On 6/16/2025 3:29 AM, Jackson Lee wrote:

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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

Yes

• Are there any recommended workflows or examples for group X timepoint interaction analysis at the vertex level?

https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova also see mris_long_slopes (which uses a QDEC file).

• 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)?

yes, I'm cc'ing Martin Reuter who has some tools to do this.

• Can QDEC handle longitudinal vertex-wise analyses involving multiple groups and timepoints, or is it more suitable for simpler designs?

QDEC is defunct now

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

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