Hi Barbara, Sorry for the late response. - the type of sequence does not matter much as long as the contrast between gray and white matter is good. - the resolution is important, because you need to be able to see the internal thin layer of white matter in the hippocampus to be able to infer its internal structure; otherwise, the segmentation of the internal boundarie will indeed be dominated by the prior knowledge, rather than the intensities. - the algorithm operates at 0.33mm (isotropic) resolution; the segmentation is provided both at that resolution and at 1mm isotropic (FS space); please see the details in the wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields If you send me the T2FLAIR and T2STIR images for a sample subject, I can take a look and give you more accurate answers ;-) Cheers, Eugenio

Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu

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From: "Barbara Kreilkamp" bakk.hbg@googlemail.com To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Friday, April 22, 2016 5:28:44 PM Subject: [Freesurfer] hippo subfield segmentation new beta version (version 6)

Dear all,

Would you please help me on this one? Thank you, best wishes, Barbara

-------- Forwarded Message -------- Subject: hippo subfield segmentation new beta version (version 6) Date: Wed, 20 Apr 2016 11:45:02 +0100 From: Barbara Kreilkamp bakk.hbg@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu

Dear all,

I've been reading the manuscript on version 6 freesurfer hippocampal subfield segmentation "A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: application to adaptive segmentation of in vivo MRI"

Can you please tell me if the type of sequence (e.g. coronal T2FLAIR vs T2STIR) and voxel sizes of .4x.4x2mm^3 vs .4x.4x4mm^3 really make a difference for this multi-modal algorithm? I previously ran recon-all on 1mm isotropic T1-w scans all with similar contrast.

It seems that the mesh fitting in version 6 is driven by the relation of the subfields to each other rather than by contrast or signal intensities; and also I notice the algorithm brings everything to isotropic space anyway.

Is this correct? Do you see a major methodological issue when using T2FLAIR (.4x.4x4mm^3) and T2STIR (.4x.4x2mm^3) subfield volumes together?

Thank you very much, Best wishes, Barbara

P.s. as a side-note, I've not noticed any major differences in subfield segmentations visually, when comparing segmentations via these two different T2 scans.

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