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Hi Simon,

This could be an issue with the affine registration or the subsequent head masking step in samseg, both of which have been upgraded/improved in the development version.

Would you be able to try the dev version and see if this resolves the issue?

Many thanks,

Koen

On Fri, Jul 30, 2021 at 5:40 AM Simon Jones spj24@cam.ac.uk wrote:

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Dear all

I have tried using SAMSEG in 7.1.1 with 7T MP2RAGE sequence data which has an inv1, inv2 and a uni images and I can create a denoised image which has a more of a traditional T1-weighted appearance. I have got some good looking results combining the uni with the inv2 except for one issue. About 20% have a small hole or slit produced within the frontal lobe. It is like an echo of the frontal sinuses and seems to appear whichever image is input. For others, the hole is outside the brain. Is this just a feature?

Thanks for your help

Simon

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