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: dwm2...@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: dwm2...@med.cornell.edu > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
