AFNI program: 3dAutomask

Usage: 3dAutomask [options] dataset
Input dataset is EPI 3D+time.
Output dataset is a brain-only mask dataset.
Method:
 + Uses 3dClipLevel algorithm to find clipping level.
 + Keeps only the largest connected component of the
   supra-threshold voxels, after an erosion/dilation step.
 + Writes result as a 'fim' type of functional dataset.
Options:
  -prefix ppp = Write mask into dataset with prefix 'ppp'.
                 [default='automask']
  -q          = Don't write progress messages (i.e., be quiet).
  -eclip      = After creating the mask, remove exterior
                 voxels below the clip threshold.
  -dilate nd  = Dilate the mask outwards 'nd' times.
  -SI hh      = After creating the mask, find the most superior
                 voxel, then zero out everything more than 'hh'
                 millimeters inferior to that.  hh=130 seems to
                 be decent (for human brains).