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Thank you for the prompt reply!
Should I spatially smooth as part of the RepeatedMeasuresAnova? I saw that it is optional. But I wonder why.  
I already used -qcach as part of recon-all. So I do not need anything from this script and I can skip it, right?
mri_surf2surf --s fsaverage --hemi lh --fwhm 5\ --sval lh.thickness.mgh \ --tval lh.thickness.sm05.mgh

Also, we were considering LME in Matlab as well before reading your response about RepeatedMeasuresAnova.
Do you think that is "good enough" for publication purposes? Or LME is the preferred method. 

Thank you!

Best regards,
Eszter




Douglas N. Greve <dgreve@mgh.harvard.edu> ezt írta (időpont: 2026. febr. 13., P, 17:58):
The first one is a more complicated model that includes a mixed effects design. Harder to set up.
The second is a paired ttest; this is simple and  good if you only have two time points.
For three time points I would use https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova



On 2/13/2026 1:22 PM, Eszter Boros wrote:

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Dear FreeSurfer Team,

We are trying to run some longitudinal data using FreeSurfer 7.4.1.
We have one group and 3 scans. We would like to see the changes between these timepoints. 
I am not sure how to proceed with the GLM because I found two tutorials.

One here is saying I should create a longitudinal qdec table including fsid-base column and years/timepoints then run mri_glmfit --osgm

The other one is saying to do a paired analysis. This one does not include the base and years data. 

How should I proceed?
Thank you!

Best regards,
Eszter



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