title: Atlas-based fiber bundle segmentation using principal diffusion directions and spherical harmonic coefficients.
abstract: OBJECTIVE
  To develop an automatic atlas-based method for segmentation of fiber bundles using High Angular Resolution Diffusion Imaging (HARDI) data.
  
  
  OBJECTIVE
  Quantitative evaluation of diffusion characteristics inside specific fiber bundles provides new insights into disease developments, evolutions, therapy effects, and surgical interventions.
  
  
  BACKGROUND
  Most of previous segmentation methods use similarity measures and strategies that do not lead to accurate segmentation results. They also suffer from subjectivity of initial seeds and regions of interest (ROI) defined by operator.
  
  
  METHODS
  We propose a novel method that uses Spherical Harmonic Coefficients (SHC) of HARDI diffusion signals to compute Orientation Distribution Function (ODF) and to extract Principal Diffusion Directions (PDDs). The proposed method selects most collinear PDD of neighbors of each voxel. Then, based on SHC and selected PDD, a similarity measure is proposed and used as a speed function in the level set framework that segments fiber bundles. To automate the process, an atlas-based method is used to select initial seeds for fiber bundles. To generate data for evaluation of the proposed method, an artificial pattern consisting of three crossing bundles intersected by a circular bundle is created. Also, two normal controls are imaged by two different HARDI protocols.
  
  
  RESULTS
  Segmentation results for different fiber bundles in simulated data and normal control data are presented. Influence of threshold selection on the proposed segmentation method is evaluated using Dice coefficient. Also, effect of increasing the number of gradient directions on accuracy of extracted PDDs is evaluated.
  
  
  CONCLUSIONS
  The proposed segmentation method has advantages over previous methods especially those that use similarity measures based on diffusion tensor imaging (DTI) data. These advantages are achieved by proper propagation of a hyper-surface in fiber crossing areas without making assumptions about diffusivity profile and selection of initial seeds or ROI.
authors.affiliation: Control and Intelligent Processing Center of Excellence, School of Electrical and Computer Engineering, University of Tehran, Tehran 14395-515, Iran. m.nazemzadeh@ece.ut.ac.ir
authors.forename: Mohammad-Reza
authors.initials: MR
authors.lastname: Nazem-Zadeh
authors.forename: Esmaeil
authors.initials: E
authors.lastname: Davoodi-Bojd
authors.forename: Hamid
authors.initials: H
authors.lastname: Soltanian-Zadeh
mesh_terms: D000465:Algorithms; D001921:Brain / Q000033:anatomy & histology*; D001931:Brain Mapping / Q000379:methods*; D038524:Diffusion Magnetic Resonance Imaging / Q000379:methods; D006801:Humans; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D008959:Models, Neurological; D009413:Nerve Fibers, Myelinated; D009434:Neural Pathways / Q000033:anatomy & histology*