Can you tar or zip the subject's folder and upload here.   ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming When the upload is complete, send an email to us and indicate the name of the file.

On 3/14/19 7:27 AM, Maria-Eleni Dounavi wrote:

External Email - Use Caution

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

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