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I have been very interested lately in the problem of filling large lesions.
I'd suggest you look at itk-snap.  Here's a link to some documentation I prepared on what seems to be working for us.
https://neuroimaging-core-docs.readthedocs.io/en/latest/pages/itk-snap_segmentation-lesion.html

itk-snap is pretty good at solving the heterogeneous tissue problem. It is a tool focused on solving segmentation problems.

-Dianne

On Tue, Dec 11, 2018 at 12:51 AM Carlotta Fabris <[log in to unmask]> wrote:
Hi Michael!

I am having the same problem, were you able to fix it?

Thank you so much,
Carlotta.

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Dianne Patterson, Ph.D.
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