Hi. I am attempting to use 3dSkullStrip with an mp2rage image. While 3dSkullStrip is running, I receive several warnings about self-intersecting surfaces. The resulting output consists of only the midbrain and white matter surrounding the midbrain. The non-stripped image does not appear to have shading. I have tried adjusting the options in 3dSkullStrip, but I have not been able to improve the output. Is there a particular combination of options in 3dSkullStrip that may be appropriate to fix this issue?
Thanks!