Projects:RegistrationLibrary:RegLib C38

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updated for v4.1 Slicer4 RegLibLogo.png Slicer Registration Library Case 38: TBI


RegLib C38 Thumb1.png lleft RegLib C38 Thumb2.png RegLib C38 Thumb3.png RegLib C38 Thumb4.png RegLib C38 Thumb5.png lleft RegLib C38 Thumb6.png RegLib C38 Thumb7.png RegLib C38 Thumb8.png
T1pre FLAIR T1post coronal T2 SWI EP50 EP75 EP100

Slicer 4.1 recommended Modules


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

  • extensive injury
  • distortions on EPI images
  • clipped FOV on T2

Key Strategies

  • we register all the scans within each exam to the T1
  • we limit registration degree of freedom to 6 DOF (rigid transformation only).


  1. Load all datasets via drag&drop or via "AddData / AddVolume" ... do not center the volumes, since they have reasonable alignment at the outset
  2. the registration procedure below is identical for all other scans in the sequence, i.e. just replace the Moving Volume and the Slicer Linear Transform", everything else can stay at default
  3. open the General Registration (BRAINS) module
    1. Fixed Image Volume: T1
    2. Moving Image Volume: T2
    3. Output Settings:
      1. Slicer BSpline Transform": none
      2. Slicer Linear Transform: create new transform, rename to "Xf1_T2"
      3. Output Image Volume: none
    4. Registration Phases: check box for Rigid only
    5. leave all other settings at defaults
    6. click: Apply; runtime < 15 sec (MacPro QuadCore 2.4GHz)
  4. this will generate the alignment transform. Note that the Slicer4.1 version of BRAINS registration does not automatically place the moving volume inside the result transform, as it did for Slicer 3.6. In order to see the result, you must either go to the Data module and drag the moving volume inside the transform node, or select to generate a resampled Output Volume, as done above. The demo movies you can download here show how to do this.

Registration Results

unregistered unregistered
registered registered