Projects:RegistrationLibrary:RegLib C31

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v3.6.1 Slicer Registration Library Case xx: TBI

Modules

• Slicer 3.6.1 recommended modules: BrainsFit

Objective / Background

We seek to align two exams (acute baseline and follow-up) as well as all series within exams into a common space for direct evaluation of regional change.

Input Data

• inter-exam
  • reference/fixed : T1_e1 baseline exam of acute TBI , 512 x 512 x 160 ; 0.5 x 0.5 x 1 mm voxel size, axial acquisition, RAS orientation.
  • moving:T1_e2 follow-up exam of acute TBI , 512 x 512 x 160 ; 0.5 x 0.5 x 1 mm voxel size, axial acquisition, RAS orientation.
• intra-exam

Registration Challenges

• we have multiple nested transforms: each exam is co-registered within itself, and then the exams are aligned to eachother
• strong pathology (hemorrhage?) present at different amounts in the two exams

Key Strategies

• we first register the scans within each exam to the T1
• second we register the follow-up T1 scan to the baseline T1
• we then nest the first alignment within the second

Procedure

• Load & Center

1. Load T1 MPRAGE datasets via Load Volume...
2. volumes are note well centered, i.e. their physical origin defined in the image header differs; we therefore first center both images:
   1. Go to Volumes module, open Info tab
   2. From Active Volume menu, select each image in turn, then click the Center Image button
   3. note how Image origin changes for T1_e1 from 121,-97,-97 to 128,-128,-80 and for T1_e2 from 129,-106,-66 to 128,-128,-80
   4. now that both images have same center their initial misalignment can be seen by placing T1_e1 in the background and T1_e in the foreground and using the toggle-switch

• Align Exam 2 to Exam 1: T1 1st pass: unmasked

1. Open Registration / BRAINSFit module
   1. Fixed Image: T1_e1, moving image: T1_e2
   2. Registration Phases: select "Initialize with CenterOfHeadAlign", Include Rigid, "IncludeScaleVersor3D" and Include Affine
   3. Output Settings: under SlicerLinear Transform, select "Create New Linear Transform, then select Rename" and rename it to Xf1_e2-e1_Affine
   4. Registration Parameters: increase the Number of Samples field to 200,000
   5. Leave all other settings at defaults & Click: Apply. Registration should complete within ~ 30 seconds
   6. Go back to the Data module: you should see the T1_e2 image moved under the newly created transform
   7. Select "T1_e1" as background and T2_e2 as new foreground, toggle to see alignment
   8. due to the strong deformations an affine alignment alone does not achieve a perfect match. We can extend the DOF to non-rigid BSpline transforms, but must be aware that doing so might remove differences of interest:

• Align Exam 2: 2nd pass: nonrigid

1. Open Registration / BRAINSFit module
   1. Fixed Image: T1_e1, moving image: T1_e2
   2. From "Initialize with previously generated transform" & select the above affine Xf1_e2-e1_Affine
   3. Registration Phases: select only Include BSpline.
   4. Output Settings: under SlicerBSpline Transform, select "Create New BSpline Transform, then select Rename" and rename it to Xf2_e2-e1_BSpl

• Align Within Exam 1:

1. Select Load Volume... and open the GRE, FLAIR and DWI images, respectively
2. Open Registration / BRAINSFit module
3. Select the presets Xf3... to Xf9... or use settings below:
   1. Registration phases: select Initialize with Center of Head Align, include rigid, include ScaleVersor3D and include Affine
   2. increase Number of Samples in Registration Parameters to 200,000

1. 1. Registration Parameters: increase the Number of Samples field to 200,000
   2. Leave all other settings at defaults & Click: Apply. Registration should complete within 3 minutes.
   3. You should see the earlier residual misalignment reduced, but strong distortions applied to the e2 image (see results below)

Registration Results

unregistered exam 1 & 2
Exam 2 aligned to Exam 1 (affine only)
Exam 2 aligned to Exam 1 (affine+BSpline)
BSpline deformation only of Exam 2