The reconstruction of skeletal movement: the soft tissue artefact issue

In 3D human movement analysis performed using stereophotogrammetric systems and skin markers, bone pose can only be estimated in an indirect fashion. During a movement, soft tissue deformations make the markers move with respect to the underlying bone generating soft tissue artefact (STA). STA has devastating effects on bone pose estimation and its compensation remains an open question. The aim of this PhD thesis was to contribute to the solution of this crucial issue. Modelling STA using measurable trial-specific variables is a fundamental prerequisite for its removal from marker trajectories. Two STA model architectures are proposed. Initially, a thigh marker-level artefact model is presented. STA was modelled as a linear combination of joint angles involved in the movement. This model was calibrated using ex-vivo and in-vivo STA invasive measures. The considerable number of model parameters led to defining STA approximations. Three definitions were proposed to represent STA as a series of modes: individual marker displacements, marker-cluster geometrical transformations (MCGT), and skin envelope shape variations. Modes were selected using two criteria: one based on modal energy and another on the selection of modes chosen a priori. The MCGT allows to select either rigid or non-rigid STA components. It was also empirically demonstrated that only the rigid component affects joint kinematics, regardless of the non-rigid amplitude. Therefore, a model of thigh and shank STA rigid component at cluster-level was then defined. An acceptable trade-off between STA compensation effectiveness and number of parameters can be obtained, improving joint kinematics accuracy. The obtained results lead to two main potential applications: the proposed models can generate realistic STAs for simulation purposes to compare different skeletal kinematics estimators; and, more importantly, focusing only on the STA rigid component, the model attains a satisfactory STA reconstruction with less parameters, facilitating its incorporation in an pose estimator

La reconstruction du mouvement du squelette : l'enjeu de l'artefact des tissus mous

In 3D human movement analysis performed using stereophotogrammetry and skin markers, bone pose can be only indirectly estimated. During a task, soft tissue deformations make the markers move with respect to the underlying bone generating soft tissue artefacts (STA), causing devastating effects on pose estimation and its compensation remains an open issue. The thesis’ aim was to contribute to the solution of this crucial issue. Modelling STA using measurable trial-specific variables is a prerequisite for its removal from marker trajectories. Two STA model architectures are proposed. A thigh marker-level model is first presented. STA was modeled as a linear combination of joint angles involved in the task. The model was calibrated with direct STA measures. The considerable number of model parameters led to defining STA approximations. Three definitions were proposed to represent STA as series of modes : individual marker displacements, marker-cluster geometrical transformations (MCGT), and skin envelope shape variations. Modes were selected using two criteria : modal energy and selecting them a priori. The MCGT allows to select either rigid or non-rigid components. It was also demonstrated that only the rigid component affects joint kinematics. A model of thigh and shank rigid component at cluster-level was then defined. An acceptable trade-off between STA compensation and number of parameters was obtained. These results lead to two main potential applications : generate realistic STAs for simulationLors de l'analyse 3D du mouvement humain basée sur des marqueurs cutanés, la position des os ne peut être qu'indirectement estimée. Au cours d'une tâche, les déformations des tissus mous génèrent des déplacements des marqueurs par rapport à l'os : les artefacts de tissus mous (STA), entraînant des effets dévastateurs sur l'estimation de la position. La compensation des STA demeure une question ouverte. L'objectif de cette thèse est de contribuer à la solution de cette question cruciale. La modélisation des STA en utilisant des variables spécifiques mesurables est une condition préalable à son élimination. Un modèle corrigeant les trajectoires individuelles de marqueurs de la cuisse, calibré par des mesures directes des STA, est d'abord présenté. Les STA sont modélisés comme une combinaison linéaire des angles articulaires impliqués. Trois représentations des STA par une série de modes sont proposées : déplacements de marqueurs individuels, transformations géométriques de clusters de marqueurs (MCGT), et variations de forme de l'enveloppe de peau. Le MCGT permet de dissocier les composantes rigides et non rigides. Il a été démontré que seule la composante rigide affecte la cinématique articulaire. Un modèle de cette composante est alors défini pour les clusters cuisse et jambe. Un compromis acceptable entre la correction des STA et le nombre de paramètres a ainsi été obtenu. Les principales applications sont de générer une simulation réaliste des STA ; et surtout, en se concentrant sur la composante rigide, le modèle permet une reconstruction satisfaisante des STA avec moins de paramètres, ce qui facilite son incorporation dans un algorithme d'estimation de la position osseus

Improving the Accuracy of CT-derived Attenuation Correction in Respiratory-Gated PET/CT Imaging

The effect of respiratory motion on attenuation correction in Fludeoxyglucose (18F) positron emission tomography (FDG-PET) was investigated. Improvements to the accuracy of computed tomography (CT) derived attenuation correction were obtained through the alignment of the attenuation map to each emission image in a respiratory gated PET scan. Attenuation misalignment leads to artefacts in the reconstructed PET image and several methods were devised for evaluating the attenuation inaccuracies caused by this. These methods of evaluation were extended to finding the frame in the respiratory gated PET which best matched the CT. This frame was then used as a reference frame in mono-modality compensation for misalignment. Attenuation correction was found to affect the quantification of tumour volumes; thus a regional analysis was used to evaluate the impact of mismatch and the benefits of compensating for misalignment. Deformable image registration was used to compensate for misalignment, however, there were inaccuracies caused by the poor signal-to-noise ratio (SNR) in PET images. Two models were developed that were robust to a poor SNR allowing for the estimation of deformation from very noisy images. Firstly, a cross population model was developed by statistically analysing the respiratory motion in 10 4DCT scans. Secondly, a 1D model of respiration was developed based on the physiological function of respiration. The 1D approach correctly modelled the expansion and contraction of the lungs and the differences in the compressibility of lungs and surrounding tissues. Several additional models were considered but were ruled out based on their poor goodness of fit to 4DCT scans. Approaches to evaluating the developed models were also used to assist with optimising for the most accurate attenuation correction. It was found that the multimodality registration of the CT image to the PET image was the most accurate approach to compensating for attenuation correction mismatch. Mono-modality image registration was found to be the least accurate approach, however, incorporating a motion model improved the accuracy of image registration. The significance of these findings is twofold. Firstly, it was found that motion models are required to improve the accuracy in compensating for attenuation correction mismatch and secondly, a validation method was found for comparing approaches to compensating for attenuation mismatch

Improving the Accuracy of CT-derived Attenuation Correction in Respiratory-Gated PET/CT Imaging

The effect of respiratory motion on attenuation correction in Fludeoxyglucose (18F) positron emission tomography (FDG-PET) was investigated. Improvements to the accuracy of computed tomography (CT) derived attenuation correction were obtained through the alignment of the attenuation map to each emission image in a respiratory gated PET scan. Attenuation misalignment leads to artefacts in the reconstructed PET image and several methods were devised for evaluating the attenuation inaccuracies caused by this. These methods of evaluation were extended to finding the frame in the respiratory gated PET which best matched the CT. This frame was then used as a reference frame in mono-modality compensation for misalignment. Attenuation correction was found to affect the quantification of tumour volumes; thus a regional analysis was used to evaluate the impact of mismatch and the benefits of compensating for misalignment. Deformable image registration was used to compensate for misalignment, however, there were inaccuracies caused by the poor signal-to-noise ratio (SNR) in PET images. Two models were developed that were robust to a poor SNR allowing for the estimation of deformation from very noisy images. Firstly, a cross population model was developed by statistically analysing the respiratory motion in 10 4DCT scans. Secondly, a 1D model of respiration was developed based on the physiological function of respiration. The 1D approach correctly modelled the expansion and contraction of the lungs and the differences in the compressibility of lungs and surrounding tissues. Several additional models were considered but were ruled out based on their poor goodness of fit to 4DCT scans. Approaches to evaluating the developed models were also used to assist with optimising for the most accurate attenuation correction. It was found that the multimodality registration of the CT image to the PET image was the most accurate approach to compensating for attenuation correction mismatch. Mono-modality image registration was found to be the least accurate approach, however, incorporating a motion model improved the accuracy of image registration. The significance of these findings is twofold. Firstly, it was found that motion models are required to improve the accuracy in compensating for attenuation correction mismatch and secondly, a validation method was found for comparing approaches to compensating for attenuation mismatch

An Investigation of Methods to Attenuate Soft Tissue Artifact of the Thigh in High Knee Flexion

Soft tissue artifact during optical motion capture, or the movement of skin markers relative to bone, is widely accepted as a significant source of error in estimations of angles and moments. In some cases, the error associated with soft tissue movement exceeds that of the physiological motion of the joint, thereby calling into question the accuracy of the data obtained and casting doubt on the ability to determine mechanical demands of a given task. While previous studies have attempted to quantify soft tissue artifact, the variability in error with placement of skin markers (i.e. location specificity), the subject investigated (i.e. subject specificity), and the requirements of the task examined (i.e. task specificity), severely compromises the ability to develop methods which minimize and compensate for soft tissue artifact. Thus, the global objective of this thesis was to investigate soft tissue artifact of the thigh in high knee flexion movements and develop recommendations to standardize data collection and processing techniques. High knee flexion was examined because knee flexion beyond approximately 100° lacks investigation despite the unique deformation of soft tissue that occurs in this range (i.e. thigh-calf contact). Additionally, the repetitive adoption of high knee flexion is associated with knee joint injury and disease; thus, to more clearly elucidate mechanisms for these injuries and disease, improvements in the accuracy and reliability of collection and processing procedures is required. Fifty participants performed squatting and kneeling movements while motion of the pelvis and lower limb was recorded with optical motion capture and force data was synchronously recorded from four embedded force plates. Six identical rigid marker clusters were distributed on the distal and middle third of the thighs, and on the anterior, lateral, and anterolateral aspect of the thighs, while one marker cluster was adhered to the pelvis, shanks, and feet. Anthropometric measures were also taken for each subject including sex, height, mass, waist circumference, thigh length, thigh proximal, middle, and distal circumference, and thigh skinfold thickness. Data processing was divided into two studies. The first study developed a non-invasive method to estimate soft tissue artifact for each thigh marker cluster which consisted of measuring the mean of the peak difference in the hip joint center position when tracked with the pelvis cluster (i.e. the gold standard) versus each of the six thigh marker clusters. Bland-Altman methods were then utilized to compare agreement between the pelvis and thigh marker clusters for each task during maximal knee flexion. Across the tasks, the mean difference ranged from -4.93 to 0.03 cm while the lower and upper limits of agreement ranged from -11.86 to -3.27 cm and -0.87 to 5.33 cm, respectively. The mid-anterolateral cluster tended to be least susceptible to soft tissue artifact across the tasks and thus would be recommended, while the lateral clusters were most susceptible and should be avoided. Utilizing the anthropometric measures for each subject, regression models were also developed to determine the association between subject anthropometry and the mean difference in hip joint center position for each marker cluster. Ten of eighteen regression models significantly predicted soft tissue artifact with poor to moderate fit (R = 0.37 to 0.63) and explained between 14 and 40% of variation in the sample. These results suggest that while soft tissue artifact is somewhat associated with measures of anthropometry, marker placement should not be adjusted based on anthropometry alone. Additionally, negative unstandardized beta coefficients and partial correlations for thigh skinfold thickness and proximal thigh circumference revealed that adipose tissue may act to dampen artifact resulting from muscular contractions. The second study evaluated the difference in peak knee joint angles and moments between the thigh marker clusters and assessed the ability of global optimization, implemented in Visual3D utilizing IK constraints, to increase precision and reliability between marker clusters. Without global optimization, there were significant differences in estimated angles and moments between the marker clusters, wherein the mean difference was up to 8.9° and 0.6 %BW*H for flexion, 5.2° and 1.0 %BW*H for abduction, 4.9° and 0.7 %BW*H for adduction, 7.5° and 0.1 %BW*H external rotation, and 9.5° and 0.1 %BW*H for internal rotation. Global optimization was partially effective in compensating for differences between marker clusters in the sagittal plane (peak mean difference decreased 2.7° and 0.4 %BW*H) but less so in the frontal and transverse plane. Additionally, while global optimization decreased the partial eta squared (i.e. measure of effect of marker cluster location) for 12 of 30 outcome measures, intraclass correlation coefficients (i.e. measure of marker cluster reliability) only increased for 2 of 30 outcome measures. These findings highlight the importance of consistent marker placement for a given subject (i.e. between legs and laboratory sessions) and between subjects, as well as the need for researchers to report marker placement and all processing methods

Measuring skeletal kinematics with accelerometers on the skin surface

The most common motion analysis method uses cameras to track the position of markers on bodily surfaces over time. Although each species has a common skeletal frame to reference recorded motions, the soft tissue covering each is not rigid. Markers, therefore, experience motion relative to the bone and do not accurately portray underlying bone activity. This limits clinical use of motion studies and the understanding of joint motion. Use of MEMS accelerometers for removing soft tissue artifact, motion relative to the bone, from surface measurements and determining the position of the underlying bone was investigated. An animal limb was modeled experimentally as a double pendulum with soft tissue as sprung masses with motions perpendicular to the pendulums. Horizontal motion was cycled at the top joint with a 25 cm stroke. Position data obtained from the mass with a Codamotion™ system and integrated accelerometer data were combined in a Kalman filter to determine global position. Acceleration data in the sensor coordinate system determined tissue artifact and were compared to measurements using CODA markers on the mass and pendulum. Removing artifact from mass position estimated pendulum position over time. In determining mass position, integrated accelerometer data experienced drift, deviating from reasonable values and were determined impractical for Kalman filter input. This led to using only the CODA-determined position as the true position. Accelerometer artifacts resulted in mean differences with the CODA markers of less than 1 mm over 3 cm displacements excluding a mass with mechanical difficulties. The largest mean difference across four tests was 0.66 mm, which is 96.17 percent accurate. Mean differences between base positions collected from accelerometers and CODA markers were found for the global x and y directions. Maximum deviations were 1.64 mm and 4.45 mm, respectively, which are 99.56 and 99.63 percent accurate. Results show the effectiveness of this procedure in calculating the location of the bases of sprung masses in two dimensions. The basis of this research contributes to the determination of bone position over time that will increase the potential of understanding fundamental, rigid body and joint motions in a clinical setting using noninvasive methods

Improving Quantification in Lung PET/CT for the Evaluation of Disease Progression and Treatment Effectiveness

Positron Emission Tomography (PET) allows imaging of functional processes in vivo by measuring the distribution of an administered radiotracer. Whilst one of its main uses is directed towards lung cancer, there is an increased interest in diffuse lung diseases, for which the incidences rise every year, mainly due to environmental reasons and population ageing. However, PET acquisitions in the lung are particularly challenging due to several effects, including the inevitable cardiac and respiratory motion and the loss of spatial resolution due to low density, causing increased positron range. This thesis will focus on Idiopathic Pulmonary Fibrosis (IPF), a disease whose aetiology is poorly understood while patient survival is limited to a few years only. Contrary to lung tumours, this diffuse lung disease modifies the lung architecture more globally. The changes result in small structures with varying densities. Previous work has developed data analysis techniques addressing some of the challenges of imaging patients with IPF. However, robust reconstruction techniques are still necessary to obtain quantitative measures for such data, where it should be beneficial to exploit recent advances in PET scanner hardware such as Time of Flight (TOF) and respiratory motion monitoring. Firstly, positron range in the lung will be discussed, evaluating its effect in density-varying media, such as fibrotic lung. Secondly, the general effect of using incorrect attenuation data in lung PET reconstructions will be assessed. The study will compare TOF and non-TOF reconstructions and quantify the local and global artefacts created by data inconsistencies and respiratory motion. Then, motion compensation will be addressed by proposing a method which takes into account the changes of density and activity in the lungs during the respiration, via the estimation of the volume changes using the deformation fields. The method is evaluated on late time frame PET acquisitions using ¹⁸F-FDG where the radiotracer distribution has stabilised. It is then used as the basis for a method for motion compensation of the early time frames (starting with the administration of the radiotracer), leading to a technique that could be used for motion compensation of kinetic measures. Preliminary results are provided for kinetic parameters extracted from short dynamic data using ¹⁸F-FDG