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Dear Martin Reuter and Bruce Fischl,

Hi all,

When we use the longitudinal pipeline of FreeSurfer, I know there are three steps: 1. cross-sectional, 2: base, 3: long. When we create the subject template, it uses median and intensity scaling in the second step ("base") based on the paper ("Within-subject template estimation ~"). Considering the base, many processes are initialized in the third step ("long").

Q1) I know when we run the base, isn't there a process to use a function such as mri_convert to adjust the image size for each time to be the same? Could creating the subject template based on the median and intensity scaling minimizes the impact of longitudinal analysis on MRI from different scanners and acquisition parameters?

Q2) In the base, I encountered the following warning, but completed the entire process without errors. ******************************************************************************* WARNING: Image parameters differ across time, maybe due to aquisition changes? Consistent changes in, e.g., resolution can potentially bias a longitudinal study! You can check image parameters by running mri_info on each input image. Will continue in 10 seconds ... ******************************************************************************* There is matrix size for each time point: Baseline (scanner1, 512 x 512 x 244 or 512 x 512 x 180) 1st follow-up (scanner1, 512 x 512 x 180) 2nd follow-up (scanner2, 448 x 448 x 192 or 448 x 448 x 208) Could I ignore the warning? Or is there anything I need to fix before running the long)? Also, could you please give me any suggestions on longitudinal analyses?

Thank you very much

Sincerely, Yoonho