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| ===Structural Analysis=== | | ===Structural Analysis=== |
− | # [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]
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− | # Scripts to run and visualize [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]] (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]
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− | #EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]]
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− | #SVM Shape Analysis (Brad, Polina, Martin)
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− | #[[Non_Rigid_Registration|Parallelization of ITK for deformable registration (Stephen, Jim, Ross)]] [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]]
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− | ## Driving problem: Congealing with B-spline (Lilla, Stephen)
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− | ## Driving problem: Non-rigid registration of anatomical MRI (Kilian, Stephen)
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− | # Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]
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− | #Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration.ppt| 4-block PPT Jan 2007]]
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− | ===Diffusion Image Analysis===
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− | #Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]
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− | #Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]
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− | #Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]
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− | #Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]
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− | #ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]
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− | #Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]
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− | #ITK Probabilistic/Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT)
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− | ===NA-MIC Kit===
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− | #Slicer3 Infrastructure Projects
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− | ##'''[[Slicer3:Architecture/Features|Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata)
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− | ##'''[[Slicer3:Data_Model|Data Model / libMRML]]''' ('''Alex''', Steve)
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− | ##'''[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
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− | ##'''[[Slicer3:Interface_Design|Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
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− | ###See [[Slicer3:UIEngineering|Slicer3:UIEngineering]]
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− | ##'''[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
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− | ###[[Slicer3:DTMRI|DTMRI]]<nowiki>: </nowiki>'''Raul''', [http://lmi.bwh.harvard.edu LMI]
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− | ###[[Slicer3:DTMRI|Tractography]]<nowiki>: </nowiki>'''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
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− | ###[[Slicer3:Editor|Editor]]<nowiki>: </nowiki>'''Steve'''
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− | ###[[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]<nowiki>: </nowiki>'''Nicole'''
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− | ###[[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]]<nowiki>: </nowiki>'''Haiying'''
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− | ###[[Slicer3:EM|EMSegment Interface]]<nowiki>: </nowiki>'''Brad Davis'''
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− | ###[[Slicer3:Slicer_Daemon|SlicerDaemon Interface (for unu, matlab)]]<nowiki>: </nowiki>'''Steve Pieper'''
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− | ##'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie)
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− | ##Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[Image:2007 AHM Programming Half Week Slicer3 Launch.ppt]]
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− | ##'''[[Slicer3:Pipeline_Integration|Pipeline Integration]]''' ('''Jags''')
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− | ##'''[[Slicer3:Grid_Interface|Grid Integration]]''' ('''Jeff Grethe''', Neil)
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− | ##'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''')
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− | #[[Slicer3:Grid_Interface|Grid Execution]] (Neil, Bill, Jim) [[Image:2007_Project_Half_Week_GridExecution.ppt]]
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− | #Tractography in Slicer3 (Lauren, Raul)
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− | #Model Hierarchies (Alex, Lauren, Kilian, Brad, Ron) -- generalize concepts from DTI and EM group nodes to support atlas hierachies like in slicer2.
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− | ===External Collaborations===
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− | #Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT 2007]]
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− | #Developing IGT workflow for Slicer3 (Simon DiMaio, Haiying Liu, Noby Hata, Stephen Aylward) [[IGT|IGT Project page in NA-MIC wiki]]
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− | #Radiology Workstation Module for Slicer3 (Pat, Steve)
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− | #vmtk module for Slicer [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 2007 Project Half Week vmtkSlicerModule.ppt]] (Luca Antiga, Jim Miller)
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− | #Hexahedral Voxel Meshing into Slicer3 [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]]
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− | ##Voxel meshing as an execuation module in Slicer3 [[Media:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 4 block PPT 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Steve Pieper)
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− | ##Mesh Quality Visualization Development [[Media:Mesh_Quality_Visualization.ppt|Mapped Quality 4 block PPT 2007]] (Curt Lisle, Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper)
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− | ##Bounding Box Projection Meshing [[Media:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 4 block PPT 2007]] (Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper, Curt Lisle)
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− | ##Tetrahedral Mesh Generation Tools in VTK [[Media:Tetmesh_VTK_Tools.ppt|VTK Tetrahedral Meshing 4 block PPT 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)
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− | #Nonhuman Primate slicer Module (Alcohol Exposure)[[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | Alcohol Exposure 4 block PPT]] (Kilian Pohl, Chris Wyatt)
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− | ----
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− | This following is a list of projects carried out at the last project week (summer 2006). For new attendees, these projects can be used as templates. For attendees involved in the last project week, please move projects from the list below to the list above if you intend to continue these projects. And please do add a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT for 2007]].
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− | === 2006 Structural Analysis ===
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− | # [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Xavier Le Faucheur, GT, Delphine Nain, GT, John Melonakos GT/GE, Jim Miller GE, Luis Ibanez, Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT 2006]]
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− | # [[NA-MIC/Projects/Structural/Shape_Analysis/ShapeStatisticsWithPermTestCorrectionAndFDR|ITK statistical analysis using non-parametric permutation analysis and false discovery rate]] (Martin Styner, UNC): [[Media:2006_06_PW_StatAnal.ppt| 4 block PPT 2006 ]]
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− | # [[NA-MIC/Projects/Structural/Shape_Analysis/Correspondence|Local curvature based correspondence in ITK]] (Ipek Oguz, Martin Styner, UNC): [[Media:2006_MIT_Project_Week_LocalCurvatureBasedCorrespondence.ppt| 4 block PPT 2006]]
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− | # [[NA-MIC/Projects/Structural/Shape_Analysis/FemaleSPDCaudates|Shape analysis of female SPD dataset]] (Jim Levitt, PNL, Marc Niethammer, PNL, Sylvain Bouix, PNL, Martin Styner, UNC): [[Media:2006_06_PW_female_SPD.ppt| 4-block PPT 2006]]
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− | # [[NA-MIC/Projects/Structural/Mesh/Mesh_Untangling|Mesh Untangling]] (Gheorghe Postelnicu, MGH, Bill Lorensen GE): [[Media:2006_Summer_Project_Week_Mesh_Untangling.ppt|4 block PPT 2006]]
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− | # [[NA-MIC/Projects/Structural/Registration/Histology_MR_Registration|MR Histology Registration]] (Gheorghe Postelnicu MGH, Bill Lorensen GE): [[Media:2006_Summer_Project_Week_MGH_Histology_MR_Registration.ppt|4 block PPT 2006]]
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− | === 2006 Diffusion Image Analysis ===
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− |
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− | # [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|ITK DTI Image Processing Modules]] (Casey Goodlett UNC, Tom Fletcher Utah, Bill Lorensen GE, John Melonakos GT/GE): [[Media:2006_Summer_Project_Week_DTI_Processing.ppt|4-block PPT 2006]]
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− | # [[NA-MIC/Projects/Diffusion_Image_Analysis/Fiber_Tools_Slicer_Integration|Fiber Tools / Slicer 3 Integration]] (Casey Goodlett UNC, Bill Lorensen GE): [[Media:2006_Summer_Project_Week_FiberTracking_Slicer_Integration.ppt|4-block PPT 2006]]
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− | # [[NA-MIC/Projects/Diffusion_Image_Analysis/Stochastic_Fiber_Tracing_Applications|Stochastic Fiber Tracing Applications]] (C-F Westin, Marek Kubicki, Raul San-Jose, AW de Vries, All LMI):[[Media:2006_Summer_Project_Week_stochastictracking.ppt| 4-block PPT 2006]]
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− | # [[NA-MIC/Projects/Diffusion_Image_Analysis/Slicer_Fiber_Anatomical_Labeling|Slicer Fiber (Model) Labeling Interface]] (Lauren O'Donnell MIT, Marek Kubicki BWH) :[[Media:2006_Summer_Project_Week_ModelLabel.ppt| 4-block PPT 2006]]
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− | === 2006 FMRI Image Analysis ===
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− | # [[NA-MIC/Projects/Structural/Conformal_Flattening_in_ITK|Conformal Flattening in ITK]](Yi Gao GT, John Melonakos GT/GE, Jim Miller GE, Luis Ibanez Kitware, Marc Niethammer BWH): [[Media:2006_Summer_Project_Week_ConformalFlattening.ppt| 4-block PPT 2006]]
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− | # [[NA-MIC/Projects/fMRI_Analysis/Spatial_Regularization_for_fMRI_Detection|Spatial Regularization in fMRI Analysis]](Wanmei Ou, Polina Golland, Sandy Wells, and Carsten) [[Media:2006_Summer_Project_Week_fMRIMRF.ppt| 4-block PPT 2006]]
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− | === 2006 NA-MIC Kit ===
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− | # [[2006_Project_Week_MIT_SlicerUI|Slicer3 Interface]] (Wendy Plesniak, Sebastien Barre, Steve Pieper, Mathieu Malaterre, Randy Gollub, Michael Halle), [[Media:2006_Summer_Project_Week_Slicer3UI.ppt|4-block PPT 2006]]
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− | # [[2006_Project_Week_MIT_Migrating_Slicer2.x_Modules_to_Slicer3|Migrating Slicer2.x Modules to Slicer3]] (Nicole Aucoin, Mathieu Malaterre, Katie Hayes, Bill Lorensen): [[Media:2006_Summer_Project_Week_Migrating_Slicer2x_Modules_to_Slicer3.ppt|4-block PPT 2006]]
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− | # [[2006_Project_Week_Kitware_Slicer3_Packaging|Slicer3 Packaging]] (Andy Cedilnik, Steve Pieper) [[Media:2006_Summer_Project_Week_Slicer3_Packaging.ppt|4-block PPT 2006]]
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− | # [[2006_Project_Week_MIT_Grid_Integration|Slicer3 Grid Integration]] (Jeff Grethe, Brendan Faherty, Steve Pieper, Katie Hayes), [[Media:2006_Summer_Project_Week_Grid_Interface_for_Slicer3.ppt|4-block PPT 2006]]
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− | # [[2006_Project_Week_MIT_LONIPipelineIntegration|Slicer3 Pipeline Integration ]] (Jagadeeswaran Rajendiran, Martin Styner, Steve Pieper), [[Media:2006_Summer_Project_Week_Jagadeeswaran_June30.ppt|4 block PPT 2006]]
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− | # [[2006_Project_MGH_File_Format_Converter|2006 Project MGH File Format Converter]](Gheorghe Postelnicu, Bill Lorensen) [[Media:2006_Summer_Project_MIT_MGH_IO.ppt|4-block PPT 2006]]
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− | # Volumetric Meshing (Kiran Shivanna, Vincent Magnotta, Nicole Grosland):[[Media:2006_Summer_Project_Week_Volumetric_Meshing.ppt|4-block PPT 2006]]
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− | # Dicom Query/Retrieve (Eduardo Suárez, Rafael Nebot, Steve Pieper, Jim Miller):[[Media:2006_Summer_Project_Week_Slicer_Query_Retrieve.ppt|4-block PPT 2006]]
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− | # A Translation Station for Imaging (Pat Mongkolwat, Alex Kogan, Tom Lechner, Steve Pieper, Wendy Plesniak):[[Media:2006_Project_Week_MIT_IntegrateSlicerWith_A_PACS_Workstation.ppt|4-block PPT 2006]]
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− | # [[NA-MIC/Projects/Slicer3_for_IGT/Converting_vtkFMRIEngine_and_vtkMRAblation_to_Slicer3_modules|Converting vtkFMRIEngine and vtkMRAblation to Slicer3 modules]] (Noby Hata, Haiying Liu, Steve Pieper, Jim Miller): [[Media:2006_Summer_Project_Week_Slicer3_IGT.ppt| 4-block ppt 2006]]
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− | === 2006 NA-MIC Kit Support for Non-Medical Data ===
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− | # ITK IO support for reading astronomy data and coordinates from FITS files (Douglas Alan IIC, Michael Halle BWH/IIC, Luis Ibanez Kitware)[[Media:2006_Summer_Project_Week_Astronomy_FITS_Reader_Prelim_Results.ppt| 4-block PPT 2006]]
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| == Logistics == | | == Logistics == |
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