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Hello Freesurfer users/experts,
I am working with Freesurfer 7.4.1 on a MacStudio (macOS 15.2). Our team has longitudinal data with 3 time points (e.g., T1, T2, T3), which has been analyzed with the main FreeSurfer longitudinal stream. So we have: ID_base (within-subject template), ID_T1.long, ID_T2.long, ID_T3.long.
We decided to look at the thalamic nuclei, but we are not sure how to run it for the 3 time points.
1) Can we just run the segmentThalamicNuclei.sh on ID_T1.long, ID_T2.long and ID_T3.long? (without using the base)
2) Or: Are we supposed to run it on the base/ (within-subject template) first and that will transfer to T1/T2/T3_long data? Are we supposed to run the recon-all -long again to get the thalamic nuclei data for the 3 timepoints?
I guess the second option would not be that productive because we need to rerun the longitudinal runs and edit the data again (to correct the pial surfaces etc.).
Thank you for your help!
Sincerely, Isa Rossellini