Making Edits to the Calcarine Sulcus
To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names.
First, select the wm volume and change the color map to Heat on the panel on the lower left. Set the opacity to ~0.15-0.25 so you can see the brainmask behind it. Then, lower the Mid to zero (where my pointer is in wm_edit_1.png; you can keep the other values at their defaults). By doing this, everything that you erase using Recon Edit will show up in red so that it is easy to see. Next, erase a line at the start of the sulcus where you want to push out the surface (wm_edit_2.png), then select the fill tool and hold shift and click inside the sulcus to erase the whole section (wm_edit_3.png). Do this for a few slices around each location that needs to be pushed out so that it has more effect, then save the wm volume and rerun recon-all.
rerun: recon-all -autorecon2-wm -autorecon3 -subjid calcarine_edits_before