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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer