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Are these really holes or are they connected to the background? If you see a hole, you can scroll through the 3D volume and "follow" the hole to see if you end up in the background.

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Dear experts,

I am using fslmaths -fillh -bin to create a binary mask of the brain tissue, however, I still see some holes in the mask when I am looking at the axial view. Is there any way to fill the holes even if they are not forming a completely closed boundary (volume)?

Thank you!

Mahmoud

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Pieter Vandemaele, MSc-Ing
GIfMI Site Manager
Ghent Institute for Functional and Metabolic Imaging
MR Department -1K12
Ghent University Hospital
De Pintelaan 185
9000 Ghent - BELGIUM

[log in to unmask]	tel: +32 (0)9 332 48 20
http://gifmi.ugent.be	fax: +32 (0)9 332 49 69
ORCID ID	0000-0002-4523-2476