I just finished my 4 hour manual editing...went to file>save volume as...then saved it to where it defaulted me, which was the mri folder of this subject. When i pull up my brainmask, it is giving me the same one that it had before i made any changes. I hope i didnt do something wrong and lost all the edits. There is 256 COR files though now in my mri folder for this subject I noticed. Maybe these are the edited slices? Just let me know how to get my final brainmask and how to proceed with running -autorecon2 on it properly. Thanks.
Quoting Bruce Fischl <[EMAIL PROTECTED]>: > it helps detect cases in which the deformation is too big (e.g. when > the > surface deforms all the way into the cerebellum), and can thus > recover from > e.g. cerebellum chopping. > > On > Wed, 28 Jun 2006 [EMAIL PROTECTED] wrote: > > > 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 > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
