Dear Bruce, thanks for the quick reply! You are right, of course. I do find errors in lh.inflated.nofix. I have attached a screenshot of the biggest errors I found.. Can you maybe guide me a little how to fix the issue? Do I just cancel the running recon-all process, and set control points and run again? Investing some time in manual editing would be fine as it's a case study...
Thanks for your help, Martin ________________________________________ Von: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fis...@nmr.mgh.harvard.edu] Gesendet: Montag, 11. Dezember 2017 22:47 An: Freesurfer support list Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst Hi Martin a defect that large means that something big went wrong (skull or dura attached, etc...). Try looking at the ?h.orig.nofix and/or the ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find defect 9 cheers Bruce On Mon, 11 Dec 2017, Loeffler, Martin wrote: > > Dear FreeSurfer team, > > > > For a case report I’m running recon-all on a patient with a giant arachnoid > cyst in the left > hemisphere. It gets stuck at this point (last message): > > CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849) > > XL defect detected... > > It is stuck here since a whole day now, so I’m not expecting it to advance… > > Following this post: > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I > looked at the wm.mgz, but did not find huge errors. > > Do you have any ideas what the problem might be or what I can do to work > around it? > > > > Thanks, > > Martin > > > > > > >
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