BrainAtlas

Link to the NAC website

• this page is under construction

Introduction

• The Surgical Planning Laboratory, in conjunction with the Neuroscience Laboratory, created a three-dimensional digitized atlas of the human brain that has been used for surgical planning, model-driven segmentation, research, and teaching, and can be found on the World Wide Web at http://www.spl.harvard.edu

The atlas was created initially as a joint effort between the Laboratory of Neuroscience of the Harvard Medical School at the Brockton VA Medical Center, Brockton, MA and the Surgical Planning Laboratory, Department of Radiology at the Brigham and Women's Hospital, Boston, MA. Dr. Shenton, one of the original people involved at the Laboratory of Neuroscience at Brockton VA Medical Center, is now Director of the Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School.

• We are pleased to make this brain atlas available to our colleagues with the following stipulations:

The data is being distributed under the Slicer license. By dowloading these data you also agree to acknowledge our contribution in any of your publications that result from the use of this atlas. Please acknowledge the following grants: P41RR013218, R01MH050740

• For your reference, here are the inital publications discussing this atlas:
  • Shenton et al. Harvard brain atlas: A teaching and visualization tool. Proceedings of Biomedical Visualization 10-17, 1995.
  • Kikinis et al. A Digital Brain Atlas for Surgical Planning, Model Driven Segmentation and Teaching. IEEE Transactions on Visualization and Computer Graphics 1996; 2(3):232-241.

Directions

• The atlas consists of
  • a brain mri of a normal subject (T1W SPGR) acquired on a 1.5T system,
  • a data set containing labels for different anatomical structures
  • 3d surface models of these structures
  • a mrml file that allows loading all of the data into 3d Slicer for visualization (see the Slicer 101 page for a link to the 3D Slicer download site and for information on how to load data and mrml files)
  • a list of label values for the segmented structures
  • inside slicer there are several pre-defined views for the motor, visual and limbic systems, diencephalon, brain stem, left cerebral hemisphere
• The tutorial explains how to view the data.
• Get the SPL-PNL-Brain_Atlas_2007 here, a list of the labels is also available.
• Get the SPL-PNL-Brain_Atlas for Slicer3 here, (you need a version of Slicer that is dated 05-15-2007 or later).