Documentation:Nightly:Registration:RegistrationLibrary:RegLib C50

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Home < Documentation:Nightly:Registration:RegistrationLibrary:RegLib C50

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Slicer Registration Library Case #50: Mouse micro-CT


this is the fixed DTI FA image. We want to align all images into this space
RegArrow NonRigid.png
this is the moving MR image, to be aligned with the reference on the left
fixed image/target
baseline CT
moving image
CT after fixation + staining


Goal is to align the two CT images pre/post fixation. The fixation process altered the tissue appearance and also caused distortions we seek to correct with non-rigid registration.

Modules used

Download (from NAMIC MIDAS)

Why 2 sets of files? The "input data" mrb includes only the unregistered data to try the method yourself from start to finish. The full dataset includes intermediate files and results (transforms, resampled images etc.). If you use the full dataset we recommend to choose different names for the images/results you create yourself to distinguish the old data from the new one you generated yourself.


micro-CT, animal, mouse, brain, intra-subject,

Video Screencasts

  1. RegLib_C50 Registration Screencast (I. Affine Registration)
  2. RegLib_C50 Registration Screencast (II. BSpline Registration)


  1. Affine Register
    1. go to the General Registration (BRAINS) module
    2. Input Images: Fixed Image Volume: baseline
    3. Input Images: Moving Image Volume: stained
    4. Output Settings:
      1. Slicer Linear Transform (create new transform, rename to: "Xf1_Affine")
      2. Output Image Volume none. No resampling required for linear transforms
    5. Registration Phases: select/check Rigid , Rigid+Scale, Affine
    6. Main Parameters:
      1. increase Number Of Samples to 300,000
    7. click: Apply; runtime ~ 1 min.
  2. BSpline Register
    1. leave baseline and stained as fixed and moving volumes
    2. Output Settings:
      1. Slicer Linear Transform select None
      2. Slicer BSpline Transform create new, rename to "Xf2_BSpline" or similar
      3. Output Image Volume: create new and rename to "stained_Xf2". Resampling is required for nonrigid transforms.
    3. Registration Phases: unchheck Rigid , Rigid+Scale, Affine and check "BSpline" only
    4. Main Parameters:
      1. increase Number Of Samples to at least 300,000
      2. BSpline Grid Size: set to 7,7,7 or similar.
    5. click: Apply; runtime < 3 min.

Registration Results

RegLib C50 unregistered.png before registration (click to enlarge)
RegLib C50 registered BSpline.gif after affine+nonrigid alignment (click to enlarge)


Many thanks to Dr.Murat Maga from Center for Developmental Biology and Regenerative Medicine in Seattle, WA for sharing the example data.