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: ni...@nmr.mgh.harvard.edu > > To: dwm2...@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: 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 > > > ______________________________________________________________________ > Hotmail: Free, trusted and rich email service. Get it now. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
