After running dwi2mask following the FBA pipeline on the mrtrix docs, the mask I get has insufficient coverage: it leaves out parts of the brain, while also including various non-brain parts:
Is there a way to fix this or proceed to the next step without using a mask? I ran subsequent steps in the pipeline and ended up getting an error: Non-positive tissue balance factor was computed. Balance factors: -nan -nan -nan, when running mtnormalise, and I was not sure how to solve this / if the mask had a role.
Please let me know if you have any ideas as to how to solve this. Thank you!
Several people I work with have successfully performed the same. Doesn’t always work perfectly though, so do QA your outputs.
@Ana_Han, when this occurs in that particular area, take into account this usually indicates your signal is literally close to or all gone in that region (did you correct for EPI distortions though? Although if the signal is all gone, it won’t come back). Even when it’s in your masks, it might not make a lot of difference in any analysis actually. That said, you’ll never know until you run things with a masks that’s a bit more complete and traces the outline of the frontal area of the brain better.
The kinds of non-brain parts that dwi2mask sometimes includes (eyeball(s) and sinus regions) are typically not a problem for any subsequent steps; typically no need to worry about those.