-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
> 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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