I am currently in the process of manual editing...just curious though, what exatly does adding an atlas do to the skullstrip process?
Quoting Nick Schmansky <[EMAIL PROTECTED]>: > 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
