University of Western Australia
Patient-Specific Biomechanical Model as Whole-Body CT Image Registration ToolMao Lia, Karol Millera, b, Grand Roman Joldesa, Barry Doylec, d, Revanth Reddy Garlapatia, Ron Kikinise, f, g and Adam Witteka*aIntelligent Systems for Medicine Laboratory, School of Mechanical and Chemical Engineering,The University of Western Australia, Crawley, Perth, AustraliabInstitute of Mechanics and Advanced Materials, Cardiff School of Engineering, Cardiff University, Wales, UKcVascular Engineering, Intelligent Systems for Medicine Laboratory, School of Mechanical and Chemical Engineering, The University of Western Australia, Crawley, Perth, AustraliadCentre for Cardiovascular Science,The University of Edinburgh, Edinburgh, UKeSurgical Planning Laboratory,Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USAfFraunhofer MEVIS, Bremen, GermanygProfessor fu?r Medical Image Computing, MZH, University of Bremen, Bremen, Germany*Corresponding author: Intelligent Systems for Medicine Laboratory, School of Mechanical and Chemical Engineering, The University of Western Australia, Crawley, Perth WA 6009, Australia. Email: adam.wittek@uwa.edu.au Abstract Whole-body computed tomography (CT) image registration is important for cancer diagnosis, therapy planning and treatment. Such registration requires accounting for large differences between source and target images caused by deformations of soft organs/tissues and articulated motion of skeletal structures. The registration algorithms relying solely on image processing methods exhibit deficiencies in accounting for such deformations and motion. We propose to predict the deformations and movements of body organs/tissues and skeletal structures for whole-body CT image registration using patient-specific non-linear biomechanical modelling. Unlike the conventional biomechanical modelling, our approach for building the biomechanical models does not require time-consuming segmentation of CT scans to divide the whole body into non-overlapping constituents with different material properties. Instead, a Fuzzy C-Means (FCM) algorithm is used for tissue classification to assign the constitutive properties automatically at integration points of the computation grid. We use only very simple segmentation of the spine when determining vertebrae displacements to define loading for biomechanical models. We demonstrate the feasibility and accuracy of our approach on CT images of seven patients suffering from cancer and aortic disease. The results confirm that accurate whole-body CT image registration can be achieved using a patient-specific non-linear biomechanical model constructed without time-consuming segmentation of the whole-body images.Keywords: Whole-Body CT, Image Registration, Patient-Specific Biomechanical Model, Non-linear Finite Element Analysis, Fuzzy-C Means, Hausdorff Distance1 IntroductionReliable and accurate radiographic image registration that aligns the source and target images is critical for application of medical imaging in cancer diagnosis, therapy planning and treatment PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5EJmFwb3M7QW1pY288L0F1dGhvcj48WWVhcj4yMDAwPC9Z
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ADDIN EN.CITE.DATA (Black et al., 1997; D'Amico et al., 2000; Jenkinson and Smith, 2001; Spicer et al., 2004; Van Sint Jan et al., 2006; Warfield et al., 2005; Zaidi, 2007). A large number of medical image registration algorithms solely relying on image processing methods have been successfully developed over the years PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5DYW88L0F1dGhvcj48WWVhcj4yMDA3PC9ZZWFyPjxSZWNO
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ADDIN EN.CITE.DATA (Cao and Ruan, 2007; Jenkinson and Smith, 2001; Sotiras et al., 2013; Wells et al., 1996). Many of them have been demonstrated to be effective for selected organs, such as the brain, breast, prostate and lungs PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5NYXR0ZXM8L0F1dGhvcj48WWVhcj4yMDAzPC9ZZWFyPjxS
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ADDIN EN.CITE.DATA (Mahfouz et al., 2003; Stromqvist et al., 2009), the whole-body CT image registration still remains a largely unsolved problem PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5MaTwvQXV0aG9yPjxZZWFyPjIwMDg8L1llYXI+PFJlY051
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ADDIN EN.CITE PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5MaTwvQXV0aG9yPjxZZWFyPjIwMDg8L1llYXI+PFJlY051
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ADDIN EN.CITE.DATA (Li et al., 2008).Therefore, patient-specific biomechanical modelling methods that account for the mechanical behaviour of organs/tissues were recommended by many researchers for registration problems involving large differences (deformations) between the source and target images PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5BbC1NYXlhaDwvQXV0aG9yPjxZZWFyPjIwMTA8L1llYXI+
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ADDIN EN.CITE.DATA (Al-Mayah et al., 2010; Hopp et al., 2013; Warfield et al., 2002; Wittek et al., 2007). Unlike image-based matching, registration algorithms using biomechanical models do not require selection of specific type of source-to-target image transformation and optimisation of the transformation parameters to maximise a selected similarity measure between the transformed and target images. Instead, they rely on principles of mechanics to compute deformations that transform source image to target image. This ensures plausibility and robustness of the predicted deformations. In particular, patient-specific biomechanical modelling has been successfully used in numerous studies on computing the brain deformations for neuroimage registration PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5YdTwvQXV0aG9yPjxZZWFyPjIwMDE8L1llYXI+PFJlY051
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ADDIN EN.CITE.DATA (Garlapati et al., 2014; Hu et al., 2007; Ji et al., 2009; Mostayed et al., 2013; Wittek et al., 2010; Xu and Nowinski, 2001).Challenges to overcome when applying biomechanical modelling for medical image registration include quick and reliable generation of patient-specific computational models, automatic segmentation of radiographic images and efficient solution of the models PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5NaWxsZXI8L0F1dGhvcj48WWVhcj4yMDEwPC9ZZWFyPjxS
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ADDIN EN.CITE.DATA (Miller, 2011; Miller et al., 2010; Mostayed et al., 2013). To facilitate rapid generation of patient-specific biomechanical models for whole-body CT image registration, we abandon time-consuming image segmentation that divides the problem domain into non-overlapping constituents with different material properties. Instead, we apply tissue classification based on the Fuzzy C-Means (FCM) algorithm to assign the constitutive properties automatically at integration points of the computation grid PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5CZXpkZWs8L0F1dGhvcj48WWVhcj4xOTg0PC9ZZWFyPjxS
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ADDIN EN.CITE.DATA (Bezdek et al., 1984; Zhang et al., 2013). This, allows us to generate the patient-specific biomechanical model automatically and rapidly. In principle, any verified method of non-linear computational mechanics accounting for both geometric and material nonlinearity can be used to solve biomechanical models for computing soft organ/tissue deformations for image registration. Non-linear finite element analysis with either implicit PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5BbGxhcmQ8L0F1dGhvcj48WWVhcj4yMDA3PC9ZZWFyPjxS
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AG==
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ADDIN EN.CITE.DATA (Joldes et al., 2009b; Miller et al., 2007; Miller et al., 2011). In this study, we adapt and apply these algorithms in registration of whole-body CT images. To demonstrate feasibility and accuracy of whole-body CT image registration using the proposed non-linear biomechanical model, we analysed sets of whole-body/torso CT images of seven patients. Deformation within the patient’s body to align a source image to target image is predicted using a patient-specific model that relies on Total Lagrangian Explicit Dynamics TLED non-linear finite element algorithm PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5NaWxsZXI8L0F1dGhvcj48WWVhcj4yMDA3PC9ZZWFyPjxS
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ADDIN EN.CITE.DATA (Fedorov et al., 2008; Garlapati et al., 2013; Garlapati et al., 2014; Huttenlocher et al., 1993). This paper is organised as follows: the proposed patient-specific non-linear finite element model and the TLED algorithm are presented in Section 2; the computational results, including accuracy evaluation, are given in Section 3 which is followed by the discussion and conclusions in Section 4. 2 Methods2.1 CT Image Datasets Used in the StudyAs CT carries health hazard due to large radiation doses, there are very strict clinical guidelines limiting the number of situations where acquiring whole-body CT should be considered (Environmental Protection Authority, 2013; American College of Radiology, 2011a; American College of Radiology, 2011b). Therefore, we created a challenging test-bed for our registration method not through registration of a large number of image datasets, but by applying them to image datasets for different diseases/pathologies: cancer (Cases II-V in Fig. 1) and aortic diseases (Cases VI and VII in Fig. 1). Each of the analysed datasets consists of two sets of images of a given patient acquired at different times. We treated one of them as moving/source image and another as a target image (Fig. 1 shows sagittal sections for each dataset). Case I is from the publicly available Slicer Registration Library (Case #20: Intra-subject whole-body/torso PET-CT (). The Slicer Registration Library contains no information about a pathology type for Case I. The CT image datasets of cancer patients (Cases II, III, IV and V) were obtained the National Biomedical Image Archive () — freely available to browse, download and use for commercial, scientific and educational purpose under the Creative Commons Attribution 3.0 Unsupported Licence. Case VI is from the University Hospital Limerick, Ireland, and CT scan data was acquired for surgical planning and treatment of abdominal aortic aneurysm. Case VII was acquired at the Fremantle Hospital, Australia, with scans taken as part of type B aortic dissection diagnosis and treatment. Local ethics approval was obtained from both institutions. All imaging datasets were anonymous and not acquired specifically for this study. The CT datasets used in this study were acquired in different resolutions (Table 1). Before conducting the analysis, we resampled them to a common resolution of 1 mm x 1 mm x 2.5 mm. Resampling was conducted using linear interpolation — we applied the “Resample Scalar Volume” procedure in 3DSlicer open source software package for medical image computing PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5GZWRvcm92PC9BdXRob3I+PFllYXI+MjAxMjwvWWVhcj48
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ADDIN EN.CITE.DATA (Fedorov et al., 2012). Table 1 Resolution (in mm) of seven CT image datasets analysed in this studySource Image (mm)Target Image (mm)Case I0.98×0.98×5.00.98×0.98×5.0Case II1.00×1.00×5.01.00×1.00×5.0Case III0.84×0.84×2.50.80×0.80×2.5Case IV0.90×0.90×2.50.98×0.98×2.5Case V1.05×1.05×2.51.06×1.06×2.5Case VI1.00×1.00×2.51.00×1.00×2.5Case VII0.86×0.86×3.00.76×0.76×3.0SourceTargetSourceTargetCase ICase IICase IIICase IVCase VCase VICase VIIFig. 1 Sagittal sections of seven CT image datasets analysed in this study. For Case I, no information about the pathology type is available. Cases II-V are patients suffering from cancer. Cases VI and VII are patients suffering from aortic disease.2.2 Patient-Specific Non-Linear Biomechanical ModelBiomechanics-based medical image registration requires incorporation of patient-specific data in the biomechanical model. However, how to generate biomechanical model quickly and reliably remains unsolved ADDIN EN.CITE <EndNote><Cite><Author>Miller</Author><Year>2011</Year><RecNum>60</RecNum><DisplayText>(Miller et al., 2011)</DisplayText><record><rec-number>60</rec-number><foreign-keys><key app="EN" db-id="dtzde0ds95xwvqef9e7vaxx0vwzwr2a2wtsz">60</key></foreign-keys><ref-type name="Book Section">5</ref-type><contributors><authors><author>Miller, K.</author><author>Wittek, A.</author><author>Joldes, G.</author></authors><secondary-authors><author>Miller, Karol</author></secondary-authors></contributors><titles><title>Biomechanical Modeling of the Brain for Computer-Assisted Neurosurgery</title><secondary-title>Biomechanics of the Brain</secondary-title></titles><periodical><full-title>Biomechanics of the Brain</full-title><abbr-1>Biol Med Phys Biomed</abbr-1></periodical><pages>111-136</pages><dates><year>2011</year><pub-dates><date>2011/01/01</date></pub-dates></dates><pub-location>New York</pub-location><publisher>Springer</publisher><urls></urls><language>English</language></record></Cite></EndNote>(Miller et al., 2011). A set of methods employed in this study can be regarded as one possible solution to this problem. 2.2.1 Element Type, Geometry and Mesh Generation for Patient-Specific Biomechanical ModelElement Type Selection In practice, in computational biomechanics tetrahedral elements are often used for spatial discretisation of the problem domain due to availability of automatic mesh generators for complex geometries of the body organs PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5XaXR0ZWs8L0F1dGhvcj48WWVhcj4yMDA3PC9ZZWFyPjxS
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ADDIN EN.CITE.DATA (Irving et al., 2006; Wittek et al., 2007). However, a 4-noded tetrahedral element has an intrinsic drawback of volumetric locking for incompressible or nearly incompressible materials such as soft tissues ADDIN EN.CITE <EndNote><Cite><Author>Hughes</Author><Year>2000</Year><RecNum>1059</RecNum><DisplayText>(Hughes, 2000)</DisplayText><record><rec-number>1059</rec-number><foreign-keys><key app="EN" db-id="aevte9adcxzvp2edtdmp9axvspzfxs2devaw" timestamp="0">1059</key></foreign-keys><ref-type name="Book">6</ref-type><contributors><authors><author>Hughes, Th. J. R.</author></authors></contributors><titles><title>The Finite Element Method: Linear Static and Dynamic Finite Element Analysis</title></titles><pages>682</pages><dates><year>2000</year></dates><pub-location>Mineola</pub-location><publisher>Dover Publications</publisher><urls></urls></record></Cite></EndNote>(Hughes, 2000). Therefore, we used under-integrated (with one Gauss point) 8-noded hexahedral elements that do not exhibit locking PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5JcnZpbmc8L0F1dGhvcj48WWVhcj4yMDA2PC9ZZWFyPjxS
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ADDIN EN.CITE.DATA (Flanagan and Belytschko, 1981; Irving et al., 2006). Practical aspects of application of hexahedral elements in biomechanical models include preventing of instabilities due to zero energy (hourglass) modes and ensuring the element quality ADDIN EN.CITE <EndNote><Cite><Author>Yang</Author><Year>2011</Year><RecNum>46</RecNum><DisplayText>(Yang and King, 2011)</DisplayText><record><rec-number>46</rec-number><foreign-keys><key app="EN" db-id="t5092rx5pwp0aie5azfve5wcvx5z0v5a5avd">46</key></foreign-keys><ref-type name="Book Section">5</ref-type><contributors><authors><author>Yang, K. H.</author><author>King, A. I.</author></authors><secondary-authors><author>Miller, K.</author></secondary-authors></contributors><titles><title>Modeling of the Brain for Injury Simulation and Prevention</title><secondary-title>Biomechanics of the Brain</secondary-title></titles><periodical><full-title>Biomechanics of the Brain</full-title><abbr-1>Biol Med Phys Biomed</abbr-1></periodical><pages>91-110</pages><dates><year>2011</year></dates><pub-location>New York</pub-location><publisher>Springer</publisher><urls></urls><language>English</language></record></Cite></EndNote>(Yang and King, 2011). For hourglass control, we used the method proposed by PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5Kb2xkZXM8L0F1dGhvcj48WWVhcj4yMDA4PC9ZZWFyPjxS
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ADDIN EN.CITE.DATA (Joldes et al., 2009b; Wittek et al., 2010). Although no commonly accepted specific guidelines regarding the required quality of hexahedral meshes in biomechanics are available, several authors have formulated their experience-based recommendations PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5JdG88L0F1dGhvcj48WWVhcj4yMDA5PC9ZZWFyPjxSZWNO
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ADDIN EN.CITE.DATA Ito et al. (2009), Shepherd and Johnson (2009) and Yang and King (2011), we used element Jacobian and warpage to assess mesh quality. We regarded hexahedral elements with Jacobian below 0.2 as unacceptable poor quality and elements with Jacobian between 0.2 and 0.3 – as questionable quality. In all models used in this study, the element Jacobian was above 0.35 and maximum warpage was 25.Patient-Specific Geometry The 3D patient-specific torso geometry was created from the CTs using the 3D SLICER (), an open-source software for visualisation, registration, segmentation and quantification of medical data developed by Artificial Intelligence Laboratory of Massachusetts Institute of Technology and Surgical Planning Laboratory at Brigham and Women’s Hospital and Harvard Medical School. Geometry creation involved application of automated level tracing algorithm available in 3D SLICER to distinguish the patient’s body from the rest of the image and creation of the 3D discrete representation (surface model) of the patient’s body. Internal organs, muscles, fat and other tissues were not segmented. Patient-Specific Mesh Generation 3D surface model of the patient’s body was used as the boundary for volumetric discretisation (meshing) using hexahedral elements. Hexahedral mesh was created using IA-FEMesh (a freely available software toolkit for hexahedral mesh generation developed at the University of Iowa) PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5Hcm9zbGFuZDwvQXV0aG9yPjxZZWFyPjIwMDk8L1llYXI+
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ADDIN EN.CITE.DATA (Grosland et al., 2009) () and HyperMesh? (a high-performance commercial finite element mesh generator by Altair, Ltd. of Troy, MI, USA). The maximum element size was designated a value of 5 mm (the maximum voxel in the analysed CTs). However, due to differences in body dimension between the patients, the generated meshes appreciably vary in size (as measured by the number of nodes and elements) as indicated in Fig. 2 and Table 2.As we used Fuzzy C-Means (FCM) algorithm for tissue classification to assign the constitutive properties automatically at integration points, there was no need to distinguish internal organs when constructing the meshes (Fig. 2). Table 2 Numbers of hexahedral elements and nodes for seven analysed casesNumber of NodesNumber of ElementsCase I55,94451,479Case II88,26582,301 Case III54,19049,950Case IV137,344128,989Case V78,57372,897Case VI86,01692,625Case VII50,88949,478Case ICase IICase IIICase IVCase VCase VICase VIIFig. 2 Patient-specific hexahedral meshes built in this study. We used Fuzzy C-Means (FCM) algorithm for tissue classification to assign the constitutive properties automatically at integration points, there was no need to distinguish internal organs when constructing the meshes.2.2.2 Load and Boundary ConditionsAs suggested in our previous studies PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5NaWxsZXI8L0F1dGhvcj48WWVhcj4yMDEzPC9ZZWFyPjxS
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ADDIN EN.CITE.DATA (Miller and Lu, 2013; Miller et al., 2011; Miller et al., 2010), for problems where loading is prescribed as forced motion of boundaries, the unknown deformation field within the domain depends very weakly on the mechanical properties of the continuum. In studies involving application of biomechanical models in image registration, the displacements to define forced motion of the boundaries are typically determined by comparing position of corresponding points in the source and target images PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5XaXR0ZWs8L0F1dGhvcj48WWVhcj4yMDEwPC9ZZWFyPjxS
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ADDIN EN.CITE.DATA (Wittek et al., 2010). Body surface (skin) appears to be one possible source of information to determine such displacements. However, there are only very few features (landmarks) on the skin that can be reliably distinguished in CT images. Therefore, we used the spine (vertebrae) when determining the displacements (between the source and target images) to prescribe forced motion of the boundaries — in CT images vertebrae are easy to distinguish from the surrounding soft tissues and their shape does not change between the images. For a given vertebra, spatial distance between the source and target position was calculated using rigid registration (a built-in algorithm from 3D SLICER) PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5GZWRvcm92PC9BdXRob3I+PFllYXI+MjAxMjwvWWVhcj48
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ADDIN EN.CITE.DATA (Fedorov et al., 2012): (1)whereis the distance vector between two corresponding points in the source and target images: in the source (moving) image and in the target (fixed) image. is the rotation transformation, is the translation transformation and is a diagonal (identity) matrix. For the seven CT image sets analysed in this study, the magnitude of the distance vector between the vertebrae in source and target images ranged from 19 mm to 21 mm.When conducting the registration, the body surface (skin) was allowed to move freely without any contact conditions and constraints. Our method, however, allows for adding correspondence between easily distinguishable surface points as constraints if desirable.2.2.3 Material PropertiesAs stated in Section Load and Boundary Conditions, our previous studies ADDIN EN.CITE <EndNote><Cite><Author>Miller</Author><Year>2013</Year><RecNum>852</RecNum><DisplayText>(Miller and Lu, 2013; Miller et al., 2011)</DisplayText><record><rec-number>852</rec-number><foreign-keys><key app="EN" db-id="t5092rx5pwp0aie5azfve5wcvx5z0v5a5avd">852</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Miller, Karol</author><author>Lu, Jia</author></authors></contributors><titles><title>On the prospect of patient-specific biomechanics without patient-specific properties of tissues</title><secondary-title>J Mech Behav Biomed Mater</secondary-title></titles><periodical><full-title>J Mech Behav Biomed Mater</full-title><abbr-1>Journal of the mechanical behavior of biomedical materials</abbr-1></periodical><dates><year>2013</year></dates><isbn>1751-6161</isbn><urls></urls></record></Cite><Cite><Author>Miller</Author><Year>2011</Year><RecNum>60</RecNum><record><rec-number>60</rec-number><foreign-keys><key app="EN" db-id="dtzde0ds95xwvqef9e7vaxx0vwzwr2a2wtsz">60</key></foreign-keys><ref-type name="Book Section">5</ref-type><contributors><authors><author>Miller, K.</author><author>Wittek, A.</author><author>Joldes, G.</author></authors><secondary-authors><author>Miller, Karol</author></secondary-authors></contributors><titles><title>Biomechanical Modeling of the Brain for Computer-Assisted Neurosurgery</title><secondary-title>Biomechanics of the Brain</secondary-title></titles><periodical><full-title>Biomechanics of the Brain</full-title><abbr-1>Biol Med Phys Biomed</abbr-1></periodical><pages>111-136</pages><dates><year>2011</year><pub-dates><date>2011/01/01</date></pub-dates></dates><pub-location>New York</pub-location><publisher>Springer</publisher><urls></urls><language>English</language></record></Cite></EndNote>(Miller and Lu, 2013; Miller et al., 2011) suggest that for problems where loading is prescribed as forced motion of boundaries, results of computation of (unknown) deformation field within the domain depend very weakly on the mechanical properties of the continuum. However, given large tissue deformations between the source and target images and overwhelming experimental evidence that soft tissues behave like hyperelastic/hyperviscoelastic continua PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5Fc3RlczwvQXV0aG9yPjxZZWFyPjE5NzA8L1llYXI+PFJl
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ADDIN EN.CITE.DATA (Bilston et al., 2001; Estes and J.H., 1970; Farshad et al., 1999; Fung, 1993; Jin et al., 2013; Miller, 2000; Miller and Chinzei, 1997, 2002; Pamidi and Advani, 1978; Prange and Margulies, 2002; Snedeker et al., 2005; Snedeker, 2005), a constitutive model compatible with finite deformation solution procedures is needed. Therefore, following ADDIN EN.CITE <EndNote><Cite><Author>Miller</Author><Year>2011</Year><RecNum>60</RecNum><DisplayText>(Miller et al., 2011)</DisplayText><record><rec-number>60</rec-number><foreign-keys><key app="EN" db-id="dtzde0ds95xwvqef9e7vaxx0vwzwr2a2wtsz">60</key></foreign-keys><ref-type name="Book Section">5</ref-type><contributors><authors><author>Miller, K.</author><author>Wittek, A.</author><author>Joldes, G.</author></authors><secondary-authors><author>Miller, Karol</author></secondary-authors></contributors><titles><title>Biomechanical Modeling of the Brain for Computer-Assisted Neurosurgery</title><secondary-title>Biomechanics of the Brain</secondary-title></titles><periodical><full-title>Biomechanics of the Brain</full-title><abbr-1>Biol Med Phys Biomed</abbr-1></periodical><pages>111-136</pages><dates><year>2011</year><pub-dates><date>2011/01/01</date></pub-dates></dates><pub-location>New York</pub-location><publisher>Springer</publisher><urls></urls><language>English</language></record></Cite></EndNote>Miller et al. (2011) we used the Neo-Hookean hyperelastic model — the simplest constitutive model that satisfies this requirement. (2)where is the second Piola-Kirchhoff stress, is the shear modulus, is the bulk modulus, is the determinant of the deformation gradient, is the first invariant of the deviatoric Right Cauchy Green deformation tensor (the first strain invariant), andis the identity matrix.Despite recent progress in magnetic resonance (MR) and ultrasound elastography PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5Ld2FoPC9BdXRob3I+PFllYXI+MjAxMjwvWWVhcj48UmVj
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ADDIN EN.CITE.DATA (Kwah et al., 2012), there is no reliable non-invasive method to determine constitutive properties of human soft tissues in-vivo ADDIN EN.CITE <EndNote><Cite><Author>Miller</Author><Year>2013</Year><RecNum>852</RecNum><DisplayText>(Miller and Lu, 2013)</DisplayText><record><rec-number>852</rec-number><foreign-keys><key app="EN" db-id="t5092rx5pwp0aie5azfve5wcvx5z0v5a5avd">852</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Miller, Karol</author><author>Lu, Jia</author></authors></contributors><titles><title>On the prospect of patient-specific biomechanics without patient-specific properties of tissues</title><secondary-title>J Mech Behav Biomed Mater</secondary-title></titles><periodical><full-title>J Mech Behav Biomed Mater</full-title><abbr-1>Journal of the mechanical behavior of biomedical materials</abbr-1></periodical><dates><year>2013</year></dates><isbn>1751-6161</isbn><urls></urls></record></Cite></EndNote>(Miller and Lu, 2013). Therefore, we adapted a method for tissue classification and material properties assignment based on the Fuzzy C-Means (FCM) algorithm. This method has been successfully used in our previous study for computation of the brain deformations due to craniotomy-induced brain shift PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5aaGFuZzwvQXV0aG9yPjxZZWFyPjIwMTM8L1llYXI+PFJl
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ADDIN EN.CITE.DATA (Bezdek et al., 1984; Zhang et al., 2013). (3)whereis data samples (i.e. pixels in CT images), is the number of cluster centres (tissue types/classes), is the weighting factor referred to in the literature ADDIN EN.CITE <EndNote><Cite><Author>Balafar</Author><Year>2010</Year><RecNum>2911</RecNum><DisplayText>(Balafar et al., 2010)</DisplayText><record><rec-number>2911</rec-number><foreign-keys><key app="EN" db-id="aevte9adcxzvp2edtdmp9axvspzfxs2devaw" timestamp="1406607413">2911</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Balafar, M. A.</author><author>Ramli, A. R.</author><author>Saripan, M. I.</author><author>Mashohor, S.</author></authors></contributors><titles><title>Review of brain MRI image segmentation methods</title><secondary-title>Artificial Intelligence Review</secondary-title><alt-title>Artif Intell Rev</alt-title></titles><periodical><full-title>Artificial Intelligence Review</full-title><abbr-1>Artif Intell Rev</abbr-1></periodical><alt-periodical><full-title>Artificial Intelligence Review</full-title><abbr-1>Artif Intell Rev</abbr-1></alt-periodical><pages>261-274</pages><volume>33</volume><number>3</number><keywords><keyword>Brain</keyword><keyword>MRI</keyword><keyword>Segmentation</keyword></keywords><dates><year>2010</year><pub-dates><date>2010/03/01</date></pub-dates></dates><publisher>Springer Netherlands</publisher><isbn>0269-2821</isbn><urls><related-urls><url>;(Balafar et al., 2010) as the fuzziness degree of clustering, is the fuzzy membership function that expresses the probability of one data sample (pixel) belonging to a specified cluster centre (tissue class), and is the spatial distance between data sample and cluster centre. We used the fuzziness degree of clustering q of 2 which is a value commonly applied for soft tissue classification PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5IYWxsPC9BdXRob3I+PFllYXI+MTk5MjwvWWVhcj48UmVj
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ADDIN EN.CITE.DATA (Hall et al., 1992; Pham and Prince, 1999).Following ADDIN EN.CITE <EndNote><Cite><Author>Pohle</Author><Year>2001</Year><RecNum>2912</RecNum><DisplayText>(Pohle and Toennies, 2001)</DisplayText><record><rec-number>2912</rec-number><foreign-keys><key app="EN" db-id="aevte9adcxzvp2edtdmp9axvspzfxs2devaw" timestamp="1406607757">2912</key></foreign-keys><ref-type name="Conference Proceedings">10</ref-type><contributors><authors><author>Pohle, Regina</author><author>Toennies, Klaus D.</author></authors></contributors><titles><title>Segmentation of medical images using adaptive region growing</title></titles><pages>1337-1346</pages><volume>4322</volume><dates><year>2001</year></dates><work-type>doi: 10.1117/12.431013</work-type><urls><related-urls><url> and Toennies (2001) and ADDIN EN.CITE <EndNote><Cite><Author>Balafar</Author><Year>2010</Year><RecNum>2911</RecNum><DisplayText>(Balafar et al., 2010)</DisplayText><record><rec-number>2911</rec-number><foreign-keys><key app="EN" db-id="aevte9adcxzvp2edtdmp9axvspzfxs2devaw" timestamp="1406607413">2911</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Balafar, M. A.</author><author>Ramli, A. R.</author><author>Saripan, M. I.</author><author>Mashohor, S.</author></authors></contributors><titles><title>Review of brain MRI image segmentation methods</title><secondary-title>Artificial Intelligence Review</secondary-title><alt-title>Artif Intell Rev</alt-title></titles><periodical><full-title>Artificial Intelligence Review</full-title><abbr-1>Artif Intell Rev</abbr-1></periodical><alt-periodical><full-title>Artificial Intelligence Review</full-title><abbr-1>Artif Intell Rev</abbr-1></alt-periodical><pages>261-274</pages><volume>33</volume><number>3</number><keywords><keyword>Brain</keyword><keyword>MRI</keyword><keyword>Segmentation</keyword></keywords><dates><year>2010</year><pub-dates><date>2010/03/01</date></pub-dates></dates><publisher>Springer Netherlands</publisher><isbn>0269-2821</isbn><urls><related-urls><url> et al. (2010), we calculated the membership functions at each cluster centre using the following formula (4)where (5)and is the Euclidean distance between the data point and cluster centre. For the image datasets analysed in this study, the minimum was achieved within 100 iterations.FCM algorithm minimises the objective function JFCM (see Eq. 3) by updating of the membership function and centres of clusters . For the image datasets analysed in this study, the minimum was achieved within 100 iterations.The only parameter that has to be selected by the analyst in Equations (3)-(5) is the number of cluster centres. Detailed explanation of how this parameter was selected for the image datasets analysed in this study is given in Section 3.1.2.3 Numerical SolutionWe used Total Lagrangian Explicit Dynamics (TLED) algorithm proposed by PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5NaWxsZXI8L0F1dGhvcj48WWVhcj4yMDA3PC9ZZWFyPjxS
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ADDIN EN.CITE.DATA Miller et al. (2007) with dynamic relaxation to improve rate of convergence to the steady state solution ADDIN EN.CITE <EndNote><Cite><Author>Joldes</Author><Year>2009</Year><RecNum>32</RecNum><DisplayText>(Joldes et al., 2009a)</DisplayText><record><rec-number>32</rec-number><foreign-keys><key app="EN" db-id="dtzde0ds95xwvqef9e7vaxx0vwzwr2a2wtsz">32</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Joldes, G. R.</author><author>Wittek, A.</author><author>Miller, K.</author></authors></contributors><auth-address>Joldes, GR
Univ Western Australia, Sch Mech Engn, Intelligent Syst Med Lab, Perth, WA 6009, Australia
Univ Western Australia, Sch Mech Engn, Intelligent Syst Med Lab, Perth, WA 6009, Australia
Univ Western Australia, Sch Mech Engn, Intelligent Syst Med Lab, Perth, WA 6009, Australia</auth-address><titles><title>Computation of intra-operative brain shift using dynamic relaxation</title><secondary-title>Computer Methods in Applied Mechanics and Engineering</secondary-title><alt-title>Comput Method Appl M</alt-title></titles><periodical><full-title>Computer Methods in Applied Mechanics and Engineering</full-title><abbr-1>Comput Method Appl M</abbr-1></periodical><alt-periodical><full-title>Computer Methods in Applied Mechanics and Engineering</full-title><abbr-1>Comput Method Appl M</abbr-1></alt-periodical><pages>3313-3320</pages><volume>198</volume><number>41-44</number><keywords><keyword>non-rigid image registration</keyword><keyword>biomechanical models</keyword><keyword>dynamic relaxation</keyword><keyword>eigenvalue estimation</keyword><keyword>image registration</keyword><keyword>mechanical-properties</keyword><keyword>tissue</keyword><keyword>deformation</keyword><keyword>models</keyword></keywords><dates><year>2009</year></dates><isbn>0045-7825</isbn><accession-num>ISI:000270702300010</accession-num><urls><related-urls><url><Go to ISI>://000270702300010</url></related-urls></urls><electronic-resource-num>DOI 10.1016/j.cma.2009.06.012</electronic-resource-num><language>English</language></record></Cite></EndNote>(Joldes et al., 2009a). This algorithm refers all variables to the original configuration, i.e. the second Piola-Kirchoff stress and Green-Lagrange strain are used. The advantage is that all the derivatives with respect to spatial coordinates can be pre-computed. Another important feature of the TLED algorithm is that it utilises central difference method to discretise the temporal derivatives so that the discretised equations are integrated in stepping forward manner without any iteration. Detailed description of the TLED-based suite of finite element procedures used in this study is given in PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5Kb2xkZXM8L0F1dGhvcj48WWVhcj4yMDA5PC9ZZWFyPjxS
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ADDIN EN.CITE.DATA Joldes et al. (2009a, b) and Miller et al. (2007). These procedures rely on explicit integration in time domain and can be easily parallelised to harness computational power of Graphics Processing Units (GPUs) as shown in ADDIN EN.CITE <EndNote><Cite><Author>Joldes</Author><Year>2010</Year><RecNum>112</RecNum><DisplayText>(Joldes et al., 2010)</DisplayText><record><rec-number>112</rec-number><foreign-keys><key app="EN" db-id="dtzde0ds95xwvqef9e7vaxx0vwzwr2a2wtsz">112</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Joldes, G. R.</author><author>Wittek, A.</author><author>Miller, K.</author></authors></contributors><auth-address>Intelligent Systems for Medicine Laboratory, School of Mechanical Engineering, The University of Western Australia, Perth, AUSTRALIA.</auth-address><titles><title>Real-Time Nonlinear Finite Element Computations on GPU - Application to Neurosurgical Simulation</title><secondary-title>Comput Methods Appl Mech Eng</secondary-title><alt-title>Computer methods in applied mechanics and engineering</alt-title></titles><alt-periodical><full-title>Computer Methods in Applied Mechanics and Engineering</full-title><abbr-1>Comput Method Appl M</abbr-1></alt-periodical><pages>3305-3314</pages><volume>199</volume><number>49-52</number><edition>2010/12/24</edition><dates><year>2010</year><pub-dates><date>Dec 15</date></pub-dates></dates><isbn>0045-7825 (Print)
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ADDIN EN.CITE.DATA (Canny, 1986; Li et al., 2013; Mostayed et al., 2013) filter in the registered (i.e. source image warped using the deformations predicted by means of a biomechanical model) and target images.2.4.2 Quantitative EvaluationFollowing our previous studies, edge-based Hausdorff distance (HD) metric (on consistent edges detected using Canny filter) is used here to objectively measure the spatial misalignment between the registered (warped using the deformations predicted by means of a biomechanical model) and target images PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5DYW5ueTwvQXV0aG9yPjxZZWFyPjE5ODY8L1llYXI+PFJl
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ADDIN EN.CITE.DATA (Canny, 1986; Garlapati et al., 2013; Garlapati et al., 2014; Mostayed et al., 2013): (6)and (7)where and are the consistent (i.e. depicting the same anatomical features) Canny edges in the deformed (registered) and target image respectively. and are the point sets that contain the consistent points from two consistent edges. Operator represents the calculation of direct distance between two points as used in the point-based HD metric ADDIN EN.CITE <EndNote><Cite><Author>Huttenlocher</Author><Year>1993</Year><RecNum>26</RecNum><DisplayText>(Huttenlocher et al., 1993)</DisplayText><record><rec-number>26</rec-number><foreign-keys><key app="EN" db-id="dtzde0ds95xwvqef9e7vaxx0vwzwr2a2wtsz">26</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Huttenlocher, D. P.</author><author>Klanderman, G. A.</author><author>Rucklidge, W. J.</author></authors></contributors><auth-address>Huttenlocher, Dp
Cornell Univ,Dept Comp Sci,Ithaca,Ny 14853, USA
Cornell Univ,Dept Comp Sci,Ithaca,Ny 14853, USA
Xerox Corp,Palo Alto Res Ctr,Syst & Practices Lab,Palo Alto,Ca 94304</auth-address><titles><title>Comparing Images Using the Hausdorff Distance</title><secondary-title>IEEE Transactions on Pattern Analysis and Machine Intelligence</secondary-title><alt-title>IEEE T Pattern Anal</alt-title></titles><periodical><full-title>Ieee Transactions on Pattern Analysis and Machine Intelligence</full-title><abbr-1>Ieee T Pattern Anal</abbr-1></periodical><alt-periodical><full-title>Ieee Transactions on Pattern Analysis and Machine Intelligence</full-title><abbr-1>Ieee T Pattern Anal</abbr-1></alt-periodical><pages>850-863</pages><volume>15</volume><number>9</number><keywords><keyword>distance transforms</keyword><keyword>model-based recognition</keyword><keyword>voronoi surface</keyword><keyword>recognition</keyword><keyword>vision</keyword></keywords><dates><year>1993</year><pub-dates><date>Sep</date></pub-dates></dates><isbn>0162-8828</isbn><accession-num>ISI:A1993LW67600001</accession-num><urls><related-urls><url><Go to ISI>://A1993LW67600001</url></related-urls></urls><electronic-resource-num>Doi 10.1109/34.232073</electronic-resource-num><language>English</language></record></Cite></EndNote>(Huttenlocher et al., 1993).From Equation (7) we construct percentile edge-based Hausdorff distance PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5Nb3N0YXllZDwvQXV0aG9yPjxZZWFyPjIwMTM8L1llYXI+
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AG==
ADDIN EN.CITE.DATA (Garlapati et al., 2013; Mostayed et al., 2013): (8)Following PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5Nb3N0YXllZDwvQXV0aG9yPjxZZWFyPjIwMTM8L1llYXI+
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ADDIN EN.CITE.DATA Garlapati et al. (2014) and Mostayed et al. (2013), we do not report here a single Hausdorff distance value, (Equation 6), but use Equation (8) to report Hausdorff distance values for different percentiles. A plot of the Hausdorff distance values for different percentiles (see Section 3.2.1) immediately reveals the percentage of edges that have acceptable misalignment errors. Following PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5Nb3N0YXllZDwvQXV0aG9yPjxZZWFyPjIwMTM8L1llYXI+
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ADDIN EN.CITE.DATA Mostayed et al. (2013), two-times the voxel size of the original CT image was regarded here as an acceptable error. 3 Results3.1 Selection of Cluster Centres for Tissue ClassificationWith exception of our preliminary analysis of a single CT scan set ADDIN EN.CITE <EndNote><Cite><Author>Li</Author><Year>2013</Year><RecNum>91</RecNum><DisplayText>(Li et al., 2013)</DisplayText><record><rec-number>91</rec-number><foreign-keys><key app="EN" db-id="dtzde0ds95xwvqef9e7vaxx0vwzwr2a2wtsz">91</key></foreign-keys><ref-type name="Book Section">5</ref-type><contributors><authors><author>Li, M.,</author><author>Wittek, A.,</author><author>Joldes, G., </author><author>Zhang, G., </author><author>Dong, F., </author><author>Kikinis, R., </author><author>Miller, K.</author></authors><secondary-authors><author>Doyle, B. J., Miller, K., Wittek, A., Nielsen, P. M. F.</author></secondary-authors></contributors><titles><title>Whole-Body Image Registration Using Patient-Specific Non-Linear Finite Element Model</title><secondary-title>Computational Biomechanics for Medicine: Fundamental Science and Patient-Specific Application</secondary-title></titles><pages>21-30</pages><dates><year>2013</year></dates><pub-location>New York</pub-location><publisher>Springer</publisher><urls></urls></record></Cite></EndNote>(Li et al., 2014), there have been no attempts to apply FCM tissue classification for biomechanical models for whole-body CT registration. Therefore, there are no guidelines regarding the number of tissue types (intensity cluster centres) (Fig. 3) that need to be distinguished to achieve desired registration accuracy. Below, we explain, how we determined the number of tissue types (cluster centres) for the Fuzzy C-Means FCM algorithm for seven CT datasets used in this study. One may expect that bones, muscles, fat, lungs, kidneys, heart, blood vessels and other abdominal organs (including liver, stomach/intestines) need to be distinguished in biomechanical models for computing the deformation for whole body CT registration. Bones and fat can be easily identified as they have distinctive image intensity (Fig. 3). On the other hand, the intensity of muscles, liver and kidneys is similar. Consequently, the FCM algorithm (solely based on image intensity) would classify them as belonging to the same tissue category. There is, however, no drawback as our previous studies on neuroimage registration PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5NaWxsZXI8L0F1dGhvcj48WWVhcj4yMDEzPC9ZZWFyPjxS
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ADDIN EN.CITE.DATA (Miller and Lu, 2013; Miller et al., 2011; Wittek et al., 2009) suggest that if the loading is prescribed via forced motion of the boundary, the results of computation of deformation field within the domain depend very weakly on the mechanical properties of the analysed continuum. In the CT scans we analysed in this study, the intensity range for lungs and bones was large, from -1100 to -200 and from 250 to 1100 respectively. Thus, we defined three intensity cluster centres for lungs and two intensity cluster centres for bones. Therefore, when assigning the material properties at the integration point using the FCM algorithm, we distinguished eight tissue classes: 1) Class 1, 2 and 3 for lungs and other gas-filled spaces (such as abdominal cavity); 2) Class 4 for fat; 3) Class 5 for muscles, liver and kidneys; 4) Class 6 for stomach and intestines; and 5) Class 7 and 8 for bones. This resulted in the FCM algorithm with eight intensity cluster centres as indicated in Table 3. The number of tissue classes was kept constant in this study, but the cluster centres have different values for different cases, i.e. the same number of intensity clusters and the different position of the cluster centres were used for all CTs in this study. Table 3 shows the position of cluster centres calculated using FCM algorithm for seven analysed cases.Table 4 shows the material property (shear modulus) calculated PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5BbGNhcmF6PC9BdXRob3I+PFllYXI+MjAwMzwvWWVhcj48
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ADDIN EN.CITE.DATA (Alcaraz et al., 2003; Bensamoun et al., 2011; Collinsworth et al., 2002; Gennisson et al., 2010; Samani et al., 2007; Watters et al., 1985) at class centres defined in Table 3 for all seven analysed cases, and an example of applying the FCM algorithm to assign the material properties (shear modulus) at the integration points of the biomechanical model is shown in Fig. 4a. Comparison of this figure with the corresponding CT slice (Fig. 4b) indicates that, with exception of very few outliers, the shear modulus assigned by the FCM algorithm is consistent with a tissue type depicted in the image at location of the integration points Fig. 3 Tissue classification for a torso CT transverse section. A certain number of organs/tissues (i.e. bones and fat) can be recognised by distinctive image intensity. Some organs/tissues have similar image intensity (i.e. kidneys, liver, small/large intestines and muscles).Table 3 Cluster centres obtained using the FCM algorithm for seven analysed CT image datasets (8 Classes)Class 1Class 2Class 3Class 4Class 5Class 6Class 7Class 8Case I-842-715-215-98-3129240641Case II-779-522-323-97-2928245590Case III-826-537-326-90-3243274661Case IV-711-519-303-104-4557253665Case V-650-481-247-89-3816238527Case VI-825-656-388-103-2052219453Case VII-704-530-319-95-1561231446Table 4 Shear modulus (×103Pa) at cluster centres for seven analysed CT image datasetsClass 1Class 2Class 3Class 4Class 5Class 6Class 7Class 8Shear modulus (kPa)0.530.530.531.073.574.02rigidrigid ADDIN EN.CITE <EndNote><Cite><Author>Alcaraz</Author><Year>2003</Year><RecNum>110</RecNum><DisplayText>(Alcaraz et al., 2003)</DisplayText><record><rec-number>110</rec-number><foreign-keys><key app="EN" db-id="dtzde0ds95xwvqef9e7vaxx0vwzwr2a2wtsz">110</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Alcaraz, J.</author><author>Buscemi, L.</author><author>Grabulosa, M.</author><author>Trepat, X.</author><author>Fabry, B.</author><author>Farre, R.</author><author>Navajas, D.</author></authors></contributors><auth-address>Navajas, D
Univ Barcelona, IDIBAPS, Fac Med, Unitat Biofis & Bioengn, Casanova 143, Barcelona 08036, Spain
Univ Barcelona, IDIBAPS, Fac Med, Unitat Biofis & Bioengn, Casanova 143, Barcelona 08036, Spain
Univ Barcelona, IDIBAPS, Fac Med, Unitat Biofis & Bioengn, Barcelona 08036, Spain
Harvard Univ, Sch Publ Hlth, Physiol Program, Boston, MA 02115 USA</auth-address><titles><title>Microrheology of human lung epithelial cells measured by atomic force microscopy</title><secondary-title>Biophysical Journal</secondary-title><alt-title>Biophys J</alt-title></titles><periodical><full-title>Biophysical Journal</full-title><abbr-1>Biophys J</abbr-1></periodical><alt-periodical><full-title>Biophysical Journal</full-title><abbr-1>Biophys J</abbr-1></alt-periodical><pages>2071-2079</pages><volume>84</volume><number>3</number><keywords><keyword>mechanical-properties</keyword><keyword>viscoelastic parameters</keyword><keyword>local measurements</keyword><keyword>living cells</keyword><keyword>cytoskeleton</keyword><keyword>fibroblasts</keyword><keyword>moduli</keyword><keyword>architecture</keyword><keyword>indentation</keyword><keyword>deformation</keyword></keywords><dates><year>2003</year><pub-dates><date>Mar</date></pub-dates></dates><isbn>0006-3495</isbn><accession-num>ISI:000183123000059</accession-num><urls><related-urls><url><Go to ISI>://000183123000059</url></related-urls></urls><language>English</language></record></Cite></EndNote>(Alcaraz et al., 2003) ADDIN EN.CITE <EndNote><Cite><Author>Alcaraz</Author><Year>2003</Year><RecNum>110</RecNum><DisplayText>(Alcaraz et al., 2003)</DisplayText><record><rec-number>110</rec-number><foreign-keys><key app="EN" db-id="dtzde0ds95xwvqef9e7vaxx0vwzwr2a2wtsz">110</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Alcaraz, J.</author><author>Buscemi, L.</author><author>Grabulosa, M.</author><author>Trepat, X.</author><author>Fabry, B.</author><author>Farre, R.</author><author>Navajas, D.</author></authors></contributors><auth-address>Navajas, D
Univ Barcelona, IDIBAPS, Fac Med, Unitat Biofis & Bioengn, Casanova 143, Barcelona 08036, Spain
Univ Barcelona, IDIBAPS, Fac Med, Unitat Biofis & Bioengn, Casanova 143, Barcelona 08036, Spain
Univ Barcelona, IDIBAPS, Fac Med, Unitat Biofis & Bioengn, Barcelona 08036, Spain
Harvard Univ, Sch Publ Hlth, Physiol Program, Boston, MA 02115 USA</auth-address><titles><title>Microrheology of human lung epithelial cells measured by atomic force microscopy</title><secondary-title>Biophysical Journal</secondary-title><alt-title>Biophys J</alt-title></titles><periodical><full-title>Biophysical Journal</full-title><abbr-1>Biophys J</abbr-1></periodical><alt-periodical><full-title>Biophysical Journal</full-title><abbr-1>Biophys J</abbr-1></alt-periodical><pages>2071-2079</pages><volume>84</volume><number>3</number><keywords><keyword>mechanical-properties</keyword><keyword>viscoelastic parameters</keyword><keyword>local measurements</keyword><keyword>living cells</keyword><keyword>cytoskeleton</keyword><keyword>fibroblasts</keyword><keyword>moduli</keyword><keyword>architecture</keyword><keyword>indentation</keyword><keyword>deformation</keyword></keywords><dates><year>2003</year><pub-dates><date>Mar</date></pub-dates></dates><isbn>0006-3495</isbn><accession-num>ISI:000183123000059</accession-num><urls><related-urls><url><Go to ISI>://000183123000059</url></related-urls></urls><language>English</language></record></Cite></EndNote>(Alcaraz et al., 2003) ADDIN EN.CITE <EndNote><Cite><Author>Alcaraz</Author><Year>2003</Year><RecNum>110</RecNum><DisplayText>(Alcaraz et al., 2003)</DisplayText><record><rec-number>110</rec-number><foreign-keys><key app="EN" db-id="dtzde0ds95xwvqef9e7vaxx0vwzwr2a2wtsz">110</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Alcaraz, J.</author><author>Buscemi, L.</author><author>Grabulosa, M.</author><author>Trepat, X.</author><author>Fabry, B.</author><author>Farre, R.</author><author>Navajas, D.</author></authors></contributors><auth-address>Navajas, D
Univ Barcelona, IDIBAPS, Fac Med, Unitat Biofis & Bioengn, Casanova 143, Barcelona 08036, Spain
Univ Barcelona, IDIBAPS, Fac Med, Unitat Biofis & Bioengn, Casanova 143, Barcelona 08036, Spain
Univ Barcelona, IDIBAPS, Fac Med, Unitat Biofis & Bioengn, Barcelona 08036, Spain
Harvard Univ, Sch Publ Hlth, Physiol Program, Boston, MA 02115 USA</auth-address><titles><title>Microrheology of human lung epithelial cells measured by atomic force microscopy</title><secondary-title>Biophysical Journal</secondary-title><alt-title>Biophys J</alt-title></titles><periodical><full-title>Biophysical Journal</full-title><abbr-1>Biophys J</abbr-1></periodical><alt-periodical><full-title>Biophysical Journal</full-title><abbr-1>Biophys J</abbr-1></alt-periodical><pages>2071-2079</pages><volume>84</volume><number>3</number><keywords><keyword>mechanical-properties</keyword><keyword>viscoelastic parameters</keyword><keyword>local measurements</keyword><keyword>living cells</keyword><keyword>cytoskeleton</keyword><keyword>fibroblasts</keyword><keyword>moduli</keyword><keyword>architecture</keyword><keyword>indentation</keyword><keyword>deformation</keyword></keywords><dates><year>2003</year><pub-dates><date>Mar</date></pub-dates></dates><isbn>0006-3495</isbn><accession-num>ISI:000183123000059</accession-num><urls><related-urls><url><Go to ISI>://000183123000059</url></related-urls></urls><language>English</language></record></Cite></EndNote>(Alcaraz et al., 2003) ADDIN EN.CITE <EndNote><Cite><Author>Samani</Author><Year>2007</Year><RecNum>880</RecNum><DisplayText>(Samani et al., 2007)</DisplayText><record><rec-number>880</rec-number><foreign-keys><key app="EN" db-id="dtzde0ds95xwvqef9e7vaxx0vwzwr2a2wtsz">880</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Samani, A.</author><author>Zubovits, J.</author><author>Plewes, D.</author></authors></contributors><auth-address>Samani, A
Univ Western Ontario, Dept Med Biophys, Med Sci Bldg, London, ON N6A 5C1, Canada
Univ Western Ontario, Dept Med Biophys, Med Sci Bldg, London, ON N6A 5C1, Canada
Univ Western Ontario, Dept Med Biophys, London, ON N6A 5C1, Canada
Sunnybrook Hlth Sci Ctr, Dept Anat Pathol, Toronto, ON M4N 3M5, Canada
Univ Toronto, Dept Med Biophys, Toronto, ON M4N 3M5, Canada</auth-address><titles><title>Elastic moduli of normal and pathological human breast tissues: an inversion-technique-based investigation of 169 samples</title><secondary-title>Physics in Medicine and Biology</secondary-title><alt-title>Phys Med Biol</alt-title></titles><periodical><full-title>Phys Med Biol</full-title><abbr-1>Physics in medicine and biology</abbr-1></periodical><alt-periodical><full-title>Phys Med Biol</full-title><abbr-1>Physics in medicine and biology</abbr-1></alt-periodical><pages>1565-1576</pages><volume>52</volume><number>6</number><keywords><keyword>magnetic-resonance elastography</keyword><keyword>mr elastography</keyword><keyword>cancer</keyword><keyword>parenchyma</keyword><keyword>lesions</keyword></keywords><dates><year>2007</year><pub-dates><date>Mar 21</date></pub-dates></dates><isbn>0031-9155</isbn><accession-num>WOS:000244714300003</accession-num><urls><related-urls><url><Go to ISI>://WOS:000244714300003</url></related-urls></urls><electronic-resource-num>Doi 10.1088/0031-9155/52/6/002</electronic-resource-num><language>English</language></record></Cite></EndNote>(Samani et al., 2007)PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5Db2xsaW5zd29ydGg8L0F1dGhvcj48WWVhcj4yMDAyPC9Z
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ADDIN EN.CITE.DATA (Bensamoun et al., 2011; Collinsworth et al., 2002; Gennisson et al., 2010) ADDIN EN.CITE <EndNote><Cite><Author>Watters</Author><Year>1985</Year><RecNum>883</RecNum><DisplayText>(Watters et al., 1985)</DisplayText><record><rec-number>883</rec-number><foreign-keys><key app="EN" db-id="dtzde0ds95xwvqef9e7vaxx0vwzwr2a2wtsz">883</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Watters, D. A. K.</author><author>Smith, A. N.</author><author>Eastwood, M. A.</author><author>Anderson, K. C.</author><author>Elton, R. A.</author></authors></contributors><auth-address>Watters, Dak
Western Gen Hosp,Wolfson Labs,Gastrointestinal Unit,Edinburgh Eh4 2xu,Midlothian,Scotland
Western Gen Hosp,Wolfson Labs,Gastrointestinal Unit,Edinburgh Eh4 2xu,Midlothian,Scotland
Univ Edinburgh,Ethicon Res Unit,Edinburgh Eh8 9yl,Midlothian,Scotland
Univ Edinburgh,Med Comp & Stat Unit,Edinburgh Eh8 9yl,Midlothian,Scotland</auth-address><titles><title>Mechanical-Properties of the Rat Colon - the Effect of Age, Sex and Different Conditions of Storage</title><secondary-title>Quarterly Journal of Experimental Physiology and Cognate Medical Sciences</secondary-title><alt-title>Q J Exp Physiol Cms</alt-title></titles><periodical><full-title>Quarterly Journal of Experimental Physiology and Cognate Medical Sciences</full-title><abbr-1>Q J Exp Physiol Cms</abbr-1></periodical><alt-periodical><full-title>Quarterly Journal of Experimental Physiology and Cognate Medical Sciences</full-title><abbr-1>Q J Exp Physiol Cms</abbr-1></alt-periodical><pages>151-162</pages><volume>70</volume><number>1</number><dates><year>1985</year></dates><isbn>0033-5541</isbn><accession-num>WOS:A1985AAW7800013</accession-num><urls><related-urls><url><Go to ISI>://WOS:A1985AAW7800013</url></related-urls></urls><language>English</language></record></Cite></EndNote>(Watters et al., 1985)(a)(b)Fig. 4 (a) Material properties (shear modulus) assignment for body tissues using FCM algorithm for Case I. Shear modulus magnitude is represented by colour scale. (b) The corresponding CT slice. Note that the points belonging to the same tissue class have similar image intensity and concentrate around the class centre. This can be seen in (a) as a spatial clustering of pixels of the same colour. Only in the boundary areas between different tissue classes, some variation of the pixel colour (shear modulus) occurs. 3.2 Results of Evaluation of the Registration Accuracy3.2.1 Qualitative Evaluation As shown in Fig. 5 (column A) and Fig. 6 (column A), for all seven whole-body/torso CT image datasets analysed in this study, large differences in the edge features between the source and target CTs were present. On the other hand, for the registered (i.e. the source images warped using the deformations predicted by biomechanical models) and target images good overlap (with some local misalignment) of edge features was observed (Fig. 5 — column B and Fig. 6 — column B). The overlap tended to be better in the posterior than anterior and lateral image parts. One possible explanation for this tendency can be that the biomechanical models for computing the tissue deformations were loaded by prescribing the vertebrae motion as described in Section 2.2.2.(A)(B)(A)(B)Case ICase II(A)(B)(A)(B)Case IIICase IV(A)(B)(A)(B)Case VCase VI(A)(B)Case VIIFig. 5 Qualitative evaluation of the registration accuracy for seven CT image datasets analysed in this study (transverse slices). For each case, (A) comparison of the edges in the source and target image; and (B) — indicates comparison of the edges in the registered (i.e. warped using the deformation computed by biomechanical models developed in this study) and target image. Edges in the source image are indicated by red colour; edges in target image — by green colour; and the edges in the registered image — by pink colour. Good overlap (with some local misalignment) between the edges in registered and target images is evident.(A)(B)(A)(B)Case ICase II(A)(B)(A)(B)Case IIICase IV(A)(B)(A)(B)Case VCase VI(A)(B)Case VII Fig. 6 Qualitative evaluation of the registration accuracy for seven CT image datasets analysed in this study (frontal slices). For each case, (A) comparison of the edges in the source and target image; and (B) — indicates comparison of the edges in the registered (i.e. warped using the deformation computed by biomechanical models developed in this study) and target image. Edges in the source image are indicated by red colour; edges in target image — by green colour; and the edges in the registered image — by pink colour. Good overlap (with some local misalignment) between the edges in registered and target images is evident.3.2.2 Quantitative Evaluation Analysis of Hausdorff Distance (HD) percentile values indicates that for Case I and Case II, the average HD (as presented in PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5TdWg8L0F1dGhvcj48WWVhcj4yMDEyPC9ZZWFyPjxSZWNO
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ADDIN EN.CITE.DATA Suh et al. (2012)) between the edges in the registered and target images was less than the original (i.e. before resampling) CT image voxel size of 5 mm (Table 1). For none of the analysed cases, the average HD was greater than two times the voxel size (10 mm for Cases I and II, 5 mm for Cases III – VI and 6mm for Case VII) — a value selected here as the allowable misalignment threshold (see section 2.4.2). Using this threshold, it can be concluded from Fig. 7 and Table 5 that 95% of edges were successfully registered for Cases I and II, 85% — for Cases III – VI and 90% for Case VII. For Cases I and II the resolution in sagittal plane was 5 mm, 2.5 mm for Cases III – VI and 3 mm for Case VII. For all seven analysed CT image datasets, the percentile edge-based HD curves tend to rise steeply around 95th percentile (Fig. 7). Therefore, it can be suggested that most edge pairs that lie between 96th and 100th percentile are possible outliers as they do not have any correspondence (i.e. edges in the source/registered and target images do not correspond to each other).No differences in the registration accuracy were observed between the datasets obtained from patients suffering from cancer (Cases II-V) and aortic disease (Cases VI and VII), (Table 5). This confirms feasibility and accuracy of our approach for patients suffering from different diseases.Table 5 95, 85, 75 and 60 –percentile, average HD metric and voxel size in inferior-superior direction (mm) for the registration accuracy of whole-body CT image of seven cases.95-percentile HD metric85-percentile HD metric75-percentile HD metric60-percentile HD metricAverage HD metricVoxel size in inferior-superior directionCase I8.866.335.835.034.935.0Case II9.217.076.325.175.205.0Case III6.705.004.473.643.772.5Case IV7.104.864.123.613.902.5Case V6.395.004.143.603.712.5Case VI8.005.004.473.723.642.5Case VII7.615.214.303.603.883.0(a)(b)(c)Fig. 7 Quantitative evaluation of the registration accuracy for seven whole-body CT image datasets analysed in this study: edge-based Hausdorff Distance (HD) between the registered (i.e. source images warped using the deformation computed by means of non-linear biomechanical models created in this study) and target images against the percentile of edges for transverse slices. The horizontal line is two times voxel size registration accuracy threshold. Plots for Cases I and II, Cases III–V and Case VII are shown separately due to the differences in image resolution (Cases I and II —sagittal resolution of 5 mm; Cases III–V — sagittal resolution of 2.5 mm; Case VII— sagittal resolution of 3.0 mm). (a) Cases I and II; (b) Cases III–VI; (c) Case VII. 4 Discussion and ConclusionsIn this study, a comprehensive patient-specific non-linear finite element model is proposed for computing the deformations within the patient’s body for registration of whole-body CT images. The proposed approach accounts for rigid body motion of bones/skeletal segments, large deformations, and non-linear constitutive properties of soft tissues. The most commonly used approach for generating patient-specific finite element models involves image segmentation to divide the human body into non-overlapping constituents with different material properties — a very tedious and time consuming process. Therefore, we replaced segmentation with the Fuzzy C-Means algorithm to quickly and automatically classify the tissues and assign the mechanical properties directly at the integration points based on this classification (see section 2.2.3). Therefore, we eliminated the need for body organ/tissue segmentation when constructing biomechanical models for registration of whole-body radiographic images. Selection of ‘fuzzy’ method rather than traditionally used “exact” (i.e. relying on image segmentation) approach to assign the mechanical properties is supported by the fact that when loading is prescribed through forced motion of the boundary (vertebrae motion in this study), the computed deformations are only very weakly sensitive to the mechanical properties of the modelled continuum providing that appropriate algorithms of non-linear computational mechanics are used PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5NaWxsZXI8L0F1dGhvcj48WWVhcj4yMDEzPC9ZZWFyPjxS
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ADDIN EN.CITE.DATA (Mostayed et al., 2013). However, some local misalignments are clearly visible in Fig. 5 and 6. One possible source of these misalignments can be that we used very sparse information (vertebrae displacements between the source and target images) to define the model loading. Although one may argue that providing more information to drive computation of the organ and tissue deformations may improve the registration accuracy, the overall results are very promising. It should be noted that to define forced motion of the boundary we relied on simple segmentation of the spine to determine vertebrae displacements between the source and target images.The present study can be regarded as a pioneering effort to solve challenging problem of whole-body CT image registration by applying a biomechanical model using non-linear finite element procedures to compute the deformations to warp a source image to the patient’s target geometry. For all the analysed image sets, the average Hausdorff distance between the pairs edges in registered and target images was within two times the voxel size, which compares well with the studies on non-rigid registration of whole-body CTs relying solely on image-processing algorithms. For instance, PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5TdWg8L0F1dGhvcj48WWVhcj4yMDEyPC9ZZWFyPjxSZWNO
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ADDIN EN.CITE.DATA Toews and Wells (2013) observed errors of an order of 6 image voxel when applying their feature-based alignment (FBA) method for inter-subject registration of human whole-body CT images.Acknowledgments The first author is a recipient of the SIRF scholarship and acknowledges the financial support of the University of Western Australia. The financial support of National Health and Medical Research Council (Grant No. APP1006031) and Australian Research Council (Discovery Grant DP120100402) is gratefully acknowledged. This investigation was also supported in part by NIH grants R01 EB008015 and R01 LM010033, and by a research grant from the Children’s Hospital Boston Translational Research Program. In addition, the authors also gratefully acknowledge the financial support of National Centre for Image Guided Therapy (NIH U41RR019703) and the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centres for Biomedical Computing can be obtained from . We would also like to thank Paul Norman (at The University of Western Australia and Fremantle Hospital), Eamon Kavanagh and Pierce Grace (at the University Hospital Limerick) for providing some of the CT datasets used in the study. NHMRC Project Grant (GNT1063986) and Career Development Fellowship (GNT1083572) are also gratefully acknowledged.References ADDIN EN.REFLIST Al-Mayah, A., Moseley, J., Hunter, S., Velec, M., Chau, L., Breen, S., Brock, K., 2010. Biomechanical-based image registration for head and neck radiation treatment. 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