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Brain-Mapping Software

Our laboratory is in the process of developing an integrated suite of software tools for surface-based analyses of the mammalian cerebral cortex, particularly in humans and macaque monkeys (see Van Essen et al., 1998; Drury et al., 1999 in Publications section). These methods emphasize the use of explicit surface reconstructions for visualizing the shape of the cerebral cortex, and for dealing with individual variability in cortical structure and function. Several software applications have already been released and are freely available to the neuroscience community. Others are in an advanced stage of development, and their availability will be posted at this web site.

This software has been developed under the auspices of the Human Brain Project (RO1-MH-60974-06), with support from NIMH, NASA, NSF, NCI, NLM, and NIDA gratefully acknowledged.

CARET & FLATMORPH

(Computerized Anatomical, Reconstruction, and Editing Toolkit) is a software package designed for the interactive viewing, editing, and manipulation of

(i) surface reconstructions (e.g. wireframe representations),
(ii) the contours used in generating these surfaces, and
(iii) experimental data associated with the 3-D volume in which these contours and surfaces reside.

CARET and FLATMORPH were developed for studies of the cerebral cortex, but are flexible and general enough to have wide applicability particularly in neuroanatomical studies.

FLATMORPH is software that allows the generation of 2-D flat maps of the surface thereby supplanting older manual techniques for the flattening of cortical layers. It uses amulti-resolution, two-stage process to flatten the surface. The first stage of FLATTEN rapidly converts the surface to a topologically correct two-dimensional map, without regard for the amount of distortion introduced. The second stage reduces distortions using a multi-resolution strategy that makes gross shape changes on a coarsely sampled map and further shape refinements on progressively finer resolution maps. The FLATTEN software will be made available in the near future and will be accompanied by its own User's Guide.

SureFit

SureFit (Surface Reconstruction by Filters and Intensity Transformations) is a new method for generating surface reconstructions of the cerebral cortex from neuroimaging data, including structural MRI or cryosection images (Van Essen, Drury, and Anderson, 1999a,b; patent pending). SureFit is based on a novel probabilistic approach to shape analysis. It includes all of the processing steps needed to generate topologically accurate reconstructions of the cortical surface. The overall process offers signficant advantages in robustness, accuracy, and speed.

SureFit is currently being beta-tested in several laboratories. If you are interested in being involved in beta testing, please contact Heather Drury (heather@v1.wustl.edu). We expect to make SureFit freely available to the neuroscience community by the end of calendar year 1999.

The current version of the SureFit User's Guide is available for downloading, once a simple registration form is completed that will allow us to keep you apprised of updates.

SuMS

Surface Management System is a database (using Sybase System 11) for the interactive viewing and comparison of a diverse spectrum of anatomical data, including surfaces (both in their original 3-D form and in their 2-D flattened form). One component of this database is a representation of a canonical hemisphere, which can be viewed as a 3-D reconstruction or as a 2-D flat map. Information about cortical geography (pattern of sulci and gyri), along with any of several areal partitioning schemes (e.g. Felleman and Van Essen, Brodmann) can be represented on any configuration of the reconstruction. SuMS will be made fully available to the community (with its own documentation) at a future date.

A preview of SuMS can be accessed from SuMS home page.

CARETdaemon

is a web interface tool that allows interactive visualization of surface-based atlases of primate cerebral cortex, including human and macaque. It has some of the functionality of CARET. CARETdaemon is especially suitable for visualizing functional neuroimaging data on 3-D reconstructions and cortical flat maps of the Visible Man. The functionality of CARETdaemon includes:

Display nodes, wire-frame, or solid (rendered) surface in either 2-D or 3-D representations

Pan, zoom, and rotate surface models
Color the surface according to geographical, functional, lobar assignments, and mean curvature calculations
Represent functional activation foci (in conjunction with the Visible Man atlas)

Requirements for running CARETdaemon include a browswer such as Netscape v3.01 and

VRML 2.0 compliant plug-in such as SGI's Cosmo Player.

CARETdaemon can be accessed from CaretDaemon Home Page.

The XANAT Database

Xanat 2.0: A Graphical Anatomical Database

Bruno Olshausen and Bill Press

Washington University School of Medicine

Department of Anatomy and Neurobiology

St. Louis, Missouri 63110

XANAT consists of two main features: a graphical database and a program for definining areas for study. (More on XANAT and its uses can be found by accessing theXANAThome page.)