Thank you @Andrew,

I have segmented again my images with the longitudinal pipeline from the dev version, and now I have a good agreement between the volumes segmented with the cross-sectional and longitudinal pipeline.

I would like to try this implementation as well to compare the results.

Can I simply make a copy of the directories from recon-all and recon-all -long, delete the files from the old segmentHA and run the new segment_subregions? or should I re-run the whole recon-all?

Regards, Andrea Dell'Orco

-- Andrea Dell'Orco Wissenschaftlicher Mitarbeiter

Neuroradiologie Charité – Universitätsmedizin Berlin Charitéplatz 1, D-10117 Berlin

Interne Besuchsadresse: CCM, Luisenstr. 7

________________________________________ From: Hoopes, Andrew AHOOPES@mgh.harvard.edu Sent: Monday, July 25, 2022 5:22:21 PM To: Freesurfer support list; Dell Orco, Andrea; Iglesias Gonzalez, Eugenio Subject: Re: [Freesurfer] [ext] Amygdala Subfields - longitudinal volumes differ a lot from the cross-sectionals

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_0S...

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 Charitéplatz 1, D-10117 Berlin Tel +49 30 450 560 185 Fax +49 30 450 7 560 280 Interne Besuchsadresse: CCM, Sauerbruchweg 5, E2

http://secure-web.cisco.com/1F0p6iM7RaFZ9LS84INNpTbTRMLmoNAJurIRelhgOdUD-v6s...

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