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