Not without scrolling through the wm volume. You will need to edit it. Have you done the troubleshooting tutorial?
On Jan 10, 2011, at 10:48 PM, Yang Liu <[email protected]> wrote: > Hi Bruce, > > Do you know how to fix it? > > Yang > > On Mon, Jan 10, 2011 at 10:43 PM, Bruce Fischl <[email protected]> > wrote: > Then I must be a topologica defect > > > > On Jan 10, 2011, at 10:37 PM, Yang Liu <[email protected]> wrote: > >> Hi Sebastian, >> >> Yes. It is Macaque. There is no aseg. >> >> Yang >> >> >> On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller >> <[email protected]> wrote: >> Hi All, >> >> >> On Jan 10, 2011, at 19:12 , Bruce Fischl wrote: >> >> > Does the aseg label that as ventricle? >> >> This pretty much looks like macaque data, so I think there is no aseg >> for that. I would love to be corrected on that point though. >> >> Best >> Sebastian >> >> > >> > >> > >> > On Jan 10, 2011, at 9:34 PM, Yang Liu <[email protected]> wrote: >> > >> >> Hi Khoa, >> >> >> >> Thanks for your reply. >> >> I attached the snapshot of the same slice with brainmask.mgz. You can see >> >> clearly that the green and yellow surface at the wrong regions. They >> >> doesn't look like ventricles to me. >> >> It is strange that even the green surface doesn't follow the original >> >> wm.mgz, though the wm.mgz as attached in the previous email >> >> has very well defined boundaries near the wrong regions. >> >> Any idea to correct this? >> >> >> >> >> >> Yang >> >> >> >> >> >> On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen <[email protected]> >> >> wrote: >> >> Hi Yang, >> >> >> >> To edit the pial surface, you want to use brainmask.mgz. >> >> >> >> As for the wm.mgz, you're right in that control points isn't the >> >> solution. Control points are to fix intensity problem, but you can also >> >> add wm voxels manually to fix any wm defects. In this case, adding that >> >> many control points would probably make the situation worse because the >> >> entire area will brighten and that would potentially extend the surfaces >> >> to include grey matter. >> >> >> >> Is the area you pointed out by any chance the ventricle? If it is, then >> >> it doesn't matter that the white surface includes it. It's hard to tell >> >> with just this image. Do you mind sending a snapshot of the brainmask.mgz >> >> for this slice? >> >> >> >> >> >> On Mon, 10 Jan 2011, Yang Liu wrote: >> >> >> >> Hi Freesurferers, >> >> >> >> I am correcting some defects in the white matter surface (yellow) and the >> >> pial surfaces (red). But I am not very sure of which volume I should work >> >> on. >> >> I did several experiments on editing one volume at a time. >> >> >> >> For pial (the red) surface, I edited brain.mgz first. I found it corrected >> >> some pial defects. >> >> However, I found one previous post here said the volume that should be >> >> edited is brainmask.mgz. >> >> So the second time I only changed brainmask.mgz. It also works. >> >> >> >> So, which one should I work on? >> >> >> >> brian.mgz or brainmask.mgz? >> >> >> >> Also, for defects on the white matter surface (the yellow one), I found >> >> the >> >> surface doesn't follow the white matter segmentation closely, although I >> >> have a good wm.mgz. (see attached image). >> >> At the location pointed by the red arrow in the attached image, both the >> >> green and yellow sufaces includes a lot of gray matter at the location. It >> >> is strange that the wm.mgz has a very well defined slice in that >> >> neighborhood. >> >> I am familiar with situations where the surfaces miss a few white matter >> >> pixels, for which I can add a few control points to improve it. >> >> >> >> How shall I edit wm.mgz to correct this? Adding more control points is >> >> not >> >> a solution, apparently. >> >> >> >> Thank you. >> >> >> >> Yang >> >> >> >> >> >> >> >> The information in this e-mail is intended only for the person to whom it >> >> is >> >> addressed. If you believe this e-mail was sent to you in error and the >> >> e-mail >> >> contains patient information, please contact the Partners Compliance >> >> HelpLine at >> >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> >> error >> >> but does not contain patient information, please contact the sender and >> >> properly >> >> dispose of the e-mail. >> >> >> >> >> >> <wrong_surfs_c39.jpg> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> [email protected] >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > _______________________________________________ >> > Freesurfer mailing list >> > [email protected] >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > The information in this e-mail is intended only for the person to whom it >> > is >> > addressed. If you believe this e-mail was sent to you in error and the >> > e-mail >> > contains patient information, please contact the Partners Compliance >> > HelpLine at >> > http://www.partners.org/complianceline . If the e-mail was sent to you in >> > error >> > but does not contain patient information, please contact the sender and >> > properly >> > dispose of the e-mail. >> >> >> -- >> Sebastian Moeller >> >> telephone: 626-807-5242 / 626-395-6523 / 626-395-6616 >> fax: 626-395-8826 >> German GSM: 0 15 77 - 1 90 31 41 >> US CDMA: + 1 - 626 - 807 - 5242 >> [email protected] >> >> Division of Biology >> MC 114-96 >> California Institute of Technology >> 1200 East California Boulevard >> CA 91125, Pasadena >> USA >> >> >
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