[Freesurfer] chose between 5.3 and 6.0

dear FS community: now i have more than 200 subjects which already finished recon-all with 5.3, since 6.0 released, i wonder should i re-run them with 6.0 as lots of changes like different surf-map and registration. i ran a bit of them as test and i found the pial problems were more than 5.3, and it seems some subcortical structures were vanished in the brainmask.mgz, though the aseg.mgz looked good. i wanna ask is my problem serious or it is usual with 6.0, and which version you think is better for cortical volume and surface thickness reserch? best regards

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