Yes, I know and I am sorry for that! I already tried to attach a tiff-file illustrating the problem yesterday, but it is unfortunately still blocked and waits for approval of a list manager (don't know what that means). I will try to send it to your fischl@nmr.mgh.harvard.edu (maybe that will work out).

The problem is that the white surface looks like it would be the pial surface and the pial surface as if it would follow the inner dura. Actually it seems as if later processing steps completely failed to differentiate between white and grey matter (what is also reflected in the wm.mgz and the aparc+aseg.mgz. To make confusion complete the aseg.mgz however seems to be completely normal (besides some minor inaccuracies in the cortex classification tshouldn't be taken too serious becausethey are in the normal range) and also the skullstrip performed quite normal (no major parts of the skull forgotten and no unwanted sections of the cerebellum). Finally, also the talairach transformation worked out perfectly... but I attached the log-file now!

So, thank you very much, I really appreciate your help!

Kind regards

Cindy

-----Ursprüngliche Nachricht----- Von: Bruce Fischl <fischl@nmr.mgh.harvard.edu> Gesendet: 25.06.2010 14:18:58 An: Cindy Eckart <cindy.eckart@web.de> Betreff: Re: [Freesurfer] Serious failure of surface reconstruction >Hi Cindy, > >it's hard to say without knowing what the strange surfaces looked like. >Were they cut off? That would probably mean the skull stripping, or the >topology fixing. Does the wm.mgz look correct? How about the aseg? > >cheers >Bruce >On Fri, >25 Jun 2010, Cindy Eckart wrote: > >> My last email seemed to be too big because of the picture, so I try it without the picture.... >> >> Dear FreeSurfers, >> >> after having now completed the automatic Freesurfer reconstruction without error message (with Fressurfer Centos X64 v4.5.0 on a Debian Machine version 5.0.4, see my email from yesterday) I realized that the white and pial surfaces were reconstructed very badly (see tiff attached). Searching within the mailing list, I found a case that might be very symilar to my problem. Unfortunatly the discussion aborts at this entry >> >> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11770.html >> >> without offering a solution. Thus, I wanted to ask if you might have any idea what might have caused this problem and how I could fix it? >> >> Thank you very much in advance! >> >> Kind regards >> >> Cindy >> ___________________________________________________________ >> WEB.DE DSL ab 19,99 Euro/Monat. Bis zu 150,- Euro Startguthaben und >> 50,- Euro Geldprämie inklusive! https://freundschaftswerbung.web.de >>