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Dear Freesurfer developers and users,

I am running the freesurfer recon-all pipeline for a big dataset and I am particularly interested in the hippocampus. For 20% of my subjects the hippocampus along with other subcortical structures are misplaced in the aseg.mgz image, which affects also the subsequent subfield analysis.

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I was wondering which steps must be followed to fix this and which surfaces need to be corrected.

So far I have corrected/checked the initial brain mask and added control points to the analysis but there is no difference in the end result.

I would be grateful if you could let me know how to tackle this issue. Apologies if a similar question has been asked in the past and I missed it.

Best Wishes,

Marialena