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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hotmail: Free, trusted and rich email service. Get it now.
Hotmail: Powerful Free email with security by Microsoft. Get it now.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_________________________________________________________________ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/196390708/direct/01/