Fig. 3: Illustration of hierarchical multi-resolution alignment to reference volume.

A hierarchical multi-resolution scheme was used to align the slab volumes to the reference structural volume. Sagittal images of the first tissue slab for each step of the alignment scheme show progressively finer alignment between the 2D coronal sections and structural reference volume. The edges of reference volume are shown in orange. For each iteration, all 2D GM segmentations are downsampled to the current resolution in the hierarchy and hence only contain morphological information at that resolution. 1 3D segmentation volumes are created by applying 2D transformations to the segmented 2D images. In the first iteration, 4mm, only rigid transformations are used to create an initial 3D GM segmentation volume, but on subsequent iterations the non-linear transformations calculated from the previous iteration are used to create the 3D segmentation volumes. 2 The reference volume (the outline of which is shown in the second and third row in orange) is then 3D non-linearly aligned to the 3D segmentation volume. 3 The alignment is then refined using 2D non-linear transformations between the original 2D segmentations and their corresponding coronal section in the aligned structural reference volume.