Differing techniques used to study the anatomy of the human brain all have their advantages and disadvantages. Magnetic resonance imaging (MRI) allows for the three-dimensional viewing of the brain and structures, precise spatial relationships and some differentiation between types of tissue, however, the image resolution is somewhat limited. Stained sections, on the other hand, offer excellent resolution and the ability to see individual nuclei (cell stain) or fiber tracts (myelin stain), however, there are often spatial distortions inherent in the staining process.

We here present an electronic anatomically labeled three-dimensional atlas of the human brain created from MRI images. In conjunction we present anatomically labeled stained sections that correspond to the three-dimensional MRI images. In this way we utilize the advantages of both methods.

MRI Specimen
The MRI subject was a 22-year-old adult male weighing 79kg with a body length of 1.87m.

Magnetic Resonance Imaging
The imaging was performed on a 1.5 Tesla LX Cardiovascular Magnetic Resonance (CVMR) system (General Electric Co., Waukesha, WI). This system is equipped with 40 milliTesla gradients with a slew rate of 150 Tesla/meter/second. The subject was placed in the magnet in the supine position with his head firmly fixed via a bite bar in a standard quadrature birdcage head coil. The subject was scanned using a 3D fast Spoiled Grass (Fast SPGR) sequence, TR 50 ms, TE 2.4 ms, FOV 24 cm, slice thickness 1.5 mm was acquired. The scan covered the entire extent of the brain in the inferior/superior direction.

Three-Dimensional Reconstruction and Reformatting
Computer-generated 3D reconstruction images were created from MRI scans in the axial (horizontal) plane, using the software programs VoxelView and VoxelMath programs (Vital Images, Inc.) at the Laser Scanning Microscopy Laboratory at Michigan State University, Dr. Joanne Whallon, Director. The 3D rendered model, wherein details of internal and external morphology are represented in three-dimensional space, was then digitally resectioned in orthogonal planes to produce corresponding virtual section series in the coronal and sagittal planes.
Stained Sections
The stained sections are from the Yakovlev-Haleem Collection in the National Museum of Health and Medicine at the Armed Forces Institute of Pathology in Washington, D. C. Sections in the coronal plane are from specimen STD-IIIA, those in the horizontal plane are from specimen SP-18, and those in the sagittal plane are from specimen VND-31-84.

Anatomical Labeling and Nomenclature
The nomenclature used is from Paxinos G, and Watson C. 1998. The Rat Brain in Stereotaxic Coordinates, 4th ed. Academic Press. San Diego, CA. 256 pp