Hi Meghana,
Depending on whether wm.mgz (or the volume in which you wish to make the edits) is loaded as the main volume or aux volume, you should select the target in the 'Tools' --> 'Configure Brush Info' as either main or aux respectively. In the example you are referring to, wm2_edits_before, wm.mgz is loaded as main volume. If you are using a similar command line for your edits, you should select 'Main volume' as 'Target' in the 'Configure Brush Info' and save the main volume after the edits. If the white surface is including Gray Matter voxels and you delete those voxels in wm.mgz, they are rendered as part of the pial surface after rerunning recon-all.
Sita.
On Fri, 4 Dec 2009, Meghana Karnik wrote:
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