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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
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