Post on 06-Jan-2016
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NA-MICNational Alliance for Medical Image Computing http://na-mic.org
NA-MIC Core 2 UpdateIsomics
Steve Pieper
Isomics, Inc.
NA-MIC Engineering Isomics Site PI
National Alliance for Medical Image Computing http://na-mic.org
Year 1 Highlights – Slicer 2.6
• Generic Readers and Writers from ITK• Linear and Non-Linear ITK Registration• Generalized DWI and DTI Coordinates• Integrated teem Tools (unu, tend, etc)• EMAtlasBrainClassifier• ITK Statistics for fMRI Ibrowser/FMRIEngine (fBIRN)• NAMICSandBox Code Included• FreeSurferReaders (mBIRN)• na-mic.org Infrastructure for Slicer Community• Draw/Draw2 Large Image Support (Simbios, NAC)• Rule Based / Baysian Segmentation (GaTech, UCI, Harvard)• ABC Tractography Filters (BWH, UCI)• CompareModule (Slicer Community)• Slicer Daemon and Slicer 3 Architecture
National Alliance for Medical Image Computing http://na-mic.org
Generic IO from ITK
• Add Volume -> Generic Readers– Uses vtkITKArchetypeImageSeriesReader– Understands Image Sequences like
• Image-1.png Image-2.png…• 00001.dcm 00002.dcm…
– Knows Volume Data Types• NIfTI, Nrrd, Meta, VTK…
– Correctly Handles Orientation• When provided
• Volumes->Export– Exports NIfTI, Nrrd, Meta, VTK– Exports Orientation to formats that support it
National Alliance for Medical Image Computing http://na-mic.org
Linear and Non-Linear Registration
• ITK Registration Framework with Slicer UI– Translation, Rigid, Affine
• Mattes MI Metric
– Demons, B-Spline– Interactive “Steering” or run to completion
• TransformVolume Module– Apply linear and non-linear transforms to
volumes and label maps– Select output orientation (AP, IS, etc)– Select output spacing, dimensions
National Alliance for Medical Image Computing http://na-mic.org
Generalized DWI, DTI
• Worked closely with Gordon Kindlmann to plus NAC LMI and wider DTI community to standardize– Scan Orientation (direction cosines)– Gradient/Tensor Measurement Frame– Reference Space– B-Value, Baseline, Gradient Definition
• Adopted NRRD format as Slicer standard for DWI/DTI– Nrrd headers for data from Core 3 (BWH, Dartmouth)
• Used in MGH / Dartmouth Collaboration and other projects (mBIRN, NAC)
National Alliance for Medical Image Computing http://na-mic.org
Integrated teem tools
• Gordon’s teem library built and distributed with Slicer 2.6– vtkTeem module used in DTMRI– Command line tools (unu, tend, etc)
available
National Alliance for Medical Image Computing http://na-mic.org
EMAtlasBrainClassifier
• Kilian Pohl (MIT, Core 1) development, adopted by Martha Shenton (BWH PNL, Core 3)
• “one click” brain segmentation from T1 and T2 scans
• Likely applicable to Primate Brains, Abdominal CT, other…
National Alliance for Medical Image Computing http://na-mic.org
ITK Statistics for fMRI
• Migrated from GSL to ITK/VNL with help from Jim Miller– New ITK Distributions library– VNL Implementation of GLM
• IBrowser/FMRIEngine from fBIRN project provide fMRI Framework for further NA-MIC Development
National Alliance for Medical Image Computing http://na-mic.org
NAMICSandBox Included
• Slicer Clustering and ITK Distributions Included from Sandbox
• Subversion repository branched for Slicer 2.6 release
• Direct Benefit from Last AHM and Programmers Week
National Alliance for Medical Image Computing http://na-mic.org
FreeSurferReaders (mBIRN)
• Nicole Aucoin in Collaboration with MGH FreeSurfer Group
• Important Link to NA-MIC as Bruce Fischl takes Active Role at MGH NA-MIC
• Rich Datatypes for Volume/Surface and Population Studies
National Alliance for Medical Image Computing http://na-mic.org
na-mic.org
• Download site for Releases, Snapshots, Data, etc
• License Clickthrough (more tracking to come)
• Slicer Dashboard
• Slicer Bug Tracker
• of course, the wiki!
National Alliance for Medical Image Computing http://na-mic.org
Draw / Draw2 & Large Image Editing
• Draw2: Simbios (Stanford NCBC) Collaboration– Chand John in Scott Delp’s group– Spline-Based editor for musculoskeletal– Co-exists with ‘classic’ Draw in Slicer 2.6
• Large Image Editing– NAC Supported Slicer Improvement to move
beyond MR to Visible Human and Microscopy– Per-session switch in Slicer 2.6
National Alliance for Medical Image Computing http://na-mic.org
Rule Based / Baysian Segmentation
• Georgia Tech Development in Response to DBP Questions
• Facilitated by the Programmers Week
• Compatible with Slicer 2.6, final Integration at this meeting
National Alliance for Medical Image Computing http://na-mic.org
ABC Tractography ROI
• Driven by UCI DBP at last year’s AHM (cull fibers to include only connectivity between selected sites)
• Implemented in collaboration with MIT and BWH/NAC
• Included in Slicer 2.6
National Alliance for Medical Image Computing http://na-mic.org
CompareModule
• Contributed by Jeremie Anquez of ENST in Paris
• New Volume Display Modes– Checkerboard “Mosaik”– 2x1,2x4…3x3 Film Sheet
Mode with Linked Cursor/Pan/Zoom/Slice Scroll
– Integrated with Transfoms/Registration
• Open Source Success Story!
National Alliance for Medical Image Computing http://na-mic.org
Slicer Daemon
• Slicerd listens on local socket• slicerget <id>
– gets volume and writes to stdout in nrrd
• slicerput [name]– reads nrrd on stdin and puts in slicer
% slicerget 0 | unu 1op exp - | slicerput
National Alliance for Medical Image Computing http://na-mic.org
ITK IO and Slicer Daemon
AntiAliasBinaryImageFilter.exe bunny.z.nrrd "| sh slicerput.tcl"
National Alliance for Medical Image Computing http://na-mic.org
UserDesktop
Slicer 3.0 Architecure
Algorithms ITK VTK SlicerModules
VTK AppsUsing ITK
Scripts ofSlicer Mods
BatchPrograms
Non-NAMICCmd tools
LONIPipeline
Birn GridData/Compute
Slicer 3.0