The easiest thing is to just run mri_preproc on the baseline scans to create a baseline stack. Then pass the baseline stack to the mri_segstats command below with --i

Dear Freesurfer Experts,

I ran a longitudinal Cth analysis and found a cluster with significant spc differences between two groups.  It was easy to obtain the mean spc values in that cluster for all the subjects. However,
I would also like to have a spreedsheet with the baseline mean Cth values in that cluster for all my subjects to correlate with other clinical measures.

My attempt was:

mri_segstats --i SPC_ANALYSIS_FOLDER/y.mgh --seg SPC_ANALYSIS_FOLDER/SUBANALYSIS/mc-z.abs.th13.sig.cluster.mgh --excludeid 0 --sum CTH_inSPC_cluster.sum

But obviously this is not the correct way to obtain for each subject the mean Cth value in that cluster.

Any help would be much appreciated!

Thanks a lot in advance,

Fred

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