Program 3dLME in the AFNI suite is a program that runs FMRI group analysis with a linear mixed-effects modeling approach. One simple criterion to decide whether 3dLME is appropriate  is that each subject has to have two or more measurements at each spatial location (except for a small portion of subjects with missing data). In other words, at least one within-subject (or repeated-measures) factor serves as explanatory variable. Input files for 3dLME can be in AFNI, NIfTI, or surface (niml.dset or 1D) format.

Now 3dLME has been fully revamped with a standard AFNI-style scripting interface. For usage and options, type the following on terminal for details:

3dLME | less

Three examples are provided in the above 'help' document. In addition, more theoretical discussions and examples can be found in the following publication:

Chen, G., Saad, Z.S., Britton, J.C., Pine, D.S., Cox, R.W. (2013). Linear Mixed-Effects Modeling Approach to FMRI Group Analysis. 
NeuroImage, http://dx.doi.org/10.1016/j.neuroimage.2013.01.047

The Group Analysis and its Hands-On slides from AFNI workshop are also good resources for various modeling approaches.