Wrapper for covbat library
Covbat is intended to correct for batch effects in functional connectivity data. Specifically, it is intended to remove scanner specific effects from functional connectivity data, so that effects of other covariates that may correlate with site or scanner are not masked by scanner effects.
The covariates themselves are not altered by running this wrapper, only the FC data is.
Wrapper to covbat.py script in MATLAB.
covbat.py script based from https://github.com/andy1764/CovBat_Harmonization/tree/master/Python with modification to correct deprecated 'iteritems' method.
Artistic License 2.0
Install python3 on your machine (tested with Python 3.8) pip install pandas (if necessary) pip install -U scikit-learn (if necessary) pip install patsy (if necessary)
covbat.py: Modified version of covbat python library covbatScript.py: Python wrapper script that is called from MATLAB runCovbatWrapper.m: MATLAB function that takes in FC data and covariates table and runs covbat on it testCovbatWrapper.m: Example script on running the covbat wrapper on random junk data
Note: covbat.py has been modified from original to replace deprecated 'iteritems' method
Note: The wrapper will generate temporary text data files in a new folder called 'tempCovbatFiles'. You shouldn't need to open or modify these files, they are only for passing data between python and matlab