na-mic national alliance for medical image computing na-mic core 2 update isomics steve pieper...

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