Derin, The tutorial pages showing which defects to look for and how to fix them start here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData this includes white matter edits: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits Nick On Fri, 2007-04-13 at 15:31 -0500, Derin Cobia wrote: > Here is a pic of the inflated.nofix, how do I know what to edit? I've > checked the wm.mgz and it looks fine (at least I can't see any errors). > Maybe I'm missing something, I've attached a shot of it as well. Thanks. > > -Derin > > > look at the ?h.inflated.nofix to see what is causing the defect, and > > correct the wm.mgz manually to remove it. Jenni: can you point Derin at > > the > > appropriate wiki page? > > > > thanks, > > Bruce > > > > > > On Fri, 13 Apr 2007, Derin Cobia wrote: > > > >> The ?h.orig.nofix looks ok, meaning it follows the white-gray boundary > >> appropriately. What should I try next? > >> > >> -Derin > >> > >>> this is probably a topology fixing problem. Look at the ?h.orig.nofix > >>> and > >>> see how it is > >>> On Fri, 13 Apr 2007, Derin Cobia wrote: > >>> > >>>> Did you mean wm.mgz? It looks fine. The orig surface is not good > >>>> either. > >>>> Here's a pic. > >>>> > >>>> -Derin > >>>> > >>>> > >>>> > >>>>> Hi Derin, > >>>>> > >>>>> What does the orig surface look like? and the wm? Are those > >>>>> correct? > >>>>> > >>>>> Jenni > >>>>> > >>>>> On Fri, 13 Apr 2007, Derin Cobia wrote: > >>>>> > >>>>>> I have two subjects where the white surface does not follow the > >>>>>> gray-white > >>>>>> gradient (see attached pic for example). Is there any way to fix > >>>>>> this? > >>>>>> I'm assuming it has to do with the limitations of my scan too (it's > >>>>>> FLASH > >>>>>> data). I'm running 3.0.4, thanks. > >>>>>> > >>>>>> -Derin > >>>>>> > >>>>>> > >>>>> > >>>> > >>> > >> > >> > >> > > _______________________________________________ > > Freesurfer mailing list > > [EMAIL PROTECTED] > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > [EMAIL PROTECTED] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
