Hi Bruce, Do you know how to fix it?
Yang On Mon, Jan 10, 2011 at 10:43 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > Then I must be a topologica defect > > > > On Jan 10, 2011, at 10:37 PM, Yang Liu <liu.yan...@gmail.com> wrote: > > Hi Sebastian, > > Yes. It is Macaque. There is no aseg. > > Yang > > > On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller > <<sebastian.moell...@rwth-aachen.de> > sebastian.moell...@rwth-aachen.de> 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 < <liu.yan...@gmail.com> >> liu.yan...@gmail.com> 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 <<k...@nmr.mgh.harvard.edu> >> k...@nmr.mgh.harvard.edu> 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> >> 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 >> >> <Freesurfer@nmr.mgh.harvard.edu>Freesurfer@nmr.mgh.harvard.edu >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > _______________________________________________ >> > Freesurfer mailing list >> > <Freesurfer@nmr.mgh.harvard.edu>Freesurfer@nmr.mgh.harvard.edu >> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> 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> >> 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 >> <moel...@caltech.edu>moel...@caltech.edu >> >> Division of Biology >> MC 114-96 >> California Institute of Technology >> 1200 East California Boulevard >> CA 91125, Pasadena >> USA >> >> >
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