Hi, there,

Does the -base step of FreeSurfer also contains three step, and can be called through recon-all as recon-all...... -autorecon1, recon-all ...... -autorecon2,  recon-all ...... -autorecon3

Thanks!

> From: nicks@nmr.mgh.harvard.edu
> To: freesurfer_zg@hotmail.com
> Date: Mon, 25 Jan 2010 12:34:47 -0500
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] images with poor resolution
>
> also the base step
>
> On Mon, 2010-01-25 at 10:41 -0600, Guang Zeng wrote:
> > Hello, Nick,
> >
> > I am using the latest 4.5.0.
> > So I only need add those -seg-wlo -segwhi flags at the "-long" step,
> > not the "-base" step, right?
> >
> > Thank!
> > Guang
> >
> > > Subject: RE: [Freesurfer] images with poor resolution
> > > From: nicks@nmr.mgh.harvard.edu
> > > To: freesurfer_zg@hotmail.com
> > > CC: freesurfer@nmr.mgh.harvard.edu
> > > Date: Mon, 25 Jan 2010 11:18:07 -0500
> > >
> > > the longitudinal stream will take any controls points added to the
> > > cross-sectional stream, but will not take any expert options or
> > special
> > > -seg-wlo -segwhi flags, so you would have to add those yourself to
> > the
> > > longitudinal stream.
> > >
> > > On Sat, 2010-01-23 at 22:02 -0600, Guang Zeng wrote:
> > > > 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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> > > >
> > > >
> > > >
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