Projects:RegistrationLibrary:RegLib C27

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

					LEGEND this indicates the reference image that is fixed and does not move. All other images are aligned into this space and resolution this indicates the moving image that determines the registration transform. this indicates images that passively move into the reference space, i.e. they have the transform applied but do not contribute to the calculation of the transform.
T2 FLAIR	T1 contr.		DTI Baseline	DTI volume
0.45 x 0.45 x 3.9 mm axial 448 x 512 x 30 RAS	0.98 x 0.98 x 1 mm axial 192 x 256 x 176 RAS		1.96 x 1.96 x 3 mm axial 128 x 128 x 40 RAS	1.96 x 1.96 x 3 mm axial 128 x 128 x 40 RAS

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 : FLAIR axial, 0.4mm resolution in plane, 4mm slices
• moving: Baseline image of acquired DTI volume, corresponds to T2w MRI , 1.96 x 1.96 x 3 mm voxel size, oblique
• tag: 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

• download dataset (DTI estimate, baseline image FLAIR & T1) (NRRD files, zip file 15 MB)
• Presets
• Tutorial only
• Complete tutorial package

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

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 cortex that might affect the registration if its contrast is different in 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%.