FBA - problems with masks

[aknodt]

i’ve been dealing with a similar issue that i’ve posted about here:

Question about FBA sensitivity to mask quality

I am new to FBA but seem to have successfully executed the analysis for most of the subjects in my dataset. One of the things I am QC’ing on everyone is the quality of the mask, and I’ve found that quite a few seem to be problematic esp according to the note in Section 8 of the tutorial (”Joint bias field correction and intensity normalisation”) stating that mtnormalise results can be sensitive to masks that contain non-brain voxels. Probably > 10% of my subjects have masks that substantially …

i unfortunately don’t have a solution for you, but maybe you could also find some improvement using synthstrip as an alternative masking strategy - it helped for some but not all of my scans. it seems like improving the masking function in mrtrix might be an active area of development. but like you i’m also still wondering what the implications of the poor masks are, and for now i am just excluding those scans where the masks aren’t very good.