Hi, I've encountered similar problems. Do you know if it's specific to the autorecon2 flag? I'm wondering if running each process separately and sequentially get around it, e.g, running recon-all -normalization2, then recon-all -segmentation, then recon-all -fill, etc...
Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -----Original Message----- From: [EMAIL PROTECTED] on behalf of Bruce Fischl Sent: Mon 21/11/2005 11:03 PM To: Martin Ystad Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Normalization problem Hi Martin, we're looking into it - it's probably a bug in recon-all. Bruce On Mon, 21 Nov 2005, Martin Ystad wrote: > I'm working on the latest developmental release for Rh. 9. and I'm > having problems with the normalization procedures on my datasets. > My datasets have large intensity inhomogeneities due to their > acquisition with a surface coil (8-ch. GE). > To fix this problem I have resorted to the use of control points. This > works if I add enough points across the brain ( over 200), and I get a > better normalization result after running "recon-all -normalization > -usecontrolpoints" and another skull-stripping on the new T1-volume. > To test whether or not this produces a good segmentaition of white > matter, I run mri_segment on my brain.mgz -volume. If I'm satisfied with > the segmentation result, I move on to the surface processing stage, and > run the -autorecon2 -script. > The problem is that after running the -autorecon2, the normalization is > completely wrong again, looking more like the first normalization done > without control points, and the wm.mgz -volume is also bad. So are the > surfaces. > How do I make freesurfer produce the same good results as I got during > the first normalization? Do I need to specify the use of control points > again, even though the brain.mgz volume looks ok? > > Thanks, > > Martin Ystad > Medical Student > University of Bergen > Institute of Biomedicine > Jonas Lies vei 91, 5009 > Bergen, Norway. > > > _______________________________________________ > 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
