Documentation:Nightly:Registration:RegistrationLibrary:RegLib C01

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Home < Documentation:Nightly:Registration:RegistrationLibrary:RegLib C01

Back to Registration Library

Slicer Registration Library Case #1: Follow-up MRI of Brain Tumor


this is the fixed baseline image.
RegArrow NonRigid.png
this is the follow-up scan, to be registered the baseline on the left
fixed image moving image

Objective / Background

Goal is to align the follow-up image with the reference/baseline scan to assess changes.

Modules used

Download (from NAMIC MIDAS)


MRI, brain, head, intra-subject, meningioma

Video Screencasts

  1. Movie/screencast showing rigid and affine registration


  1. Rigid Registration: open the General Registration (BRAINS) module
    1. Input Images: Fixed Image Volume: MRMeningioma_1
    2. 'Input Images: Moving Image Volume: MRMeningioma_2
    3. Output Settings:
      1. Slicer Linear Transform (create new transform, rename to: "Xf1_Rigid")
      2. Output Image Volume none
    4. Registration Phases: select/check Rigid
    5. Initialization Phases: none
    6. Main Parameters:
    7. Leave all other settings at default
    8. click: Apply; runtime < 10 sec
  2. Affine registration: We have now increase the DOF to 12 in the form of an affine transform that also corrects scale and allows shear.

Registration Results

RegLib C01 unregistered.png baseline and follow-up before registration (click to enlarge)
300px after rigid alignment. Note the residual shape differences (click to enlarge)
RegLib C01 affine.png after affine registration (click to enlarge)

Discussion: Key Strategies

  • The affine registration seeks to address residual distortions that are typical for longitudinal MRI. However to prevent the tumor (and putative tumor change) from affecting the registration, we mask out the tumor so that it does not contribute to the registration. The assumption is thus that aside from the tumor we expect the two serial scans to be matching exactly, i.e. any differences in size or shape is considered an artifact we wish to remove by registration.