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 >> <[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 >>>>> >>>>> >>>>> > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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 _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
