NA-MIC National Alliance for Medical Image Computing NA-MIC Core 2 Update Isomics Steve Pieper Isomics, Inc. NA-MIC Engineering Isomics Site PI

National Alliance for Medical Image Computing 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 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 it

National Alliance for Medical Image Computing 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 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 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 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 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 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 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 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 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 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 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 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 Slicer Daemon Slicerd listens on local socket slicerget –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 ITK IO and Slicer Daemon AntiAliasBinaryImageFilter.exe bunny.z.nrrd "| sh slicerput.tcl"

National Alliance for Medical Image Computing User Desktop Slicer 3.0 Architecure AlgorithmsITKVTK Slicer Modules VTK Apps Using ITK Scripts of Slicer Mods Batch Programs Non-NAMIC Cmd tools LONI Pipeline Birn Grid Data/Compute Slicer 3.0