Projects:RegistrationDocumentation:RegLib 12 LiverTumorAblation1

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v3.6.3 Slicer Registration Library Case #12:
Intra-subject liver & kidney CT / MRI: preop-scan to intra-op scan

Input

fixed image/target		moving image

Modules

Slicer 3.6.3 recommended modules:

• BrainsFit

Objective / Background

This is a typical case of image fusion from preop planning: we seek to align the preoperative MRI and CT (which have better tumor visibility) to the intra-operative CT.

Keywords

abdominal CT, abdominal MRI, liver, kidney, surgical planning, image fusion, tumor, nonrigid

Input Data

• reference/fixed : intra-operative CT, 1x1x5 mm voxel size, 512x512x41, axial
• moving 1: pre-operative MRI, 0.8x0.8x2.5 mm voxel size, 512x512x96, axial
• moving 2: pre-operative contrast CT, 0.9x0.9x5 mm voxel size, 512x512x42, axial

Overall Strategy

1. run rigid/affine registration (BRAINSfit) with initialization
2. run 7x7x7 nonrigid registration (BRAINSfit BSpline) using the above affine as input

Procedures

• Phase I: Register Rigid/Affine

1. open Registration : BrainsFit module (presets: BRAINSfit_Xf1 or _Xf2
   1. Registration Phases:
      1. select/check Include Affine registration phase
      2. for affine also select/check Include Scale Versor 3D and Include Affine registration phase
   2. Registration Parameters: increase Number Of Samples to 200,000
      1. select a new transform "Linear Transform", rename to "Xf1_affine"
   3. Leave all other settings at default

• Phase II: [optional]: generate skull mask

1. open Skull Stripper for Structural MRI Module (Extension module)
2. increase Iterations" to 200 and Subdivisions to 12
3. both results will have to be edited manually using the Editor module.

• Phase III: Register BSpline

1. open Registration : BrainsFit module (presets: BRAINSfit_Xf3 or _Xf4
   1. select a new volume "Output Image Volume, rename to "DTI_base_Xf1"
   2. Registration Parameters: increase Number Of Samples to 200,000
   3. Registration Parameters: set Number Of Grid Subdivisions to 7x7x7
   4. Leave all other settings at default
   5. if using masks, set the Mask Processing Mode to "ROI" and select the two labelmaps generated in phase II as Input Masks

Registration Results

unregistered	original unregistered
rigid	affine
rigid registered	affine registered
BSpline (7x7x7) unmasked	BSpline (7x7x7) masked
nonrigid registered (7x7x7 BSpline unmasked)	nonrigid registered (7x7x7 BSpline masked)

Download

• Data
  • RegLib_C12_Data , image data, resets & solution transforms (NRRD files, zip file 41 MB)
• Presets
  • RegLib_C12_Presets Presets for BRAINSFIT registration (.mrml file 12 kB)
  • Link to User Guide: How to Load/Save Registration Parameter Presets