearn, fslpy, mne-python, bioread, nipype

Prepare the folder structure specified here under Expected folder structure. Copy the data from link to the corresponding folders in the project folder. Copy the code from this repository to corresponding folders in the project folder. Finally, run the main script main_voxel_based.py from the project folder.

Scripts description:

• main_voxel_based.py - screens the subjects and runs list, run all the relevant scripts on all of them, then runs the second level analysis.

• Gastric initial preprocessing:

  • egg_analysis/preprocess_gastric.py - Preprocessing the EGG data

• Brain initial preprocessing:

  • brain_analysis/run_fmriprep.py - Running fMRIprep using Docker SDK
  • brain_analysis/fmriprep_cleaning.py - Confound regression
  • ppu_analysis/add_cardiac_confound.py - Adds cardiac confound to fmriprep confounds file based on niphlem RETROICOR method
  • brain_analysis/brain_preprocessing.py- additional preprocessing steps - spatial smooting + bandpass filtering

• Assessing gastric-brain synchrony:

  • synchrony_analysis/signal_slicing.py - slicing the EGG signal according to the fMRI
  • synchrony_analysis/voxel_based_analysis.py - subject-level analysis of gastric-brain coupling
  • synchrony_analysis/voxel_based_second_level.py - second level analysis of gastric-brain coupling

• Additional important scripts:

  • config.py - defines global variables that are shared across analysis scripts, mainly preprocessing options.
  • dataframes/brain_meta_data.csv - a table listing all runs with relevant meta-data, quality control measures and manual configurations if exist (dominant channel, etc.).
  • gastric_utils.py - EGG processing related functions
  • spect_utils.py - spectrogram related analysis functions

Expected folder structure:

Folder structure inside [main_project_path]:

|-- BIDS_data
|   |-- soroka
|   |   |-- sub-LA
|   |   |-- sub-...
|-- fmriprep
|   |-- out
|   |-- tmp
|   |-- freesurfer
|   |-- run_logs
|-- physio
|   |-- sub-LA
|   |-- sub-...
|-- code
|   |-- egg_analysis
|   |-- brain_analysis
|   |-- ppu_analysis
|-- plots
|   |-- brain_gast
|-- derivatives
|   |-- brain_gast

• BIDS_data - contains the raw data in BIDS format
• fmriprep - contains the fmriprep outputs and temporary files
• physio - contains the electrogastrogram + oximeter data
• code - contains the analysis scripts
• plots - contains the plots generated by the analysis scripts (mainly for quality control)
• derivatives - contains the analysis outputs and intermediate files

Citing

If you use this code, please cite:

Levakov, G., Ganor, S. & Avidan, G. (2023), “Reliability and validity of brain-gastric phase synchronization”, Human brain mapping, (under review).

Issues

Please raise an issue if you have any questions/ comments regarding the code.