Projects:RegistrationLibrary:RegLib C03

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updated for v4.1 Slicer Registration Library Case #3: Diffusion Weighted Image Volume: align with structural reference MRI

Input

fixed image/target T2		moving image 2a DTI baseline	moving image 2b DTI tensor

Modules

• Slicer 4.1 recommended modules: BrainsFit, Resample DTI Volume, Diffusion Tensor Estimation
• for the Slicer 3.6.3 version of this case see here

Objective / Background

Goal is to align the DTI image with the structural reference T2 scan that provides accuracte anatomical reference.

• Alternate Versions: this example covers the most basic form of directly registering a DTI + baseline to a T2. There is another (more advanced) version that show how to address additional issues of a strong initial rotation and strong voxel-anisotropy for the raw DWI image acquired. You will find the advanced version here.

Download

• Image Data:
  • RegLib_C03_Data: main registration package: register DTI (Data,Presets, Transforms, zip file 61 MB)

Procedure

This assumes you have the following: 1) a T2 reference image, 2) a DTI baseline image and 3) the DTI volume (both obtained from the Diffusion Tensor Estimation module).

• Image Data:
• Overview:

1. Using General Registraion (BRAINS), register DTI_baseline to T2 (affine+nonrigid) w/o masking

1. Resample the DTI with above transform with the Resample DTI Volume module

1. open Registration : General Registration (BRAINS) module
   1. Input Images: fixed = T2 , moving = DTI_base
   2. Output Settings:
      1. Slicer BSpline Transform (create new transform, rename to: "Xf1_DTbase-T2_BSpline")
      2. Slicer Linear Transform none
      3. Output Image Volume (create new volume, rename to: "DTIbaseline_Xf1"
   3. Registration Phases: select/check Rigid , Rigid+Scale, Affine, BSpline
   4. Main Parameters:
      1. increase Number Of Samples to 200,000
      2. set B-Spline Grid Size to 5,5,5
   5. Leave all other settings at default
   6. click: Apply; runtime < 1 min.
2. Resample DTI
3. Open the Resample DTI Volume module (found under: All Modules)
   1. Input Volume: select DTI
   2. Output Volume: select create new Diffusion Tensor Volume,and rename it to DTI_Xf2
   3. Reference Volume: select T2
   4. Transform Parameters: select transform "Xf2_DTI-T2_masked, Deformation Field: none ; check the displacement checkbox
   5. Leave all other settings at defaults
   6. Click Apply; runtime ~ 2 min.
4. Go to the Volumes module, select the newly produced DTI_Xf2 volume
5. under the Display tab, select Color Orientation from the Scalar Mode menu
6. set T2 as background and new DTI_Xf2 volume as foreground
7. fade between back- and foreground to see DTI overlay onto the T2 image

Registration Results (click to enlarge)

baseline & T2 before registration	baseline to T2 after affine+nonrigid alignment	DTI and T2 before & after registration

Keywords

MRI, brain, head, intra-subject, DTI, DWI

Discussion: Key Strategies

• the strong EPI-based distortions of the DTI image make nonrigid registration necessary
• initial alignment & overlap is sufficient so that no "initialization" methods are necessary and registration can succeed without.
• contrast & initial pose are similar enough for registration to succeed without any masking. However the DTI estimation procedure does provide an optional mask that is usually very helpful in registering cases with more "distracting" image content. For an example see the extended version of this case here.
• the DTI in this example is isotropic and hence can be resampled directly. If the DTI contains strong anisotropy of ratios 1:3 or greater, reorienting the DTI can lead to strong artifacts (e.g. in axial direction appear as blue cast in the color orientation view). In that case it is necessary to resample the DWI in the original orientation to an isotropic size before reorienting. It may also be advisable to first reorient the DWI and perform the DTI estimation afterwards.