3D reconstruction of the lower limb anatomical structures
ORASIS’09, Trégastel, 2009, June 11th
François Chung1, Jérôme Schmid2, Olivier Clatz1, Nadia Magnenat-Thalmann2, Hervé Delingette1
1 Asclepios Team, INRIA Sophia-Antipolis 2 MIRALab, Université de Genève
3D reconstruction of the lower limb anatomical structures 2
Main methods Volumic representation (a) Surfacic representation (b) Segments (c)
Bones a) Finite Element Method1
b) B-Splines2, meshes3
c) Stick-figure4
Muscles a) Finite Element Method5
b) B-Splines2, meshes3
c) Action lines6
[1] Majumder 2004, [2] Fernandez 2003, [3] Aubel 2002, [4] Kang 2003, [5] Hirota 2001, [6] Jensen 1975
Lower limb representations
3D reconstruction of the lower limb anatomical structures 3
Motivation and overview
Delineation
Mesh extraction
Smoothing
Attachments
Interpenetration removal
Tendons
3D reconstruction method Fast Accurate Subject specific
3D reconstruction of the lower limb anatomical structures 4
MRI acquisition
6 acquisitions Limited FOV Registration step
Specific protocol1
Slice thickness Hip and knee (2 mm) Long bones (10 mm) Foot (4 mm)
Subject Female (25 years old) Written consent Medical-ethical committee
[1] Gilles 2007
3D reconstruction of the lower limb anatomical structures 5
Overview
Delineation
Mesh extraction
Smoothing
Attachments
Interpenetration removal
Tendons
3D reconstruction of the lower limb anatomical structures 6
Manual MRI segmentation Bones Fat Muscles Tendons
Delineation using standard
radiologist books Gray’s Anatomy Netter’s Atlas of Human Body
Delineation: overview
Cortical
Spongious
3D reconstruction of the lower limb anatomical structures 7
Delineation: Gray vs Netter
3D reconstruction of the lower limb anatomical structures 8
Delineation: results
raw MRI semi-transparent labelling
labelling
Bones
Fat
3D reconstruction of the lower limb anatomical structures 9
Overview
Delineation
Mesh extraction
Smoothing
Attachments
Interpenetration removal
Tendons
3D reconstruction of the lower limb anatomical structures 10
Mesh extraction
labelling mesh
Marching Cubes1
[1] Lorensen 1987
3D reconstruction of the lower limb anatomical structures 11
Overview
Delineation
Mesh extraction
Smoothing
Attachments
Interpenetration removal
Tendons
3D reconstruction of the lower limb anatomical structures 12
Generated 3D models are not smooth Interslice distance (up to 10mm) Slight errors made during a manual segmentation
Manual delineation correction Very slow
Model correction Refine1
Internal constraints (C2)1 => Increase model rigidity
[1] Delingette 1999
Smoothing
3D reconstruction of the lower limb anatomical structures 13
Smoothing: results
Bumps
3D reconstruction of the lower limb anatomical structures 14
Overview
Delineation
Mesh extraction
Smoothing
Attachments
Interpenetration removal
Tendons
3D reconstruction of the lower limb anatomical structures 15
Tendons mainly attach muscles to bones Tissues from both structures are stuck together
Meshes modelling these structures should also be stuck together Not the case a priori (inaccuracy, smoothing, ...)
Splines to define attachment regions1 [1] Gilles 2006
Attachments
3D reconstruction of the lower limb anatomical structures 16
Overview
Delineation
Mesh extraction
Smoothing
Attachments
Interpenetration removal
Tendons
3D reconstruction of the lower limb anatomical structures 17
Models shape changed (smoothing+attachment) Models are likely to penetrate each other (muscles)
To solve this issue, pairwise procedure: Distance map is created for each model If vertices from another model inside, force applied
Models still smooth after the correction
Interpenetration removal
3D reconstruction of the lower limb anatomical structures 18
Interpenetration removal: results
before after
3D reconstruction of the lower limb anatomical structures 19
Overview
Delineation
Mesh extraction
Smoothing
Attachments
Interpenetration removal
Tendons
3D reconstruction of the lower limb anatomical structures 20
Quite easy to detect in the MRI Uniform appearance in the images Region growing based method is enough to segment
an important part of these structures Maximum intensity ridge tracing method1
(used for blood vessels segmentation)
In some regions, difficult to follow through slices Landmarks are placed manually and linked as tubular
structures that follow a centreline
[1] Aylward 2002
Tendons
3D reconstruction of the lower limb anatomical structures 21
Tendons: manual landmark placement
Extensor Hallucis Longus
Big toe
3D reconstruction of the lower limb anatomical structures 22
Results
An atlas composed of models is constructed from the manual segmentation of the entire lower limb Bones: 6 (thigh: 3 and leg: 3) Muscles: 34 (thigh: 21 and leg: 13) Tendons: a pair for each muscle (proximal-distal) Skin
A total of 109 models have been generated
3D reconstruction of the lower limb anatomical structures 23
Results: bones
3D reconstruction of the lower limb anatomical structures 24
Results: muscles
3D reconstruction of the lower limb anatomical structures 25
Results: tendons
3D reconstruction of the lower limb anatomical structures 26
Results: overview
3D reconstruction of the lower limb anatomical structures 27
Results: image rendering
3D reconstruction of the lower limb anatomical structures 28
Evaluation and validation by medical expert Proposed method does not guarantee absence of errors,
nor perfect segmentation Smoothing, interpenetration removal, … Intra and inter-expert variability
Corrections still possible Manual landmarks placement, image gradient Forces applied to the mesh
Trade-off between segmentation and reconstruction
Validation and discussion
3D reconstruction of the lower limb anatomical structures 29
Few data, few literature Global lower limb segmentation
Group of foot bones
Cartilage and ligaments
Models used as a) ground truth Manual vs auto seg. comparison
Models used for b) automatic segmentation methods Priors (PCA), model’s internal forces
Models used for c) subject-specific lower limb modelisation1
Motion capture / EMG / force plate [1] Schmid 2009
Conclusion and future work
Thank you for your attention
3D reconstruction of the lower limb anatomical structures