# 9.10. **Linear Mixed-Effects (LME) Modeling**¶

## 9.10.1. Introduction¶

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