Linear mixed effects (lme) Matlab toolbox. Implements both univariate and mass-univariate analyses. Jorge Luis Bernal Rusiel, 2012.

If you use these tools in your analyses please cite:

Bernal-Rusiel J.L., Greve D.N., Reuter M., Fischl B., Sabuncu M.R., 2013. Spatiotemporal Linear Mixed Effects Modeling for the Mass-univariate Analysis of Longitudinal Neuroimage Data, Neuroimage 81C, 358-370.

Bernal-Rusiel J.L., Greve D.N., Reuter M., Fischl B., Sabuncu M.R., 2012. Statistical Analysis of Longitudinal Neuroimage Data with Linear Mixed Effects Models, Neuroimage 66C, 249-260.

in addition to (for the longitudinal image processing):

Reuter M., Schmansky N.J., Rosas H.D., Fischl B, 2012.Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis, NeuroImage 61(4), pp. 1402-1418, 2012, http://dx.doi.org/10.1016/j.neuroimage.2012.02.084

These Matlab tools are freely distributed and intended to help neuroimaging researchers when analyzing longitudinal neuroimaging (LNI) data. The statistical analysis of such type of data is arguable more challenging than the cross-sectional or time series data traditionally encountered in the neuroimaging field. This is because the timing associated with the measurement occasions and the underlying biological process under study are not usually under full experimental control.

There are two aspects of longitudinal data that require correct modeling: The mean response over time and the covariance among repeated measures on the same individual. I hope these tools can serve for such modeling purpose as they provide functionality for exploratory data visualization, model specification, model selection, parameter estimation, inference and power analysis including sample size estimation. They are specially targeted to be used with Freesurfer's data but can be used with any other data as long as they are loaded into Matlab and put into the appropriate format.

The lme Matlab toolbox is also distributed within Freesurfer since Freesurfer's v5.2 release. An optional sample dataset which can be used to become familiar with the LME Matlab tools can be found at ftp://surfer.nmr.mgh.harvard.edu/pub/data/long_mixed_effects_tools-data.tar.gz

Please take a look at the wiki for more info on the usage of this toolbox.