Projects:RegistrationLibrary:RegLib C27

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v3.6.1 Slicer Registration Library Exampe #27: Diffusion Weighted Image Volume: align with structural reference MRI

Input

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

Modules

• Slicer 3.6.1 recommended modules: BrainsFit

Objective / Background

This is a typical example of DTI processing. Goal is to align the DTI image with a structural scan that provides accuracte anatomical reference. The DTI contains acquisition-related distortion and insufficient contrast to discern anatomical detail. For treatment planning and evaluation, location of functionally critical fiber tracts relative to the pathology is sought.

Keywords

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

Input Data

• reference/fixed : T1 axial, 0.98 x 0.98 x 1 , 192 x 256 x 176
• reference/fixed : FLAIR axial, 0.4mm resolution in plane, 4mm slices, 448 x 512 x 30
• moving: Baseline image of acquired DTI volume, corresponds to T2w MRI , 1.96 x 1.96 x 3 mm voxel size, oblique, 128 x 128 x 40
• moving: Tensor data of DTI volume, oblique, same orientation as Baseline image. The result Xform will be applied to this volume. The original DWI has 64 directions, the extracted DTI volume has 9 scalars, i.e. 128 x 128 x 40 x 9

Overall Strategy

1. Register FLAIR to T1 (affine) & resample
2. Resample DWI to isotropic voxel size: use T1 as size reference
3. Convert DWI -> DTI, incl. mask & baseline extraction
4. Register DTI_baseline to FLAIR (affine+nonrigid) w/o masking
5. Resample DTI with above transform

Procedures

• Phase I: register FLAIR to T1

1. open Registration : BrainsFit module (presets: Xf1_FLAIR-T2)
   1. Registration Phases:
   2. set T1 as fixed and FLAIR as moving image
      1. select/check Include Rigid registration phase
      2. select/check Include Affine registration phase
   3. Output Settings:
      1. select a new transform "Output Transform", rename to "Xf1_FLAIR-T1"
      2. select a new volume "Output Image Volume, rename to "FLAIR_Xf1"
   4. Registration Parameters: increase Number Of Samples to 200,000
   5. Leave all other settings at default
   6. click: Apply; runtime < 1 min.
   7. click: Apply

• Phase II: Resample DWI to isotropic voxel size

1. go to Filtering / Resample Scalar/Vector/DWI module
2. Input Volume: "DWI", Reference Volume: "T1", Output Volume: "create new Diffusion Weighted Volume", rename to "DWI_iso"
3. Click: Apply
4. save new DWI_iso to disk
5. depending on RAM of your machine, consider deleting the original DWI node

• Phase III: DWI -> DTI

1. open "Diffusion Tensor Estimation" module
2. Input DWI Volume: DWI_iso, Output DTI Volume: create new, rename to "DTI_iso"
3. Output Baseline: create new, rename to "DTI_iso_base"
4. Otsu Threshold Mask: create new, rename to "DTI_iso_mask"
5. check box: "Estimation Parameters": "WLS"
6. check boxes for Remove Islands and Apply Mask
7. Click: Apply

• Phase IV: Register DTI (unmasked)

1. open Registration : BrainsFit module (presets: Xf2_DTI-FLAIR_unmasked)
   1. Registration Phases:
   2. set FLAIR as fixed and DTI_iso_base as moving image
      1. select/check Include Rigid registration phase
      2. select/check Include Affine registration phase
      3. select/check Include BSpline registration phase
   3. Output Settings:
      1. select a new transform "Slicer BSpline Transform", rename to "Xf1_DTI-FLAIR_unmasked"
      2. select a new volume "Output Image Volume, rename to "DT_iso_base_Xf1"
   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 V: Resample DTI

1. Open the Resample DTI Volume module (found under: All Modules)
   1. Input Volume: select DTI_iso
   2. Output Volume: select New DTI Volume, rename to DTI_iso_Xf2
   3. Reference Volume: select T1
   4. Transform Parameters: select transform "Xf2_DTI-FLAIR_unmasked
   5. check box: output-to-input
   6. Leave all other settings at defaults
   7. Click Apply; runtime ~ 3 min.
2. Go to the Volumes module, select the newly produced DTI_Xf2 volume
3. under the Display tab, select Color Orientation from the Scalar Mode menu
4. set T1 as background and new DTI_Xf2 volume as foreground
5. Set fade slider to see DTI overlay onto the T2 image

for more details see the tutorial(s) under Downloads above

Registration Results

Download

• Data
  • RegLib_C27_Data DWI, DTI, T1, FLAIR, Presets & solution transforms (NRRD files, zip file 145 MB)
• Presets
  • RegLib_C27_Preproc_Presets Presets for DWI resampling & DTI estimation (.mrml file 8 kB)
  • RegLib_C27_Presets Presets for FLAIR and DTI registration & DTI resampling (.mrml file 12 kB)
  • Link to User Guide: How to Load/Save Registration Parameter Presets
• Documentation
  • RegLib_C27_Tutorial.ppt step-by-step tutorial Powerpoint (.ppt file 2.6MB)
  • RegLib_C27_Tutorial.pdf step-by-step tutorial PDF (.pdf file 3.8MB)

Discussion: Registration Challenges

• The DTI contains acquisition-related distortions (commonly EPI acquisitions) that can make automated registration difficult.
• the two images often have strong differences in voxel sizes and voxel anisotropy. If the orientation of the highest resolution is not the same in both images, finding a good match can be difficult.
• there is widespread and extensive pathology in the right hemisphere that might affect the registration if contrast is different between the baseline and structural reference scan.

Discussion: Key Strategies

• because the pathology appears similar in the FLAIR as in the DTI baseline, we choose the FLAIR as reference
• masking is likely necessary to obtain good results.
• in this example the initial alignment of the two scans is pretty good already. No initial affine alignment is needed.
• these two images are not too far apart initially, so we reduce the default of expected translational misalignment
• because speed is not that critical, we increase the sampling rate from the default 2% to 15%.