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]> > 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]>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/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 . 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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