Difference between revisions of "NA"

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== Description ==
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Core 1: Algorithms
  
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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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* Eric Grimson: [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=7015019&p_grant_num=5R01NS051826-02&p_query=&ticket=23536649&p_audit_session_id=114807056&p_keywords= 5R01NS051826-02 Computational Modeling of Anatomical Shape Distributions]
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* David Kennedy: [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=7056141&p_grant_num=5K12MH069281-03&p_query=&ticket=23536693&p_audit_session_id=114807056&p_keywords= 5K12MH069281-03 Neuroimaging Neuroinformatics Training Program], [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=6941591&p_grant_num=5R01NS034189-11&p_query=&ticket=23536693&p_audit_session_id=114807056&p_keywords= 5R01NS034189-11 Anatomic Morphologic Analysis of MR Brain Images]
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* Allen Tannenbaum:
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* Guido Gerig: [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=6690190&p_grant_num=1P50MH064065-01A19002&p_query=&ticket=25176558&p_audit_session_id=165467414&p_keywords= 1P50MH064065-01A19002 Core--Neuroimaging and morphology],
  
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This page outlines the steps we will take to code the Conformal Flattening mapping in ITK.
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[http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=6613380&p_grant_num=2P01CA047982-12A10005&p_query=(Neuroimaging)&ticket=25176624&p_audit_session_id=165467414&p_audit_score=32&p_audit_numfound=1&p_keywords=Neuroimaging 2P01CA047982-12A10005 Shape of Subcortical Brain Structures in Schizophrenia], [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=6988774&p_grant_num=1U54EB005149-010004&p_query=(Neuroimaging)&ticket=25176647&p_audit_session_id=165467414&p_audit_score=21&p_audit_numfound=1&p_keywords=Neuroimaging 1U54EB005149-010004 STRUCTURAL ANALYSIS OF ANATOMICAL SHAPES AND OF WHITE MATTER TRACTS], [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=6613382&p_grant_num=2P01CA047982-12A19003&p_query=(imaging)&ticket=25176711&p_audit_session_id=165467414&p_audit_score=7&p_audit_numfound=1&p_keywords=imaging 2P01CA047982-12A19003 Core--Validation Methodology]
  
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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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* Ross Whitaker:
  
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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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Core 3: DBP
  
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The process of the algorithm is brifly given below:
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* Martha Shenton: [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=7141113&p_grant_num=7K05MH070047-03&p_query=&ticket=23604627&p_audit_session_id=115583617&p_keywords= 7K05MH070047-03 Clinical Symptons & Brain Abnormalities in Schizophrenia], [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=7115712&p_grant_num=5R01MH050740-12&p_query=&ticket=23604627&p_audit_session_id=115583617&p_keywords= 5R01MH050740-12 Computerized Image Analyses of MR Scans in Schizophrenia]
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* Andy Saykin: [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=6934525&p_grant_num=5R01AG019771-05&p_query=&ticket=23604676&p_audit_session_id=115583617&p_keywords= 5R01AG019771-05 Memory Circuitry in MCI and Early Alzheimer's Disease], [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=7106608&p_grant_num=5R01CA101318-04&p_query=&ticket=23604676&p_audit_session_id=115583617&p_keywords= 5R01CA101318-04 Neural Mechanisms of Chemotherapy-Induced Cognitive Dis]
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* Steven Potkin: [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=7107205&p_grant_num=5P20RR020837-03&p_query=&ticket=23605260&p_audit_session_id=115583617&p_keywords= 5P20RR020837-03 Transdisciplinary Imaging Genetics Center (1 of 2)(RMI)], [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=7088050&p_grant_num=1U24RR021992-01A1&p_query=&ticket=23605260&p_audit_session_id=115583617&p_keywords= 1U24RR021992-01A1 Function BIRN]
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* Jim Kenndy: [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=7253142&p_grant_num=5P01MH056193-100001&p_query=&ticket=23605262&p_audit_session_id=115583617&p_keywords= 5P01MH056193-100001 Genetics of childhood onset depression: relation to psychophysiologic measures]
  
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# 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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=== Compiled for Mike Ackermann on 17:13, 13 September 2006 (EDT) ===
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# 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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# Having the mapping <span class="texhtml">''f''</span>, the original surface can be mapped to a plane.
 
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# Further, the plane can be mapped to a sphere by the stereographic projection.
 
  
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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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* NCBC NA-MIC
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* DBP Title: STRUCTURAL AND FUNCTIONAL CONNECTIVITY IN SCHIZOPHRENIA
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* PI: Martha Shenton
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* Grant #:5K05MH070047-04
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* HSA:
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* funding ends: 31-AUG-2009
  
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== Current Status ==
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----
  
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* We have written and tested the itkConformalFlatteningFilter
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* NCBC NA-MIC
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* Our paper on this was accepted for oral presentation at the 2006 MICCAI Open-source Workshop
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* DBP Title: STRUCTURAL AND FUNCTIONAL CONNECTIVITY IN SCHIZOPHRENIA
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* PI: Martha Shenton
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* Grant #:5R01MH050740-12
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* HSA*: Douglas Meinecke
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* funding ends: 30-JUN-2010
  
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== Next Steps ==
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----
  
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* We will help integrate this into the ITK CVS repository
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* NCBC NA-MIC
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* DBP Title: STRUCTURAL AND FUNCTIONAL CONNECTIVITY IN SCHIZOPHRENIA
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* PI: Andrew Saykin
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* Grant #:5R01AG019771-05
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* HSA*:
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* funding ends: 31-AUG-2007
  
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== Members ==
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----
  
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* Yi Gao (Gatech)
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* NCBC NA-MIC
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* John Melonakos (Gatech)
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* DBP Title: STRUCTURAL AND FUNCTIONAL CONNECTIVITY IN SCHIZOPHRENIA
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* Jim Miller (GE)
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* PI: Andrew Saykin
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* Luis Ibanez (Kitware)
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* Grant #:5R01CA101318-04
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* HSA*:
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* funding ends: 31-MAY-2008
  
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== Links ==
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----
  
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* [[NA-MIC/Projects/fMRI_Analysis/Conformal_Flattening_for_fMRI_Visualization|Conformal Flattening for fMRI Visualization]]
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* NCBC NA-MIC
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* DBP Title: TRANSDISCIPLINARY IMAGING GENETICS CENTER
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* PI: Steven Potkin
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* Grant #: 5P20RR020837-03
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* HSA*: Greg Farber
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* funding ends: 31-JUL-2007
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----
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* NCBC NA-MIC
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* DBP Title: FUNCTIONAL IMAGING BIOINFORMATICS RESEARCH NETWORK (FBIRN)
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* PI: Steven Potkin
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* Grant #: 1U24RR021992-01A1
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* HSA*: Greg Farber
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* funding ends: 30-NOV-2010
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----
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* NCBC NA-MIC
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* DBP Title: FUNCTIONAL IMAGING AND GENETICS IN SCHIZOPHRENIA:THE SEARCH FOR ENDOPHENOTYPES
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* PI: James Kennedy
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* Grant #: 5P01MH056193-100001
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* HSA*: Rajeev Chandok
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* funding ends:June 30, 2007.

Revision as of 13:28, 18 December 2006

Home < NA

Core 1: Algorithms

2P01CA047982-12A10005 Shape of Subcortical Brain Structures in Schizophrenia, 1U54EB005149-010004 STRUCTURAL ANALYSIS OF ANATOMICAL SHAPES AND OF WHITE MATTER TRACTS, 2P01CA047982-12A19003 Core--Validation Methodology

  • Ross Whitaker:

Core 3: DBP

Compiled for Mike Ackermann on 17:13, 13 September 2006 (EDT)

  • NCBC NA-MIC
  • DBP Title: STRUCTURAL AND FUNCTIONAL CONNECTIVITY IN SCHIZOPHRENIA
  • PI: Martha Shenton
  • Grant #:5K05MH070047-04
  • HSA:
  • funding ends: 31-AUG-2009
  • NCBC NA-MIC
  • DBP Title: STRUCTURAL AND FUNCTIONAL CONNECTIVITY IN SCHIZOPHRENIA
  • PI: Martha Shenton
  • Grant #:5R01MH050740-12
  • HSA*: Douglas Meinecke
  • funding ends: 30-JUN-2010
  • NCBC NA-MIC
  • DBP Title: STRUCTURAL AND FUNCTIONAL CONNECTIVITY IN SCHIZOPHRENIA
  • PI: Andrew Saykin
  • Grant #:5R01AG019771-05
  • HSA*:
  • funding ends: 31-AUG-2007
  • NCBC NA-MIC
  • DBP Title: STRUCTURAL AND FUNCTIONAL CONNECTIVITY IN SCHIZOPHRENIA
  • PI: Andrew Saykin
  • Grant #:5R01CA101318-04
  • HSA*:
  • funding ends: 31-MAY-2008
  • NCBC NA-MIC
  • DBP Title: TRANSDISCIPLINARY IMAGING GENETICS CENTER
  • PI: Steven Potkin
  • Grant #: 5P20RR020837-03
  • HSA*: Greg Farber
  • funding ends: 31-JUL-2007
  • NCBC NA-MIC
  • DBP Title: FUNCTIONAL IMAGING BIOINFORMATICS RESEARCH NETWORK (FBIRN)
  • PI: Steven Potkin
  • Grant #: 1U24RR021992-01A1
  • HSA*: Greg Farber
  • funding ends: 30-NOV-2010
  • NCBC NA-MIC
  • DBP Title: FUNCTIONAL IMAGING AND GENETICS IN SCHIZOPHRENIA:THE SEARCH FOR ENDOPHENOTYPES
  • PI: James Kennedy
  • Grant #: 5P01MH056193-100001
  • HSA*: Rajeev Chandok
  • funding ends:June 30, 2007.
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