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:

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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