Hello, Nick,

I read your answer to this thread posted few months ago.
Currently, I met the same kind of problem, and I used the method you recommended below, it works pretty well on my cases.
My question is:

The results of my data have been improved in FS cross-sectional stream, if I want to send them to the FS longitudinal stream,
Could I just need follow the general FS longitudinal stream or I still need the -expert <path_to>/xopts.txt and -seg-wlo wlo -seg-ghi ghi options
somewhere in the longitudinal stream?

Thanks!
Guang



> From: nicks@nmr.mgh.harvard.edu
> To: dwm2003@med.cornell.edu; freesurfer@nmr.mgh.harvard.edu
> Date: Mon, 5 Oct 2009 19:11:15 -0400
> Subject: Re: [Freesurfer] images with poor resolution
>
> 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
> >
> >
>
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