1 / 18

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)

kieve
Download Presentation

NA-MIC Core 2 Update Isomics

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related