Projects:RegistrationLibrary:RegLib C06

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updated for v4.1 Registration Library Case #6: Breast MRI Treatment Assessment

fixed image/target pre Rx MRI		moving image post Rx MRI

Versions

For the Slicer 3.6 version of this tutorial see here

Modules

• Slicer 3.6.1 recommended modules:
  • Robust Multiresolution Affine
  • Fast Nonrigid BSpline

Objective / Background

We seek to align the post-treatment (PostRx) scan with the pre-treatment scan to compare local effects (left side only).

Keywords

MRI, breast cancer, intra-subject, treatment assessment, change detection, non-rigid registration

Download

• Data:
  • RegLib_C06_BreastCancer_Data.zip (Data,Presets, Solution, zip file 85 MB)
• Presets
  • Registration parameter presets file (.mrml file 20 kB)
  • Link to User Guide: How to Load/Save Registration Parameter Presets
• Documentation
  • download guided tutorial (PowerPoint, 2.6 MB)
  • download guided tutorial (PDF, 1 MB)

Input Data

• reference/fixed : 0.44 x 0.44 x 5 mm , 784 x 784 x 30
• moving: 0.68 x 0.68 x 1.5 mm, 515 x 515 x 93

Methods

• Phase 1: Extract left breast image of PreRx and PostRx scan

1. Open the Crop Volume module
   1. 1. Input volume: "PreRx"
      2. Input ROI: "Create new annotation ROI"
      3. ROI visibilité: turn on
      4. Isotropic output voxel: yes (checkbox)
      5. Interpolator: "WindowedSinc" (radio button)
      6. place/drag the color markers visible in the slice views to enclose the left breast only (right side of image)
   2. click on Crop! button
2. go to the Data module
   1. several new nodes were created: look for the "PreRx_subvolume-scale_1" entry, double click and rename to "PreRx_Left"
3. repeat the same for the "PostRx" image
4. Save intermediate results.

• Phase 2: MRI Bias field inhomogeneity correction

1. Open the N4ITKBiasFieldCorrection module
   1. Input Image: PreRx_left
   2. Mask Image: none
   3. Output Volume: create & rename new: "PreRx_left_n4"
   4. leave all parameters at defaults
   5. Apply.
2. repeat for the Post_Rx image.
3. save intermediate results

• Phase 3: Build masks

1. open the Foregroud masking (BRAINS) module (under Segmentation:Specialized)
   1. Input Image Volume: PreRx_left
   2. Output Mask: create & rename new: "PreRx_mask"
   3. Output Image clipped by ROI: none
   4. Configuration Parameters:
      1. ROI Auto Dilate Size: 0.1
      2. defaults for the rest
   5. Apply
2. repeat for Post_Rx_left_n4
3. save intermediate results

• Phase 4: Affine pre-Registration

1. open the General Registration (BRAINS) module
   1. Fixed Image Volume: PreRx_left_n4
   2. Moving Image Volume: PostRx_left_n4
   3. Output Settings:
      1. Slicer BSpline Transform": none
      2. Slicer Linear Transform: create & rename new transform, rename to "Xf1_Affine"
      3. Output Image Volume: none
   4. Registration Phases: check boxes for Rigid , Rigid+Scale and Affine
   5. Main Parameters:
      1. Number Of Samples: 200,000
   6. Leave all other settings at default
   7. Apply
   8. this should generate a first alignment. To see it you need to:

t and also 2 masks. We already have a DWI mask, so we care not about "DWI_mask_ROIauto", but we will use the T1_mask_ROIauto" output to edit/cleanup and use as mask in the subsequent nonrigid registration

• Phase IV: T1 mask

1. open the Editor module
2. select "T1_mask_ROIauto" as the volume to edit
3. select the Erosion tool and click Apply until all of the segmented skull areas are removed
4. select the Brush tool and manually fill in missing areas. Note that this need not be extremely accurate along the edges, since it will serve as a registration mask. To skip this step load the "T1_mask_edit.nrrd" file from the downloaded dataset.

• Phase V: Nonrigid Registration

1. open the General Registration (BRAINS) module
   1. Fixed Image Volume: T1_n4
   2. Moving Image Volume: DWI_baseline
   3. Output Settings:
      1. Slicer BSpline Transform": create new transform, rename to "Xf2_DWI-T1_BSpline"
      2. Slicer Linear Transform: none
      3. Output Image Volume: create new volume, rename to "DWI_baseline_Xf2"
   4. Registration Phases: check boxes for BSpline only
   5. Main Parameters:
      1. Number Of Samples: 200,000
      2. B-Spline Grid Size: 5,5,5
   6. Mask Option: select ROI button
      1. ROI Masking input fixed: select " "T1_mask_ROIauto" or "T1_mask_edit" edited in phase III above
      2. ROI Masking input moving: select "DWI_mask" created in phase I above
   7. Leave all other settings at default
   8. click: Apply

Registration Results

Discussion: Registration Challenges

• soft tissue deformations during image acquisition cause large differences in appearance
• the large tumor recession represents a significant pre/post difference in image content that will influence unmasked intensity-driven registration, which becomes a problem for the non-rigid portion of registration, particularly at higher DOF, because the registration will try to "recreate" the tumor area from the postRx image in order to match the content.
• contrast enhancement and pathology and treatment changes cause additional differences in image content
• the surface coils used cause strong differences in intensity inhomogeneity.
• we have strongly anisotropic voxel sizes with much less through-plane resolution
• resolution and FOV change between the two scans

Discussion: Key Strategies

• because of the strong changes in shape and position, we break the problem down and register each breast separately.
• we perform a bias-field correction on both images before registration
• we use the Multires version of RegisterImages for an initial affine alignment
• the nonlinear portion is then addressed with a BSpline or DiffeomorphicDemons algorithm
• because accuracy is more important than speed here, we increase the sampling rate (i.e. the number of points sampled for the BSpline registration)