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Dear FreeSurfer team,
We are using the Freesurfer longitudinal pipeline, and we had questions
about accounting for different scanners and acquisition parameters.
We are looking at 3 different timepoints with 2 different scanners (scanner
1 was used for time points 1 and 2, scanner 2 was used for time point 3).
Timepoint 1 (scanner1, 512 x 512 x 244 or 512 x 512 x 180)
Timepoint 2 (scanner1, 512 x 512 x 180)
Timepoint 3 (scanner2, 448 x 448 x 192 or 448 x 448 x 208)
Q1: Does creating the subject template based on median and intensity
scaling help address the issue of different scanners and acquisition
parameters when conducting longitudinal analyses? If it is not sufficient
to address the scanner/acquisition issue, do you have any recommendations
as to next steps to account for this? We have seen others use LongCombat
harmonization or linear mixed effects models to address this issue, is that
something you would consider as well?
Q2: In a similar vein, when we received the warning below in the "base"
step of longitudinal analysis, we were wondering how much it was affecting
our results. Would it be helpful to resample the images? Do you have
suggestions on other avenues we could consider to address this warning and
have robust and reliable results?
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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 ...
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Thank you
Sincerely,
Yoonho
--
*Hwang, Yoonho*
*Research professor*
*Institute of Human Genomic Study,*
*College of Medicine, Korea University*
*#123, Jeokgeum-ro, Danwon-gu, Ansan-si, Gyeonggi-do, **15355, Republic of
Korea.*
*Email: ken.lmsta...@gmail.com <ken.lmsta...@gmail.com>*
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