Upload the subject and we will take a look
On Apr 19, 2011, at 8:03 AM, Allie Rosen <rosen.al...@gmail.com> wrote: > Hi, > > This (recon-all after wm.mgz and brainmask.mgz edits) didn't work. The part > that wasn't included in the pial or white matter surfaces is still not > included. The intensities in the white matter regions are no different than > in white matter regions that were included in the white matter. Any other > suggestions? > > Thanks, > Allie > > > > On Mon, Apr 18, 2011 at 7:53 PM, Allie Rosen <rosen.al...@gmail.com> wrote: > 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 <fis...@nmr.mgh.harvard.edu> > 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 <rosen.al...@gmail.com> 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 <s...@nmr.mgh.harvard.edu> >> 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 >> <s...@nmr.mgh.harvard.edu>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 >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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