MNI Macaque Atlas

Contributed by ChrisFiloGorgolewski on Oct. 24, 2016

Collection: An MRI based average macaque monkey stereotaxic atlas and space (MNI monkey space)

Description: The macaque average atlas is comprised of 25 T1-weighted MRIs of normal young adult macaque brains (18 Macaca fascicularis, 7 Macaca mulatta). This atlas is not based on a single subject but instead is an average constructed from the averaged position, orientation and scale from all the individual subjects and is representative of both the intensities and spatial positioning of anatomical structures. Image pre-processing included non-uniform intensity correction and intensity normalization with a range of 0–100. One monkey out of 25 macaques was chosen to serve as the initial target. Registration of the remaining 24 macaque monkeys to the chosen was initialized using manually identified homologous landmarks that included the center of the left and right eyeballs, the anterior commissure (AC), the posterior apex of the 4th ventricle as seen in a midline sagittal image, the most anterior aspect of the genu and the most posterior aspect of the corpus callosum, and the intersection of the central sulcus with the longitudinal fissure. The ANIMAL algorithm (Collins et al., 1995) was used to estimate the nonlinear deformation field that best aligned local neighbourhoods between each monkey volume and the average target. The nonlinear registration began by estimating a grid with 3mm spacing. Each MRI volume was resampled through the recovered nonlinear transformation, and all resampled volumes were averaged together on a voxel-by-voxel basis to create a mean intensity image. To remove the potential bias of the initial atlas used for registration, all deformation fields were average together and then the average deformation was inverted and then applied to the mean intensity volume to create a spatially unbiased, average intensity atlas volume that is used as the target for the next registration step. This process was repeated twice, using a grid spacing of 2mm, and then 1mm.

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