Dear Victor,

We model the alveus in the atlas but don’t write it in the final segmentation because it’s unreliable and tends to leak out (mostly because of partial voluming, which messes up parameter estimation and segmentation).

If you have small holes in the CA1 region over bright pixels, they have most likely been segmented as alveus. If they are black (cysts), they get segmented as CSF.

If the rest of the anatomy looks good, it’s OK to use these cases in your analyses.

Cheers,

/Eugenio

On 22 Jun 2021, at 09:51, Zeng, Victor (BIDMC - Keshavan - Psychiatry) <vzeng@bidmc.harvard.edumailto:vzeng@bidmc.harvard.edu> wrote:

​Hi,

Sometimes I see empty space inside the CA1 in the FS7 hippo parcellations. These are voxels of bright intensities. Is this where the alveus is supposed to be labelled and are these brain scans that we should still be using for hippo?

Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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