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BRAINS (Brain Research: Analysis of Images, Networks, and Systems)
Iowa Mental Helath Clinical Research Center
BRAINS2 is an innovative, versatile software package created for the analysis of images of the human brain.
The package contains manual and automated tools for structural identi cation and methods for tissue
classi cation and cortical surface generation. BRAINS2 is most commonly used to analyze magnetic resonance
(MR) scans, but the package can also be used to analyze images acquired with positron emission tomography
(PET), single photon emission computed tomography (SPECT), and functional magnetic resonance (fMR).
The BRAINS2 package was developed as a replacement for the BRAINS package. (BRAINS is an acronym for
Brain Research: Analysis of Images, Networks, and Systems.) The BRAINS2 package was designed
to support multiple computer platforms and was implemented in such a way that it would function like an
image processing toolbox, providing image processing modules that can be linked together in many ways to
achieve an almost unlimited number of image analysis strategies.
BRAINS2 takes full advantage of the latest hardware and software technology standards to allow it to be
used on platforms other than the Linux and SGI systems we ourselves use. BRAINS2 uses object-oriented
approaches, OpenGL, and X11 to implement the GUI. The object-oriented design speci es that BRAINS2
have speci c routines (access functions) for interaction with every object. For example, images must have
the information about them obtained or set using the image object access functions.
There are three main parts to the BRAINS2 implementation: the toolbar and command line interface, the
GUI, and the kernel. Using the toolbar and command line interface, the user can load, save, and operate on
objects. The GUI displays viewable objects, like images, ROIs, and surfaces. The kernel is a set of image
processing routines, which can be linked together through the command language. In terms of data,
BRAINS2 is backward compatible with BRAINS and links together a series of processing steps to mimic the
behavior of BRAINS. A fundamental set of library routines has been implemented in BRAINS2 for structural
NIfTI-1 support
NIfTI-1 is supported at this time. Our developers have implemented the NIfTI-1 IO system in the ITK software package, which intern is used in BRAINS.

Nancy C. Andreasen
Hans J. Johnson (
How to get
Request a password from the website
Current version
Current version release date
Open source
Copyright Agreement
Available free of charge
Requires OpenGL, X11 and a 24 bit graphics card.
Technical publications
Andreasen NC, Cohen G, Harris G, et al. Image processing for the study of brain structure and function: Problems and programs. Journal of Neuropsychiatry and Clinical Neuroscience 1992; 4:125-133.

Andreasen NC, Cizadlo T, Harris G, et al. Voxel Processing Techniques for the antemortem study of neuroanatomy and neuropathology using magnetic resonance imaging. Journal of Neuropsychiatry and Clinical Neuroscience 1993; 5:121-130.

Cohen G, Andreasen NC, Alliger R, et al. Segmentation Techniques for the classification of brain tissue using magnetic resonance imaging. Psychiatry Research: Neuroimaging 1992; 45:33-51

Andreasen NC, Rajarethianam R, Cizadlo T, et al. Automatic atlas based volume estimation of human brain regions from MR images. Journal of Computer Assisted Tomography 1996; 20:98-106.

Harris G, Andreasen NC, Cizadlo T, et al. Improving tissue classification in MRI: A three-dimensional multispectral discriminant analysis method with automated training class selection. Journal of Computer Assisted Tomography 1999; 23:144-154.

Magnotta VA, Andreasen NC, Schultz SK, et al. Quantitative in vivo measurement of gyrification in the human brain: Changes associated with aging. Cerebral Cortex 1999; 9:151-160.

Magnotta VA, Heckel D, Andreasen NC, et al. Measurement of brain structures with artificial neural networks: Two-dimensional and three-dimensional applications. Radiology 1999; 211:781-790.

Ward J, Wooteman W, Magnotta VA, Andreasen NC. Color Enhancement of Multispectral Magnetic Resonance Images: Improving the Visualization of Subcortical Structures. Journal of Computer Assisted Tomography. 25(6):942-949, 2001.

Magnotta VA, Harris G, O'Leary DS, Andreasen NC, Heckel D. BRAINS2: A Structural Imaging Processing Toolbox. Computerized Medical Imaging and Graphics, In Press.

Crespo-Facorro B, Kim JJ, Andreasen NC, O'Leary DS, Wiser AK, Bailey JM, Harris G, Magnotta VA. Human Frontal Cortex: An MRI-Based Parcellation Method. NeuroImage, 10:500-519, 1999.

Applications publications
Piven J, Saliba K, Bailey J, et al. An MRI Study of autism: the cerebellum revisited. Neurology 1997; 49:546-551, 1997

Piven J, Bailey J, Ranson BJ, et al. An MRI Study of the corpus callosum in autism. American Journal of Psychiatry 1997; 154(8):1051-1056.

Sears LL, Vest C, Mohamed S, et al. An MRI study of the basal ganglia in autism. Progress in Neuro-Psychopharmacology & Biological Psychiatry 1999; 23:613-624.

Swayze VW, Johnson VP, Hanson JW, et al. Magnetic resonance imaging of brain anomalies in fetal alcohol syndrome. Pediatrics 1997; 99:232-240.

Crespo-Facorro B, Kim JJ, Andreasen NC, O'Leary DS, Magnotta V. Regional Frontal Abnormalities in Schizophrenia: A Quantitative Grey Matter Volume and Cortical Surface Size Study. Biological Psychiatry, 48:110-119, 2000.

Pantel J, O'Leary DS, Cretsinger K, Bockholt HJ, Keefe H, Magnotta VA, Andreasen NC. A New Method for the In Vivo Measurement of the Human Hippocampus with High Neuroanatomical Accuracy. Hippocampus, 10:752-758, 2000.

Crespo-Facorro B, Kim JJ, Andreasen NC, Spinks R, O'Leary DS, Bockholt HJ, Harris G, Magnotta VA. Cerebral cortex: a topographic segmentation method using magnetic resonance imaging. Psychiatry Research Neuroimaging 100: 97-126, 2000.

White TJ, O'Leary DS, Magnotta VA, Arndt S, Flaum M, Andreasen NC. Anatomic and functional variability: The effects of filter size in group fMRI data analysis. NeuroImage 13: 577-588, 2001.

Stephan KE, Magnotta VA, White T, Arndt S, Flaum M, O'Leary DS & Andreasen NC. Effects of Olanzapine on cerebellar functional connectivity in schizophrenia measured by fMRI during a simple motor task. Psychological Medicine 31: 1065-1078, 2001.

Shultz SK, O'Leary DS, Ponto LLB, Arndt S, Magnotta V, Watkins GL, Hichwa RD, Andreasen NC. Age and Regional Cerebral Blood Flow in Schizophrenia: Age Effects in Anterior Cingulate, Frontal and Parietal Cortex. Journal of Neuropsychiatry and Clinical Neurosciences. 14(1):19-24, 2002.

Other information
atlas, functional, NIfTI-1 support, registration, segmentation, statistical, surface analysis, visualization, volume, warping
cygwin, HPUX, IRIX, Linux, MacOS, SunOS, UNIX, Windows
IATR listing last updated
30 Nov 2005