Hi Peter, After completing your Talairach and skullstrip edits have you regenerated the brainmask.mgz? I'd recommend running the rest of recon-all (-autorecon2 & -autorecon3) to see how the surfaces come out.
After that you can go ahead with intensity normalization (with control points), and wm/pial edits if necessary. It is only necessary to add control points and to make edits to the brainmask/wm volumes to correct inaccuracies in the surfaces. Intensity normalization and wm edits will influence both wm and pial surfaces. Pial edits only influence the pial surface. The pial surface grows out from the wm surface so wm edits will affect the pial surface as well
intensity normalization -> wm surf -> pial surf
You can perform all 3 types of editing at the same time and then rerun from the second intensity normalization step onwards in the recon-all stream.
Freesurfer tries to normalize wm to 110, but inevitably not all wm is normalized exactly to 110. Placing a control point on any voxel with an intensity less than 110 tells freesurfer to boost the intensity of that voxel to 110, as well as adjust the proximal intensities of other voxels nearby to a lesser degree. Voxels with intensities less than 110 can be included in the wm surface. This will be the case if the first steep drop-off in intensity (presumed to be the gm/wm boundary) is detected at a point where voxels are below 110. Freesurfer is looking for relative steep gradients in intensity which should correspond to the gm/wm boundary and the pial/csf boundary. I assume the wm voxels at 70 you see within the wm surface are located in a different area of the brain from the non-wm voxels of the same intensity which are not being included in the wm surface. In other words the relative differences in intensity between the gm and wm differ in those two areas. -Louis
On Mon, 1 Jul 2013, Peter Boulos wrote:
Resending, would greatly appreciate some input so I can move forward: I have a fairly basic question regarding the order in which I should perform the edits. After running the full recon on all of my subjects I have now completed the Talairach edits and the skull strip edits on my subjects. At this point I am attempting to seek out help in terms of performing the edits on white/grey matter border from a more experienced user but have a couple of days before I can meet with them. Therefore, can I go ahead and do the pial surface edits before or does the intensity normalization and white/grey boundary edits need to be done first before the pial surface? As in will those edits alter what I do in later steps? Also, I am having a hard time understanding what I am doing with intensity normalization. Am I just ensuring that there are sections of an intensity of 110 in the white matter boundaries of each subject? Am I only looking for white matter that appears to be left out in a disastrous way in this step or should I be very meticulous about this? I am confused because I have areas considered white matter in free surfer that appear to be white matter by visual inspection that have intensities as low as 70 but then areas of the same intensity outside of the boundary. I realize that the program is probably using intensity data along with location data but do not understand how I am supposed to ensure that whether something with an intensity lower than 110 is indeed white matter by visual inspection alone. I apologize for the simplicity of my understanding at this point and thank you for your time.
Peter