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
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
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/
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.
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. http://clk.atdmt.com/GBL/go/196390710/direct/01/
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.
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
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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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-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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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
> > 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
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-
Guang Zeng -
Nick Schmansky