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Thanks, Antonin. The ASEG has definitely oversegmented the hippo. Those large regions were ASEG and the subfield module disagree are mostly partial voluming of the lateral ventricle and the cerebral white matter or the fimbria, and are thus NOT hippocampus. Having said that, it is also true that the subfield module undersegments the fimbria a bit; I’m pretty sure this is because some of the fimbria voxels (the most lateral ones) get assigned to the alveus instead (which we don’t shown in the segmentation, as it’s not very reliable…) I hope this helps, /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: Thursday, 4 July 2019 at 07:31 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Doubts in hippocampal subfields labeling

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Dear Eugenio,

I have uploaded the subject as file hippocampal_subfields_labeling.tar.gz to your server surfer.nmr.mgh.harvard.edu. RAS coordinates of the unlabeled area are -31,-27,-9. Thank you in advance,

Antonin

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.comhttps://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jeiglesias.com&data=02%7C01%7C%7C43a65c8534384affac9e08d700493365%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636978186706804839&sdata=IQZT2941gn6uS8bagfzRYCl1zHYj2Nr6QD0A9QbSzfo%3D&reserved=0

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Antonin Skoch

a...@ikem.cz

Reply-To: Antonin Skoch a...@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

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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