This might be related to a small bug in the previous longitudinal code, which affected volume rescaling. It should be fixed now. You could try out the new implementation: https://surfer.nmr.mgh.harvard.edu/fswiki/SubregionSegmentation

Best,

Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Andrea Dell'Orco <andrea.dellorco@charite.de>
Date: Tuesday, June 21, 2022 at 10:06 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [ext] Amygdala Subfields - longitudinal volumes differ a lot from the cross-sectionals

        External Email - Use Caution       

Ops I have forgot:

Freesurfer 7.1.1,

no special flags in recon-all.

Just the subjects have a little processing before recon-all, but I do
not think this can lead to some problem only on the left hemisphere.



>          External Email - Use Caution
>
> 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_0S04A9X5thwWY_4fEhSd-jO6E-9ayRY0XOalS_l_UwoZfqgLuPgrHO9gy8-fJwasgdw5jxcsAEvOuetKOo_-ks3z-utNjBwTcyTVJ5QsG_G_hNIZRTFjNQBRP20TZGauK6v3qgy2ecQvHiAn_2Z03W6FA8MNcRcx0-IVMEQLNdBiosVRO60RFuEUover0QGAglNFCOaQ3eJE8ygT8xFwqhEMoHJr7BfVBb3CIlQuvLId91YmGOn-CiLE4kot2e_8d1hQvWN6cJLg5K364kF7Kkj_kAZro5kcdO-ZJthDyjWrATEXDN9DHxb4LW1KZ88/https%3A%2F%2Fcharitede-my.sharepoint.com%2F%3Ap%3A%2Fg%2Fpersonal%2Fandrea_dellorco_charite_de%2FEU3Za9DDG-pDv8XfcB4fBNAB53JTlqbZnzKhSXOnSvBYSQ%3Fe%3DGLKyYP
>
> Do someone has some idea, what can be the problem?
>
> Regards,
>
> Andrea Dell'Orco
>
--
Andrea Dell'Orco
HiWi

Charité – Universitätsmedizin Berlin
NeuroCure Clinical Research Center NCRC

AG Kognitive Neurologie
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