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 https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel https://secure-web.cisco.com/12qS0acHTgwXhZDIytchwCnsXkPJ57shyJ2uQEuf0WkwB9mHKD_F025ScXa3x_w6UTTa033qwm9kh39bvL8QtSvm8CzIADZLkiusS96akb1z7Siecnj7s395hVQx4WyNGElMWwb5UKSw3mj-CbSpGMOKq3YCyjB9ujY2NWo0MWY1Vhhq37r9GIi0_ozz0pFf6kISjrCpP2gtQ4TraV2331sVFRPyTvzn4MrLoSitQycAeOPXH9hHu8ZnMwgdRSeIExNfOYfuHghbnsJJq87iJb0iR7b1qKZO_NbkvTRmuxKJL3coCXnVN9HVgiWtgh7U8lO6tJwVADL19Th516PqsyQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalTwoStageModel
The other one is saying to do a paired analysis. This one does not include the base and years data. https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis https://secure-web.cisco.com/1voT6D0EOLTXJrVgGSmPK-onn8JIxg74dwxqLG9An8DuChONQTsGe_Ofrr8nuwU-pri3bChh8YFXTyJ9ZinYiCLKxWXtDm2HnFq-Z9QFa0hy8KhVjsDJ5vAtZWGokRHhPQD_rDPKdYl1iAbMIIAtei1aXlzfgpfB5x61LVSxzxTMT_9qREac9pwiqNLZ7c1H_bCt-iJlBnAqBR9BXIOAbpHKJWzarwCGRO9ys1uXBGar4DfjHmoSBozw1WA8mud3SeKpgobTnFDkAA9MK2rQn8nk0V703KLn6BKSkpTNKRMmeFeneh_h0HcLXp4cAjLtzZjsqqlGJLtQSBpWXKFowOA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPairedAnalysis
How should I proceed? Thank you!
Best regards, Eszter
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