1. Harmo- Harmonization step

Linear regression - R 4.2.2  
ComBat - Matlab2020a  
SMA - Matlab2020a  
ICVAE - Python3.6.5  

2. Efficiency(Residual site effect) - Evaluation step

mean and variance of residual site effect -TSP3/CoRR/FCP_SiteStats.m  
covariance of residual site effect - randomforest_predictsite_LOO.m  

3. Identifiability - Evaluation step

To calculate the random chance of identifiability - ChanceLevelCalculation.m, stirling2.m   
Evaluation - Identifiability.R	  

notice：The Identifiability test for SMA target site choices is also in the   
Identifiability.R file.  

4. Test-retest Reliability - Evaluation step

5. Replicability - Evaluation step

statistics - FCP_MalevsFemale.m  
calculate the dice of replicability - DICEall.m  

6. Misuse - Evaluation step

SexinSeparateSites.m  

7. SMA Target site Choice - Practice Experiments

Test-retest reliability of CoRR - CoRR-ChangeTS-TestRetestReliability  
	statistics - TargetSiteChoice.m  
	Calculate dice - Targetsitechoice_Dice.m  
Check if the sample size or distribution of Z variates affect stability - FCP-Bootstrapping-Stability  
	sample size - bootstrappingExps.m  
	distribution - bootstrappingExps2.m  

Harmonization tools

ComBat

Codes:
https://github.com/Jfortin1/ComBatHarmonization

Citations:

1. Jean-Philippe Fortin, Drew Parker, Birkan Tunc, Takanori Watanabe, Mark A Elliott, Kosha Ruparel, David R Roalf, Theodore D Satterthwaite, Ruben C Gur, Raquel E Gur, Robert T Schultz, Ragini Verma, Russell T Shinohara. Harmonization Of Multi-Site Diffusion Tensor Imaging Data. NeuroImage, 161, 149-170, 2017
2. Jean-Philippe Fortin, Nicholas Cullen, Yvette I. Sheline, Warren D. Taylor, Irem Aselcioglu, Philip A. Cook, Phil Adams, Crystal Cooper, Maurizio Fava, Patrick J. McGrath, Melvin McInnis, Mary L. Phillips, Madhukar H. Trivedi, Myrna M. Weissman, Russell T. Shinohara. Harmonization of cortical thickness measurements across scanners and sites. NeuroImage, 167, 104-120, 2018
3. W. Evan Johnson and Cheng Li, Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics, 8(1):118-127, 2007.

CovBat

Codes:
https://github.com/andy1764/CovBat_Harmonization
Citation:
Chen, A. A., Beer, J. C., Tustison, N. J., Cook, P. A., Shinohara, R. T., Shou, H., & The Alzheimer's Disease Neuroimaging Initiative (2022). Mitigating site effects in covariance for machine learning in neuroimaging data. Human Brain Mapping, 43(4), 1179–1195. https://doi.org/10. 1002/hbm.25688

SMA

Codes:
https://github.com/hzhoustat/PNAS2018
Citation:
https://www.pnas.org/doi/full/10.1073/pnas.1719747115