Projects:RegistrationLibrary:RegLib C29

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v3.6.1 Slicer Registration Library Case #29: Intra-subject Brain DTI

Input

fixed image/target T1 SPGR		moving image 1 T2		moving image 2a DTI baseline	moving image 2b DTI tensor

Modules

• Slicer 3.6.1 recommended modules: BrainsFit

Objective / Background

This is a classic case of a multi-sequence MRI exam we wish to spatially align to the anatomical reference scan (T1-SPGR). The scan of interest is the DTI image to be aligned for surgical planning/reference.

Download

• DATA
  • Registration Library Case 29 (full set) (Data & Solution Xforms, incl. DTI + DWI + resampled DTI, zip file 140 MB)
  • Registration Library Case 29 (small set) (excl. DWI and resampled DTI images, use if interested in registration portion only, zip file 44 MB)
  • Registration Library Case 29 (suppl. set) (DWI and resampled DTI images only, use if interested in DWI-DTI conversion, zip file 95 MB)
• PRESETS:
  • Registration Library Case 29: Parameter Presets (presets for registration and resampling) 16kB, load via ImportScene..)

Link to User Guide: How to Load/Save Registration Parameter Presets

• TUTORIALS:
  • Powerpoint Tutorial (.ppt PowerPoint file, 1.5 MB)
  • Powerpoint Tutorial as PDF (PDF file 2.1 MB)

Keywords

MRI, brain, head, intra-subject, DTI, T1, T2, non-rigid, tumor, surgical planning

Input Data

• reference/fixed : T1 SPGR , 0.5x0.5x1 mm voxel size, 512 x 512 x 176
• moving 1: T2 0.5x0.5x1.5 mm voxel size, 512 x 512 x 92
• moving 2a: DTI baseline: 1 x 1 x 3 mm, 256 x 256 x 41
• moving 2b: 1 x 1 x 3 mm, 256 x 256 x 41 x 9 (tensor), original: DWI 256 x 256 x 41 x 32 directions

Registration Challenges

• The DWI sequence (EPI) contains strong distortions we seek to correct via non-rigid alignment
• The DWI sequence also contains strong intensity inhomogeneity (coil bias)
• the DTI baseline is similar in contrast to a T2, albeit at much lower resolution
• we have different amounts of voxel-anisotropy
• a direct registration of the DTI_baseline to the SPGR will fail, hence a 2-step approach is required

Key Strategies

• Slicer 3.6.1 recommended modules: BrainsFit
• to align the DTI with the T1 we need 2 registration steps: 1.align the T2 with the T1 and 2. align the DTI with the T2. The DTI baseline scan has contrast most similar to the T2 and hence is best registered against the T2. However the structural reference scan with highest resolution and tissue contrast is the T1.
• we therefore use the following approach: 1) we first co-register the T2 with the SPGR T1. 2) we register the DTI baseline to the registered/resampled T2; 3) resample the DTI volume with the new transform
• the DTI-T2 registration includes non-rigid deformation to correct for the strong distortions from the EPI acquisition. Because of the nonrigid component a mask of the brain parenchyma helps greatly in obtaining a meaningful transform.
• The DTI estimation provides an automated mask for the DTI_baseline scan, but we have no mask for the T2. We can either obtain one through separate segmentation or by sending the DTI_mask through an additional registration step. In this example we show the latter.
• thus the full pipeline is this:

1. Affine align T2-T1, incl. resampled T2 volume = T2r
2. Affine+BSpline align of DTI_baseline to T2r (unmasked)
3. Resample DTI_mask with above BSpline -> mask for the T2r
4. repeat Affine+BSpline align of DTI_base to T2r, WITH masks
5. resample DTI with result Affine+BSpline transform

Procedures

• Phase I: LOAD DATA

1. download example dataset
2. load into 3DSlicer 3.6.1 (Load Scene)
3. To convert the DWI into a DTI: use the Converters / DICOM to NRRD Converter module

• Phase II: Register T2 to T1

1. open Registration : BrainsFit module
   1. Registration Phases:
   2. select/check Include Rigid registration phase
   3. select/check Include Affine registration phase
   4. select a new transform Output Transform
2. Registration Parameters: increase Number Of Samples to 200,000
3. Leave all other settings at default
4. click apply; runtime ca. 1-2 min.
5. Resample T2 into T1 space
   1. Open Resample Scalar/Vector/DWI Volume module (Filtering menu)
   2. Input Volume: T2, Reference Volume: T1
   3. Output Volume: create new volume, rename to "T2_Xf1"
   4. Interpolation Type: select ws (windowed sinc)
   5. Click Apply.
   6. Upon completion, go to Volumes module to adjust window & level
   7. Active Volume: select T2_Xf1
   8. Open Display tab and adjust window & level, e.g. 1300/700

• Phase III:REGISTER DTI TO T2_Xf1

1. open Registration : BrainsFit module
   1. Registration Phases:
   2. set T2_Xf1 as fixed and DTI_baseline as moving image
      1. select/check Include Rigid registration phase
      2. select/check Include Affine registration phase
      3. select/check Include BSpline registration phase
      4. select Include Rigid registration phase
      5. select Include Affine registration phase
      6. select Include BSpline registration phase
   3. Output Settings:
      1. select a new transform "Slicer BSpline Transform", rename to "Xf2_DTI-T1_unmasked"
      2. select a new volume "Output Image Volume, rename to "DT_base_Xf2"
   4. Registration Parameters: increase Number Of Samples to 200,000
   5. Registration Parameters: set Number Of Grid Subdivisions to 5,5,3
   6. Leave all other settings at default
   7. click: Apply; runtime < 1 min.

• Phase IV: Resample DTI_mask
  • we use the above Xform to produce a mask for the T1.

1. Open Resample Scalar/Vector/DWI Volume module
   1. Input Volume: DTI_mask; Output volume: create new volume, rename to "DTI_mask_Xf2"
   2. Transform Node: "Xf2_DTI-T1_unmasked"
   3. select/check: output-to-input
   4. Interpolation Type: select: nn
   5. click: Apply

• Phase V:REGISTER DTI TO T2_Xf1 with masking

1. open Registration : BrainsFit module
   1. Registration Phases: as before: rigid, affine, BSpline
   2. set T2_Xf1 as fixed and DTI_baseline as moving image
   3. All parameters as in Phase III
   4. Output BSpline Transform: create new , rename to "Xf3_DTI-T1_masked"
   5. Output Volume: create new, rename to "DTI_base_Xf3"
   6. Control of Mask Processing
      1. select/check: ROI (rightmost box)
      2. Input Fixed Mask: select "DTI_mask_Xf2"
      3. Input Moving Mask: select "DTI_mask"
   7. click: Apply; runtime < 1 min.

• Phase VI: Resample DTI

1. Load the combined transform (Add Data)
2. Open the Resample DTI Volume module (found under: All Modules)
   1. Input Volume: select DTI
   2. Output Volume: select New DTI Volume, rename to DTI_Xf2
   3. Reference Volume: select T1
   4. Transform Parameters: select transform "Xf2_DTI-T1
   5. check box: output-to-input
   6. Leave all other settings at defaults
   7. Click Apply; runtime < 1 min.
3. Go to the Volumes module, select the newly produced DTI_Xf2 volume
4. under the Display tab, select Color Orientation from the Scalar Mode menu
5. set T1 as background and new DTI_Xf2 volume as foreground
6. Set fade slider to see DTI overlay onto the SPGR image

for more details see the tutorial(s) under Downloads

Registration Results

registered (cycles show T1 and T2 and color DTI overlay)