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

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%.