Hello Veronica,
(1) if BET functions well, then any further brain extraction ('cleaning up')
is not necessary, at least theoretically. The reason for cleaning step is to
null out voxels outside the brain which have not been clearly identified as
extrabrain voxels by the segmentation process. The overall result is quite
satisfying as I think most VBM users would confirm and significant results in
the critical peripheral area should be looked at carefully anyway.
BET, uses a different method and tends be more conservative, it sometimes
still has problems with the orbita and skull base area, and needs tuning of
the f and g parameter for a sequence.
So to my experience, the SPM2 function delivers a good result and I skipped
any extra steps. However, if you want to look if normalisation is improved by
previous BET this is another story - you will just need the stripped brain
for that purpose.
But it is definitely worth comparing some cases (optimized BET versus SPM),
esp. with regard to the venous sinuses / dural tissue and the above mentioned
areas.
(2) In SPM2 you can also switch it off in the defaults for segmentation.
best regards,
Philipp
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