Projects:RegistrationLibrary:RegLib C21

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v3.6.3 Slicer Registration Library Case #21: Intra-subject knee MRI

Input

fixed image/target		moving image

Modules

• Slicer 3.6.3 recommended modules: BrainsFit,

Objective / Background

atlas building, priors, cartilage segmentation

Keywords

knee, MRI

Input Data

• reference/fixed : subject 58 MRI: 0.47 x 0.47 x 1.55 mm , 256 x 256 x 60; sagittal
• moving: subject 64 MRI: 0.55 x 0.55 x 1.5 mm , 256 x 256 x 60; sagittal

Download

• Data
  • RegLib C20 example data set; incl Presets and solutions (zip file 9.6 MB)
  • Registration Presets (.mrml files 16kB)
  • Link to User Guide: How to Load/Save Registration Parameter Presets

Registration Results

rigid
rigid
affine alignment
BSpline registration of full volumes. 9 x 9 x 5 grid

Procedures

• Phase 1: rigid alignment

1. Go to the BRAINSfit module
   1. select Presets "Xf1_Rigid" or set the parameters as given below:
   2. fixed image: "58_MRI", moving image: "64_MRI"
   3. Initialize with previous transform: select "Off"
   4. Initialize Transform Mode: check box for use MomentsAlign
   5. check Include Rigid registration Phase box.
   6. Output: under Slicer Linear Transform, select new and rename to "Xf1_Rigid" or similar
   7. Registration Parameters: set "Number of Samples" to 150,000 at least
   8. leave rest at defaults
   9. Click Apply

• Phase 2: affine alignment

1. Go to the BRAINSfit module
   1. same as Phase 1 above, except:
   2. Initialize with previous transform: select "Xf1_Rigid" from phase 1 above
   3. Initialize Transform Mode: check box for Off
   4. check Include ScaleVersor" , "Include ScaleSkewVersor" and "Include Affine" registration Phase box.
   5. Registration Parameters: set "Number of Samples" to 200,000 at least
   6. Output: under Slicer Linear Transform, select new and rename to "Xf2_Affine" or similar

• Phase 3: Masking

1. Before allowing nonrigid deformations we must mask the aliasing present:
   1. Go to the Editor module.
   2. Select 58_MRI as Master Volume, choose the threshold tool and threshold at intensity ~68 to separate from the background.
   3. Select the Brush tool and cut connections between the aliasing portions and the rest of the image
   4. Select Island Tool and remove aliasing portions
   5. Select Dilate tool to fill holes
   6. Save. Repeat for the 64_MRI volume

• Phase 4: BSpline alignment

1. Go to the BRAINSfit module
   1. Initialize with previous transform: select "Xf2_Affine" from phase 2 above
   2. Output: under Slicer BSpline Transform, select new and rename to "Xf3_BSpline" or similar
   3. Output Image Volume: select new and rename to "64_MRI_Xf3" or similar
   4. Registration Parameters: set "Number of Samples" to 300,000 at least
   5. Number of Grid Subdivisions: 7,7,5
   6. Maximum B-Spline Displacement: set to 5 [mm]
   7. Masking: check ROI box, Input Fixed Mask: "58_MRI-label", Input Moving Mask: "64_MRI-label" generated in Phase 3 above.
   8. Click Apply
2. Note to compare the different registrations: to see the Rigid or Affine registrations, drag the 64_MRI volume inside/onto the respective transform node. To see the BSpline registrations, select the "64_MRI_Xf3" volume as fore- or background.

Discussion: Registration Challenges

• inter-subject registration: content differences are large, as are relative limb positions
• aliasing: both MRIs have aliasing with part of the anatomy wrapping around to the other edge of the image. This needs to be masked for detailed registration

Discussion: Key Strategies

• to calculate the transform, we use the images with the most accurate geometric representation and the smallest expected change, i.e. we align the follow-up CT to the baseline CT and then apply the transforms to the PET image.
• because of the non-rigid differences due to posture and breathing we will need to apply a 2-step registration with an affine alignment followed by a BSpline.