Hi,
I have been running recon1 recently and I have noticed that for some of my participants big chunks are missing in the brainmask.mgz. Out of 20 participants, five participants have this problem. The pattern is similar across participants: the missing parts start around slice 70-50 at the bottom (cerebellum) and then move upward. The data can be found in:
/autofs/space/boggart_001/users/oosterwi/construct_struc
It concerns constr011 (which I corrected using the clone method), and constr012, constr016, constr019 and constr020 (which still show the problem).
I think it can be solved by cloning the T1 (aux volume) as is explained in the Freesurfer tutorial. Still, I wonder whether this is the best solution, and why this is happening in the first place.
I appreciate any help or feedback on this. Thanks in advance! kind regards, Suzanne Oosterwijk