Hi Yang, Are the slices before and after this slice the same as this one?
> 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]> >> [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]> 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]> 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 >>> >> <[email protected]>[email protected] >>> >> <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] >>> > <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 >>> <[email protected]>[email protected] >>> >>> Division of Biology >>> MC 114-96 >>> California Institute of Technology >>> 1200 East California Boulevard >>> CA 91125, Pasadena >>> USA >>> >>> >> > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
