brain image preprocessing

19 sec read

  1. convert between different image formats
  2. strip skull (FSL bet, or Bet for gui)
    bet brain.nii brain_noskull.nii
  3. 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.
  4. 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



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