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. Author manuscript; available in PMC: 2018 Oct 20.
Published in final edited form as: Curr Protoc Mol Biol. 2017 Jul 5;119:29A.5.1–29A.5.38. doi: 10.1002/cpmb.40

Figure 14: Diagram of Steps B3–6 for aligning non-contrast and contrast-enhanced brain images.

Figure 14:

A diagrammatic representation of the alignment procedures described in Steps B3-B6. In Step B3, non-contrast enhanced brain images from Step B2 are affine transformed (NC1, NC2, NC3 etc). In Step B4 these aligned non-contrast-enhanced images are averaged, and then re-aligned against their averaged image. These re-aligned images are then averaged to create the MDA. In Step B5, each set of contrast-enhanced images from Step B2 (C1a-x, C2a-x, C3a-x, etc., where 1,2,3,…n are the mice numbers, and a,b,c,…x are experimental time points) are aligned to their respective non-contrast-enhanced image from the same animal using a rigid body rotation. In Step B6, the re-aligned non-contrast-enhanced images for each mouse (NC1r, NC2r, etc.) representing the “step 3 images” from the output of Step B4.2, are warped to the MDA, to obtain a Warp field for each mouse (WF1, WF2, etc.). The warp field is then applied to all rigid body aligned contrast images for each mouse from Step B5, one mouse at a time, to produce the output with all images from the dataset aligned-warped (NC1.w, NC2.w, etc and C1a.w, C1b.w etc.; C2a.w, C2b.w, etc) where *.w indicates that images that have been warped.