Documentation:Nightly:Registration:RegistrationLibrary:RegLib C20

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Slicer Registration Library Case #20: Align PET/CT pair follow-up to baseline

Input

fixed image/target baseline PET/CT		moving image follow-up PET/CT

Modules used

• General Registration (BRAINS)
• Resample Volume (BRAINS)
• TransformVisualizer

Download (from NAMIC MIDAS)

• RegLib_C20.mrb: input data, masks and result transforms (Slicer mrb file. 12 MB).

Keywords

PET/CT, full-body, intra-subject, nonrigid

Procedure

It is possible to perform both steps of affine and BSpline registration in a single pass within the General Registration (BRAINS) module, but to better show/judge progress we perform each separately and feed the results of one the the next step. Hence we first run an affine registration, then use that as starting point for a BSpline registration.

1. Compute Affine Registration: open to the General Registration (BRAINS) module
   1. Input Images: Fixed Image Volume: CT_1
   2. Input Images: Moving Image Volume: CT_2
   3. Output Settings:
      1. Slicer Linear Transform: (create new transform, rename to: "Xf1_Affine")
      2. Output Image Volume: none (we need no resampled volume at this stage, only the transform)
   4. Initialization: none
   5. Initialize Transform Mode: switch to Off (there is sufficient overlap)
   6. Registration Phases: 'check Rigid, Rigid+Scale and Affine only
   7. Main Parameters:
      1. increase Number Of Samples to at least 200,000
   8. Leave all other settings at default
   9. click: Apply; runtime < 2 min.
   10. check the result
       1. Place "CT_1" in the background and "CT_2" in the foreground
       2. switch to the Data module, verify that the "CT_2" node is inside the newly created "Xf1_Affine" node. The registration module should do that automatically for you. You may see a small "+" next to the "Xf1_Affine" node, click on it to reveal the contents.
       3. fade between background and foreground to judge the alignment.
2. Compute BSpline Registration: return to the General Registration (BRAINS) module
   1. Input Images: Fixed Image Volume: CT_1
   2. Input Images: Moving Image Volume: CT_2
   3. Output Settings:
      1. Slicer BSpline Transform: Create and rename new. Rename to "Xf2_BSpline"
      2. Slicer Linear Transform: set to none
      3. Output Image Volume: Create and rename new. Rename to "CT_2_Xf2" (we need a resampled volume to visualize the result. Nonrigid transforms cannot be visualized on the fly)
   4. Initialization: for the Initialization transform select the "Xf1_Affine" transform created above.
   5. Initialize Transform Mode: switch to Off
   6. Registration Phases: uncheck Rigid+Scale and Affine and select BSpline only
   7. Main Parameters:
      1. increase Number Of Samples to 300,000
      2. set B-Spline Grid Size to 11,11,7
   8. Leave all other settings at default
   9. click: Apply; runtime for this will be more than 1 minute, depending on CPU.
   10. check the result
       1. Place "CT_1" in the background and "CT_2_Xf2" in the foreground
       2. fade between background and foreground to judge the alignment.
3. Apply transform to PET

Registration Results

|before registration (click to enlarge)

|after affine registration (click to enlarge)

|BSpline deformation grid (click to enlarge)