na-mic core 2 update isomics

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


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


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


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)


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


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…


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


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


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


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!


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


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


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


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!


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


ITK IO and Slicer Daemon

AntiAliasBinaryImageFilter.exe bunny.z.nrrd "| sh slicerput.tcl"


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

na-mic core 2 update isomics

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