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== Description ==
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= NA-MIC Internal Collaborations =
  
A general description of this project is given on page: [[NA-MIC/Projects/fMRI_Analysis/Conformal_Flattening_for_fMRI_Visualization|Conformal Flattening for fMRI Visualization]].
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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|cores]] of NA-MIC.
  
This page outlines the steps we will take to code the Conformal Flattening mapping in ITK.
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== Diffusion Image Analysis ==
  
For the detail of the algorithm please refer to the paper: S. Angenent, S. Haker, A. Tannenbaum, and R. Kikinis, “On the Laplace-Beltrami operator and brain surface flattening,” IEEE Trans. on Medical Imaging, Vol. 18, pp. 700-711, 1999.
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=== Fiber Tract Extraction and Analysis ===
  
An angle preserving flattening mapping is proposed in this paper. The explicit transform is obtained by solving a partial differential equation. Such transform will map the original surface to a plane(flattening) and then one can use classic stereographic transformation to map the plane to a sphere.
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# [[NA-MIC/Projects/Diffusion_Image_Analysis/Fiber_Tract_Statistics|Fiber Tract Statistics]] (Utah, UNC)
 +
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Diffusion_measures_alongs_fiber_tracts_of_the_cingulum_bundle|Diffusion measures alongs fiber tracts of the cingulum bundle]] (Harvard, MIT, UNC)
 +
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Clustering_of_anatomically_distinct_fiber_tracts|Clustering of anatomically distinct fiber tracts]] (Harvard, MIT)
 +
# [[Algorithm:GATech:Finsler_Active_Contour_DWI|Anisotropic Conformal Metrics for DTI Tractography]] (Georgia Tech, Harvard)
 +
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Corpus_Callosum_Fiber_Tractography_in_Schizophrenia|Corpus Callosum Fiber Tractography in Schizophrenia]] (Dartmouth, Harvard, MIT)
  
The process of the algorithm is brifly given below:
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=== Fractional Anisotropy Analysis ===
  
# The conformal mapping <span class="texhtml">''f''</span> is defined on the originla surface <span class="texhtml">Σ</span> as [[Image:89ff38a84b2fcde5fa7c5ea0f8c97a6b.png|\triangle f = (\frac{\partial}{\partial u} - i\frac{\partial}{\partial v})\delta_p]]. In that <span class="texhtml">''u''</span> and <span class="texhtml">''v''</span> are the conformal coordinates defined on the surface and the <span class="texhtml">δ<sub>''p''</sub></span> is a Dirac function whose value is non-zero only at point <span class="texhtml">''p''</span>. By solving this partial differential equation the mapping <span class="texhtml">''f''</span> can be obtained.
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# [[NA-MIC/Projects/Diffusion_Image_Analysis/Corpus_Callosum_Regional_FA_analysis_in_Schizophrenia|Corpus Callosum Regional FA analysis in Schizophrenia]] (Harvard, UNC, Dartmouth)
# To solve that equation on the discrete mesh representation of the surface, finite element method(FEM) is used. The problem is turned to solving a linear system <span class="texhtml">''D''''x'' = ''b''</span>. Since b is complex vector, the real and imaginary parts of the mapping <span class="texhtml">''f''</span> can be calculated separately by two linear system.
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# [[NA-MIC/Projects/Diffusion_Image_Analysis/Fractional_Anisotropy_of_the_Corpus_Callosum_and_Anterior_Commissure|Fractional Anisotropy of the Corpus Callosum and Anterior Commissure]] (Harvard, MIT, Dartmouth)
# Having the mapping <span class="texhtml">''f''</span>, the original surface can be mapped to a plane.
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# [[NA-MIC/Projects/Diffusion_Image_Analysis/Fractional_Anisotrophy_in_the_Uncinate_Fasciculus_in_Schizophrenia_and_Bipolar_I_Disorder--replication_and_extension_of_Kubicki_study|Fractional Anisotrophy in the Uncinate Fasciculus in Schizophrenia and Bipolar I Disorder--replication and extension of Kubicki study]] (Dartmouth, Harvard)
# Further, the plane can be mapped to a sphere by the stereographic projection.
 
  
The code for doing this is currently local codes, not having been embeded into ITK class hierarchy. This is what we are working on now.
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=== Path of Interest Analysis ===
  
== Current Status ==
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# [[NA-MIC/Projects/Diffusion_Image_Analysis/Integrity_of_Fronto-Temporal_Circuitry_in_Schizophrenia_using_Path_of_Interest_Analysis|Integrity of Fronto-Temporal Circuitry in Schizophrenia using Path of Interest Analysis]] (Dartmouth, MGH, Isomics, Harvard)
  
* We have written and tested the itkConformalFlatteningFilter
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=== Validation ===
* Our paper on this was accepted for oral presentation at the 2006 MICCAI Open-source Workshop
 
  
== Next Steps ==
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# [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Validation|DTI Validation]] (UCI, MGH, UNC, MIT)
  
* We will help integrate this into the ITK CVS repository
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=== Algorithm/Software Infrastructure ===
  
== Members ==
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# [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software/Algorithm Infrastructure]] (Utah, UNC)
 +
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Tensor_based_statistics|Tensor based statistics]] (Harvard, Utah)
 +
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Diffusion_tensor_image_filtering|Diffusion tensor image filtering]] (Utah, Harvard)
 +
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Non-rigid_EPI_Registration|Non-rigid EPI Registration]] (Harvard/MGH, Kitware, Dartmouth)
 +
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Fiber_Tools_Slicer_Integration|Fiber Tools Integration with Slicer 3]] (UNC, GE, Isomics)
  
* Yi Gao (Gatech)
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== Structural Image Analysis ==
* John Melonakos (Gatech)
 
* Jim Miller (GE)
 
* Luis Ibanez (Kitware)
 
  
== Links ==
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=== Image Segmentation ===
  
* [[NA-MIC/Projects/fMRI_Analysis/Conformal_Flattening_for_fMRI_Visualization|Conformal Flattening for fMRI Visualization]]
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# [[Algorithm:GATech:Knowledge_Based_Bayesian_Segmentation|Knowledge-Based Bayesian Classification and Segmentation]] (Georgia Tech, Kitware)
 +
# [[NA-MIC/Projects/Structural/Segmentation/Interleaved_Segmentation_and_Registration|Brain Tissue Classification and Subparcellation of Brain Structures]] (Harvard, MIT, Kitware)
 +
# [[Algorithm:GATech:Rule_Based_Segmentation|Rule based segmentation: Striatum]] (Georgia Tech, Harvard, Isomics, Kitware)
 +
# [[Algorithm:GATech:Rule_Based_Segmentation|Rule based segmentation: DLPFC]] (Georgia Tech, UCI, Isomics, Kitware)
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# [[Algorithm:GATech:Multiscale_Shape_Segmentation|Multiscale Shape Segmentation Techniques]] (Georgia Tech, Harvard)
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# [[NA-MIC/Projects/Structural/Segmentation/Stochastic_Methods_for_Segmentation|Stochastic Methods for Segmentation]] (Georgia Tech)
 +
# [[Algorithm:GATech:Statistical_Segmentation_Slicer_2|Statistical/PDE methods for Segmentation]] (Georgia Tech)
 +
 
 +
=== Image Registration ===
 +
 
 +
# [[Algorithm:GATech:Optimal_Mass_Transport_Registration|Optimal Mass Transport for Registration]] (Georgia Tech, Harvard)
 +
 
 +
=== Morphometric Measures and Shape Analysis ===
 +
 
 +
# [[NA-MIC/Projects/Structural/Shape_Analysis/Caudate_and_Corpus_Callosum|Shape Analysis for the caudate and corpus callosum data]] (Harvard, UNC, Georgia Tech, Dartmouth)
 +
# [[NA-MIC/Projects/Structural/Shape_Analysis/Hippocampus|Shape Analysis of the hippocampus]] (Dartmouth, UNC, Harvard)
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# [[Algorithm:GATech:Multiscale_Shape_Analysis|Multiscale Shape Analysis applied to Caudate and Hippocampus]] (Georgia Tech, Harvard, UNC)
 +
# [[NA-MIC/Projects/Structural/Shape_Analysis/Using_LONI_Pipeline|UNC Shape Analysis with LONI pipeline for clinical investigators]] (UNC, UCLA)
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# [[NA-MIC/Projects/Structural/Population_Studies|Population Studies]] (UNC, GE)
 +
# [[NA-MIC/Projects/Structural/Morphometric_Measures/Mild_Cognitive_Impairment|Multi-site morphometry in Mild Cognitive Impairment]] (UCI, mBIRN?)
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# [[NA-MIC/Projects/Structural/Morphometric_Measures/Schizophrenia/Muti-site_Morphometry|Multi-site morphometry in Schizophrenia]] (UCI, FBIRN)
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# [[NA-MIC/Projects/Structural/Shape_Analysis/Automated_shape_model_construction|Automated shape model construction]] (Utah, Harvard)
 +
# [[NA-MIC/Projects/Structural/Morphometric_Measures/Schizophrenia/Neural_Substrates_of_Apathy|Neural substrates of apathy in schizophrenia]] (Dartmouth, Isomics)
 +
 
 +
== fMRI Analysis ==
 +
 
 +
=== Functional Activation Analysis ===
 +
 
 +
# [[NA-MIC/Projects/fMRI_Analysis/Neural_Substrates_of_Working_Memory_in_Schizophrenia:_A_Parametric_3-Back_Study|Neural Substrates of Working Memory in Schizophrenia: A Parametric 3-Back Study]] (Dartmouth, Harvard)
 +
# [[NA-MIC/Projects/fMRI_Analysis/Brain_Activation_during_a_Continuous_Verbal_Encoding_and_Recognition_Task_in_Schizophrenia|Brain Activation during a Continuous Verbal Encoding and Recognition Task in Schizophrenia]] (Dartmouth, Harvard)
 +
# [[NA-MIC/Projects/fMRI_Analysis/Fronto-Temporal_Connectivity_in_Schizophrenia_during_Semantic_Memory|Fronto-Temporal Connectivity in Schizophrenia during Semantic Memory]] (Dartmouth, Harvard)
 +
# [[NA-MIC/Projects/fMRI_Analysis/Imaging_Phenotypes_in_Schizophrenics_and_Controls|Imaging Phenotypes in Schizophrenics and Controls]] (UCI, Toronto)
 +
# [[NA-MIC/Projects/fMRI_Analysis/Attentional_Circuits_in_Schizophrenia_as_revealed_by_fMRI_and_PET|Attentional Circuits in Schizophrenia as revealed by fMRI and PET]] (UCI)
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 +
=== Algorithm and Software Infrastructure ===
 +
 
 +
# [[NA-MIC/Projects/fMRI_Analysis/fMRI_Statistics_Software_Infrastructure|fMRI Statistics Software Infrastructure]] (GE, Isomics, Kitware, MIT)
 +
# [[NA-MIC/Projects/fMRI_Analysis/Spatial_Regularization_for_fMRI_Detection|Spatial Regularization for fMRI Detection]] (MIT, Harvard)
 +
# [[Algorithm:GATech:Conformal_Flattening_Registration|Conformal Flattening for fMRI Visualization]] (Georgia Tech, Harvard)
 +
 
 +
== NA-MIC Kit ==
 +
 
 +
=== NAMIC Software Process ===
 +
 
 +
# [[NA-MIC/Projects/NA-MIC_Kit/CMake_-_NAMIC_Kit_Building|CMake - NAMIC Kit Building]] (Kitware)
 +
# [[NA-MIC/Projects/NA-MIC_Kit/CPack_-_NAMIC_Kit_Distribution|CPack - NAMIC Kit Distribution]] (Kitware)
 +
# [[NA-MIC/Projects/NA-MIC_Kit/Dart_2_and_CTest_-_Software_Quality|Dart 2 and CTest - Software Quality]] (GE, Kitware)
 +
 
 +
=== Software Infrastructure ===
 +
 
 +
# [[NA-MIC/Projects/NA-MIC_Kit/Slicer3|Slicer 3]] (Isomics, GE, Kitware, UCSD, UCLA)
 +
# [[NA-MIC/Projects/NA-MIC_Kit/Coordinate_Systems|Coordinate Systems]] (GE, Isomics)
 +
# [[NA-MIC/Projects/NA-MIC_Kit/IO_Unification|IO Unification]] (GE, Isomics)
 +
# [[NA-MIC/Projects/NA-MIC_Kit/Licenses_Unification|Licenses Unification]] (Kitware, Isomics)
 +
# [[NA-MIC/Projects/NA-MIC_Kit/Grid_Computing|Grid Computing]] (UCSD, UCLA, GE, Kitware, Isomics)
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# [[NA-MIC/Projects/NA-MIC_Kit/KWWidgets|KWWidgets]] (Kitware)
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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/MRML|MRML]] (Isomics, Kitware, GE)
 +
# [[NA-MIC/Projects/NA-MIC_Kit/Teem|Teem]] (Harvard/BWH)
 +
 
 +
=== Training & Dissemination ===
 +
 
 +
# [[NA-MIC/Projects/NA-MIC_Kit/Training_Material_and_Workshops_for_NA-MIC_Kit|Training Material and Workshops for NA-MIC Kit]] (Harvard/MGH, Harvard/BWH)
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# [[NA-MIC/Projects/NA-MIC_Kit/Dissemination|Dissemination for NA-MIC]] (Isomics, Kitware, Harvard)
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 +
== Other Projects ==
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 +
# [[Non_Rigid_Registration|Non-Rigid Registration]]
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 +
= NA-MIC External Collaborations =
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 +
This section describes all external collaborations with NA-MIC. Details for the primary funding mechanism for collaborating with NCBCs are provided [[Collaborator:Resources|here]].
 +
 
 +
== PAR-05-063 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 [[NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development|here]], while the rest of this section contains links to the specific active projects in this collaboration.
 +
 
 +
=== Meshing Algorithms ===
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 +
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)
 +
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)
 +
 
 +
=== Automated Segmentation ===
 +
 
 +
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)
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 +
=== Image Registration ===
 +
 
 +
# [[Evaluation_of_Inter-Modality_Registration]] (Iowa/Isomics)
 +
 
 +
=== Validation ===
 +
 
 +
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning]] (Iowa)
 +
# [[FE_Mesh_Validation]] (Iowa)

Latest revision as of 14:04, 18 December 2006

Home < NA

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

  1. Fiber Tract Statistics (Utah, UNC)
  2. Diffusion measures alongs fiber tracts of the cingulum bundle (Harvard, MIT, UNC)
  3. Clustering of anatomically distinct fiber tracts (Harvard, MIT)
  4. Anisotropic Conformal Metrics for DTI Tractography (Georgia Tech, Harvard)
  5. Corpus Callosum Fiber Tractography in Schizophrenia (Dartmouth, Harvard, MIT)

Fractional Anisotropy Analysis

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

Path of Interest Analysis

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

Validation

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

Algorithm/Software Infrastructure

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

Structural Image Analysis

Image Segmentation

  1. Knowledge-Based Bayesian Classification and Segmentation (Georgia Tech, Kitware)
  2. Brain Tissue Classification and Subparcellation of Brain Structures (Harvard, MIT, Kitware)
  3. Rule based segmentation: Striatum (Georgia Tech, Harvard, Isomics, Kitware)
  4. Rule based segmentation: DLPFC (Georgia Tech, UCI, Isomics, Kitware)
  5. Multiscale Shape Segmentation Techniques (Georgia Tech, Harvard)
  6. Stochastic Methods for Segmentation (Georgia Tech)
  7. Statistical/PDE methods for Segmentation (Georgia Tech)

Image Registration

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

Morphometric Measures and Shape Analysis

  1. Shape Analysis for the caudate and corpus callosum data (Harvard, UNC, Georgia Tech, Dartmouth)
  2. Shape Analysis of the hippocampus (Dartmouth, UNC, Harvard)
  3. Multiscale Shape Analysis applied to Caudate and Hippocampus (Georgia Tech, Harvard, 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, Harvard)
  9. Neural substrates of apathy in schizophrenia (Dartmouth, Isomics)

fMRI Analysis

Functional Activation Analysis

  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)

Algorithm and Software Infrastructure

  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)

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

Training & Dissemination

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

Other Projects

  1. Non-Rigid Registration

NA-MIC External Collaborations

This section describes all external collaborations with NA-MIC. Details for the primary funding mechanism for collaborating with NCBCs are provided here.

PAR-05-063 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. Novel Hexahedral Meshing Algorithms (Iowa)
  2. 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)

Validation

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