Projects:RegistrationLibrary:RegLib C11

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Slicer Registration Library Exampe #11: Co-registration of two anatomic brain atlases for merging of structure labels

			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.
Target Atlas		2nd (older) Atlas containing labels for thalamic nuclei
0.9375 x 0.9375 x 1.5 mm axial 256 x 256 x 124 T1w, PA		0.9375 x 0.9375 x 1.5 mm axial 256 x 256 x 124 T1w, PA

Objective / Background

This is an example of sparse atlas co-registration. Not all atlases have an associated reference image that can be used for registration. Because the atlas represents a map of a particular tissue class probability, its contrast differs significantly from the target image.

Keywords

MRI, brain, head, inter-subject, probabilistic atlas, atlas-based segmentation

Input Data

• reference/fixed : T1w axial, 1mm resolution in plane, 3mm slices
• moving: Probabilistic Tissue atlas,

Methods

1. build brain mask for fixed image using Skull Stripping module. Settings: 100 iterations, 20 subdivisions. New Volume: RegLib_C10_MRI_AtlasSegmentation_fixed_mask
2. manually edit brain mask with Editor module. required manual fix at frontal and occipital lobe
3. run Register Images , Settings:

• Fixed Image:
• Moving Image:
• Resample Image:
• Load Transform:
• Save Transform: RegLib_C10_MRI_AtlasSegmentation_Xform_Affine_wmsk
• Initialization: Centers of Mass,
• Registration: PipelineAffine
• Expected offset: 10
• Expected Rotation: 0.2
• Expected Scale: 0.1
• Expected Skew: 0.05
• Fixed Image Mask: RegLib_C10_MRI_AtlasSegmentation_fixed_mask
• Affine Max Iteration: 80
• Affine Sampling Ratio: 0.05

1. (alternatively automated Affine Registration: Register Images Multires (Slicer 3.5) also produces good results
2. run Deformable B-spline Registration module. Settings:

• Grid Size: 5
• Histogram Bins: 50,
• Spatial Samples: 50000,
• initial transform: RegLib_C10_MRI_AtlasSegmentation_Xform_Affine_wmsk

Registration Results

Download

• download entire package (Data,Tutorial, Solution, zip file 14 MB)
• Presets
• Tutorial only
• Image Data only

Discussion: Registration Challenges

• Because the atlas represents a probabilistic image (i.e. contains blurring from combining multiple subjects), its contrast differs significantly from the target image.
• The atlas has strong rotational misalignment that can cause difficulty for automated affine registration.
• The two images represent different anatomies, a non-rigid registration is required

Discussion: Key Strategies

• Because of the strong differences in image contrast, Mutual Information is recommended as the most robust metric.
• masking (skull stripping) is highly recommended to obtain good results.
• because speed is not that critical, we increase the sampling rate for both affine and BSpline registration
• we also expect larger differences in scale & distortion than with regular structural scans: so we significantly (2x-3x) increase the expected values for scale and skew from the defaults.
• a good affine alignment is important before proceeding to non-rigid alignment to further correct for distortions.

Acknowledgments

• dataset provided by Killian Pohl, Ph.D.