Hi Doug, thank for your suggestion. I will give it a try.
Yang On Tue, Jan 11, 2011 at 10:57 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > You can also run defect-seg to create segementations and annotations of the > defects. This can be quite handy when tracking down defects. Run it with > --help to get info on how to use it. > > doug > > > Bruce Fischl wrote: > >> 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 >> >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >
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