Hi Bruce,I am editing aseg to correct the boundaries that excluded the lateral ventricle. The problem with lateral ventricle has been solved after running the process with -noaseg flag. But the boundaries in the middle, is crossing to the other hemesphere in some cases. I even tried -autorecon2-cp, the problem still exists. aparc+aseg has not been updated after running the process.
Does Celine's case apply to mine? Here is your answer to Celine: Hi Celine the only existing way to correct this would be to create two volumes in addition to brain.finalsurfs.mgz (say, lh.brain.finalsurfs.mgz and rh.brain.finalsurfs.mgz) and edit each of them to remove voxels in the contralateral hemisphere that are causing problems, then rerun mris_make_surfaces for each hemi, using the appropriate volume. At some point I guess we should put an intersection check into it for the contra hemicheers Bruce Could you help me with the exact command line? Thank you in advance for your help,Maryam