Running Freesurfer v4.0.5 on RHEL5 linux system.

General Question: after using the “Edit Segmentation” tool and saving edits by overwriting the aseg.mgz file generated during $recon-all -autorecon-all…which command should I pass to re-enter the analysis pipeline at the most appropriate spot? I understand that after edits to the wm.mgz file, it is fine to re-enter the pipeline with $recon-all -autorecon2-wm -autorecon3. But unable to find much in the Wiki wrt *aseg.mgz* edits and subsequent re-processing (other than “how to” accomplish edits).

Specific info: Unusual case with enlarged lateral ventricles (particularly posteriorly). Review of the aseg.mgz after completing $recon-all –autorecon-all  indicated that the right lateral ventricle (posterior portion) was partially incorrectly labeled in a range of slices (COR: 86-48) with a “cocktail” of labels, including the following: Right-Lateral-Ventricle; Right-Cerebral-White-Matter; Right-Cerebral-Cortex; None; WM-hypointensities.

After editing *wm.mgz* to fill-in missing voxels in the problem areas and re-running $recon-all -autorecon2-wm -autorecon3, segmentation labels of problem areas still required edits.  After using the “Edit Segmentation” tool, I have now saved my edits by overwriting *aseg.mgz*. So which command should I pass to re-enter the pipeline?

Many Thanks for any advice you can provide.

Jenifer