This section is ONLY relevant for the manual editing step. For full pre-processing steps, refer back to here.
Below is a previous guide from James - Note it uses the older versions of FreeSurfer (v6.0 and below).
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ONCE MANUAL EDITS ARE COMPLETE
Surface Check: Open tkmedit as if you were doing manual edits (we will use this later). Then, open a new terminal window and enter the command below. Here we are looking at a 3D construction of each hemisphere to check for any problems (i.e. spikes or holes).
Code Block tksurfer FTD### lh inflated.Change the rotation from 90 to 30 degrees, then use the rotation arrows above to rotate the brain to check the whole surface (See Figure G. in sidebar).
If there is a spot you want to check, double click on it (which will make a little blue dot) then hit the save button circled in red. Go to the tkmedit tool box and click the folder with the + sign (appears like the button circled in green) to open the saved location in the tkmedit window we opened earlier. It will place the small red cross on the exact spot you saved on the inflated version. You may need to scroll back and forth through the slices to find the exact location.
This step is a final quality check. We want to use the surface check to highlight any locations where we have potentially missed a section of brain that is not included or a section of non-brain that has been included.
Address issues found by doing more manual edits and rerunning autorecon2/3 as above.
NOTE: There will always be a spike on either hemisphere where the optic nerve enters the brain. This spike is ignored.
Once you have done this for the left hemisphere, repeat the process for the right:
Code Block tksurfer FTD### rh inflated.
Last pre-processing step
Continue with pre-processing step - qcache (outlined in the main section of manual pre-processing steps here).