Hi Allie, Can you upload the subject? I'll take a look and see if I can figure out what's wrong.
-Khoa On Tue, 19 Apr 2011, Allie Rosen 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> >>> 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>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/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 >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
