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