3D MRI Data Viewer System on Neuroimaging-platform
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1
AIST, Human Technology Reserch Inst, Japan
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2
Kyoto University, Primate Res. Inst, Japan
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3
Kanazawa Institute of Technology, Japan
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4
ATR-Promotions, Japan
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5
Natl. Inst. Info & Comm Technol., Biol. ICT Grp, Japan
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6
Osaka University, Japan
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7
RIKEN, Japan
Purpose: It is important in neuroscience research and education to visualize three-dimensional brain structures. We have developed 3D MRI Data Viewer System, which enables viewing 3D or 2D MR images by using ordinary Web browsers. This 3D MRI Data Viewer is utilized in "Brain Explorer" of NeuroImaging-platform (http://nimg.neuroinf.jp/) to demonstrate a Japanese (Adult, male) brain that was provided by Tohoku University's "The Japanese brain database" and a Japanese monkey (3 years 8 months old, male) brain that was scanned in AIST (National Institute of Advanced Industrial Science and Technology). Brain Explorer is intended not to be glanced at but to be used as an interactive visual dictionary. For this purpose, this Viewer has many functions to promote the use in study. DATA specification: Human MRI data are reconstructed from T1 weighted images (FOV 250mm, slice thickness 1.5mm). We removed the skin from scanned images. When we reconstruct volume data from MRI data, we interpolate them to obtain isotropic voxels. Voxel length is 0.9766mm. This volume data is adjusted on Talairach coordinate system. The origin is the posterior margin of the anterior commissure (AC) at the midsagittal plane. Horizontal zero plane includes AC-PC (Posterior commissure) line. Japanese monkey data are reconstructed from sagittal T1 weighted images (FOV 120mm, slice thickness 1.2mm). We show both head and brain (skin removed from data) images. We reconstruct the volume data in the same way as for the human's. Voxel length is 0.46875mm. The volume data are adjusted on Horsley-Clarke coordinates by using spatial markers scanned with the head. Horizontal zero plane is 10 mm superior to the Frankfurt zero plane including the center of ear canal and inferior rim of the orbit. Coronal zero plane includes the straight line passing the center of ear canals. The origin is the point of intersection of horizontal, coronal and sagittal zero-planes. Web application: This Viewer system is implemented as the client-server model. Any workstations or personal computers installed with Apache (httpd server), PHP (Lightweight scripting language) can be a server of this system. Proper operation was checked on Linux, Windows XP/Vista/7 and Mac OS X. NIMG-PF uses Linux machine as a server. Users can access the server and view data with Web browsers. Image processing programs on the server create slice images and surface-rendered 3D images of the selected data on demand from the user's Web browser. We confirm that this Web application works by usual Web browsers such as IE7, IE8, Safari3, FireFox3.5, Opera10, and Google Chrome. We build the user interface using JavaScript and DHTML, so users can operate this application interactively. Clicking a point on the image leads to getting cross sections at an arbitrary point (a cursor, red cross). Dragging the cursor leads to getting the positional information on the tip tool or to moving the cursor, depending on modes. The title of control area has hyper-link of presently displayed images. A user can share what one see with another person by sending the URL. Summary: We have developed 3D MRI Data Viewer System on NIMG-PF, which enables users to view slices and rendered surface image of the brain from arbitrary angles, and to measure the position of arbitrary brain structure on standard anatomical coordinates. We hope that users use this web application as a visual dictionary in their studies.
Conference:
Neuroinformatics 2010 , Kobe, Japan, 30 Aug - 1 Sep, 2010.
Presentation Type:
Poster Presentation
Topic:
Digital atlasing
Citation:
Matsuda
K,
Higo
N,
Oishi
T,
Niki
K,
Suzuki
R,
Masaki
S,
Fujimaki
N,
Ichikawa
K and
Usui
S
(2010). 3D MRI Data Viewer System on Neuroimaging-platform.
Front. Neurosci.
Conference Abstract:
Neuroinformatics 2010 .
doi: 10.3389/conf.fnins.2010.13.00042
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Received:
10 Jun 2010;
Published Online:
10 Jun 2010.
*
Correspondence:
Keiji Matsuda, AIST, Human Technology Reserch Inst, Tsukuba Ibaraki, Japan, k.matsuda@aist.go.jp