CCB Biological Projects

Name Description Literature Details Data
Skull-stripping automatic removal of extra-cerebral tissue      
Global Segmentaiton Accurate and automated WM/GM/CSF Brain Segmentation      
http://www.loni.ucla.edu/twiki/pub/CCB/CcbBiologicalProjects/REX_BEMA.pdf
http://www.loni.ucla.edu/twiki/pub/CCB/CcbBiologicalProjects/Rottenberg_Seg_Comparison.pdf
http://www.loni.ucla.edu/twiki/pub/CCB/CcbBiologicalProjects/Shattuck01.pdf
http://www.pascal-network.org/Workshops/IOR04/Programme/
Online Lecture Notes on Digital Image Analysis and Understanding
Cortical Shape Representation Using Directed Graphs
Shape Modeling and Representation Primer
Wavelet-based Segmentation, Denoising and Registration
Fast Image Segmentaiton using Wavelets
http://cvs.sourceforge.net/viewcvs.py/eeg/mri_toolbox/segmentation/
Bayesian Complete and Automated Anatomical Segmentation of the Adult MOUSE Brain
A Unified Framework for Automated Spatial Registration and Volume Segmentation of the Brain (Mike Brady's Group)
Another Unified Framework for Automated Spatial Registration and Volume Segmentation of the Brain (PhD Thesis by YM Wang)

Bayesian Complete and Automated Anatomical Segmentation of the Adult HUMAN Brain

The most comlete tutorial on level-set-based tools for brain image progessing - a must-read for anyone using level-sets

The ultimage goal of the Global Segmentation is to accurately estimate the White Matter, Gray Matter and the Cerebro-Spinal Fluid in the entire brain. Sample data can be obtain from this CCB Download places: http://www.loni.ucla.edu/CCB/Resources/; http://www.loni.ucla.edu/CCB/Resources/CCB_SIG_SEG_TestData.zip and https://services.loni.ucla.edu/ida/login.jsp?search=true

Name Description Literature Details Data
Regional Segmentation Accurate and automated WM/GM/CSF subcortical Segmentation      
Microarray Analysis Develop new mathematical and statistical methods for microarray data analysis Math/Stat of Microarray Modeling Workshop at IMA    
Cortical modeling Cortical Surface Representation http://www.loni.ucla.edu/twiki/pub/CCB/CcbBiologicalProjects/Implicit_Parametric_Representation.pdf      
Topo-Surface Topologically correct surface representation of the cortex      
Cortical ribbon (inner & outer surface), thickness assessment      
Shape Representation parametric or implicit Mathematical Definition of Biological Shape, Form and Size    
Hippocampus Modeling      
Caudate Modeling      
Ventricles Ventricular surface modeling      
Feature Extraction Major sulcal curves http://www.loni.ucla.edu/ad/AD_protocol/sulcal.html    
Gyri Modeling Major Gyri      
Modeling single structures across species        
Auto Feature Extraction Unsupervised learning (and modeling) of distributions of feature morphologies (e.g., Bayesian adaptive probability priors on anatomical shapes) Lecture Notes and Code Samples    
Vasculature Automated vasculature segmentation and atlasing (MRA)      
Cytoarchitectonics Automatic cytoarchitectonic delineation      
Lesions WM: stroke, multiple sclerosis; GM: tumors, atrophy      
DTI Segmentation & denoising of DTI data      

Attachment sort Action Size Date Who Comment
REX_BEMA.pdf manage 721.7 K 05 Apr 2005 - 21:34 Main.ccb LONI BEMA Segmentation Comparison
Rottenberg_Seg_Comparison.pdf manage 457.5 K 05 Apr 2005 - 21:35 Main.ccb Rottenberg Segmentation Review
Shattuck01.pdf manage 1207.5 K 05 Apr 2005 - 21:36 Main.ccb Shattuck Brain Suite
Shape_Representation_3dm_10_reconstruction.pdf manage 2912.6 K 08 Jun 2005 - 20:36 Main.ccb Shape Modeling and Representation Primer
91-pdf.pdf manage 1185.6 K 10 Jun 2005 - 00:37 Main.ccb Wavelet-based Segmentation, Denoising and Registration
sdarticle.pdf manage 424.7 K 10 Jun 2005 - 00:47 Main.ccb Fast Image Segmentaiton using Wavelets
Implicit_Parametric_Representation.pdf manage 286.3 K 21 Jul 2005 - 19:04 Main.ccb Implicit and Parameteric Surfaces: Pros & Cons
Ali_MouseAutoSeg.pdf manage 1784.1 K 08 Aug 2005 - 19:06 Main.ccb A.Ali's Complete Automatic Mouse Brain Segmentation
Fischl_HumanAutoSeg.pdf manage 451.8 K 08 Aug 2005 - 19:07 Main.ccb Fischl's Complete Automated Human Brain Segmentation
Complete_LevelSet_SegmentationTutorial.pdf manage 699.4 K 10 Aug 2005 - 22:30 Main.ccb The Complete Level-Set Brain Image Processing Archive
Brady_Unified_Registr_Segment.pdf manage 202.7 K 26 Aug 2005 - 19:28 Main.ccb Unified Framework for Spatial Registration and Volume Segmentation
Thesis_YMWang.pdf manage 2735.4 K 19 Sep 2005 - 19:58 Main.ccb YM Wang's PhD Thesis on Unified Statistical Framework for Registration and Segmentation (2000)
01318723.pdf manage 1189.2 K 23 Nov 2005 - 00:51 Main.ccb  
Monteiro_ShapeFormSize_Paper.pdf manage 165.0 K 14 Jan 2006 - 01:18 Main.ccb Mathematical Definition of Biological Shape, Form and Size