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