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Core 1 & Core 3 Projects. Existing projects: Core 1 & 3. Harvard and University of North Carolina Shape analysis of caudate Automatic Segmentation of corpus callosum based on Diffusion Fiber Tracking Model ITK SNAP : Level set semiautomatic segmentation tool

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Existing projects core 1 3
Existing projects: Core 1 & 3

Harvard and University of North Carolina

Shapeanalysis of caudate

Automatic Segmentation of corpus callosum based on Diffusion Fiber Tracking Model

ITK SNAP: Level set semiautomatic segmentation tool

Statistical analysis of DTI measures along white matter fibers

[Participants: UNC: Isabelle Corouge, Martin Styner, Guido Gerig

PNL: Sylvain Bouix, Marek Kubicki, James Levitt,

Marc Niethammer, Martha Shenton]


Existing projects core 1 31
Existing projects: Core 1 & 3

Harvard and Massachusetts Institute of Technology

Diffusion measures along cingulum bundle fiber tracts

Clustering of specific fiber tracts based on location & regions they connect

Atlas of human brain white matter fiber bundles using automatic population based clustering

FA/Trace measures of corpus callosum and anterior commissure

[Participants: MIT: Lauren O’Donnell, CF Westin, Scott Hoge, Raul San Jose, Eric Grimson

PNL: Marc Niethammer, Sylvain Bouix, Marek Kubicki, Mark Dreusicke, Martha Shenton]

Brain tissue classification and subparcellation of brain structures

[Participants: MIT: Kilian Pohl, Sandy Wells, Eric Grimson

PNL: Sylvain Bouix, Motaki Nakamura, Min-Seong Koo, Martha Shenton]


Existing projects core 1 32
Existing projects: Core 1 & 3

Harvard and Georgia Tech

Semiautomatic segmentation and parcellation of basal ganglia

[Participants: GTech: Ramsey Al-Hakim,

Delphine Nain, Allen Tannenbaum

PNL: Sylvain Bouix, James Levitt, Marc Niethammer, Martha Shenton]


Existing projects core 1 33
Existing projects: Core 1 & 3

UCI and Georgia Tech

Semiautomatic segmentation and parcellation of cortical and subcortical areas

[Participants: GTech: Ramsey Al-Hakim, Delphine Nain, Allen Tannenbaum

UCI: Jim Fallon, Vid Petrovic, Martina Panzenboeck]


Existing projects core 1 34
Existing projects: Core 1 & 3

UCI and UNC

Automated DTI tractography and atlas development


Existing projects core 1 35
Existing projects: Core 1 & 3

Harvard and Utah

New anisotropic measures for white matter diffusion

[Participants: Utah: Tom Fletcher, Ross Whitaker

PNL: Sylvain Bouix, Marek Kubicki,

Martha Shenton]


Quantitative fiber tract analysis uci and unc
Quantitative Fiber Tract AnalysisUCI and UNC

  • For clinical studies

    • UNC: neonatal studies in autism, SZ

  • For neuroanatomy and connectivity exploration

  • NAMIC collaboration with UC Irvine (Jim Fallon)

  • NAMIC collaboration with Shenton/Marek

  • UNC: Krabbe’s disease

  • UNC: Neonatal & Autism Studies

  • UNC: Healthy Aging Study

[Fallon]


Rule based brain segmentation
Rule-Based Brain Segmentation

  • We are developing common tools needed for rule-based semi-automatic segmentation algorithms

  • 3 Prototype programs have been created to segment different brain structures based on neurological rules and minimal user input


Common tool thumb extraction uci and gatech
Common tool: “Thumb” Extraction: UCI and GaTech

  • Extraction of “thumbs” using an intensity-based energy minimized using Fast Marching methods

  • Applications to rule-based algorithms

  • Currently being ported from Matlab to VTK

“Thumb”

John Melonakos (GaTech), Jim Fallon (UCI)


Example: Segmentation of Putamen: UCI/Ga Tech

MRI image of striatum showing the putamen.

Gradient of the image showing edge information.

  • The user specifies several points on

    the border of the Putamen on each slice.

  • The algorithm finds the lowest cost

    outline of the structure based on edge

    information in the image.

  • A 3D model is created for analysis

Shawn Lankton (GaTech), Jim Fallon (UCI)


Example rule based segmentation of the striatum in slicer harvard gatech
Example: Rule Based Segmentation of the Striatum in Slicer: Harvard/GaTech

  • Begin with manually segmented label of total striatum

  • Manually input most superior/dorsal point on putamen and anterior commissure; striatum is delineated automatically based on rules of Dr. James Levitt.

Most superior/dorsal point on putamen

Anterior commissure

Ramsey Al-Hakim (GaTech), James Levitt (SPL)


Example path of interest analysis dartmouth mgh isomics
Example: Path-of-interest analysis (Dartmouth/MGH/Isomics) Harvard/GaTech

• Path-of-interest reconstruction

•Dartmouth DTI data

•Slicer visualization

http://www.na-mic.org/Wiki/index.php/Progress_Report:DTI_Path_of_interest_analysis

Saykin (Dartmouth), West (Dartmouth), Snyder (MGH), Tuch (MGH), Pieper (Isomics)


Example rule based segmentation of the striatum in slicer harvard gatech1

Pre Caudate Harvard/GaTech

Post Caudate

Post Putamen

Nucleus Accumbens

Pre Putamen

Example: Rule Based Segmentation of the Striatum in Slicer: Harvard/GaTech

Anterior/Superior View of Delineated Striatum

Automatically marked label (blue lines input by user to designate superior/dorsal point on putamen)

Ramsey Al-Hakim (GaTech), James Levitt (SPL)


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