Inside FEAT there is a masking stage, but it is deliberately large to avoid removing any parts of the brain. Normally it is fine to just mask your final results with a tighter brain mask if you see much outside of the brain. However, only do this after
carefully checking that your registrations are OK, as this can be the sign that some registrations are not good.
As for your masking approach - I would advise against it. This can cause biases to the motion correction. I think it is better to mask your final results, not the initial data.
Dear experts,
I have problem in my fMRI data analysis. in some of my cases I have activation outside or on the skull. after examination i saw that the problem is EPI brain extraction. so we decided to run bet on each individual volume separately. to do this first i
ran fslsplit first, then bet ,and then fslmerge. i have some question regarding this method:
1- is this method correct?
2- should i do this for each subject, or only those with activation outside skull.
3- what is the problem for my subject? is this ghosting effect?
Thank you all,
Ashkan
