Surgical Planning Laboratory - Brigham & Women's Hospital - Boston, Massachusetts USA - a teaching affiliate of Harvard Medical School

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Multi-modality MRI-based Atlas of the Brain

1Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
2Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
3Center for Morphometric Analysis, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA.
Publication Date:
SPL 2017 Jan;
Atlas, Brain, MRI based, Multi-modality
Appears in Collections:
SPL, CNI, Download Data, NAC, SLICER
P41 RR013218/RR/NCRR NIH HHS/United States
P41 EB015902/EB/NIBIB NIH HHS/United States
Generated Citation:
Halle M., Talos I-F., Jakab M., Makris N., Meier D., Wald L., Fischl B., Kikinis R. Multi-modality MRI-based Atlas of the Brain. SPL 2017 Jan;
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The Neuroimage Analysis Center's Computational Clinical Anatomy Core and the Surgical Planning Laboratory at Brigham and Women's Hospital is pleased to make available a multi-modality MRI-based atlas of the brain. Data was acquired at the Martinos Center for Biomedical Imaging (courtesy Dr. Lawrence Wald) on a Siemens 3T scanner, using a multi-array head coil, in a healthy, 42 year old male. The data set consists of : 1. a volumetric whole head MPRAGE series (voxel size 0.75 mm isotropic). 2. a volumetric whole head T2-weighted series (voxel size 0.75 mm isotropic). 3. a downsampled version of both acquisitions at 1mm isotropic resolution. 4. a per voxel labeling of the structures based on the 1mm volumes. 5. a color file mapping label values to RadLex-ontology derived names and colors suitable for display. 6. MRML files for displaying the volumes in 3D Slicer version 3.6 or greater, available for download. The atlas data is made available under terms of the 3D Slicer License section B.
The Slicer4 version also consists of 1. hypotalamic parcellation (courtesy Nikos Makris [Neuroimage. 2013]) 2. cerebellar parcellation (courtesy Nikos Makris [J Cogn Neurosci. 2003], [Neuroimage. 2005]) 3. head and neck muscles segmentation 4. anatomical model hierarchy 5. several pre-defined Scene Views (“anatomy teaching files”). All in a mrb (Medical Reality Bundle) archive file that contains the mrml scene file and all data for loading into Slicer 4 for displaying the volumes in 3D Slicer version 4.0 or greater, available for download.
This work is funded as part of the Neuroimaging Analysis Center, grant number P41 RR013218, by the NIH's National Center for Research Resources (NCRR) and grant number P41 EB015902, by the NIH's National Institute of Biomedical Imaging and Bioengineering (NIBIB) and the Google Faculty Research Award.
Contributors: Ilwoo Lyu and Martin Styner-Sulcal Curves, Samira Farough-Ventricular System, Ibraheem Naeem and Maria Naeem-Head and Neck Muscles, George Papadimitriou-Cerebellar Parcellation, Madiha Tahir-White Matter.
This atlas maybe viewed with our Open Anatomy Browser.

Additional Material
10 Files (1GB)
BrainAtlas-Snapshot.jpg (273.752kB) nac-hncma-atlas-2017Jan-Slicer4-7Version.mrb (213MB)
nac-hncma-atlas-2016Sep-Slicer4-5Version.mrb (212MB)
September 2016: Updated Visual and Auditory System
nac-hncma-atlas-2015Nov-Slicer4-4Version.mrb (210MB)
nac-hncma-atlas-2015April-Slicer4-4Version.mrb (179MB)
April 2015: Updated for Slicer 4.4 and reorganized to support authoring on GitHub
nac-hncma-atlas-2013Nov-Slicer4Version.mrb (205MB)
November 2013: Adjusted labels
nac-hncma-atlas2013-Slicer4Version.mrb (176MB)
August 2013: Major Sulci added
nac-hncma-atlas2012b-Slicer4Version.mrb (202MB)
May 2013: Skin, Caudate Nucleus, Putamen, Nucleus Accumbens update
nac-brain-atlas2012-Slicer4Version.mrb (199MB) (168MB)