Dana,

First I would run:

recon-all -s subid -clean

to remove any prior control points and edits.

Then I would open nu.mgz:

tkmedit subjid nu.mgz

and *sparingly* put control points well into white matter areas on a few
different slices.  you only need a half dozen or so.  to add control
points, see:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints

except you will add them to nu.mgz, to make sure that T1.mgz gets
created properly.

Then create a file name xopts.txt containing these lines:

mri_normalize -gentle

Then run:

recon-all -s subjid -autorecon1 -expert <path_to>/xopts.txt

and when done, open brainmask.mgz

tkmedit subjid brainmask.mgz

and check again to get a sense of the low value for white matter and
high value for gray matter, then run:

recon-all -s subjid -autorecon2 -seg-wlo wlo -seg-ghi ghi

replacing wlo and ghi with those values.

if the surfaces still look bad, you can add a line to the xopts.txt
file :

mris_make_surfaces -max_gray val -min_gray_at_white_border val

replacing the two 'val's with something you find appropriate, then run:

recon-all -s subjid -autorecon2-pial -autorecon3 \
  -expert <path_to>/xopts.txt

good luck!

Nick


On Mon, 2009-10-05 at 16:56 -0400, Dana W. Moore wrote:
> Hi Nick,
>
> Below is Bruce's response to a problem I'm having with the gray/white
> segmentation. (Pasted below, you can see the brainmask.mgz volume and
> surfaces--the entire brain is labeled as white matter).  I could use
> some guidance in carrying out his advice.  He says to adjust the
> intensity normalization using control points and then use expert opts
> for mri_segment and mris_make_surfaces.
>
> When I look at the brain.mgz volume, the white matter tends to have an
> intensity of 110, as it should, but the gray matter at times goes as
> high as 115.  I was thinking, I could set ghi to 115 and wlo to 110.
> Then, I am not sure how to actually run the corrections and what
> language to use to implement the control points and mri_segment
> adjustments.  I will save control points and then run: recon-all
> -autorecon2-cp -autorecon3 -subjed <subject>.  Can I somehow include
> the mri_segment adjustments into this command, or do I have to run
> that separately?
>
> I am also not sure how options for mris_make_surfaces might help.
>
> I appreciate your help with this!
>
> Thanks,
> dana
>
> 
>
>
> []
>
> At 04:40 PM 10/2/2009, Bruce Fischl wrote:
> > Hi Dana,
> >
> > it looks like the gray/white density estimation failed. Try setting
> > them with the expert opts for mri_segment and mris_make_surfaces
> > (Nick can point you in the right direction if you can't figure it
> > out). Things like max gm at white border and such.
> >
> > cheers,
> > Bruce
>
>
> p.s. it also looks like the intensity normalization went too far due
> to the low contrast. You'll probably need to add some control points
> and run it with the -gentle option
>
>
>
> >  On Fri, 2 Oct 2009, Dana W. Moore wrote:
> >
> > > Hi everyone,
> > >
> > > I am trying to salvage some images that were done with poor
> > > gray/white boundary contrasts. First, FreeSurfer includes an area
> > > of dura in the skull strip.  I tried adjusting the watershed but
> > > it made no differences. FreeSurfer is subsequently unable to
> > > detect the gray/white boundary and labels the dura as cortex:
> > >
> > > []
> > >
> > >
> > >
> > > Looking at the raw images, the gray/white boundaries are faint but
> > > visible. Is there anything I can adjust to try to make this work
> > > with FreeSurfer?
> > >
> > > Thanks,
> > > Dana
> > >
> > >
> > > Dana W. Moore, Ph.D.
> > > Neuropsychology Fellow
> > > Cornell Neuropsychology Service
> > > Weill Medical College of Cornell University
> > > New York Presbyterian Hospital
> > > Department of Neurology & Neuroscience
> > > 428 East 72nd Street, Suite 500
> > > New York, NY 10021
> > > Phone: 212-746-2823
> > > Fax: 212-746-5584
> > > Email: dwm2003@med.cornell.edu
>
> Dana W. Moore, Ph.D.
> Neuropsychology Fellow
> Cornell Neuropsychology Service
> Weill Medical College of Cornell University
> New York Presbyterian Hospital
> Department of Neurology & Neuroscience
> 428 East 72nd Street, Suite 500
> New York, NY 10021
> Phone: 212-746-2823
> Fax: 212-746-5584
> Email: dwm2003@med.cornell.edu
>
>