Online Interface to a 3D MRI Simulated Brain Database
CHRIS A. COCOSCO, VASKEN KOLLOKIAN, REMI K.-S. KWAN, G. BRUCE PIKE, ALAN C. EVANS
McConnell Brain Imaging Centre, Montréal Neurological Institute,
McGill University, Montréal, Canada
The increased importance of automated computer techniques for anatomical brain mapping from MR images and quantitative brain image analysis methods leads to an increased need for validation and evaluation of the effect of image acquisition parameters on performance of these procedures. Validation of analysis techniques of in-vivo acquired images is complicated due to the lack of reference data (``ground truth''). Also, optimal selection of the MR imaging parameters is difficult due to the large parameter space. BrainWeb makes available to the neuroimaging community, online on WWW, a set of realistic simulated brain MR image volumes (Simulated Brain Database, SBD) that allows the above issues to be examined in a controlled, systematic way.
The 3D simulated MR images are generated by varying specific imaging parameters and artifacts in an MRI simulator, which:
A pre-computed SBD was generated by varying specific imaging sequence and artifact parameters. The set of these of parameters was chosen according to the values typically encountered in modern MRI systems . For two anatomical models (normal, and with moderate MS lesions), simulated volumes for three imaging sequences are available online (T, T, PD), each with several values of slice thickness, noise and intensity INU levels (Fig. 4).
In addition, BrainWeb allows a remote user to run their own custom MRI simulation (on our server) with any of several pulse sequences and source digital phantoms, and arbitrary values of the acquisition artifacts (Figs. 5, 6). After the simulation is finished, the user can preview the result online or download it, everything being done through the WWW interface.
All 3D image volumes are in stereotaxic space, and can be interactively explored with practically any WWW browser in three simultaneous orthogonal views at any cursor position in the volume (Fig. 7). Each simulated brain image, as well as the source digital phantoms, can be downloaded in a variety of file and data compression formats.
SBD can be used to:
BrainWeb provides to the international research community a convenient access to this resource through the Internet. The full SBD, the online interface for controlling the MR simulator, as well as the anatomical models (phantoms) used as input to it, are available on WWW at ``http://www.bic.mni.mcgill.ca/brainweb/''. We are currently working on extending BrainWeb to include fMRI and PET simulated data.
This work supported by the U.S. Human Brain Map Project and the International Consortium for Brain Mapping (ICBM). Contributions to this project were made by Peter Neelin, Alex Zijdenbos, John Sled, and Louis Collins from the McConnell Brain Imaging Centre.
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