yes, with the current version it seems to almost never fail.
On Fri, 14 Dec
2007, Nick Schmansky wrote:
Simon or Martin,
If you have a chance, can you try the -multistrip option of recon-all
with a subject that you know fails the default fs skullstrip? That
option launches eight instances of mri_watershed all with different
parameter combos, and the best one is selected. If all of those fail,
can you send us the failed subject data? We are always looking for test
cases.
The command is: recon-all -s <subj> -multistrip
Nick
On Fri, 2007-12-14 at 14:47 +0000, Simon Rushton wrote:
I've found it varies. A couple of brains that didn't go through with
the FS brain extraction tool went through with BET. Maybe recon-all
could include an option to try BET? Obviously have the most reliable
tool as default but allow the user to easily test an alternative tool
before starting to dig deep into other things?
simon
On 14 Dec 2007, at 09:40, Martin Kavec wrote:
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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