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 ansk@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.schofield@yahoo.com To: Freesurfer Support List freesurfer@nmr.mgh.harvard.edu, Antonin Skoch ansk@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