View source for EM Segmentation For Orthopaedic Applications

'''Objective:'''

* To utilize the Slicer3 Expectation Maximization Algorithm for segmentation of the phalanx bones of the hand.

'''Progress:'''

* We have utilized the Slicer2.7 EM Segmentation Module for segmentation of the phalanx bones
*# Registration was performed outside of Slicer using ITK registration algorithms that are available in the IaFeMesh software. This includes Thin plate spline, B-Spline and rigid registration algorithms.
*# Probability map information was created from a single subject used as the atlas image and filtered using a Gaussian filter.
* Initial evaluation has been performed 
**Reliability assessed on fourteen specimens that also had the index finger segmented, and two specimens that had the index, middle, ring and little fingers manually segmented
**Validation assessed using the laser scanning of the index finger (proximal, middle, and distal) phalanx bones in five specimens
* Work is underway to develop a Slicer2.7 tutorial for this segmentation ([[Image:Draft_EM_Segment_Tutorial_9_12.pdf|Draft Copy]])

'''Results:'''

{| class="wikitable" border="1" cellpadding="2"
|+Relative Overlap with Manual Rater
|-
! Finger !! Phalanx Segment !! Average Relative Overlap
|-
! Index (14 subjects)
| Proximal || 0.87
|-
!
| Medial || 0.80
|-
!
| Distal || 0.70
|-
! Middle (2 subjects)
| Proximal || 0.79
|-
!
| Medial || 0.77
|-
!
| Distal || 0.71
|-
! Ring (2 subjects)
| Proximal || 0.76
|-
!
| Medial || 0.82
|-
!
| Distal || 0.80
|-
! Pinky (2 subjects)
| Proximal || 0.70
|-
!
| Medial || 0.73
|-
!
| Distal || 0.72
|}

* Example of Validation Results is shown below in the figures





'''To Do:'''
*Update the the tutorial to support the Slicer3 Workflow
**Tutorial will be developed by Austin Ramme - In progress
*Slicer3 Segmentation applied to the femur
**Using BRAINSFit for mapping of probability information to the subject images

'''Manuscript:'''
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.


'''Key Investigators:'''

* Iowa: Austin Ramme, Nicole Grosland, and Vincent Magnotta

'''Links:'''
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)]


'''Figures:'''

[[Image:EM-Segment-Phalanx.png|left|thumb|300px|Surface models from EM Segmentation generated via Slicer3]]

[[Image:EM-Segment-Proximal.png|left|thumb|450px|Results of the EM Segmentation for the Proximal Pahalanx]]

[[Image:EMSegment-Phalanx-DistanceMap.jpg|left|thumb|300px|Validation of EM Segmentation for the phalanx bones of the hand. Distance of automated segmentation versus physical laser surface scanning]]