Does the aseg label that as ventricle?
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
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