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Dear Antonin, It is difficult to see what’s going on in the images you sent. Would you mind uploading the subject, or at least sending us the image without the segmentation overlaid (and ideally, a sagittal view as well)? Cheers, /Eugenio

-- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Antonin Skoch ansk@ikem.cz Reply-To: Antonin Skoch ansk@ikem.cz, Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 2 July 2019 at 21:43 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Doubts in hippocampal subfields labeling

External Email - Use Caution Dear experts,

I noticed that systematically in most of my subjects there is area in hippocampal region, labeled in aseg as hippocampus, but NOT labeled as hippocampus in hippocampal subfields segmentation (it has zero value there). See screenshots with norm.mgz overlaid by 1) aseg, 2) hippocampal subfields segmentation.

According to T1 and T2 signal, it should neither be white matter and also probably not a ventricle/CSF. Neocortex is not located here. It has similar signal intensity as hippocampus, so I think that it should be hippocampus, but I am puzzled by hippocampal subfields segmentation results there. Why it is not labeled?

Could you please help me to clarify this? My concern is to correctly label this area. I could upload the example subject if it is of any help.

Regards,

Antonin Skoch