A 3D high resolution ex vivo white matter atlas of the common squirrel monkey (Saimiri sciureus) based on diffusion tensor imaging

Abstract

Modern magnetic resonance imaging (MRI) brain atlases are high quality 3-D volumes with specific structures labeled in the volume. Atlases are essential in providing a common space for interpretation of results across studies, for anatomical education, and providing quantitative image-based navigation. Extensive work has been devoted to atlas construction for humans, macaque, and several non-primate species (e.g., rat). One notable gap in the literature is the common squirrel monkey - for which the primary published atlases date from the 1960's. The common squirrel monkey has been used extensively as surrogate for humans in biomedical studies, given its anatomical neuro-system similarities and practical considerations. This work describes the continued development of a multi-modal MRI atlas for the common squirrel monkey, for which a structural imaging space and gray matter parcels have been previously constructed. This study adds white matter tracts to the atlas. The new atlas includes 49 white matter (WM) tracts, defined using diffusion tensor imaging (DTI) in three animals and combines these data to define the anatomical locations of these tracks in a standardized coordinate system compatible with previous development. An anatomist reviewed the resulting tracts and the inter-animal reproducibility (i.e., the Dice index of each WM parcel across animals in common space) was assessed. The Dice indices range from 0.05 to 0.80 due to differences of local registration quality and the variation of WM tract position across individuals. However, the combined WM labels from the 3 animals represent the general locations of WM parcels, adding basic connectivity information to the atlas.

Keywords: brain atlas; diffusion tensor imaging; magnetic resonance imaging; neuroanatomy; squirrel monkey; tractography; white matter atlas.

Figure 1

Flowchart of iterative algorithm to construct anatomical atlas.

Figure 2

The pipeline for iterative definition of one bundle – the left cingulum in native space of one monkey. The ‘reference’ is taken from [17].

Figure 3

Axial, coronal and sagittal sections of anatomical monkey brain atlas with 300×300×300µm³ resolution. The images were acquired by gradient echo 3D sequence. The blue lines indicate the locations of the sections on the left side.

Figure 4

Axial, coronal and sagittal sections of anatomical monkey brain atlas with 300×300×300µm³ resolution. The images were acquired by gradient echo multi-slice sequence. The blue lines indicate the locations of the sections on the left side.

Figure 5

Sagittal, coronal and axial view of white matter parcels CCg (green), CCb (red), CCs (blue), FCCb (pink), FMn (dark green) and FMj (light blue) in the MRI common space.

Figure 6

Sagittal, coronal and axial view of white matter parcels Cing (light blue), F (purple), AC (red) and PC (yellow) in the MRI common space.

Figure 7

Sagittal, coronal and axial view of white matter parcels ICa (yellow), ICg (light blue), ICp (orange), CP (green). CST (pink), CRa (dark green), CRs (purple), CRdp (dark blue) and CRp (red) in the MRI common space.

Figure 8

Sagittal, coronal and axial view of white matter parcels SLFI (yellow), SLFII (light blue), SLFIII (red), MLF (blue) and ILF (purple) in the MRI common space.

Figure 9

Sagittal, coronal and axial view of white matter parcels EC (yellow), UF (red) and IIT (blue) in the MRI common space.

Figure 10

Sagittal, coronal and axial view of white matter parcels IFOF (yellow) in the MRI common space.