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NA-MIC Core 2 Update Isomics

NA-MIC Core 2 Update Isomics. Steve Pieper Isomics, Inc. NA-MIC Engineering Isomics Site PI. 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)

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NA-MIC Core 2 Update Isomics

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  1. NA-MIC Core 2 UpdateIsomics Steve Pieper Isomics, Inc. NA-MIC Engineering Isomics Site PI

  2. 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

  3. 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

  4. 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

  5. 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)

  6. 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

  7. 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…

  8. 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

  9. 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

  10. 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

  11. 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!

  12. 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

  13. 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

  14. 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

  15. 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!

  16. 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

  17. ITK IO and Slicer Daemon AntiAliasBinaryImageFilter.exe bunny.z.nrrd "| sh slicerput.tcl"

  18. Slicer 3.0 Architecure User Desktop Slicer3.0 Algorithms ITK VTK Slicer Modules Scripts of Slicer Mods VTK Apps Using ITK Batch Programs Non-NAMIC Cmd tools LONI Pipeline Birn Grid Data/Compute

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