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  Back to [[NA-MIC_Collaborations:New|NA-MIC Collaborations]]
 
  Back to [[NA-MIC_Collaborations:New|NA-MIC Collaborations]]
 
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= NA-MIC Internal Collaborations =
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{| cellpadding="10" border="1"
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| style="width:33%" | [[Image:CingulumAllSubjectsFibers.png|300px]]
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| style="width:33%" | [[Image:Sulcaldepth.png|300px]]
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| style="width:33%" | [[Image:Mit_fmri_clustering_parcellation2_xsub.png|300px]]
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|-align="center"
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== [[NA-MIC_Internal_Collaborations:DiffusionImageAnalysis|Diffusion Image Analysis]] ==
 
== [[NA-MIC_Internal_Collaborations:DiffusionImageAnalysis|Diffusion Image Analysis]] ==
  
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== [[NA-MIC_Internal_Collaborations:StructuralImageAnalysis|Structural Image Analysis]] ==
 
== [[NA-MIC_Internal_Collaborations:StructuralImageAnalysis|Structural Image Analysis]] ==
  
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== [[NA-MIC_Internal_Collaborations:fMRIAnalysis|fMRI Analysis]] ==
 
== [[NA-MIC_Internal_Collaborations:fMRIAnalysis|fMRI Analysis]] ==
  
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=== Algorithm and Software Infrastructure ===
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|}
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= Driving Biological Problems (2007 - 2010): Roadmap Projects =
  
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{| cellpadding="10"
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{| cellpadding="10" border="1"
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| style="width:15%" | [[Image:Brain-flat.PNG|200px]]
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| style="width:15%" | [[Image:Cingulum1.jpg|200px]]
 
| style="width:85%" |
 
| style="width:85%" |
  
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== [[Projects:ConformalFlatteningRegistration|Conformal Flattening]] ==
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== [[ProjectWeek200706:ContrastingTractographyMeasures|Contrasting Tractography Measures]] ==
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This project represents a new initiative to build upon a shared vision among Cores 1, 3 and 5 that the field of medical image analysis would be well served by work in the area of validation, calibration and assessment of reliability in DW-MRI image analysis. [[ProjectWeek200706:ContrastingTractographyMeasures|More...]]
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<font color="red">'''New: '''</font>  [[SanteFe.Tractography.Conference|Contrasting Tractography Methods Conference]], Santa Fe, October 1-2, 2007.
  
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The goal of this project is for better visualizing and computation of neural activity from fMRI brain imagery. Also, with this technique, shapes can be mapped to shperes for shape analysis, registration or other purposes. Our technique is based on conformal mappings which map genus-zero surface: in fmri case cortical or other surfaces, onto a sphere in an angle preserving manner. [[Projects:ConformalFlatteningRegistration|More...]]
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<font color="red">'''New: '''</font> Y. Gao, J. Melonakos, and A. Tannenbaum. Conformal Flattening ITK Filter. ISC/NA-MIC Workshop on Open Science at MICCAI 2006.
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| | [[Image:ProstateDiagram.png|200px]]
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== [[ProjectWeek200706:BrachytherapyNeedlePositioningRobotIntegration|Brachytherapy Needle Positioning Robot Integration]] ==
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The Queen’s/Hopkins team is developing novel devices and procedures for cancer interventions, including biopsy and therapies.  Our goal for the programming week is to design and start implementing software for the new MRI Brachytherapy needle positioning robot.  [[ProjectWeek200706:BrachytherapyNeedlePositioningRobotIntegration|More...]]
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<font color="red">'''New: '''</font>  Meeting at JHU on July 17-19, 2007.
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|-
  
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== NA-MIC Kit ==
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| | [[Image:Lupus.png|200px]]
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=== NAMIC Software Process ===
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== [[DBP2:MIND:Roadmap|Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus]] ==
  
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{| cellpadding="10"
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Our goal is to automatically, or with little or no manual human rater input, accurately tissue classify our example lupus data-set into gray, white, csf, and lesion classes. 
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<font color="red">'''New: '''</font>  Participants in the Summer 2007 NA-MIC Project Week.
  
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=== Software Infrastructure ===
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|-
  
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{| cellpadding="10"
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| | [[Image:Itksnap.jpg|200px]]
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| style="width:15%" |
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| style="width:85%" |
 
  
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== [[ProjectWeek200706:CorticalThicknessForAutism|Cortical Thickness for Autism]] ==
  
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=== Training & Dissemination ===
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Our goal is to begin a longitudinal study of early brain development by cortical thickness in autistic children and controls (2 years with follow-up at 4 years). We want to be able to make statistical group comparisons. [[ProjectWeek200706:CorticalThicknessForAutism|More...]]
  
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{| cellpadding="10"
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<font color="red">'''New: '''</font>  Participation in the NA-MIC Summer 2007 Project Week.
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| style="width:15%" |
 
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| style="width:85%" |
 
  
 
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|}
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== NA-MIC Kit ==
  
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== Other Projects ==
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=== NAMIC Software Process ===
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# [[NA-MIC/Projects/NA-MIC_Kit/CMake_-_NAMIC_Kit_Building|CMake - NAMIC Kit Building]] (Kitware)
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# [[NA-MIC/Projects/NA-MIC_Kit/CPack_-_NAMIC_Kit_Distribution|CPack - NAMIC Kit Distribution]] (Kitware)
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# [[NA-MIC/Projects/NA-MIC_Kit/Dart_2_and_CTest_-_Software_Quality|Dart 2 and CTest - Software Quality]] (GE, Kitware)
  
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{| cellpadding="10"
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=== Software Infrastructure ===
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| style="width:15%" | [[Image:vxl.gif|200px]]
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# [[NA-MIC/Projects/NA-MIC_Kit/Slicer3|Slicer 3]] (Isomics, GE, Kitware, UCSD, UCLA)
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| style="width:85%" |
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## [[NA-MIC/Projects/NA-MIC_Kit/MRML|MRML]] (Isomics, Kitware, GE)
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## [[NA-MIC/Projects/NA-MIC_Kit/Coordinate_Systems|Coordinate Systems]] (GE, Isomics)
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## [[NA-MIC/Projects/NA-MIC_Kit/IO_Unification|IO Unification]] (GE, Isomics)
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## [[NA-MIC/Projects/NA-MIC_Kit/Execution_Model|Execution Model]] (GE)
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## [[NA-MIC/Projects/NA-MIC_Kit/Grid_Computing|Grid Computing]] (UCSD, GE, Kitware, Isomics)
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# [[NA-MIC/Projects/NA-MIC_Kit/Licenses_Unification|Licenses Unification]] (Kitware, Isomics)
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# Toolkits
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## [[NA-MIC/Projects/NA-MIC_Kit/KWWidgets|KWWidgets]] (Kitware)
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## [[NA-MIC/Projects/NA-MIC_Kit/Teem|Teem]] (Harvard/BWH)
  
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== [[Projects:FreeSurferNumericalRecipiesReplacement|Numerical Recipies Replacement]] ==
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=== Training & Dissemination ===
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# [[NA-MIC/Projects/NA-MIC_Kit/Training_Material_and_Workshops_for_NA-MIC_Kit|Training Material and Workshops for NA-MIC Kit]] (MGH, BWH)
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# [[NA-MIC/Projects/NA-MIC_Kit/Dissemination|Dissemination for NA-MIC]] (Isomics, Kitware, Harvard)
  
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Our objective is to replace algorithms using the proprietary Numerical Recipes for C source base in FreeSurfer in the efforts to open-source FreeSurfer. This project has been completed through the use of the open source packages VXL (VNL) and Cephes. This includes the complete replacement of all Numerical Recipes in C code, and the implementation of a battery of unit tests for each replaced function. Currently the open source release is at a beta stage, and 25 beta releases of the source have been made. We anticipate a complete open source release in first quarter 2008. [[Projects:FreeSurferNumericalRecipiesReplacement|More...]]
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== Other Projects ==
  
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<font color="red">'''New: '''</font> Completed
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# [[Non_Rigid_Registration|Non-Rigid Registration]]
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# [[NA-MIC/Projects/Diffusion_Image_Analysis/FreeSurfer_NRRD_IO|FreeSurfer NRRD IO]]
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|}
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# [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|FreeSurfer Numerical Recipies Replacement]]
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# [https://www.slicer.org/wiki/Slicer3:Fluorescence_and_Electron_Microscopy_Support Slicer3 Fluorescence and Electron Microscopy Support]

Latest revision as of 17:08, 10 July 2017

Home < NA-MIC Internal Collaborations:New
Back to NA-MIC Collaborations

NA-MIC Internal Collaborations

CingulumAllSubjectsFibers.png Sulcaldepth.png Mit fmri clustering parcellation2 xsub.png

Diffusion Image Analysis

Structural Image Analysis

fMRI Analysis

Driving Biological Problems (2007 - 2010): Roadmap Projects

Cingulum1.jpg

Contrasting Tractography Measures

This project represents a new initiative to build upon a shared vision among Cores 1, 3 and 5 that the field of medical image analysis would be well served by work in the area of validation, calibration and assessment of reliability in DW-MRI image analysis. More...

New: Contrasting Tractography Methods Conference, Santa Fe, October 1-2, 2007.

ProstateDiagram.png

Brachytherapy Needle Positioning Robot Integration

The Queen’s/Hopkins team is developing novel devices and procedures for cancer interventions, including biopsy and therapies. Our goal for the programming week is to design and start implementing software for the new MRI Brachytherapy needle positioning robot. More...

New: Meeting at JHU on July 17-19, 2007.

Lupus.png

Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus

Our goal is to automatically, or with little or no manual human rater input, accurately tissue classify our example lupus data-set into gray, white, csf, and lesion classes.

New: Participants in the Summer 2007 NA-MIC Project Week.

Itksnap.jpg

Cortical Thickness for Autism

Our goal is to begin a longitudinal study of early brain development by cortical thickness in autistic children and controls (2 years with follow-up at 4 years). We want to be able to make statistical group comparisons. More...

New: Participation in the NA-MIC Summer 2007 Project Week.

NA-MIC Kit

NAMIC Software Process

  1. CMake - NAMIC Kit Building (Kitware)
  2. CPack - NAMIC Kit Distribution (Kitware)
  3. Dart 2 and CTest - Software Quality (GE, Kitware)

Software Infrastructure

  1. Slicer 3 (Isomics, GE, Kitware, UCSD, UCLA)
    1. MRML (Isomics, Kitware, GE)
    2. Coordinate Systems (GE, Isomics)
    3. IO Unification (GE, Isomics)
    4. Execution Model (GE)
    5. Grid Computing (UCSD, GE, Kitware, Isomics)
  2. Licenses Unification (Kitware, Isomics)
  3. Toolkits
    1. KWWidgets (Kitware)
    2. Teem (Harvard/BWH)

Training & Dissemination

  1. Training Material and Workshops for NA-MIC Kit (MGH, BWH)
  2. Dissemination for NA-MIC (Isomics, Kitware, Harvard)

Other Projects

  1. Non-Rigid Registration
  2. FreeSurfer NRRD IO
  3. FreeSurfer Numerical Recipies Replacement
  4. Slicer3 Fluorescence and Electron Microscopy Support
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