Hi Bruce, Thanks! The -bigventricles flag worked like a charm! But I have now run into other cases with fuzzy data and thin cortex that are not captured, such as the picture below:
Any tips on filing them out? Thank you. On Sunday, April 23, 2017 3:41 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: yes, that is correct. An alternative would be editing the aseg directly. Editing the wm will help the surfaces but not correct the aseg. But as Antonin suggests, try running with -bigventricles and see if that fixes your problems cheers Bruce On Sun, 23 Apr 2017, Shane Schofield wrote: > Thank you. I will try that. Do I run that command after editing the wm.mgz > to fill in the ventricles? I noticed that the voxels (value = 255) are still > 255 in the new WM.mgz after autorecon2-wm. Is this correct? > > > On Sunday, April 23, 2017 1:33 PM, Antonin Skoch <a...@ikem.cz> wrote: > > > Dear Shane, > > I would suggest to run: > > recon-all -bigventricles -s subject -autorecon2 -autorecon3 (-T2pial or > -FLAIRpial if you have 3D T2 or 3D FLAIR). This should help to correct aseg > in case of such large ventricles. > > Antonin Skoch > > > From: Shane Schofield <shane.schofi...@yahoo.com> > To: Freesurfer Support List <freesurfer@nmr.mgh.harvard.edu>, Antonin Skoch > <a...@ikem.cz> > Sent: 4/22/2017 11:30 PM > Subject: Filling in missing ventricles in WM > > Hi Freesurfer Experts and Antonin, > > About an earlier question on XL Defects > > I have used your suggestions to check the orig.nofix surfaces and I > think the skull and missing ventricle voxels are causing the problem. > Picture pasted. > > Inline image > I have removed the WM voxels in the skull, filled in the ventricles > by adding WM voxels (brush value = 255 ), and ran the command > recon-all -s subject -autorecon2-wm -autorecon3 > Recon-all was completed successfully and the surfaces look good. > However, the aseg volume in the lateral ventricles are still wrong. > Inline image > At the crosshair, the WM value is 255 and the ASEG value is 0. Should > I be editing the aseg now? Or should I be doing something else to the > wm.mgz? > Appreciate your tips! > Best Wishes, > Shane > > > > >_______________________________________________ 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.
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