In my experience, the FreeSurfer's brain extraction works better than the
BET. Although, now with an option of iterative BET in the latest FSL, the
outcomes are much better than before. In cases where brain extraction
failed in my analysis, I found that it was the bias field correction which
didn't do the best job, though the images looked ok. In these cases, even
playing with watershed parameters didn't provide statisfactory results. So
I tried FLS's bias correction followed by the watershed, and this always
helped.
Martin
On Thu, 13 Dec 2007, Bruce Fischl wrote:
Hi Simon,
yes, you would need to skip the watershed step (it is our skull stripping),
or better yet, replace it with bet, since at some points we need the skull on
e.g. to do TIV estimation. Do you find our skullstripping is failing? In our
hands the current version is extremely robust - working on 99% of the brains
we test.
cheers,
Bruce
On Thu, 13 Dec 2007, Simon Rushton wrote:
I've been having problems with a few brains (errors during processing). I
found advice on the web about running BET (the FSL brain extraction tool)
prior to running recon-all
http://lcni.uoregon.edu/mediawiki/index.php/SOFT:FSL_FreeSurfer
I've tried this and that has helped. (Searching the mail archive I see
that at least one other person on this list appears to be doing the same.)
My question is, is this a sensible thing to do? I ask because looking at
the output I see that at least one of the early processing stages appears
to expect a non-stripped brain:
mri_watershed -brain_atlas /Applications/freesurfer/average/
RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta T1.mgz
brainmask.auto.mgz
Does this suggest that I either should not try the BET trick or that if I
do that I should make some modifications to the recon-all scripts?
simon
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