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.
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.
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
