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Dear FreeSurfer developers,

Hi,

Prior to the FreeSurfer-based longitudinal analysis, it's inevitable that the scanner will change over time in a long follow-up study. We had multiple follow-up data for the same subjects [e.g., baseline and 1st follow-up (scanner 1), 2nd follow-up (scanner 2)].

I applied the longitudinal pipeline of FreeSurfer to the data as follows:

1. Cross-sectional process for each time point
2. Create template (recon-all -base long_base -tp long_tp1 -tp long_tp2 -tp long_tp3 -all -parallel -openmp 4)
3. Longitudinal process

In process 2, 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 are resolutions of our data 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)

Can I ignore the warning? Or is there anything I need to fix before doing process 3 (longitudinal process)?

Also, could you please give me any suggestions on longitudinal analyses?

Thank you very much

Sincerely,

Yoonho

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