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