Dear FreeSurfer community,

I'm currently working on a study involving three groups, each with two timepoints, and I'm interested in analysing vertex-wise cortical thickness using FreeSurfer's longitudinal pipeline. I have already run recon-all, -base, and -long for all subjects.

I would appreciate any clarification or recommendations on the following points:

• Is it appropriate to perform vertex-wise group comparisons after longitudinal processing using mri_glmfit
• Are there any recommended workflows or examples for group X timepoint interaction analysis at the vertex level?
• Is it possible to conduct linear mixed-effects models (LME) at the vertex level within FreeSurfer (e.g., random intercepts for subject), or would this require extracting thickness data and performing the analysis externally (e.g., in R or Python)?
• Can QDEC handle longitudinal vertex-wise analyses involving multiple groups and timepoints, or is it more suitable for simpler designs?

I'd love to know if others have implemented similar longitudinal vertex-wise analyses and whether you used QDEC, custom scripts, or external tools!

Warm regards,

Jackson Lee