national alliance for medical image computing project week june 26-30, 2006 participants: 56 na-mic...

National Alliance for Medical Image Computing

http://na-mic.org

Project Week June 26-30, 2006

Participants: 56• NA-MIC (38), Collaborators (18)

– NA-MIC: Algorithms Core (11), Engineering Core (13), DBP Core (9), Service Core (2), Training Core (2), Dissemination Core (1)

– Collaborators: NWU (3), Iowa (1), JHU (1), Harvard IIC (1), Canary Islands IT (2), MIT (3), BWH (7)

Projects: 21• Along the 4 NA-MIC Themes:

– Structural Analysis (4)

– DTI Analysis (4)

– fMRI Analysis (2)

– NA-MIC Kit (10)

– Non medical outreach - Astronomy data visualization (1)


http://na-mic.org

Project Week June 26-30, 2006

Structural Analysis1. ITK Spherical Wavelet Transform Filter2. False Discovery Rate for Shape Analysis3. Local curvature based correspondence in ITK 4. Mesh Untangling

NA-MIC (16)

Collaborator (6)

Diffusion Image Analysis1. ITK DTI Image Processing Modules 2. Fiber Tools / Slicer 3 Integration3. Stochastic Fiber Tracing Applications 4. Slicer Fiber (Model) Labeling Interface

fMRI Analysis1. Conformal Flattening in ITK2. Spatial Regularization in fMRI

NA-MIC Kit1. Slicer3 Interface 2. Migrating Slicer2.x Modules to Slicer3 3. Slicer3 Packaging 4. Slicer3 Grid Integration 5. Slicer3 Pipeline Integration 6. MGH File Format Converter7. Volumetric Meshing8. Dicom Query/Retrieve 9. A Translation Station for Imaging10. Slicer3 for IGT: Converting vtkFMRIEngine and vtkMRAblation to Slicer3 modulesNon-Medical Data Support:1. Non-Medical Data Support: ITK IO support for astronomy data & coordinates from FITS files


http://na-mic.org

Structural/Shape Analysis

1. ITK Spherical Wavelet Transform Filter2. ITK Statistical analysis using non-parametric permutation & false discovery rate3. Local curvature based correspondence in ITK 4. Mesh Untangling

NA-MIC

Collaborator


http://na-mic.org

3D shape analysis using Spherical Wavelets:

Develop algorithm and ITK software module for Spherical Wavelet computation

Delphine Nain, GT (algorithms)Xavier Le Faucheur, GT (algorithms)Martin Styner, UNC (algorithms)John Melonakos, GT /GE (algorithms/ software)

Luis Ibanez, Kitware (software)Jim Miller, GE (software)

Algorithms: decomposition of a scalar signal defined on a spherical mesh into spherical wavelet coefficients and vice-versa in order to represent shapes and learn a multiscale shape probability prior from a population of shapes.

Software: convert current non ITK Spherical Wavelet computation to ITK compatible classes

Clinical: Comparison to current results on segmentation of the caudate nucleus

Plan/Expected Challenges/PublicationTeam

Accomplished by end of Programming Week

-creation of a more detailed structure -creation of the base class SphericalWaveletObject (SWO)

.

Expected Date for Insight Journal Publication: After the “project Week” in July

2006 Summer PrWeek

SWOSignal to Coeffs Filter

Coeffs to Signal FilterSWO


http://na-mic.org

False Discovery Rate for Shape Analysis:

Develop algorithm and ITK software module for False Discovery Rate (FDR) analysis.

Martin Styner, UNC (algorithms)

Jim Miller, GE Research (software support)

Jim Levitt, VA Brockton, Harvard (clinical data)

Algorithms: False Discovery Rate(FDR) for local shape analysis.

Software: Convert current non-ITK statistical analysis to ITK-compatible classes for current method. Add new implementation for FDR

Clinical: Comparison to current results on male SPD caudate study.



- New Software classes for FDR - Testing on male SPD caudate data

- Less conservative then permutation test based correction

- Dissemination to BWH for other studies- Initial work on Insight Journal publication

Expected Date for Insight Journal Publication: Submission to MICCAI open source workshop during project week or one week after that.

2006 Summer PrWeek

RawRaw

FDRFDR

PermTestPermTest


http://na-mic.org

Correspondence Based on Local Curvature:

Developing methods in ITK for using local curvature features to establish population based correspondence

Ipek Oguz, UNC (algorithms) (contact)Martin Styner, UNC (algorithms)

Bill Lorenson, GE (software support)Sebastien Barre, Kitware (software support)

Jim Levitt, VA Brockton, Harvard (clinical data)

Algorithms: Test with different combinations of features to see which one(s) leads to higher quality correspondence.

Software: improve computational efficiency. Visualization of results using MeshVisu from last project week

Clinical: Validation of results.


Accomplished by end of Programming Week• Finished the correspondence code, fixing some I/O issues.• Mostly finished the IJ paper for the correspondence• Fixed many bugs and flaws in KWMeshVisu, making it ready for distribution• Started the IJ paper for KWMeshVisu

Expected Date for Insight Journal Publication: Plan to submit before July 9th

2006 Summer PrWeek

Subject 1 Subject 2

Phi

Theta


http://na-mic.org

Mesh Untangling:

Gheorghe Postelnicu, MGH (algorithms) (contact)Bill Lorensen, GE (algorithms)

Algorithms: perform untangling of meshes in the context of FEM bio-mechanical models. Starting points are Smoothing methods or local untangling methodsSoftware: Proper insertion in ITK framework.

Clinical: Useful as post-processing step in FEM modelization (registration)


Accomplished by end of Programming WeekTested visualization methods for tetrahedra. Currently using Matlab, planning on using Paraview.

Expected Date for Insight Journal Publication:

Is this a continuation of a previous programming week project? If so, please include that slide as well.

2006 Summer PrWeek


http://na-mic.org

Diffusion Image Analysis

1. ITK DTI Image Processing Modules 2. Fiber Tools / Slicer 3 Integration3. Stochastic Fiber Tracing Applications (BWH LMI)4. Slicer Fiber (Model) Labeling Interface

NA-MIC

Collaborator


http://na-mic.org

ITK DTI Image Processing Modules:Develop algorithms and ITK filters for processing DTI images.

Casey Goodlett, UNC (algorithms) (contact)Thomas Fletcher, Utah (algorithms)John Melonakos, GT/GE (algorithms)

Bill Lorensen, GE (software)Luis Ibanez, Kitware (software)

Algorithms: Extend existing work on DTI and DWI filtering and registration.

Software: Evaluate which filters to move into ITK.Design ITK Tractography framework




•Filters placed in sandbox•ITK Tractography class diagrams•Discussion of processing DTIin presence of scanner noise

2006 Summer PrWeek


http://na-mic.org

Fiber Tools/Slicer 3 Integration:Integration of UNC Fiber Tools with Slicer 3.

Casey Goodlett, UNC (algorithms) (contact)Thomas Fletcher, Utah (algorithms)John Melonakos, GT/GE (algorithms)

Bill Lorensen, GE (software)

Algorithms: Extend existing work on DTI and DWI filtering and registration.

Software: Evaluate which filters to move into ITK.Proof of concept integration of existing tools with Slicer3.Design ITK Tractography framework




•Slicer3/FiberTracking Integration•Filters placed in sandbox•ITK Tractography class diagrams

2006 Summer PrWeek


http://na-mic.org

Stochastic Fiber Tracing:Develop method and Algorithm for stochastic fiber tracing. Use with Schiz data to find connection probabilities between f-MRI activated ROI's.

C-F Westin, LMI, General advisorOla Friman, Algorithm designMarek Kubicki, SPL, Clinical applicationRaul San-Jose , LMI, Vtk implementation AW de Vries, LMI, Algorithm design, implementation and execution

Algorithms: trace fibers in a stochastic matter. Find connection probabilities between ROIs.

Software: computational speed. Implementation in slicer

Clinical: - find difference in connection probabilities between populations. Perform tracing between f-MRI activated regions (gray matter).



•Estimate of sample's size needed and confidence bound on results.•GUI development•First results on schiz data: Map of connection probabilities


2006 Summer PrWeek


http://na-mic.org

Fiber Model Interactive Labeling Interface:

Develop Slicer module for anatomical labeling of fiber clusters for white matter atlas building.

Lauren O’Donnell, MIT (algorithms) (contact)

Marek Kubicki, BWH (clinical)

Software: New user interface for creating model hierarchies in slicer2.

Clinical: Apply user interface to labeling of fiber cluster vtk models for white matter atlas creation.



The new ModelInteraction module has been added to slicer2 CVS. Models can be grouped using the mouse and keyboard to select, and groups can be named anatomically. The module exports/imports to the MRML tree in the existing ModelHierarchy format.

2006 Summer PrWeek


http://na-mic.org

fMRI Analysis

NA-MIC

Collaborator

fMRI Analysis• Conformal Flattening in ITK• Spatial Regularization in fMRI


http://na-mic.org

Conformal Flattening:Write ITK Conformal Flattening Filter. This is useful for the visualization of irregular surfaces. In the special case of FMRI visualization, the flattened view facilitates the understanding of the mapping of function to spatial location.

Yi Gao, GT (algorithms)John Melonakos, GT/GE (algorithms)

Jim Miller, GE (software)Luis Ibanez, Kitware (software)

Algorithms: Use conformal mapping to map an irregular surface onto a sphere while preserving the angle. This is useful for visualization of FMRI where it is important to map function to spatial location.

Software: itkConformalFlatteningFilterGoals: 1) Apply to brain surface meshes

2) Write Insight Journal paper 3) Add to ITK CVS


Accomplished by end of Programming WeekAccomplishments: 1) Applied to brain surface meshes

2) Wrote Insight Journal paperhttp://insight-journal.org/dspace/handle/1926/225(note: this was accepted for oral presentation at the 2006

MICCAI open source workshop)

Expected Date for Insight Journal Publication: after the programming week

2006 Summer PrWeek


http://na-mic.org

MRF Spatial Regularization for fMRI :

Develop algorithm and ITK filter for angle preserving mapping of irregular surface.

Wanmei Ou, MIT (algorithms)Polina Golland, MIT (algorithms)Sandy Wells, MIT (algorithms)Carsten, Richer BWH (software, but left)Luis Ibanez (software)

fBIRN data (clinical)

Algorithms: Use Markov Random Field to perform spatial regularization for fMRI detection.

Software: written in VTK. Proper insertion in ITK framework

Clinical:



We converted 50% of the IsingMeanFieldApproximation imagefilter from vtk to itk. The source code has been putIn the NAMIC sandbox:fMRI-MarkovRandomFields

2006 Summer PrWeek


http://na-mic.org

NA-MIC Kit

NA-MIC

Collaborator

NA-MIC Kit1. Slicer3 User Interface 2. Migrating Slicer2.x Modules to Slicer3 3. Slicer3 Packaging 4. Slicer3 Grid Integration 5. Slicer3 LONI Pipeline Integration for Shape Analysis6. MGH I/O: File Format Converter7. Volumetric Meshing (UIowa)8. Dicom Query/Retrieve (IT Canary Islands)9. A Translation Station for Imaging (NWU)10. Slicer3 for IGT (BWH)Non-Medical Data Support:• ITK IO for astronomy data (Harvard IIC)


http://na-mic.org

Slicer3 UI:

Design and implement Slicer3’s UI; provide C++ infrastructure for module UI development.

Wendy Plesniak, BWHSebastien Barre, KitwareMathieu Malaterre, KitwareMichael Halle, BWH

Software: • Spec out slicer’s Nav/Zoom widget for controlling 3D view

• Implement 3D and Slice View reconfiguration



•Nav/Zoom widget specification as shown, implementation begun.•Reconfiguring views implemented: conventional, four-up, (lightbox still in progress)one-up 3D, one-up slice, view tabbed 3D view (icons, view examples shown below).•Documented feature requests and results of UI design discussion at meeting.

2006 Summer PrWeek

• Share infrastructure for building Slicer3 module GUI’s;

• Gather Slicer feature requests, features to keep, and discuss usability issues.


http://na-mic.org

Migrating Slicer2.x Modules to Slicer3:Integrate Slicer 2 modules into Slicer 3.

(algorithms)

Nicole Aucoin, BWH (software) (contact)Mathieu Malaterre, Kitware (software) Katie Hayes, BWH (testing)Bill Lorensen, GE (exec model support)

(clinical)

Algorithms:

Software: Port to VTK 5, gold standard tests, move Model Maker to Slicer 3 (CLI framework done)

Clinical:



2006 Summer PrWeek

Created nightly regression tests for Base, vtkTensorUtil, vtkDTMR:I User:Mathieu/Week.Converted Slicer 2.6 TCL ModelMaker to VTK 5.0 C++ code and created a stand alone executable callable from Slicer3. Picture showsoverlay of Slicer 2 and Slicer 3 models (differencedue to different decimation class). Project URL


http://na-mic.org

Slicer3 Packaging:Use CPack to generate Slicer3 installers.

(algorithms)

Andy Cedilnik, Kitware (software) Steve Pieper, BWH (testing)

(clinical)

Algorithms:

Software: Adopt CPack as a slicer packaging tool

Clinical:



•Work on issues with Slicer build system for NIHworkshop•Make Slicer2 work on Intel Mac

Place your picture/movie here.

2006 Summer PrWeek


http://na-mic.org

Grid Interface for Slicer3:Integrate BIRN Grid Intrrface into Slicer 3 Execution Model.

(algorithms)

Brendan Faherty, UCSD (software) (contact)Jeff Grethe, UCSD (software)Steve Pieper, Isomics (Slicer)Bill Lorenson, GE (CLI)Jim Miller, GE (CLI)

(clinical)

Algorithms:

Software: finish and test grid-interface / Slicer3 module

Clinical:



2006 Summer PrWeek

Finished XML to GI interfacesHand strawman execution through GIInstalled Condor and GI-Remote on Slicerl

Goal for All Hands

Launch ClRegistration from within Slicer3 CLI Module launcherPackage NAMIC-KIT for Grid Installation (RPM)


http://na-mic.org

LONI Pipeline UNC Shape Analysis & Slicer 3 Execution Model

Jagadeeswaran, UCLA (Core 2) ([email protected])Martin Styner, UNC (algorithms)Steve Pieper, Isomics (Core 2)

Algorithms: Continue developing the UNC-shape pipeline (from AHM 2006)Gather bug reports/ feature requests for GUI, executionContinue development on modules for Slicer 3 execution modelDiscuss output specifications for interaction with Slicer 3


Accomplished by end of Programming WeekUNC shape pipeline works (4 subjects)

Features: Side Effect Outputs, Argument Lists, Client Threading LimitsNeeds debugging of StatNonParamTestPDMFunctionMartin compiles for LONI grid - can stress test for > 4 subjects

Slicer 3 Demo Refactored code for batch-mode pipeline Batch-mode Pipeline spews .module parameters for Slicer Batch-mode Pipeline tested for simple .modules Formulating input format specs, stress testing, monitoring

2006 Summer PrWeek


http://na-mic.org

ITK MGH I/O:Develop classes to provide valid IO between ITK images and MGH format.

Gheorghe Postelnicu, MGH (algorithms) (contact)Bill Lorensen (GE)

Algorithms: none

Software: Interface properly the cosines and other useful information.



Accomplished by end of Programming Week• Completed the Input and tested it in the case of different types of input data (scalar, vector);• Created new class to accommodate the data structure: itk::OrientedVectorImage, based on itk::VectorImage• Wrote output functions for both compressed and uncompressed formats• Initial Testing.• Code checked in the sandbox.


Is this a continuation of a previous programming week project? If so, please include that slide as well.

2006 Summer PrWeek


http://na-mic.org

Volumetric mesh generation:

Develop high quality volumetric mesh using projection techniques.Plan/Expected Challenges/PublicationTeam


2006 Summer PrWeek

Vincent Magnotta, Iowa (contact)Kiran Shivanna, Iowa Nicole Grosland, Iowa

Algorithms: Implement projection methods for volumetric mesh generation for musculoskeletal biomechanics applications.

Software: Visualization of resulting mesh in VTK.

Implementation of multiple bounding box mesh generation.Mesh smoothing to improve mesh quality.


http://na-mic.org

Slicer 3 dicom query/retrieveDevelop slicer 3 module for query/retrieval of data from PACS.

Eduardo Suárez, IT Canarias (algorithms)

Rafael Nebot, IT Canarias (software)Steve Pieper, Isomics (software)Jim Miller, GE research (software)

Software: Add dicom module to Slicer for query/retrieve. This module would have the look and feel of Slicer 3. It would be developed against the KWwidgets, and initially dcmtk. This module would return a directory/file hierarchy in a first step and would connect to Slicer in a second step. It is expected to be finished by AHM 2007.



We started the analysis of this module.We have been talking to Pat Mongkolwat from NW University to see whether there is a meeting point in our needs. It seems at the moment the two efforts should stay independet and continue to discuss progress

2006 Summer PrWeek


http://na-mic.org

A Translation Station for Imaging Integrate a radiology clinical workstation with 3D Slicer

David S. Channin, NWU (Requirements/Architecture)Pat Mongkolwat, NWU (Architecture/software)Tom Lechner, NWU (software)Alex Kogan, NWU (software)

Steve Pieper, Isomics (software)Wendy Plesniak, BWH (software)

Algorithms: Use existing Slicer 3 platform and modules

Software: IHE workflow functionality, PACS connectivity, hanging protocols and other radiology clinical functions with the SLICER research platform

Clinical: Provide advanced 3D imaging tools to radiologists



Place your picture/movie here.

Expected Date: RSNA 2006 meeting (Nov 26th – Dec 1st)

2006 Summer PrWeek

Requirements and Architecture: A typical radiology workstation requirements; Design to work seamlessly with Slicer 3

- Create a scene without the typical Slicer 3 GUI

Things to add- Slicer 3 logo and other contributors’ logos- Configurable 4 scenes layout- Minimize interaction steps for each module


http://na-mic.org

Slicer3 for Image Guided Therapy (IGT):

Convert vtkMRAblation and vtkFMRIEngine to Slicer3 modules.

Noby Hata, BWH (software)Haiying Liu, BWH (software)Steve Pieper, Isomics (software)Jim Miller, GE (software)

Algorithms:

Software: Build Slicer3 modules for IGT applications.

Clinical:



• MRAblation has been converted to Slicer3 loaded module.• It has been tested using different data sets.• Thermal maps (output volumes) look the same as (similar to) those from Slicer2.6

2006 Summer PrWeek


http://na-mic.org

NA-MIC kit for non-medical data:

Develop and test a FITS IO reader for ITK to allow astronomy data to be imported directly into Slicer.

Douglas Alan (Harvard IIC) (software)Michael Halle (BWH/IIC) (software)

Luis Ibanez, Kitware (software) ??



ITK FITSIO now reads in multi-dimensionalimage from FITS file.

Skeleton code for reading headers

Still need physical to data unit conversion

Expected Date for Insight Journal Publication: September ‘06..

2006 Summer PrWeek

Plan: Build simple ITK reader for FITS that imports a multi-dimensional data volume and associated metadata into ITK. Build in hooks to support interpretation of headers to provide world coordinate system conversion.

Challenges: Handling dimensionless and non-rectilinear coordinate systems (although this issue can be deferred).

national alliance for medical image computing project week june 26-30, 2006 participants: 56 na-mic...

Documents

itk software module

dti analysis

spherical mesh

local shape analysis

itkcompatible classes

itk io support

spherical wavelet coefficients

filteritk statistical