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Dear Freesurfers,
I hope this email finds you well. I am writing to you because I have concerns about how acquisition parameters are biasing the results of a longitudinal study I am running on Niftis that I have processed with Synth_SR.
Specifically, when I run the -base command, I receive a message indicating that the scan parameters do not match and that this may bias the results. As a test, I compared longitudinal MRIs for one subject using both T1 and FLAIR scans. I then used the long_mris_slopes function on both pairs and compared the resulting long.volume-pc1.FWHM10.fsaverage.mgh files. Surprisingly, I found that the areas of significance were different between the two scans.
This suggests that the acquisition parameters used in the scans are biasing the results of my longitudinal study. I am therefore seeking advice on how to correct for this issue. Do you have any recommendations or best practices for ensuring that acquisition parameters do not bias longitudinal study results? Any advice or guidance you can provide would be greatly appreciated.
Thank you for your time and consideration. I look forward to hearing back from you soon.
Best regards, Nicolas