Projects:RegistrationLibrary:RegLib C47

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updated for v4.1
Slicer Registration Library Case #47: Liver Tumor Cryoablation

Input

fixed image/target		moving image

Slicer4 Modules used

• BrainsFit

Objective / Background

We seek to align a pre-operative MRI with the intra-operative CT for surgical guidance.

Keywords

MRI, CT, IGT, intra-operative, liver, cryoablation, change detection, non-rigid registration

Input Data

• reference/fixed : pr-op CT, 0.95 x 0.95 x 5 mm voxel size
• moving: intra-op MRI, 0.78 x 0.78 x 2.5 mm axial,

Discussion: Registration Challenges

• large differences in FOV
• strong differences in image contrast between MRI & CT
• we have strongly anisotropic voxel sizes with much less through-plane resolution
• there is a related example for pre-operative contrast CT to MRI in Library Case #12

Procedures

• Phase I: MR-CTpre registration

1. Following the concept of manual registration, we create an initial transform that roughly aligns the MR to the pre-op CT.
2. open General Registraion (BRAINS) module
   1. Input Images
      1. Fixed Image Volume: CT_intraop
      2. Moving Image Volume: MRI_preop
   2. Output Settings:
      1. Slicer BSpline Transform none
      2. Slicer Linear Transform (create new transform, rename to: "Xf1_MRI-CT_Affine")
      3. Output Image Volume none
   3. Registration Phases: select/check Rigid , Rigid+Scale, Affine
   4. Leave all other settings at default
   5. click: Apply
3. switch to the Data module
   1. click on the "MRI_intra" node, and drag it onto the transform node "Xf1_MRI-CT_Affine" created above
   2. this should yield a rough alignment as shown in the result section below. We will use this to initialize a more refined nonrigid registration

• Phase II: nonrigid registration

1. open General Registraion (BRAINS)module
   1. Input Images
      1. Fixed Image Volume: CT_intraop
      2. Moving Image Volume: MRI_preop
   2. Output Settings:
      1. Slicer BSpline Transform (create new transform, rename to: "Xf2_MRI-CT_BSpline")
      2. Slicer Linear Transform none
      3. Output Image Volume create new volume, rename to "MRI_Xf2"
   3. Initialization
   4. Initialization transform: select "" created in phase 1 above
   5. 'Initialize Transform Mode: Off
   6. Registration Phases: select/check BSpline only
   7. Main Parameters
   8. Number Of Samples: 200,000
   9. B-Spline Grid Size: 7,7,5
   10. Leave all other settings at default
   11. click: Apply

Registration Results

	unregistered MRI & CT
	after linear (affine) registration
after nonrigid registration	after nonrigid registration
	comparing kidney alignment at different registration stages

Download

• download input image data (Input Data, NRRD images, zip file 42 MB)

Acknowledgments

Thanks to Dr.Stuart Silverman and Dr. Nobuhiko Hata for sharing this case.