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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