STEP 3.5 : creating a union mask

• STEP 3.5 : creating a union mask

• • use 3dAutomask to create a 'brain' mask for each run
  • create a mask which is the union of the run masks (since we need only one main mask; not 9 masks from individual runs)
  • this mask can be applied in various ways:
  • • During the scaling operation
    • In 3dDeconvolve (so that time is not wasted on background voxels)
    • To group data, in standard space
    • • may want to use the intersection of all subject masks
      • foreach run ( $runs )
      • 3dAutomask -dilate 1 -prefix rm.mask_r$run \
      • pb03.$subj.r$run.blur+orig
      • end
    • -dilate 1 : dilate the mask by one voxel (just to ensure that none of the voxels along the perimeter of the brain get accidently clipped away and excluded from the mask).