Carbonate rocks are among the sedimentary systems which preserve information on the formation and diagenetic history expressed in its composition (distribution of its major rock-forming components ...(RFC). For estimating RFC proportions at the micro-scale, a simple counting of visible RFCs in thin sections using overlaid grids is a long-used, well-established technique. However, computer tomography (CT) analysis provides us with quantitative data in 3D at both the scale of the entire sample and a resolution defined by dimensions of the voxels at the micro-scale. The quantitative data expressed in Hounsfield units (HU) correlates with the density of RFCs. In this work statistical properties of CT-based data for selected freshwater carbonate samples from the Danube-Tisza Interfluve have been assessed using histograms and boxplots. Univariate statistical parameters characterize each sample. The maximum-likelihood method of mixture analysis has been adapted to recover and estimate the parameters of these subpopulations. Subpopulations have been defined in the form of overlapping intervals using statistical parameters gained (mean±2STD). Five major components have been defined: empty and partially or entirely filled pores by calcite, limestone micrite, dolomite micrite matrix and limonite saturated matrix.
Diffeomorphic shape registration allows for the seamless geometric alignment of shapes. In this study, we demonstrated the use of a registration algorithm to automatically seed anthropological ...landmarks on the CT images of the pelvis. We found a high correlation between manually and automatically seeded landmarks. The registration algorithm makes it possible to achieve a high degree of automation with the potential to reduce operator errors in the seeding of anthropological landmarks. The results of this study represent a promising step forward in effectively defining the anthropological measures of the human skeleton.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, PRFLJ, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
•Almost automatic procedure to the development of innovative computational clinical tools.•Method of detection of the principal directions of anisotropy for the bone tissue.•Identification of the ...principal factors and quantification of influence on the procedure's accuracy.•Capability of customisation of the procedure.
The use of modelling techniques that combine CT data and bone tissue micromechanics is spreading in computational biomechanics. Finite Element models show great potential in surgical planning of intervention and in prediction of stress and strain fields through a non-invasive method. The main challenge pertains to the reliable characterization of bone mechanical behaviour. An almost automatic procedure is here defined, which provides computational models of bony structures considering the actual anisotropy of bone tissue response. The innovative aspect resides on the automatic detection of the directions of anisotropy as the eigenvectors of a three-dimensional distribution matrix of HU values.
:The procedure combines CT data and micromechanics modelling techniques. Regarding a specific location, the procedure reports both the orthotropic elastic constants, by the analysis of the local HU value, and the anisotropic material directions, by the analysis of the HU values distribution around the specific location.
The procedure returns the distribution of bone tissue orthotropic elasticity tensor. The procedure proves to correctly respect the differentiation between cortical and trabecular bone. Principal directions show to be consistent with experimental data from ultrasound measurements. Regarding the material mapping from voxel to FE model, the developed strategies show to be reliable, leading to marginal errors (lower than 10%) for most of CT voxels (more than 90%). The computational analyses of typical structural loading conditions lead to strain values that are comparable with results from strain gauges experimentations. The development and the exploitation of FE models of different bony structures allow assessing the reliability of the procedure for cortical bone.
The results highlight the potentialities of the procedure in providing accurate patient-specific biomechanical models of bony structures starting from CT data. The accuracy and the automatism of the procedure are important factors for the development of real time clinical tools. The main limitations of this work remain the not fully automatism and the reliability assessment, which is based mainly on cortical bone regions only.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Purpose:
Primary goal of this study is to select optimal registration schemes in the framework of interstitial lung disease (ILD) follow‐up analysis in CT.
Methods:
A set of 128 multiresolution ...schemes composed of multiresolution nonrigid and combinations of rigid and nonrigid registration schemes are evaluated, utilizing ten artificially warped ILD follow‐up volumes, originating from ten clinical volumetric CT scans of ILD affected patients, to select candidate optimal schemes. Specifically, all combinations of four transformation models (three rigid: rigid, similarity, affine and one nonrigid: third order B‐spline), four cost functions (sum‐of‐square distances, normalized correlation coefficient, mutual information, and normalized mutual information), four gradient descent optimizers (standard, regular step, adaptive stochastic, and finite difference), and two types of pyramids (recursive and Gaussian‐smoothing) were considered. The selection process involves two stages. The first stage involves identification of schemes with deformation field singularities, according to the determinant of the Jacobian matrix. In the second stage, evaluation methodology is based on distance between corresponding landmark points in both normal lung parenchyma (NLP) and ILD affected regions. Statistical analysis was performed in order to select near optimal registration schemes per evaluation metric. Performance of the candidate registration schemes was verified on a case sample of ten clinical follow‐up CT scans to obtain the selected registration schemes.
Results:
By considering near optimal schemes common to all ranking lists, 16 out of 128 registration schemes were initially selected. These schemes obtained submillimeter registration accuracies in terms of average distance errors 0.18 ± 0.01 mm for NLP and 0.20 ± 0.01 mm for ILD, in case of artificially generated follow‐up data. Registration accuracy in terms of average distance error in clinical follow‐up data was in the range of 1.985–2.156 mm and 1.966–2.234 mm, for NLP and ILD affected regions, respectively, excluding schemes with statistically significant lower performance (Wilcoxon signed‐ranks test, p < 0.05), resulting in 13 finally selected registration schemes.
Conclusions:
Selected registration schemes in case of ILD CT follow‐up analysis indicate the significance of adaptive stochastic gradient descent optimizer, as well as the importance of combined rigid and nonrigid schemes providing high accuracy and time efficiency. The selected optimal deformable registration schemes are equivalent in terms of their accuracy and thus compatible in terms of their clinical outcome.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
The design of optimized scaffolds for tissue engineering and regenerative medicine is a key topic of current research, as the complex macro- and micro-architectures required for scaffold applications ...depend not only on the mechanical properties but also on the physical and molecular queues of the surrounding tissue within the defect site. Thus, the prediction of optimal features for tissue engineering scaffolds is very important, for both its physical and biological properties.The relationship between high scaffold porosity and high mechanical properties is contradictory, as it becomes even more complex due to the scaffold degradation process. Biomimetic design has been considered as a viable method to design optimum scaffolds for tissue engineering applications. In this research work, the scaffold designs are based on biomimetic boundary-based bone micro-CT data. Based on the biomimetic boundaries and with the aid of topological optimization schemes, the boundary data and given porosity is used to obtain the initial scaffold designs. In summary, the proposed scaffold design scheme uses the principles of both the boundaries and porosity of the micro-CT data with the aid of numerical optimization and simulation tools.
Reverse engineering and medical image-based modeling technologies allow manufacturing of 3D biomodels of anatomical structures of human body. These techniques are based on anatomical information from ...scanning data such as CT and MRI, whose scanners are used for scanning data acquisition of the external and internal geometry of anatomical structures. These 3D biomodels have many medical applications such surgical training, preoperative planning, surgical simulation, diagnosis and treatments. 3D virtual models of human body structures based on CT are increasingly being used in clinical practice. A data processing methodology is required to obtain an accurate 3D model suitable for manufacturing using AM, and specially the FDM technologies. This study shows a step-by-step methodology to process the CT information in bounded uncertainty conditions in order to obtain the STL models of the degenerated bone components, and to manufacture the 3D biomodels for surgery analysis with optimal design and details, and with an adequate accuracy to ensure proper results by surgeons analysis.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
A three-dimensional (3D) understanding of muscle attachment footprints became increasingly relevant for musculoskeletal modeling. The established method to project attachments as points ignores ...patient-specific individuality. Research focuses on investigating certain muscle groups rather than comprehensively studying all muscles spanning a joint. Therefore, we present a reliable method to study several muscle attachments in order to reconstruct the attachment sites in 3D based on CT imaging for future applications in musculoskeletal modeling. For the present feasibility study, 23 knee-related muscle attachments were CT-scanned postmortem from four nonadipose male specimens. For this, the specific muscle attachments were dissected and marked with a barium sulfate containing paint (60 g BaSO4 in 30 mL water and 10 mL acrylic paint). Subsequently, bone geometries and muscle attachments were reconstructed and evaluated from CT datasets. Bone morphology and footprint variations were studied. Exemplarily, variations were high for pes anserinus insertions (mean 56%) and the origins of M. biceps femoris (mean 54%). In contrast, the origins of the vastus muscles as well as the insertion of the Achilles tendon showed low variation (mean 9% and 13%, respectively). Most attachment sites showed variation exceeding the individuality of bone morphology. In summary, the present data were consistent with the few published studies of specific muscle footprints. Our data shed light on the high variability of muscle attachments, which need to be addressed when studying muscle forces and movements through musculoskeletal modeling. This is the first step to achieving a more profound understanding of muscle morphology to be utilized in numerical simulations.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
The share of chronic odontogenic rhinosinusitis is 40% among all chronic rhinosinusitis. Using automated information systems for differential diagnosis will improve the efficiency of decision-making ...by doctors in diagnosing chronic odontogenic rhinosinusitis. Therefore, this study aimed to develop an intelligent decision support system for the differential diagnosis of chronic odontogenic rhinosinusitis based on computer vision methods. A dataset was collected and processed, including 162 MSCT images. A deep learning model for image segmentation was developed. A 23 convolutional layer U-Net network architecture has been used for the segmentation of multi-spiral computed tomography (MSCT) data with odontogenic maxillary sinusitis. The proposed model is implemented in such a way that each pair of repeated 3 × 3 convolutions layers is followed by an Exponential Linear Unit instead of a Rectified Linear Unit as an activation function. The model showed an accuracy of 90.09%. To develop a decision support system, an intelligent chatbot allows the user to conduct an automated patient survey and collect patient examination data from several doctors of various profiles. The intelligent information system proposed in this study made it possible to combine an image processing model with a patient interview and examination data, improving physician decision-making efficiency in the differential diagnosis of Chronic Odontogenic Rhinosinusitis. The proposed solution is the first comprehensive solution in this area.
•A two-stage variational approach for segmenting 3D bone CT data is proposed.•Well-separated regions are identified by a flux-augmented Chan–Vese model.•A phase-field fracture inspired method is ...presented to remove fine-scale contacts.•Accuracy, robustness and automation is demonstrated for 3D femur and vertebra.
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We present a two-stage variational approach for segmenting 3D bone CT data that performs robustly with respect to thin cartilage interfaces. In the first stage, we minimize a flux-augmented Chan–Vese model that accurately segments well-separated regions. In the second stage, we apply a new phase-field fracture inspired model that reliably eliminates spurious bridges across thin cartilage interfaces, resulting in an accurate segmentation topology, from which each bone object can be identified. Its mathematical formulation is based on the phase-field approach to variational fracture, which naturally blends with the variational approach to segmentation. We successfully test and validate our methodology for the segmentation of 3D femur and vertebra bones, which feature thin cartilage regions in the hip joint, the intervertebral disks, and synovial joints of the spinous processes. The major strength of the new methodology is its potential for full automation and seamless integration with downstream predictive bone simulation in a common finite element framework.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
We present a theoretical overview and a performance evaluation of a novel
z
-sampling technique for multidetector row CT (MDCT), relying on a periodic motion of the focal spot in the longitudinal ...direction (
z
-flying focal spot) to double the number of simultaneously acquired slices. The
z
-flying focal spot technique has been implemented in a recently introduced MDCT scanner. Using
32
×
0.6
mm
collimation, this scanner acquires 64 overlapping 0.6 mm slices per rotation in its spiral (helical) mode of operation, with the goal of improved longitudinal resolution and reduction of spiral artifacts. The longitudinal sampling distance at isocenter is 0.3 mm. We discuss in detail the impact of the
z
-flying focal spot technique on image reconstruction. We present measurements of spiral slice sensitivity profiles (SSPs) and of longitudinal resolution, both in the isocenter and off-center. We evaluate the pitch dependence of the image noise measured in a centered 20 cm water phantom. To investigate spiral image quality we present images of an anthropomorphic thorax phantom and patient scans. The full width at half maximum (FWHM) of the spiral SSPs shows only minor variations as a function of the pitch, measured values differ by less than 0.15 mm from the nominal values 0.6, 0.75, 1, 1.5, and 2 mm. The measured FWHM of the smallest slice ranges between 0.66 and 0.68 mm at isocenter, except for pitch 0.55 (0.72 mm). In a centered
z
-resolution phantom, bar patterns up to
15
lp
∕
cm
can be visualized independent of the pitch, corresponding to 0.33 mm longitudinal resolution. 100 mm off-center, bar patterns up to
14
lp
∕
cm
are visible, corresponding to an object size of 0.36 mm that can be resolved in the
z
direction. Image noise for constant effective mAs is almost independent of the pitch. Measured values show a variation of less than 7% as a function of the pitch, which demonstrates correct utilization of the applied radiation dose at any pitch. The product of image noise and square root of the slice width (FWHM of the respective SSP) is the same constant for all slices except 0.6 mm. For the thinnest slice, relative image noise is increased by 17%. Spiral windmill-type artifacts are effectively suppressed with the
z
-flying focal spot technique, which has the potential to maintain a low artifact level up to pitch 1.5, in this way increasing the maximum volume coverage speed that can be clinically used.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
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