Hello, Nick,

Thanks a lot.
The reason I ask is because in your previous reply to the "images with poor resolution" thread, you explained that in order to fix the problem, we need first
(1) add ctr points, then run recon-all -s subjid -autorecon1 -expert <path_to>/xopts.txt
(2) 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

It looks to me that I can not use -all directly here at the -base step, I had to do it step by step. That's why I need to know if the -base step is divided to three steps and three steps only.

Thanks!
Guang

> From: nicks@nmr.mgh.harvard.edu
> To: freesurfer_zg@hotmail.com
> Date: Mon, 25 Jan 2010 16:17:43 -0500
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] images with poor resolution
>
> -base triggers creation of the base subject, and requires the usual
> additional flags to run the entire stream. -all is the what is
> recommended here:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing
>
> but you could also run the stages separately.
>
>
> On Mon, 2010-01-25 at 15:05 -0600, Guang Zeng wrote:
> > Hi, there,
> >
> > Does the -base step of the FreeSurfer longitudinal stream also
> > contains three step,
> > and can be called through recon-all as recon-all -base ......
> > -autorecon1,
> >
> > recon-all -base ...... -autorecon2,
> > recon-all
> > -base...... -autorecon3
> >
> > Thanks!
> >
> >
> >
> > ______________________________________________________________________
> > From: freesurfer_zg@hotmail.com
> > To: nicks@nmr.mgh.harvard.edu
> > Date: Mon, 25 Jan 2010 13:57:58 -0600
> > CC: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] images with poor resolution
> >
> > 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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