[Freesurfer] Amygdala Subfields - longitudinal volumes differ a lot from the cross-sectionals

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Dear all,

I have a Cohort of subjects with multiple time points. I have segmented the T1w with the normal recon-all and sub fields and then with the longitudinal pipeline as described in the wiki.

When I compare the sub fields Volumes, there is a good agreement, with the expected variability,  between longitudinal and not longitudinal for the Whole Hippocampus rh and lh.

The Volumes for the amygdala are on the other hand, really different, especially for the left Whole amygdala.

Here some plots with the correlation longitudinal vs non-longitudinal pipeline: https://secure-web.cisco.com/14VEQLZEbs96z59Y5ty9CueQKgO9cELG9hY62vKSTRXY_0S...

Do someone has some idea, what can be the problem?

Regards,

Andrea Dell'Orco