Re: [Freesurfer] bad midline cut

oh, sorry, you are correct. I guess you need to edit the aseg.presurf.mgz since that is what mri_fill is given as a segmentation. Sorry for the mistake Bruce

On Tue, 26 Sep 2017, Gabor Perlaki wrote:

If I accurately understand the recon-all script, then -noaseg sets UseAseg=0, but "autorecon2-noaseg" is a different flag, which only sets the following things.

case "-autorecon2-cp":
case "-autorecon2-noaseg":
case "-autorecon2-wm":
  set DoNormalization2 = 1;
  set DoSegmentation   = 1;
  set DoFill           = 1;
  set DoTessellate     = 1;
  set DoSmooth1        = 1;
  set DoInflate1       = 1;
  set DoQSphere        = 1;
  set DoFix            = 1;
  set DoMaskBFS        = 1;
  set DoWhiteSurfs     = 1;
  set DoSmooth2        = 1;
  set DoInflate2       = 1;
  set DoSegStats       = 0;
  set DoCurvStats      = 1;
  breaksw

Best Regards,

Gabor