Documentation:Nightly:Registration:RegistrationLibrary:RegLib C40

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Slicer Registration Library Case #40:
micro-CT of material wood sample

Input

fixed image/target		moving image

Modules used

• General Registration (BRAINS)

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.

• RegLib_C40.mrb
  (input data only, Slicer mrb file. 40 MB)
  
• RegLib_C40_full.mrb
  (input data + results, Slicer mrb file. 100 MB).

Description

We have 2 micro-CT scans of a material (wood) sample under different environmental conditions (e.g. moisture). We seek to use a nonrigid registration to capture and model the structural changes (deformations) that occur when conditions change. We register the two volumes to eachother and then interpret the deformation in this registration as a surrogate of the change that occurred.

Keywords

micro-CT, deformation modeling

Procedure

1. Affine Registration: open the General Registration (BRAINS) module.
   1. Fixed Image Volume: "sample1"
   2. Moving Volume: "sample2"
   3. Registration phases: check boxes for Rigid" ,"Scale", "Affine"
   4. Slicer Linear Transform: select "create new transform", rename to "Xf1_Affine" or similar
   5. leave rest at defaults. Click Apply
   6. registration should take ~ 10 secs.
   7. use fade slider to verify alignment; compare with result snapshots shown below. Alignment will not be perfect but should be better than before.
   8. note: you can also change the colormaps for the fixed and moving volumes to better judge the alignment: go to the Volumes module and in the Display tab, select "green" and "magenta" as the respective colormaps for the two volumes.
2. Nonrigid Registration: open the General Registration (BRAINS).
   1. Fixed/Moving Image Volume: as above
   2. Registration phases: uncheck boxes for rigid, scale and affine and check box for BSpline
   3. Output: Slicer Linear transform: set to None
   4. Output: Slicer BSpline transform: create new, rename to "Xf2_BSpline" or similar
   5. Output Image Volume: create new, rename to "sample2_Xf2"; Pixel Type: "unsigned short"
   6. Registration Parameters: increase Number Of Samples to 300,000; Number of Grid Subdivisions: 5,5,5
   7. Leave all other settings at default
   8. click apply

Registration Results

baseline and follow-up before registration (click to enlarge)
after affine alignment. Note the residual shape differences (click to enlarge)
after nonrigid BSpline registration (click to enlarge)
| visualization of the nonrigid deformation component only

Acknowledgments

Registration problem and dataset kindly provided by Alessandra Patera from the Swiss Federal Institute of Technology (ETHZ) in collaboration with the Swiss Federal Laboratories for Material Science and Technology (EMPA).