Hi Bruce, I followed the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits.
But I couldn't find similar examples as mine in the tutorial. I don't really understand why don't the yellow and green surfaces follow the boundary of wm.mgz, especially the boundary is well defined in the slices. Yang On Mon, Jan 10, 2011 at 10:56 PM, Bruce Fischl <[email protected]>wrote: > 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]> > [email protected]> wrote: > >> Then I must be a topologica defect >> >> >> >> On Jan 10, 2011, at 10:37 PM, Yang Liu < <[email protected]> >> [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]><[email protected]> >> [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]><[email protected]> >>> [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]><[email protected]> >>> [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><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 >>> >> <[email protected]> <[email protected]> >>> [email protected] >>> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer><https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> > _______________________________________________ >>> > Freesurfer mailing list >>> > <[email protected]> <[email protected]> >>> [email protected] >>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer><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> >>> 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]> <[email protected]>[email protected] >>> >>> Division of Biology >>> MC 114-96 >>> California Institute of Technology >>> 1200 East California Boulevard >>> CA 91125, Pasadena >>> USA >>> >>> >> >
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