Projects:RegistrationLibrary:RegLib C19

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Slicer Registration Library Exampe #19: Multi-contrast group analysis: intra- and inter-subject registration of multi-contrast 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.
reference T1, subject 1	moving T2, subject 1	moving MRA, subject 1		reference T1, subject 2	moving T2, subject 2	moving MRA, subject 2
1mm isotropic 176 x 256 x 176 PA	1mm isotropic 192 x 256 x 128 PA	0.51 x 0.51 x 0.8 mm 448 x 448 x 128 PA		1mm isotropic 176 x 256 x 176 PA	1mm isotropic 192 x 256 x 128 PA	0.51 x 0.51 x 0.8 mm 448 x 448 x 128 PA

Objective / Background

This is an example of inter-subject registration via surface matching. The structures of interest are a small subset of the entire image, hence registration is not driven by image intensities but rather two model surfaces derived from the labelmaps.

Keywords

multi-stage registration, MRI, brain, head, multi-contrast, inter-subject, group analysis, MRA, T2

Input Data

• reference/fixed : T1w coronal, 1mm isotropic. Called A1_gray
• reference/fixed : labelmap , aligned with above. Called A1_label
• moving: T1w coronal, 0.9 inplane, 1.5mm coronal slices. Called A0_gray
• moving: labelmap , aligned with above. Called A0_label

Methods

1. Visualize & browse A0 data: determine label range of thalamic nuclei labels in A0_label: 500-526
2. Visualize & browse A1 data: determine label range of thalamus lables in A1_label: 10 and 49
3. Build label mask of thalamus for A0: Editor module
   1. Create Labelmap From”: A0_labels

Registration Results

Download

• download entire tutorial package (Original Data, Intermediate Results, Solution, zip file 74 MB)
• download old atlas dataset (MRI+labelmap,thalamic nuclei models, list of labels+names), zip file 5.4 MB)
• download new atlas dataset (MRI T1+T2, labelmap, thalamus model), zip file 126MB)
• download result merged new atlas dataset (MRI T1+T2, new merged labelmaps (2x) incl. thalamic nuclei, colormap file with label names), zip file 126 MB)
• download full step-by-step tutorial (PowerPoint, zip file, 2.5 MB)
• obsolete: download compare set (New Atlas, 2 merged versions (full & clipped), thalamus models, Xform, Merged colormap, zip file, 67 MB)

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

Discussion: Registration Challenges

• Because the structures of interest are a very small subset of the image without distinct grayscale contrast
• the two atlases represent different anatomies and hence some residual misalignment is inevitable
• the two labelmaps have different resolutions and different smoothness of structure outlines. Some need filtering to remove spurious surface details that would distract the registration algorithm

Discussion: Key Strategies

• Because the structures of interest are a very small subset of the image without distinct grayscale contrast, we co-register surfaces rather than intensity volumes

Acknowledgments

• dataset provided by Ron Kikinis, M.D. and Florin Talos, M.D.