strip skull (FSL bet, or Bet for gui) bet brain.nii brain_noskull.nii
register to a standard brain (FSL flirt, or Flirt for gui)
Select avg152T1_brain.img as reference, use rigid body (6 parameters)
A mat file will be produced.
register to a standard brain, with skull
First perform step 2 and 3
Then run Flirt, click button “Utils”, select “Apply FLIRT transform”
Input the mat file, the original image file (with skull). Output size: select the original image. Output file: give a new name
