This is a basic question about the process for manual edits and the autorecon commands. I am going to follow the recommended reconstruction page (on fs wiki) to make manual edits on my data. The page says that you can make all the manual edits at once. But my question is, how do you go about running the autorecon commands specific to each type of edit? Do you run each command separately after you're done saving all your manual edits? It seems that some of the steps are redundant (like running autorecon 3 more than once). Also, if I make changes to skullstip, will I have to do the recon again before doing additional edits?
Here is an example where my questions would need to be addressed. Say I had to add control points to wm, and erase some voxels from the pial. Do I make edits and run the commands to fix these problems separately (i.e. make wm edits and subsequently run appropriate recon steps specified in wiki, then make pial edits and run specified recon steps), or do I make any types of edits at once (control points, add/delete voxels, etc.) and then run each command separately, or do I make any types of edits at once and somehow combine these different commands into one step? I'm sorry if this is confusing - I am just trying to grasp how to approach manual edits in the "order" listed in the recommended reconstruction page. Thank you! Elissa
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