na-mic national alliance for medical image computing na-mic core 2 update isomics steve pieper...
DESCRIPTION
National Alliance for Medical Image Computing Generic IO from ITK Add Volume -> Generic Readers –Uses vtkITKArchetypeImageSeriesReader –Understands Image Sequences like Image-1.png Image-2.png… dcm 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 itTRANSCRIPT
NA-MICNational Alliance for Medical Image Computing http://na-mic.org
NA-MIC Core 2 UpdateIsomics
Steve PieperIsomics, 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