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
