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Hi AJ,

The longitudinal stream does not account for inter-scanner variability, but does reduce biases related to registering subsequent timepoints to the initial one.

Perhaps longitudinal experts could confirm, but I would run the longitudinal stream, then account for scanner differences afterwards.

-Paul

On Sun, Jul 4, 2021 at 10:03 AM AJ <ajcns1969@gmail.com> wrote:

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Hi,
I am running Freesurfer on longitudinal datasets all obtained on 3T scanners. Unfortunately,  many of the MRIs were done on different scanners,  Phillips and GE.   
Would longitudinal pipeline help reduced scanner variability or should I process crossectionally each time point separately and normalize these time points with eTIV?

Many thanks
AJ
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