Hi Bruce, I am running recon-all tonight using wm voxels that I manually added (I also edited brainmask.mgz to add missing grey matter). To me it doesn't really look like a case of the white matter not having a high enough intensity. It simply looks like the whole lobe was ignored, regardless of intensity. But I'll check tomorrow to see if the intensity is low.
Thanks, Allie On Mon, Apr 18, 2011 at 7:38 PM, Bruce Fischl <[email protected]>wrote: > What is the intensity of the white matter in the regions you drew in? A > couple of control points might help if it is less than 110 > > > > On Apr 18, 2011, at 12:36 PM, Allie Rosen <[email protected]> wrote: > > Hi Sita, > > Thanks for all the responses! I've actually had the same problem for > multiple subjects. I'm using version 5.0.0. I'll try fixing the cerebellum > as well. I've attached pictures of where I am adding wm voxels. They aren't > really in the same places as in the online tutorials. Could you take a quick > look to see if they're in the right place? > > Thanks, > Allie > > > > > On Mon, Apr 18, 2011 at 12:31 PM, Sita Kakunoori <<[email protected]> > [email protected]> wrote: > >> >> Hi Allie, >> >> pial surface which looks like this can only be corrected by correcting the >> wm.mgz. Also I would suggest to try and fix the cerebellum and see if it >> corrects the surfaces as well. Since part of the cerebellum is stripped off, >> it's probably affecting the segmentation as well but I could be wrong. what >> version of freesurfer are you using. >> >> >> Sita. >> >> >> >> On Mon, 18 Apr 2011, Allie Rosen wrote: >> >> Hi Sita, >>> >>> Can I still add voxels to wm.mgz even though the points would be outside >>> even the pial boundary? >>> >>> Thanks >>> Allie >>> >>> >>> >>> On Mon, Apr 18, 2011 at 12:18 PM, Sita Kakunoori >>> < <[email protected]>[email protected]>wrote: >>> >>> >>>> Hi Allie, >>>> >>>> This probably needs white matter edits but it's hard to tell from one >>>> slice. Please refer to our white matter edits wiki and toplogical >>>> defects >>>> wiki and see if it helps in fixing the errors in your datasets. Also it >>>> looks like part of the Cerebellum is stripped off. You might want to >>>> correct >>>> that as well. >>>> >>>> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits> >>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits >>>> >>>> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect> >>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect >>>> >>>> >>>> Sita. >>>> >>>> >>>> >>>> >>>> On Mon, 18 Apr 2011, Allie Rosen wrote: >>>> >>>> Hi, >>>> >>>>> >>>>> Once processed, several of my subjects have had errors around the >>>>> occipital >>>>> lobe. Attached is an example. I've already tried editing brainmask.mgz >>>>> and >>>>> running recon-all, but as you can see, this didn't change the pial or >>>>> wm >>>>> borders. What can I do to fix this? >>>>> >>>>> Thank you, >>>>> Allie Rosen, MSc Candidate >>>>> Graduate Student, Department of Neurosurgery >>>>> Toronto Western Hospital 14-327 >>>>> 399 Bathurst St. >>>>> University of Toronto >>>>> >>>>> >>>>> >>>> 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. >>>> >>>> >>>> >>> > <2.png> > > <3.png> > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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