Hi everyone,
I’m trying to run FBA on my muti-shell dataset of 600 patients and have a few questions about step 11 in the documentation (computing the template mask as the intersection of all subject masks in template space).
The template mask I’m getting does have a few holes in it and the documentation recommends to go back to resolve the causes, however since these are patients who will naturally have atrophy and abnormal brain morphology, I’m not sure what “resolve” means in this case. Should I exclude these subjects, or manually edit their masks in order to cover regions where there is no brain tissue?
The other issue is that with 600 subjects, it is quite impractical to check every single mask and find the abnormal ones. I have tried averaging sets of masks in order to know which subset contains abnormal masks but this too is quite a lot of manual work. Has anyone done this in some other clever way?
One alternative I had in mind was creating a template mask with only a subset of subjects, e.g. the 40 subjects I used to generate the FOD template in step 9. I’m not sure if this is good or problematic, this template mask will of course not be the intersection of all 600 subjects, but maybe that is not an issue?
Thank you in advance!
