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 extend outside the brain, often including areas around the nasal cavity as shown, or large parts of the spine etc.
A solution that seems to work well for most subjects is using freesurfer’s synthstrip to calculate another mask (light yellow in the image) and then use the intersection of the two as the final mask. However , a few of these are ending up too aggressive, resulting in large parts of the brain being excluded - as shown here with cerebellum and occipital lobe. In this situation, neither masks works on its own, and the intersection isn’t good either.
I’m wondering if i need to try another masking tool, manually correct the mask in these situations, or proceed with the default more inclusive mask for all steps but mtnormalise , since the note also mentions that the step is less sensitive to missing brain voxels whereas others are moreso (however my intuition is that this is referring to fewer missing voxels than the attached).
Any suggestions are appreciated - thanks!
