Hi Bruce,

Actually I need to skip the whole aseg process as this is incompatible to the high resolution volumes I'm using. I read that prior to the aseg files the talairach transform was used to delete the cerebellum and that the cutting planes correctly. Is it possible to use this again?

I also tried using seed points, though the cerebellum was never erased.

Regards, Falk

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, May 18, 2009 2:07 PM To: Falk Lüsebrink Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_fill

p.s. you can pick seed points in the callosum and pons in tkmedit and see if that fixes your problem, but if there is something else going on then it may not (e.g. if the aseg is badly wrong) On Mon, 18 May 2009, Falk Lüsebrink wrote:

Hi FreeSurfers,

At the end of mri_fill I’m told to check the filled volume as the cerebellum may be included. It is and also the brainstem. But actually I don’t know how to fix this. Do I need to include the seed points for cc and pons for better cutting planes? Do I need to manually

edit the volume?

If the latter is better are there any other tools available besides

tkmedit?

If I try to add or delete voxels of a high resolution volume tkmedit seems to skin every second slice.

Regards,

Falk