Neuroimage Analysis Center
http://www.spl.harvard.edu/nac
NAC Engineering Core
Steve Pieper, Core PI
SPL; Isomics, Inc.
An NCRR National
Resource Center
Overview of NAC Engineering Core
• Was BIRN Core, but split per NIH
request
– NAC Engineering Core
– mBIRN Grant
– fBIRN Grant (Sandy took lead)
• Mainly do 3D Slicer development
• Also sponsored by NA-MIC, NCIGT,
R01, SBIR, others…
Neuroimage Analysis Center
-2-
http://www.spl.harvard.edu/nac
An NCRR National Resource Center
Slicer2
• Mature and stable, but
becoming difficult to
maintain and extend
• Needed:
– New look and feel
– More modularity
– Generalized data
model
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Neuroimage Analysis Center
-3-
http://www.spl.harvard.edu/nac
Load Medical Image Data: MR, CT in DICOM, GE,
Analyze…
XML-based File Format: MRML (Medical Reality Markup
Language)
Interactive Editor: Draw, Threshold, Math Morphology…
Automated Segmenters: EM Segmentation, Fast
Marching, Level Sets…
Visualization: Model Building, Stereo Rendering,
Animation…
Registration: Manual, ITK, CNI
Measurement: Fiducial-Based, Volumetric, Polyhedral
Intersection, Vessel Cross-Section, Osteotomy Planning
IGT: Tracked Probes, Real-Time Images, Robot Control
Additional Application-Specific Features in Modules…
An NCRR National Resource Center
Slicer2 DTI
Neuroimage Analysis Center
-4-
http://www.spl.harvard.edu/nac
An NCRR National Resource Center
Slicer2 fMRI
Neuroimage Analysis Center
-5-
http://www.spl.harvard.edu/nac
An NCRR National Resource Center
Slicer3 Effort
• Collaboration of
NAC, NA-MIC, BIRN,
NCIGT, Others…
• Base Development
at BWH, GE,
Kitware, Isomics
• Module
Development at
MGH, BWH, UNC,
Utah, MIT, UCLA,
UCSD…
Neuroimage Analysis Center
-6-
http://www.spl.harvard.edu/nac
An NCRR National Resource Center
Near Term Plans
• 3D Slicer 2.7 Release Candidate
– February 2007
– Bug fixes, performance enhancements
• 3D Slicer 3.0 Base Release
– March 2007
– Essential feature (load/save, view, transforms,
models…)
• 3D Slicer 3.1 Release
– June 2007
– Application modules (DTI, EMSegment)
Neuroimage Analysis Center
-7-
http://www.spl.harvard.edu/nac
An NCRR National Resource Center
Longer term plans
• Slicer3 Informatics
– XNAT (mBIRN), HID (fBIRN), MIDAS (Kitware)
– Query Atlas (mBIRN, fBIRN)
• Execution Model for Grid Computing (mBIRN,
NA-MIC)
• DICOM / IHE Clinical Workflows (pending with
Northwestern)
• FEM Meshing / Visualization (Iowa, ongoing)
• DTI (NAC, NA-MIC, mBIRN)
• Interoperability (NAC, mBIRN)
– FreeSurfer, FSL, MATLAB, NumPy…
• Image Guided Therapy (NCIGT, NAC)
Neuroimage Analysis Center
-8-
http://www.spl.harvard.edu/nac
An NCRR National Resource Center
Slicer3 Execution Model
• Standardized command line syntax and
exchange of data (parameters, volumes, models,
seed points…)
• Slicer3 auto-generates GUI
• Modules are “just executables”
– (but they can also be shared libraries)
• Modules can be written in a variety of
languages/toolkits (ITK, VTK, Tcl, Python,
MATLAB, C, C++…)
• Modules can be used for scripting, batch
processing
• Simple wrappers to translate syntax can allow
interoperability
Neuroimage Analysis Center
-9-
http://www.spl.harvard.edu/nac
An NCRR National Resource Center
Slicer 2.6 Functionality: FreeSurfer
Neuroimage Analysis Center
-10-
http://www.spl.harvard.edu/nac
An NCRR National Resource Center
BIRN Query Atlas in Slicer3
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Re-Architecture of the
QueryAtlas
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Integrates with BIRN IT
Efforts
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Advanced Label Features
Built-In
Real-Time Interaction with
Labels
“Right Click” on Models and
Images to Initiate Queries
Based on NA-MIC Software
Engineering Methodology
Anatomy-Based Access to
Web Resources
Auto Convert and Load
BIRN Data
Leverages mBIRN Data
Formats and Analysis
(FreeSurfer)
fBIRN is Building Functional
QueryAtlas Integrated with
mBIRN QueryAtlas
Neuroimage Analysis Center
-11-
http://www.spl.harvard.edu/nac
An NCRR National Resource Center
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Neuroimage Analysis Center - NA-MIC