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When you do the corrections for multiple comparisons, you will get a file with "ocn" in the name. This is the output cluster number where the vertices have values 0 to NumberOfClusters. You can use this with mri _segstats to extract the values from the input subjects, eg,
mri_segstats --seg ocn.mgh --i thickness.lh.stack.tp1.mgh --avgwf thickness.lh.stack.tp1.dat --excludeid 0
The output thickness.lh.stack.tp1.dat will be a table of data where each row is a subject and each column is a cluster matched to the .sum file
It is assumed above that thickness.lh.stack.tp1.mgh is the stack of thicknesses from all your subjects for time point 1, you can do the same for tp2

On 4/20/2023 12:56 AM, Eszter Boros wrote:

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Dear FreeSurfer Team,

        
We are doing a longitudinal analysis with Freesufer 7.1.1 (two-stage longitudinal model), and  we would like to extract the Cortical thickness values from the significant clusters (before and after treatment changes) to visualize the individual values/changes.

        
I am wondering how I can do that?

        

        
Please let me know if you need any more information.

Thank you for your answer in advance!

All the best,
Eszter Boros

      

      

      

      
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