Hi Lars
sure, if you can a better strip give it a try. Dura is really hard to get
rid of , and depending on your bandwidth and readout direction you also can
find fat shifting down to touch the edge of cortex
cheers
Bruce
On Tue, 1 Mar 2016, Lars M. Rimol wrote:
Hi,
We have run recon-all on 33 healthy subjects in their 20ies with FreeSurfer
version 5.3.0, on a Linux CentOS 6.7. The original T1's look good
(example image attached). We used the braindeer tool(http://brainder.org/201
1/09/10/quickly-inspect-freesurfer-cortical-surfaces/) to check the quality
of the cortical reconstruction, and we find that in 10-15 subjects the cort
ical surface reconstruction was unsuccessful. We think it may
have to do with an incomplete skull strip (please see attached images). In o
rder to get rid of residual dura (and some skull) we changed
watershed first to 20 then to 5, using these commands:
1) recon-all -skullstrip -wsthresh 20 -clean-bm -subjid <subject name>
2) recon-all -autorecon-pial -subjid <subject name>
( We also tried: recon-all -skullstrip -clean-bm -multistrip -subjid <subjec
t name> )
None of this changed the outcome much. Neither did -gcut .....
An alternative is of course manual editing, but we are wondering whether usi
ng BEaST to do the skull strip, and then replacing the brainmask.mgz
with the brainmasking resulting from BEaST (and then recon-all -autorecon-pi
al -subjid <subject name> ), could be a workable solution.
Would you recommend to do that/ not to do that?
Thank you!
sincerely yours,
Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway
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