Hello.
I'm a new Freesurfer question, and I was wondering if you could answer a couple of questions for me.
First some background: After having done the autorecon1 and autorecon2 steps successfully, and after also checking and making sure that the original white matter surface registered well to Talairach space, I am now at the point of checking the white matter surface. There are definitely places that should be included as white matter that were left out. In those spots, I have added control points and have had no trouble.
My questions though are about spots in the cortex where the white matter surface has included gray matter. I believe I should use the Edit Voxels Tool to fix this, but I am not entirely sure how I should "Configure the Brush Info" or "Configure the Volume Brush". For the Brush Info, should I set the Target as the Main Volume, the Aux Volume or the Main and Aux Volume? I am not sure which I should select. From the tutorial ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits), it looks like I should select the Aux Volume and then save that in order to run: recon-all -autorecon2-wm -autorecon3 -subjid wm2_edits_before.
But, I'm concerned about what the tutorial means as the deletion of voxels by this editing tool. Would reclassifying these voxels as non-white matter automatically render them as part of the pial surface when the above script is run? Or, would they be reclassified as non-brain tissue?
Also, I would appreciate it if you could direct me on how to set the Volume Brush Info appropriately.
Thank you in advance for your help, Meghana