First have a look at the troubleshooting wiki pages at: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData
In particular, Subject 1 has a skull strip problem, and the fix info is here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix I'm guessing you have seen this page since you have already attempted one type of fix (adjusting the watershed parameters). The alternative fix is the slice-by-slice manual editing. You could also try adding the wsatlas flag: recon-all -s (subject) -skullstrip -wsatlas which will use an atlas to help with the skull-strip. Does the contrast of your image look good? That is, comparing your orig.mgz to that of the sample subject 'bert' included with freesurfer? Nick On Wed, 2006-06-28 at 10:09 -0400, [EMAIL PROTECTED] wrote: > I am having trouble with one of my skull strips, and getting very > extreme results. When I re-run the skullstrip using different watershed > values, anything at 56% or below takes 75%+ of the brain out, and as > soon as I jump to 57% or higher, it leaves on almost all of the skull, > except for maybe 5% of it. Is this indicative of a more complicated > problem, and what is my next step (other than manually taking off the > skull), if any? > Thanks > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
