Hi!
I have a problem with creating the template mask for FBA. My template mask excludes a part of the brain. This, of course, results in my fixel mask also missing this part. I already excluded 3 participants who had particularly bad masks. Would you suggest excluding even more participants to get a better mask, or is there anything else that could be done?
I’m in a similar situation, so hoping you get some answers.
My initial run of mrtrix processing resulted in a high rate of very bad masks, so i ended up creating the masks outside of mrtrix with a combination of fsl’s bet and freesurfer’s synthstrip. this solved a lot of problems for me, but even with that my group mask is similar to yours.
i’m not an FBA expert, but i think for most purposes this should be fine, as you’ve got most white matter regions covered. i’m primarily looking to extract regional summary measures using tractseg and just trying to make sure that this won’t cause any issues with that process.
