Hi Yang, if you send us the surfaces and the wm.mgz/brainmask.mgz we'll take a look. You need to find the reason for the topological defect in the wm.mgz. By defition to correct a defect the orig (green) surface can no longer follow the boundary of the wm.mgz. If it did it would have a defect! You can also look at the orig.nofix and/or the inflated.nofix to see where the defect is in that region
cheers Bruce On Tue, 11 Jan 2011, Yang Liu wrote: > 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 > <fis...@nmr.mgh.harvard.edu>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 <liu.yan...@gmail.com> wrote: >> >> 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> >> 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> >>> 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> >>> 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> >>>> 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> >>>> 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> >>>> 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> >>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> <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 >>>>> <Freesurfer@nmr.mgh.harvard.edu> <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> >>>> 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 >>>> <moel...@caltech.edu> <moel...@caltech.edu>moel...@caltech.edu >>>> >>>> Division of Biology >>>> MC 114-96 >>>> California Institute of Technology >>>> 1200 East California Boulevard >>>> CA 91125, Pasadena >>>> USA >>>> >>>> >>> >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
