A toolbox to quantify and adjust for session and site effects in fMRI time-series

This toolbox implements a number of approaches to correct fMRI time-series or volumes for session specific artifacts and site effects, aka "batch Effects".

Contents

This toolbox has 3 types of functions.

• Primary functions to measure reliability, implement alternatives to the standard correlation matrix that adjust for nuisance variation or artifacts.

• Demo functions that illustrate the function API and usage of primary functions. These functions start with demo_

• Analysis functions that perform a detailed case study of a particular method or pipeline on a dataset. These functions start with analyze_

Primary functions

• siteEffects: A class containing useful methods for diagnosis of site effects and other metrics of improvement.

  • siteEffects.within_group_error()
  • siteEffects.test_retest_mccc()

• projpca, demo_projpca: Multivariate correction on time-series data tensor. Provides residual time-series after regressing out site effects can be used to infer correlation matrices. Disclaimer: This function is still being tested, unfinished.

Demo functions

• demo_successive_normalization: Demonstrates examples of calling ggmClass for data cleaning and correlation estimation. Is a wrapper around local functions that combine different forms of standardization of data matrix with a variety of covariance estimators. Exported figures can be found in tmp/<date>/demo_successive_norm_*.png

• demo_conditional_correlation.m: Demonstrates examples of calling ggmClass for data cleaning and correlation estimation. Is a wrapper around local functions that perform factor model based decomposition of the observed covariance by conditioning on covariates.

• demo_robust_covariance.m: Demonstrates examples of calling ggmClass to call robust estimators of the covariance or correlation matrix.

Analysis functions

• analyze_etkinlab_sessioneffects.m: To be documented

• analyze_etkinlab_siteeffects.m: To be documented

• analyze_abide_siteeffects.m: To be documented

Installation

Use the --recursive setting to make sure the ggmClass and connectivity-diagnostics submodule are added. Disclaimer: You will need to have keyless ssh login to github to access private repositories.

git clone --recursive git@github.com:TheEtkinLab/fmri-site-effects.git

Modify setup.m to specificy paths to matlab-library or your local equivalent. To add package dependencies, run setup using

run('setup.m')