Diffusion MRI brain extraction

Community SlicerDMRI
1

I found two bugs on the brain mask extraction utility (Diffusion Brain Masking) from diffusion images.

  1. It creates a mask which is just a plain square. I think it is the problem with the option ‘Remove islands in Brain Mask’

  2. If I disable this option, then inverted mask generated.

Please, find images attached.
Stable release 4.10 works fine.

Package: Slicer-4.11.0-2019-07-22-linux-amd64
OS: Ubuntu 18.04.2 LTS

Screenshot%20from%202019-07-23%2015-13-00
Screenshot%20from%202019-07-23%2015-13-001920×956 110 KB

2

THanks. Yes this is due to a bug in ITK 5. I have not yet had time to push the information upstream somehow. There is a workaround in the nightly but it fails if the background is larger than the brain volume. This is helpful if you can share your dataset at a later time for testing.