I made white matter and pial edits to my volume. Do I need to run -autorecon2-wm and when that is finished run -autorecon2-pial?
No. If you made both white matter and pial edits, you only need to run -autorecon2-wm which is higher up in the processing stream (before the steps of -autorecon2-pial). By running -autorecon2-wm, it will perform the steps necessary to fix a white matter edit and then all the remaining steps in -autorecon2 including those steps that -autorecon2-pial would run. The OtherUsefulFlags wiki shows the hierarchy of the -autorecon2 flag shortcuts (-autorecon2-cp starts before -autorecon2-wm which starts before -autorecon2-pial). In general, you should start the processing stream at the earliest step where you made an manual intervention and the rest will be taken care of. Don’t forget to run -autorecon3!
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