Dear Freesurfer Experts,

I'm sorry if I have not been clear with my question so far. I have completed the cortical analysis on a number of subjects using 5.3, with all requiring some editing and re-running.

Now that I have the final surfaces, to update the aseg.mgz, I would like to run: recon-all -subjid subject -surfsegedit before examining the aseg.mgz more closely.

Looking at one aseg.mgz (for example) I can see that edits could be made to label more of the cerebellar cortex as well as some relabelling of the brainstem.

After performing edits such as these to aseg.mgz (and possibly to other subcortical structures) would I then run: recon-all -subjid subject -aparc2aseg -segstats -wmparc

to update stats/aseg.stats, aparc+aseg.mgz, aparc.a2009s+aseg.mgz wmparc.mgz, and stats/wmparc.stats without changing the cortical stats files such as lh.aparc.stats?

Using this approach, I'm hoping that I can begin the group analysis of the cortex using lh.aparc.stats (and the like) while the subcortical review is underway, without having to re-run this group analysis with subsequent updates of lh.aparc.stats that would occur by running -autorecon3 (or similar) to update aseg.stats, aparc+aseg.mgz, etc.

Please let me know if this approach is valid, any suggestion would be appreciated.

Thanks,

P