the Problem is that they were labeled as cortex in the aseg but as "unknown" in the aparc, so they get labeled as "unkown" in the aparc+aseg
the Resolution is still not clear. I was directed to follow instructions https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit, but the 'unkonwn' voxels are omitted from this inflated view and there is no instruction on how to find the specific coordinates of the unknowns seen on freeview (unkonwn voxels or others). Processing in the latest dev 8/22/15 did not resolve the issue as well. On Aug 25, 2015, at 3:45 PM, Douglas N Greve wrote: > The non-labeled voxels in the aparc+aseg near hippocampus. I think the > resolution was that they were labeled as cortex in the aseg but as > "unknown" in the aparc, so they get labeled as "unkown" in the > aparc+aseg (since that is what they are) > > On 08/25/2015 06:42 PM, fmri wrote: >> sorry, what was ? >> >> >> On Aug 25, 2015, at 3:18 PM, Douglas N Greve wrote: >> >>> wasn't this brought up on the list a few weeks back? >>> >>> On 08/25/2015 06:08 PM, fmri wrote: >>>> Dear Freesurfer experts, >>>> >>>> on aparc+aseg.mgz there is Hippocampus labeled over WM regions. >>>> >>>> There are cortex "Unknown" voxels that persist through out all of our >>>> scans. >>>> >>>> What files should be edited and what recons should be processed after >>>> edits to get a complete freesurfer data set. >>>> >>>> Thanks >>>> >>>> Joe >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> 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 . 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. >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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 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.
