Projects:RegistrationLibrary:RegLib C30

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v3.6.1 Slicer Registration Library Case #30: Intra-subject Brain DTI

Input

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

Modules

• Slicer 3.6.1 recommended modules: BrainsFit, Skull Stripping Module, N4 MRI Bias Field Correction

Objective / Background

This is a common case of a DTI exam with no T2 available as structural reference and a T1 that has strong field inhomogeneity. We wish to spatially align the DTI to the anatomical reference scan (T1-SPGR).

Download

• DATA
  • Registration Library Case 30 (registration set) (Data & Solution Xforms, incl. DTI, zip file 18 MB)
  • Registration Library Case 30 (DWI+resampled DTI set) (original DWI + resampled DTI only, zip file 53 MB)
• PRESETS:
  • Registration Library Case 30: Parameter Presets (presets for bias correction, mask generation, registration & resampling) 12kB, load via ImportScene..)
  • Link to User Guide: How to Load/Save Registration Parameter Presets
• Documentation:
  • 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, non-rigid,

Input Data

• reference/fixed : T1 , 1x1x1.1 mm voxel size, 256 x 256 x 193
• moving: DTI baseline: 2.5 x 2.5 x 2.5 mm, 128 x 112 x 44
• moving DTI tensor: : 2.5 x 2.5 x 2.5 mm, 128 x 112 x 44 x 9 (tensor), original: DWI 256 x 256 x 41 x 36 directions

Registration Challenges

• The DTI sequence (EPI) has a low resolution, a clipped FOV and distortions we seek to correct via non-rigid alignment
• the DTI baseline is similar in contrast to a T2, but we have only a T1 as structural reference

Key Strategies

• Slicer 3.6.1 recommended modules: BrainsFit
• to align the DTI with the T1 we need 2 preprocessing steps: 1. reduce the bias field inhomogeneity in the reference T1 and 2. obtain a skull-stripping / brain mask for the T1
• The DWI is already isotropic and hence no resampling is required before obtaining the DTI
• 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 T1. We can either obtain one through separate segmentation or by sending the DTI_mask through an additional registration step. We use the former here.
• thus the full pipeline is this:

1. Bias Field Correction of T1 -> T1_bc
2. Skull Stripping of T1_bc

1. DWI -> DTI estimation (incl. DTI_base and DT_mask output)

1. Affine registration of DTI_baseline to T1_bc, unmasked
2. non-rigid (BSpline) registration of DTI_baseline to T1_bc, masked, using above affine as starting pose
3. 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 DTI superimposed on SPGR and T2 registered (cycles show T1 and T2 and color DTI overlay)