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
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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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