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# [[NA-MIC/Projects/Diffusion_Image_Analysis/FreeSurfer_NRRD_IO|FreeSurfer NRRD IO]]
# [[NA-MIC/Projects/Diffusion_Image_Analysis/FreeSurfer_NRRD_IO|FreeSurfer NRRD IO]]
# [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|FreeSurfer Numerical Recipies Replacement]]
# [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|FreeSurfer Numerical Recipies Replacement]]
# [http://www.slicer.org/slicerWiki/index.php/Slicer3:Fluorescence_and_Electron_Microscopy_Support Slicer3 Fluorescence and Electron Microscopy Support]
# [https://www.slicer.org/wiki/Slicer3:Fluorescence_and_Electron_Microscopy_Support Slicer3 Fluorescence and Electron Microscopy Support]

Latest revision as of 14:07, 10 July 2017

Home < NA-MIC Collaborations:Old

Resources for New External Collaborators: Click here


NA-MIC External Collaborations

This section describes external collaborations with NA-MIC that are funded by NIH under the "Collaboration with NCBC" PAR. (Details for this funding mechanism are provided here).

PAR-05-063: R01CA124377 An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

This project is a NCBC collaboration grant. Collaborators include Kevin Cleary and Noby Hata. The master page for this collaboration is here, while the rest of this section contains links to the specific active projects in this collaboration.


To be added.

PAR-05-063: R01EB005973 Automated FE Mesh Development

This project is a NCBC collaboration grant. Collaborators include Nicole Grosland, Vincent Magnotta, Steve Pieper, and Simon Warfield. The master page for this collaboration is here, while the rest of this section contains links to the specific active projects in this collaboration.

Meshing Algorithms

  1. Voxel Meshing Module (Iowa)
  2. Novel Hexahedral Meshing Algorithms (Iowa)
  3. Hex vs Tet Mesh Comparisons (Iowa/Isomics/BWH)

Automated Segmentation

  1. Integration of Neural Network Algorithms (Iowa)

Image Registration

  1. Evaluation_of_Inter-Modality_Registration (Iowa/Isomics)
  2. Inter-slice Motion Correction for fMRI (OSU)


  1. Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning (Iowa)
  2. FE_Mesh_Validation (Iowa)

Mesh Quality Visualization

  1. FE Mesh Quality Visualization (Iowa/Isomics)
  2. Standalone FE Mesh Quality Viewer
  3. Mesh Quality Command Line Module

PAR-05-063: R01AA016748 Measuring Alcohol and Stress Interaction with Structural and Perfusion MRI

This project is a NCBC collaboration grant. Collaborators include James B Daunais, Robert Kraft, Chris Wyatt, William Wells, and Kilian Pohl. The master page for this collaboration is here, while the rest of this section contains links to the specific active projects in this collaboration.

Rhesus Probabalistic Atlas

  1. WM/GM Atlas
  2. Subcortical Atlas


  1. Rhesus ICV Extraction
  2. Rhesus EM Segmentation

PAR-05-057: BRAINS Morphology and Image Analysis

This project is not an NCBC collaboration grant, but instead a Continued Development and Maintenance of Software grant. The intent of this application is to update the BRAINS image analysis software developed at the University of Iowa. The collaborators include Vincent Magnotta, Hans Johnson, Jeremy Bockholt, and Nancy Andreasen. There are three main thrusts of this application as outlined below.

Implement a Automated Brain Analysis Pipeline

Code Refactoring for Cross Platform Support

Validation of Pipeline Using MIND MCIC Sample

Children's Pediatric Cardiology Collaboration with SCI/SPL/Northeastern

Smallkidcxr.png 27y-leftabdcan-T6SQ-voltage-withheart4.png 27y-leftabdcan-T6SQ-current4.png 27y-leftabdcan-T6SQ-heart-cut3.png


Placement of Implantable Cardiac Defibrillators(ICDs)is a unique and challenging problem for children due to the variety of shapes and sizes, ranging from neonate to adolescent. As a result, a variety of novel implant techniques have been employed. Although these have generally been successful inasmuch as they result in a clinically acceptable defibrillation threshold, nothing is known about the mechanisms by which this threshold is attained, the optimal geometries for defibrillation, and whether unsafe electric field strengths are a result of novel implant approaches. Finite element modeling has been shown in adult torso models to correlate well with clinical results. Our goal is to model defibrillation in child torso models to gain insight into this important problem. We are also interested in developing new orientations in adults with the goal of lowering DFTs and providing options in patients with contraindications to standard techniques.

Goals of Project

1. Create 3D models of children based on CT and MRI datasets for modeling internal and external defibrillation in the SCIRun environment. The processes required address the larger question of how to take any CT or MRI DICOM dataset, segment it into various label maps, combine those label maps in a hierarchical manner, then import and utilize them in the SCIRun/BioPSE environment. This represents part of an expanding collaboration between SCI and SPL to integrate open source tools to allow creation, visualization, and computational modeling of image based 3D models.

2. Create modules which allow insertion of electrode shapes into finite element models in in the SCIRun environment.

3. Utilize the above innovations to model the placement of internal defibrillator electrodes to maximize efficacy, minimize potential cardiac damage, and gain further insight into optimizing defibrillation in children of various sizes as shown above.

Slicer and SPL Tools in the Project

Outline of Torso Segmentation Problem

Segmentation Tools Currently Utilized

Tools In Development and Wishlist

Building and Running SCIRun on SPL Machines

SCRun on SPL Machines

NA-MIC Internal Collaborations

This is a list of all collaborative projects within NA-MIC. These projects form the basis of the progress reports submitted to the NIH. These collaborations are between team members of the various cores of NA-MIC.

Diffusion Image Analysis

Fiber Tract Extraction and Analysis

Continued from 2006

  1. Fiber Tract Statistics (Utah, UNC)
  2. Diffusion measures alongs fiber tracts of the cingulum bundle (BWH, MIT, UNC)
  3. Clustering of anatomically distinct fiber tracts (BWH, MIT)
  4. Geodesic Active Contours for Fiber Tractography and Fiber Bundle Segmentation (Georgia Tech, BWH)
  5. Corpus Callosum Fiber Tractography in Schizophrenia (Dartmouth, BWH, MIT)

New in 2007

  1. Tensor estimation and Monte-Carlo simulation (UNC, Utah)
  2. ITK Stochastic Tractography Filter (MIT, BWH)
  3. Volumetric White Matter Connectivity (Utah)
  4. DTI Atlas-Building (UNC, BWH)
  5. Inferior Frontotemporal Connections in Schizophrenia (BWH, MIT)
  6. Automatic Clustering of Corpus Callosum and FA Analysis (BWH, MIT)
  7. FA Analysis of Fornix Tractography in Schizophrenia (BWH, MIT)
  8. A Diffusion Tensor Imaging and Genetics Study of Psychosis Across the Lifespan - Project in Recruitment Phase (Toronto, BWH)

Fractional Anisotropy Analysis

Continued from 2006

  1. Corpus Callosum Regional FA analysis in Schizophrenia (BWH, UNC, Dartmouth)
  2. Fractional Anisotropy of the Corpus Callosum and Anterior Commissure (BWH, MIT, Dartmouth)
  3. Fractional Anisotrophy in the Uncinate Fasciculus in Schizophrenia and Bipolar I Disorder--replication and extension of Kubicki study (Dartmouth, BWH)

New in 2007

  1. Geodesic Active Contours for Fiber Tractography and Fiber Bundle Segmentation (Georgia Tech, BWH)
  2. Corpus Callosum Probabilistic Subdivision and FA Analysis (BWH, UNC)

Path of Interest Analysis

Continued from 2006

  1. Integrity of Fronto-Temporal Circuitry in Schizophrenia using Path of Interest Analysis (Dartmouth, MGH, Isomics, BWH)

New in 2007

  1. ITK implementation of POIStats, and Integration into Slicer3 (MGH, Isomics),
  2. Dartmouth Data Image Format Compatibility in Application of POIStats (MGH, Isomics, Kitware, Dartmouth)
  3. Anatomical Connectivity of Regions of Functional Activation (BWH)


Continued from 2006

  1. DTI Validation (UCI, MGH, UNC, MIT)

Algorithm/Software Infrastructure

Continued from 2006

  1. DTI Software/Algorithm Infrastructure (Utah, UNC)
  2. Tensor based statistics (BWH, Utah)
  3. Diffusion tensor image filtering (Utah, BWH)
  4. Non-rigid EPI Registration (MGH, Kitware, Dartmouth)
  5. Fiber Tools Integration with Slicer 3 (UNC, GE, Isomics)

New in 2007

  1. Rician Noise Remvoal in Diffusion Tensor MRI (Utah)
  2. Finsler Tractography in ITK (Georgia Tech, Kitware): 4-block PPT Jan 2007
  3. Finsler Levelsets in ITK (Georgia Tech, Kitware): 4-block PPT Jan 2007
  4. Restoration of DWI data using a Rician LMMSE Estimator (BWH)

Structural Image Analysis

Image Segmentation

Continued from 2006

  1. Knowledge-Based Bayesian Classification and Segmentation (Georgia Tech, Kitware)
  2. Brain Tissue Classification and Subparcellation of Brain Structures (BWH, MIT, Kitware)
  3. Rule based segmentation: Striatum (Georgia Tech, BWH, Isomics, Kitware)
  4. Rule based segmentation: DLPFC (Georgia Tech, UCI, Isomics, Kitware)
  5. Multiscale Shape Segmentation Techniques (Georgia Tech, BWH)
  6. Stochastic Methods for Segmentation (Georgia Tech)
  7. Statistical/PDE methods for Segmentation (Georgia Tech)
  8. Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms (MGH)

New in 2007

  1. EMSegmenter Software Development (BWH, MIT, Kitware) 4-block PPT Jan 2007
  2. Expanded neuroanatomy training for algorithm development at GA Tech, to expand the rules set for semiautomated segmmentation/shape analysis of frontal cortex (UCI, Georgia Tech)

Image Registration

Continued from 2006

  1. Optimal Mass Transport for Registration (Georgia Tech, BWH)

New in 2007

  1. Parallelization of ITK for deformable registration (Kitware, GE, Utah), 4-block PPT Jan 2007
  2. Group-wise Registration of Medical Images (MIT, BWH, MGH), 4-block PPT Jan 2007

Morphometric Measures and Shape Analysis

Continued from 2006

  1. Shape Analysis for the caudate and corpus callosum data (BWH, UNC, Georgia Tech, Dartmouth)
  2. Shape Analysis of the hippocampus (Dartmouth, UNC, BWH)
  3. Multiscale Shape Analysis applied to Caudate and Hippocampus (Georgia Tech, BWH, UNC)
  4. UNC Shape Analysis with LONI pipeline for clinical investigators (UNC, UCLA)
  5. Population Studies (UNC, GE)
  6. Multi-site morphometry in Mild Cognitive Impairment (UCI, mBIRN?)
  7. Multi-site morphometry in Schizophrenia (UCI, FBIRN)
  8. Automated shape model construction (Utah, BWH)
  9. Neural substrates of apathy in schizophrenia (Dartmouth, Isomics)
  10. Cortical Surface Shape Analysis Based on Spherical Wavelets (MGH)
  11. Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops (MGH)

New in 2007

  1. ITK Spherical Wavelet Transform Filter (Georgia Tech,GE, Kitware): 4-block PPT Summer 2006, 4-block PPT Jan 2007
  2. UNC shape analysis with Spherical Wavelet Features (GaTech, UNC): 4-block PPT Jan 2007
  3. Integrating KWMeshVisu into Slicer (UNC, Kitware), 4-block PPT Jan 2006, 4-block PPT Jan 2007
  4. Integrating UNC Shape Analysis into Slicer (UNC, Kitware)
  5. Correspondence of complex structures using (Curvature + Location) MDL (UNC)
  6. Qdec - a GUI front-end tool for GLM-based group analysis of Freesurfer-processed subject morphometry data (MGH): Freesurfer wiki page
  7. Adaptive, Particle-Based Sampling for Shapes and Complexes (Utah, UNC)
  8. Thickness Slicer3 Module (BWH, Isomics)
  9. Genus Zero Slicer3 Module (BWH, Isomics)
  10. Morphometry of Frontal circuitry in patients with schizophrenia with and without co-occurring substance use disorder (Dartmouth, Isomics)

fMRI Analysis

Functional Activation Analysis

Continued from 2006

  1. Neural Substrates of Working Memory in Schizophrenia: A Parametric 3-Back Study (Dartmouth, Harvard)
  2. Brain Activation during a Continuous Verbal Encoding and Recognition Task in Schizophrenia (Dartmouth, Harvard)
  3. Fronto-Temporal Connectivity in Schizophrenia during Semantic Memory (Dartmouth, Harvard)
  4. Imaging Phenotypes in Schizophrenics and Controls (UCI, Toronto)
  5. Attentional Circuits in Schizophrenia as revealed by fMRI and PET (UCI)
  6. Serotonergic / dopaminergic genes and processing of threatening stimuli in panic disorder: an imaging genetics study (Toronto)

Algorithm and Software Infrastructure

Continued from 2006

  1. fMRI Statistics Software Infrastructure (GE, Isomics, Kitware, MIT)
  2. Spatial Regularization for fMRI Detection (MIT, Harvard)
  3. Conformal Flattening for fMRI Visualization (Georgia Tech, Harvard)


NAMIC Software Process

Continued from 2006

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

Software Infrastructure

Continued from 2006

  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

Continued from 2006

  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