I ran SS Warper over a dataset of 21 subjects. The results are perfect, except for two subjects. Lets call them subject 1 and 2.
Subject 1: in the quality control images of the file the whole head (skull plus brain) looks totally deformed after running SS Warper. Then, I ran skullstripping again but with adding “-deoblique” first, and “-deoblique_refitly” in a third try. Those two additional steps did also not yield better results. The images I added actually stem from the third try, but the results look like that for all skullstripping attempts.
Subject 2: the result looks very noisy. I realized that the raw data of this subject also has this noisy “flickering” effect. Is there a way to reduce this effect in AFNI? I am afraid that this effect leads to meaningless results in further computations concerning brain data.
Here is my script for skullstripping:
for subject in Subject1 Subject2 …
-deoblique_refitly \ # added for the problematic subject1)
The first two pictures are from subject 1. The third picture is from subject 2. The picture preview looks messy; please just open them via right click and open in a new tab to take a proper look at them.