Fully automatic online geometric calibration for non-circular cone-beam CT orbits using fiducials with unknown placement

BACKGROUND

Cone-beam CT (CBCT) with non-circular scanning orbits can improve image quality for 3D intraoperative image guidance. However, geometric calibration of such scans can be challenging. Existing methods typically require a prior image, specialized phantoms, presumed repeatable orbits, or long computation time.

PURPOSE

We propose a novel fully automatic online geometric calibration algorithm that does not require prior knowledge of fiducial configuration. The algorithm is fast, accurate, and can accommodate arbitrary scanning orbits and fiducial configurations.

METHODS

The algorithm uses an automatic initialization process to eliminate human intervention in fiducial localization and an iterative refinement process to ensure robustness and accuracy. We provide a detailed explanation and implementation of the proposed algorithm. Physical experiments on a lab test bench and a clinical robotic C-arm scanner were conducted to evaluate spatial resolution performance and robustness under realistic constraints.

RESULTS

Qualitative and quantitative results from the physical experiments demonstrate high accuracy, efficiency, and robustness of the proposed method. The spatial resolution performance matched that of our existing benchmark method, which used a 3D-2D registration-based geometric calibration algorithm.

CONCLUSIONS

We have demonstrated an automatic online geometric calibration method that delivers high spatial resolution and robustness performance. This methodology enables arbitrary scan trajectories and should facilitate translation of such acquisition methods in a clinical setting.

Notice of Removal: Fourier Diffusion Models: A Method to Control MTF and NPS in Score-Based Stochastic Image Generation

Removed.

Design and fabrication of 3D-printed patient-specific soft tissue and bone phantoms for CT imaging

The objective of this study is to create patient-specific phantoms for computed tomography (CT) that possess accurate densities and exhibit visually realistic image textures. These qualities are crucial for evaluating CT performance in clinical settings. The study builds upon a previously presented 3D printing method (PixelPrint) by incorporating soft tissue and bone structures. We converted patient DICOM images directly into 3D printer instructions using PixelPrint and utilized calcium-doped filament to increase the Hounsfield unit (HU) range. Density was modeled by controlling printing speed according to volumetric filament ratio to emulate attenuation profiles. We designed micro-CT phantoms to demonstrate the reproducibility, and to determine mapping between filament ratios and HU values on clinical CT systems. Patient phantoms based on clinical cervical spine and knee examinations were manufactured and scanned with a clinical spectral CT scanner. The CT images of the patient-based phantom closely resembled original CT images in visual texture and contrast. Micro-CT analysis revealed minimal variations between prints, with an overall deviation of ± 0.8% in filament line spacing and ± 0.022 mm in line width. Measured differences between patient and phantom were less than 12 HU for soft tissue and 15 HU for bone marrow, and 514 HU for cortical bone. The calcium-doped filament accurately represented bony tissue structures across different X-ray energies in spectral CT (RMSE ranging from ± 3 to ± 28 HU, compared to 400 mg/ml hydroxyapatite). In conclusion, this study demonstrated the possibility of extending 3D-printed patient-based phantoms to soft tissue and bone structures while maintaining accurate organ geometry, image texture, and attenuation profiles.

Tunable neural networks for CT image formation

Optimization of CT image quality typically involves balancing variance and bias. In traditional filtered back-projection, this trade-off is controlled by the filter cutoff frequency. In model-based iterative reconstruction, the regularization strength parameter often serves the same function. Deep neural networks (DNNs) typically do not provide this tunable control over output image properties. Models are often trained to minimize the expected mean squared error, which penalizes both variance and bias in image outputs but does not offer any control over the trade-off between the two. We propose a method for controlling the output image properties of neural networks with a new loss function called weighted covariance and bias (WCB). Our proposed method uses multiple noise realizations of the input images during training to allow for separate weighting matrices for the variance and bias penalty terms. Moreover, we show that tuning these weights enables targeted penalization of specific image features with spatial frequency domain penalties. To evaluate our method, we present a simulation study using digital anthropomorphic phantoms, physical simulation of CT measurements, and image formation with various algorithms. We show that the WCB loss function offers a greater degree of control over trade-offs between variance and bias, whereas mean-squared error provides only one specific image quality configuration. We also show that WCB can be used to control specific image properties including variance, bias, spatial resolution, and the noise correlation of neural network outputs. Finally, we present a method to optimize the proposed weights for a spiculated lung nodule shape discrimination task. Our results demonstrate this new image quality can control the image properties of DNN outputs and optimize image quality for task-specific performance.

Design and fabrication of 3D-printed patient-specific soft tissue and bone phantoms for CT imaging

The objective of this study is to create patient-specific phantoms for computed tomography (CT) that have realistic image texture and densities, which are critical in evaluating CT performance in clinical settings. The study builds upon a previously presented 3D printing method (PixelPrint) by incorporating soft tissue and bone structures. We converted patient DICOM images directly into 3D printer instructions using PixelPrint and utilized stone-based filament to increase Hounsfield unit (HU) range. Density was modeled by controlling printing speed according to volumetric filament ratio to emulate attenuation profiles. We designed micro-CT phantoms to demonstrate the reproducibility and to determine mapping between filament ratios and HU values on clinical CT systems. Patient phantoms based on clinical cervical spine and knee examinations were manufactured and scanned with a clinical spectral CT scanner. The CT images of the patient-based phantom closely resembled original CT images in texture and contrast. Measured differences between patient and phantom were less than 15 HU for soft tissue and bone marrow. The stone-based filament accurately represented bony tissue structures across different X-ray energies, as measured by spectral CT. In conclusion, this study demonstrated the possibility of extending 3D-printed patient-based phantoms to soft tissue and bone structures while maintaining accurate organ geometry, image texture, and attenuation profiles.

Design and fabrication of 3D-printed patient-specific soft tissue and bone phantoms for CT imaging

The objective of this study is to create patient-specific phantoms for computed tomography (CT) that have realistic image texture and densities, which are critical in evaluating CT performance in clinical settings. The study builds upon a previously presented 3D printing method (PixelPrint) by incorporating soft tissue and bone structures. We converted patient DICOM images directly into 3D printer instructions using PixelPrint and utilized stone-based filament to increase Hounsfield unit (HU) range. Density was modeled by controlling printing speed according to volumetric filament ratio to emulate attenuation profiles. We designed micro-CT phantoms to demonstrate the reproducibility and to determine mapping between filament ratios and HU values on clinical CT systems. Patient phantoms based on clinical cervical spine and knee examinations were manufactured and scanned with a clinical spectral CT scanner. The CT images of the patient-based phantom closely resembled original CT images in texture and contrast. Measured differences between patient and phantom were less than 15 HU for soft tissue and bone marrow. The stone-based filament accurately represented bony tissue structures across different X-ray energies, as measured by spectral CT. In conclusion, this study demonstrated the possibility of extending 3D-printed patient-based phantoms to soft tissue and bone structures while maintaining accurate organ geometry, image texture, and attenuation profiles.

Three-dimensional printing of patient-specific computed tomography lung phantoms: a reader study

In modern clinical decision-support algorithms, heterogeneity in image characteristics due to variations in imaging systems and protocols hinders the development of reproducible quantitative measures including for feature extraction pipelines. With the help of a reader study, we investigate the ability to provide consistent ground-truth targets by using patient-specific 3D-printed lung phantoms. PixelPrint was developed for 3D-printing lifelike computed tomography (CT) lung phantoms by directly translating clinical images into printer instructions that control density on a voxel-by-voxel basis. Data sets of three COVID-19 patients served as input for 3D-printing lung phantoms. Five radiologists rated patient and phantom images for imaging characteristics and diagnostic confidence in a blinded reader study. Effect sizes of evaluating phantom as opposed to patient images were assessed using linear mixed models. Finally, PixelPrint's production reproducibility was evaluated. Images of patients and phantoms had little variation in the estimated mean (0.03-0.29, using a 1-5 scale). When comparing phantom images to patient images, effect size analysis revealed that the difference was within one-third of the inter- and intrareader variabilities. High correspondence between the four phantoms created using the same patient images was demonstrated by PixelPrint's production repeatability tests, with greater similarity scores between high-dose acquisitions of the phantoms than between clinical-dose acquisitions of a single phantom. We demonstrated PixelPrint's ability to produce lifelike CT lung phantoms reliably. These phantoms have the potential to provide ground-truth targets for validating the generalizability of inference-based decision-support algorithms between different health centers and imaging protocols and for optimizing examination protocols with realistic patient-based phantoms. Classification: CT lung phantoms, reader study.

Deep Learning CT Image Restoration using System Blur Models

Restoration of images contaminated by blur is an important processing tool across modalities including computed tomography where the blur induced by various system factors can be complex with dependencies on acquisition and reconstruction protocol, and even be patient-dependent. In many cases, such a blur can be modeled and predicted with high accuracy providing an important input to a classical deconvolution approach. While traditional deblurring methods tend to be highly noise magnifying, deep learning approaches have the potential to improve upon classic performance limits. However, most network architectures base their restoration on data inputs alone without knowledge of the system blur. In this work, we explore a deep learning approach that takes both image inputs as well as information that characterizes the system blur to combine modeling and deep learning approaches. We apply the approach to CT image restoration and compare with an image-only deep learning approach. We find that inclusion of the system blur model improves deblurring performance - suggesting the potential power of the combined modeling and deep learning technique.

Revealing pelvic structures in the presence of metal hip prothesis via non-circular CBCT orbits

As the expansion of Cone Beam CT (CBCT) to new interventional procedures continues, the burdensome challenge of metal artifacts remains. Photon starvation and beam hardening from metallic implants and surgical tools in the field of view can result in the anatomy of interest being partially or fully obscured by imaging artifacts. Leveraging the flexibility of modern robotic CBCT imaging systems, implementing non-circular orbits designed for reducing metal artifacts by ensuring data-completeness during acquisition has become a reality. Here, we investigate using non-circular orbits to reduce metal artifacts arising from metallic hip prostheses when imaging pelvic anatomy. As a first proof-of-concept, we implement a sinusoidal and a double-circle-arc orbit on a CBCT test bench, imaging a physical pelvis phantom, with two metal hip prostheses, housing a 3D-printed iodine-filled radial line-pair target. A standard circular orbit implemented with the CBCT test bench acted as comparator. Imaging data collection and processing, geometric calibration and image reconstruction was completed using in-house developed software programs. Imaging with the standard circular orbit, image artifacts were observed in the pelvic bones and only 33 out of the possible 45 line-pairs of the radial line-pair target were partially resolvable in the reconstructed images. Comparatively, imaging with both the sinusoid and double-circle-arc orbits reduced artifacts in the surrounding anatomy and enabled all 45 line-pairs to be visibly resolved in the reconstructed images. These results indicate the potential of non-circular orbits to assist in revealing previously obstructed structures in the pelvic region in the presence of metal hip prosthesis.

Quantitative Dual-Energy Imaging of Bone Marrow Edema Using Multisource Cone-Beam CT with Model-Based Decomposition

Purpose

We investigated the feasibility of dual-energy (DE) detection of bone marrow edema (BME) using a dedicated extremity cone-beam CT (CBCT) with a unique three-source x-ray unit. The sources can be operated at different energies to enable single-scan DE acquisitions. However, they are arranged parallel to the axis of rotation, resulting in incomplete sampling and precluding the application of DE projection-domain decompositions (PDD) for beam-hardening reduction. Therefore, we propose a novel combination of a model-based "one-step" DE two-material decomposition followed by a constrained image-domain change-of-basis to obtain virtual non-calcium (VNCa) images for BME detection.

Methods

DE projections were obtained using an "alternating-kV" protocol by operating the peripheral two sources of the CBCT system at low-energy (60 kV, 0.105 mAs/frame) and the central source at high-energy (100 kV, 0.028 mAs/frame), for a total of 600 frames over 216° of gantry rotation. Projections were processed with detector lag, glare and fast Monte Carlo (MC)-based iterative scatter corrections. Model-based material decomposition (MBMD) was then implemented to obtain aluminum (Al) and polyethylene (PE) volume fraction images with minimal beam-hardening. Statistical ray weights in MBMD were modified to account for regions with highly oblique sampling by the peripheral sources. To generate the VNCa maps, image-domain decomposition (IDD) constrained by the volume conservation principle (VCP) was performed to convert the Al and PE MBMD images into volume fractions of water, fat and cortical bone. Accuracy of BME detection was evaluated using physical phantom data acquired on the multi-source extremity CBCT scanner.

Results

The proposed framework estimated the volume of BME with ~10% error. The MC-based scatter corrections and the modified MBMD ray weights were essential to achieve such performance - the error without MC scatter corrections was >30%, whereas the uniformity of estimated VNCa images was 3x improved using the modified weights compared to the conventional weights.

Conclusions

The proposed DE decomposition framework was able to overcome challenges of high scatter and incomplete sampling to achieve BME detection on a CBCT system with axially-distributed x-ray sources.

PixelPrint: A collection of three-dimensional printed CT phantoms of different respiratory diseases

Imaging is often a first-line method for diagnostics and treatment. Radiological workflows increasingly mine medical images for quantifiable features. Variability in device/vendor, acquisition protocol, data processing, etc., can dramatically affect quantitative measures, including radiomics. We recently developed a method (PixelPrint) for 3D-printing lifelike computed tomography (CT) lung phantoms, paving the way for future diagnostic imaging standardization. PixelPrint generates phantoms with accurate attenuation profiles and textures by directly translating clinical images into printer instructions that control density on a voxel-by-voxel basis. The present study introduces a library of 3D printed lung phantoms covering a wide range of lung diseases, including usual interstitial pneumonia with advanced fibrosis, chronic hypersensitivity pneumonitis, secondary tuberculosis, cystic fibrosis, Kaposi sarcoma, and pulmonary edema. CT images of the patient-based phantom are qualitatively comparable to original CT images, both in texture, resolution and contrast levels allowing for clear visualization of even subtle imaging abnormalities. The variety of cases chosen for printing include both benign and malignant pathology causing a variety of alveolar and advanced interstitial abnormalities, both clearly visualized on the phantoms. A comparison of regions of interest revealed differences in attenuation below 6 HU. Identical features on the patient and the phantom have a high degree of geometrical correlation, with differences smaller than the intrinsic spatial resolution of the scans. Using PixelPrint, it is possible to generate CT phantoms that accurately represent different pulmonary diseases and their characteristic imaging features.

Task-Driven CT Image Quality Optimization for Low-Contrast Lesion Detectability with Tunable Neural Networks

Low-contrast lesions are difficult to detect in noisy low-dose CT images. Improving CT image quality for this detection task has the potential to improve diagnostic accuracy and patient outcomes. In this work, we use tunable neural networks for CT image restoration with a hyperparameter to control the variance/bias tradeoff. We use clinical images from a super-high-resolution normal-dose CT scan to synthesize low-contrast low-dose CT images for supervised training of deep learning CT reconstruction models. Those models are trained using with multiple noise realizations so that variance and bias can be penalized separately. We use a training loss function with one hyperparameter called the denoising level, which controls the variance/bias tradeoff. Finally, we evaluate the CT image quality to find the optimal denoising level for low-contrast lesion detectability. We evaluate performance using a shallow neural network model classification model to represent a suboptimal image observer. Our results indicate that the optimal networks for low-contrast lesion detectability are those that prioritize bias reduction rather than mean-squared error, which demonstrates the potential clinical benefit of our proposed tunable neural networks.

Approaches for Three Material Decomposition using a Triple-Layer Flat-Panel Detector

X-ray spectral imaging has been increasingly investigated in radiography and interventional imaging. Flat-panel detectors with more than one detection layer have demonstrated advantages in providing separate soft tissue and bone images. Current dual-layer flat-panel detectors (DL-FPD) have limited capability to further differentiate between iodinated contrast agent and bony/calcified structures. In this work, we investigate a triple-layer flat-panel detector (TL-FPD) and the feasibility of three-material (water/calcium/iodine) decomposition. A physical model of TL-FPD, including system geometry, spectrum sensitivities, blur and noise models was developed. Using simulated triple-layer projections, three-material decompositions were performed using three different processing methods: polynomial-based, model-based, and a machine learning-based method (ResUnet). We find that the polynomial-based method leads to very noisy images with poor differentiation between calcium and iodine maps. The model-based method achieved much lower noise levels than the polynomial-based method but exhibited residual errors between the iodine and calcium channels. The ResUnet method offered the best decompositions among the investigated methods in terms of root mean square error from the ground truth and noise in the material maps. These preliminary results demonstrate the feasibility of three-material decomposition using TL-FPD and suggest a path for clinical translation of single-shot contrast/iodine differentiation in radiography and fluoroscopy.

Three-material decomposition using a dual-layer flat panel detector in the presence of soft tissue motion

Digital subtraction angiography (DSA) is a widely used technique for the visualization of contrast-enhanced structures. However, temporal subtraction DSA is challenged by misregistration artifacts due to patient motion and incomplete separation of iodine contrast agent from background soft tissue and bone. In this work, we propose an approach that allows three-material decomposition using a dual-layer flat panel detector in the presence of soft tissue motion. We assume the calcium signal (bone) remains stationary in the pre- and post-contrast images but allow soft tissues to move freely (e.g. cardiac motion). The dual-layer pre- and post-injection images form and ensemble of four measurements that permits material decomposition of four bases (pre- and post-injection soft tissue, calcium, and iodine). We apply two different processing techniques: 1) a modified lookup table and; 2) a model-based material estimation. These are compared with previously proposed DSA methods using temporal subtraction and hybrid (dual-energy) subtraction. Investigations were performed using an XCAT thorax phantom simulating a breath-hold. The pre- and post-contrast measurements were simulated at different time points within a cardiac cycle. Both the lookup table and model-based algorithms eliminate motion artifact as a result of soft tissue motion and allow good separation of iodine, bone, and soft tissue. While the lookup table algorithm contains high noise at the simulated dose level, the model-based algorithm produced iodine images that allow the visualization of major vessels around the heart. In contrast, traditional temporal DSA is susceptible to subtraction artifacts and hybrid DSA shows increased noise.

Technical note: Extended longitudinal and lateral 3D imaging with a continuous dual-isocenter CBCT scan

BACKGROUND

The clinical benefits of intraoperative cone beam CT (CBCT) during orthopedic procedures include (1) improved accuracy for procedures involving the placement of hardware and (2) providing immediate surgical verification.

PURPOSE

Orthopedic interventions often involve long and wide anatomical sites (e.g., lower extremities). Therefore, in order to ensure that the clinical benefits are available to all orthopedic procedures, we investigate the feasibility of a novel imaging trajectory to simultaneously expand the CBCT field-of-view longitudinally and laterally.

METHODS

A continuous dual-isocenter imaging trajectory was implemented on a clinical robotic CBCT system using additional real-time control hardware. The trajectory consisted of 200° circular arcs separated by alternating lateral and longitudinal table translations. Due to hardware constraints, the direction of rotation (clockwise/anticlockwise) and lateral table translation (left/right) was reversed every 400°. X-ray projections were continuously acquired at 15 frames/s throughout all movements. A whole-body phantom was used to verify the trajectory. As comparator, a series of conventional large volume acquisitions were stitched together. Image quality was quantified using Root Mean Square Deviation (RMSD), Mean Absolute Percentage Deviation (MAPD), Structural Similarity Index Metric (SSIM) and Contrast-to-Noise Ratio (CNR).

RESULTS

The imaging volume produced by the continuous dual-isocenter trajectory had dimensions of L = 95 cm × W = 45 cm × H = 45 cm. This enabled the hips to the feet of the whole-body phantom to be captured in approximately half the imaging dose and acquisition time of the 11 stitched conventional acquisitions required to match the longitudinal and lateral imaging dimensions. Compared to the stitched conventional images, the continuous dual-isocenter acquisition had RMSD of 4.84, MAPD of 6.58% and SSIM of 0.99. The CNR of the continuous dual-isocenter and stitched conventional acquisitions were 1.998 and 1.999, respectively.

CONCLUSION

Extended longitudinal and lateral intraoperative volumetric imaging is feasible on clinical robotic CBCT systems.

Design Optimization of Spatial-Spectral Filters for Cone-Beam CT Material Decomposition

Spectral CT has shown promise for high-sensitivity quantitative imaging and material decomposition. This work presents a new device called a spatial-spectral filter (SSF) which consists of a tiled array of filter materials positioned near the x-ray source that is used to modulate the spectral shape of the x-ray beam. The filter is moved to obtain projection data that is sparse in each spectral channel. To process this sparse data, we employ a one-step direct model-based material decomposition (MBMD) to reconstruct basis material density images directly from the SSF CT data. To evaluate different possible SSF designs, we define a new Fisher-information-based predictive image quality metric called separability index which characterizes the ability of a spectral CT system to distinguish between the signals from two or more materials. This spectral CT performance metric can be used to optimize spectral CT system design. We conducted simulation-based design optimization study to find optimized combinations of filter materials, filter thicknesses, filter widths, and source settings. Finally, we present MBMD results using simulated SSF CT measurements from the optimized designs to demonstrate the ability to reconstruct basis material density images and to show the benefits of the optimized designs. Our results indicate that optimizing SSF CT for separability leads to high-performance at material discrimination tasks.

Model-based three-material decomposition in dual-energy CT using the volume conservation constraint

Objective. We develop a model-based optimization algorithm for ‘one-step’ dual-energy (DE) CT decomposition of three materials directly from projection measurements. Approach. Since the three-material problem is inherently undetermined, we incorporate the volume conservation principle (VCP) as a pair of equality and nonnegativity constraints into the objective function of the recently reported model-based material decomposition (MBMD). An optimization algorithm (constrained MBMD, CMBMD) is derived that utilizes voxel-wise separability to partition the volume into a VCP-constrained region solved using interior-point iterations, and an unconstrained region (air surrounding the object, where VCP is violated) solved with conventional two-material MBMD. Constrained MBMD (CMBMD) is validated in simulations and experiments in application to bone composition measurements in the presence of metal hardware using DE cone-beam CT (CBCT). A kV-switching protocol with non-coinciding low- and high-energy (LE and HE) projections was assumed. CMBMD with decomposed base materials of cortical bone, fat, and metal (titanium, Ti) is compared to MBMD with (i) fat-bone and (ii) fat-Ti bases. Main results. Three-material CMBMD exhibits a substantial reduction in metal artifacts relative to the two-material MBMD implementations. The accuracies of cortical bone volume fraction estimates are markedly improved using CMBMD, with ∼5–10× lower normalized root mean squared error in simulations with anthropomorphic knee phantoms (depending on the complexity of the metal component) and ∼2–2.5× lower in an experimental test-bench study. Significance. In conclusion, we demonstrated one-step three-material decomposition of DE CT using volume conservation as an optimization constraint. The proposed method might be applicable to DE applications such as bone marrow edema imaging (fat-bone-water decomposition) or multi-contrast imaging, especially on CT/CBCT systems that do not provide coinciding LE and HE ray paths required for conventional projection-domain DE decomposition.

Practical workflow for arbitrary non-circular orbits for CT with clinical robotic C-arms

Non-circular orbits in cone-beam CT (CBCT) imaging are increasingly being studied for potential benefits in field-of-view, dose reduction, improved image quality, minimal interference in guided procedures, metal artifact reduction, and more. While modern imaging systems such as robotic C-arms are enabling more freedom in potential orbit designs, practical implementation on such clinical systems remains challenging due to obstacles in critical stages of the workflow, including orbit realization, geometric calibration, and reconstruction. In this work, we build upon previous successes in clinical implementation and address key challenges in the geometric calibration stage with a novel calibration method. The resulting workflow eliminates the need for prior patient scans or dedicated calibration phantoms, and can be conducted in clinically relevant processing times.

PixelPrint: Three-dimensional printing of patient-specific soft tissue and bone phantoms for CT

Patient-based CT phantoms, with realistic image texture and densities, are essential tools for assessing and verifying CT performance in clinical practice. This study extends our previously presented 3D printing solution (PixelPrint) to patient-based phantoms with soft tissue and bone structures. To expand the Hounsfield Unit (HUs) range, we utilize a stone-based filament. Applying PixelPrint, we converted patient DICOM images directly into FDM printer instructions (G-code). Density was modeled as the ratio of filament to voxel volume to emulate attenuation profiles for each voxel, with the filament ratio controlled through continuous modification of the printing speed. Two different phantoms were designed to demonstrate the high reproducibility of our approach with micro-CT acquisitions, and to determine the mapping between filament line widths and HU values on a clinical CT system. Moreover, a third phantom based on a clinical cervical spine scan was manufactured and scanned with a clinical spectral CT scanner. CT image of the patient-based phantom closely resembles the original CT image both in texture and contrast levels. Measured differences between patient and phantom are around 10 HU for bone marrow voxels and around 150 HU for cortical bone. In addition, stone-based filament can accurately represent boney tissue structures across the different x-ray energies, as measured by spectral CT. This study demonstrates the feasibility of our 3D-printed patient-based phantoms to be extended to soft-tissue and bone structure while maintaining accurate organ geometry, image texture, and attenuation profiles for spectral CT.

Local Linearity Analysis of Deep Learning CT Denoising Algorithms

The rapid development of deep-learning methods in medical imaging has called for an analysis method suitable for non-linear and data-dependent algorithms. In this work, we investigate a local linearity analysis where a complex neural network can be represented as piecewise linear systems. We recognize that a large number of neural networks consists of alternating linear layers and rectified linear unit (ReLU) activations, and are therefore strictly piecewise linear. We investigated the extent of these locally linear regions by gradually adding perturbations to an operating point. For this work, we explored perturbations based on image features of interest, including lesion contrast, background, and additive noise. We then developed strategies to extend these strictly locally linear regions to include neighboring linear regions with similar gradients. Using these approximately linear regions, we applied singular value decomposition (SVD) analysis to each local linear system to investigate and explain the overall nonlinear and data-dependent behaviors of neural networks. The analysis was applied to an example CT denoising algorithm trained on thorax CT scans. We observed that the strictly local linear regions are highly sensitive to small signal perturbations. Over a range of lesion contrast from 0.007 to 0.04 mm^-1, there is a total of 33992 linear regions. The Jacobians are also shift-variant. However, the Jacobians of neighboring linear regions are very similar. By combining linear regions with similar Jacobians, we narrowed down the number of approximately linear regions to four over lesion contrast from 0.001 to 0.08 mm^-1. The SVD analysis to different linear regions revealed denoising behavior that is highly dependent on the background intensity. Analysis further identified greater amount of noise reduction in uniform regions compared to lesion edges. In summary, the local linearity analysis framework we proposed has the potential for us to better characterize and interpret the non-linear and data-dependent behaviors of neural networks.

Tunable Neural Networks for Multi-Material Image Formation from Spectral CT Measurements

Quantitative estimation of multi-material density images is an important goal for Spectral CT imaging. However, material decomposition is a poorly-conditioned nonlinear inverse problem. Maximum-likelihood model-based material decomposition results in very noisy material density image estimates. One increasingly popular strategy for noise reduction is to apply deep neural networks for multi-material image formation. The most common loss function is mean squared error with respect to supervised target images such as ground truth or higher-dose cases. However, we believe that the mean-squared error loss function has several issues for multi-material image formation. In this work, we present a new loss function which includes multiple noise realizations with separate weights on covariance and bias for joint denoising of all material bases. By modulating these weights, it is possible to tune the image quality of neural network output images. To demonstrate our proposed approach, we conducted a simulation of a water/calcium/gadolinium spectral CT imaging scenario using a deep neural network for multi-material image denoising. Our results show that by changing the weights of our proposed loss function, it is possible to control the tradeoff between variance and bias for individual materials as well as the control over the bias coupling between materials.

Universal orbit design for metal artifact elimination

Objective.Metal artifacts are a persistent problem in CT and cone-beam CT. In this work, we propose to reduce or even eliminate metal artifacts by providing better sampling of data using non-circular orbits.Approach.We treat any measurements intersecting metal as missing data, and aim to design a universal orbit that can generally accommodate arbitrary metal shapes and locations. We adapted a local sampling completeness metric based on Tuy's condition to quantify the extent of sampling in the presence of metal. A maxi-min objective over all possible metal locations was used for orbit design. A simple class of sinusoidal orbits was evaluated as a function of frequencies, maximum tilt angles, and orbital extents. Experimental implementation of these orbits were performed on an imaging bench and evaluated on two phantoms, one containing metal balls and the other containing a pedicle screw assembly for spine fixation. Metal artifact reduction (MAR) performance was compared amongst three approaches: non-circular orbits only, algorithmic correction only, and a combined approach.Main results.Theoretical evaluations of the objective favor sinusoidal orbits with large tilt angles and large orbital extents. Furthermore, orbits that leverage redundant azimuthal angles to sample non-redundant data have better performance, e.g. even or non-integer frequency sinusoids for a 360° acquisition. Experimental data support the trends observed in theoretical evaluations. Reconstructions using even or non-integer frequency orbits present less streaking artifacts and background details with finer resolution, even when multiple metal objects are present and even in the absence of MAR algorithms. The combined approach of non-circular orbits and MAR algorithm yields the best performance. The observed trend in image quality is supported by quantitative measures of sampling and severity of streaking artifact.Significance.This work demonstrates that sinusoidal orbits are generally robust against metal artifacts and can provide an avenue for improved image quality in interventional imaging.

Assessment of Boundary Discrimination Performance in a Printed Phantom

Printed phantoms hold great potential as a tool for examining task-based image quality of x-ray imaging systems. Their ability to produce complex shapes rendered in materials with adjustable attenuation coefficients allows a new level of flexibility in the design of tasks for the evaluation of physical imaging systems. We investigate performance in a fine "boundary discrimination" task in which fine features at the margin of a clearly visible "lesion" are used to classify the lesion as malignant or benign. These tasks are appealing because of their relevance to clinical tasks, and because they typically emphasize higher spatial frequencies relative to more common lesion detection tasks. A 3D printed phantom containing cylindrical shells of varying thickness was used to generate lesions profiles that differed in their edge profiles. This was intended to approximate lesions with indistinct margins that are clinically associated with malignancy. Wall thickness in the phantom ranged from 0.4mm to 0.8mm, which allows for task difficulty to be varied by choosing different thicknesses to represent malignant and benign lesions. The phantom was immersed in a tub filled with water and potassium phosphate to approximate the attenuating background, and imaged repeatedly on a benchtop cone-beam CT scanner. After preparing the image data (reconstruction, ROI Selection, sub-pixel registration), we find that the mean frequency of the lesion profile is 0.11 cyc/mm. The mean frequency of the lesion-difference profile, representative of the discrimination task, is approximately 6 times larger. Model observers show appropriate dose performance in these tasks as well.

Performance Assessment Framework for Neural Network Denoising

The proliferation of deep learning image processing calls for a quantitative image quality assessment framework that is suitable for nonlinear, data-dependent algorithms. In this work, we propose a method to systematically evaluate the system and noise responses such that the nonlinear transfer properties can be mapped out. The method involves sampling of lesion perturbations as a function of size, contrast, as well as clinically relevant features such as shape and texture that may be important for diagnosis. We embed the perturbations in backgrounds of varying attenuation levels, noise magnitude and correlation that are associated with different patient anatomies and imaging protocols. The range of system and noise response are further used to evaluate performance for clinical tasks such as signal detection and classification. We performed the assessment for an example CNN-denoising algorithm for low does lung CT screening. The system response of the CNN-denoising algorithm exhibits highly nonlinear behavior where both contrast and higher order lesion features such as spiculated boundaries are not reliably represented for lesions perturbations with small size and low contrast. The noise properties are potentially highly nonstationary, and should be assumed to be the same between the signal-present and signal-absent images. Furthermore, we observer a high degree dependency of both system and noise response on the background attenuation levels. Inputs around zeros are effectively imposed a non-negativity constraint; transfer properties for higher background levels are highly variable. For a detection task, CNN-denoised images improved detectability index by 16-18% compared to low dose CT inputs. For classification task between spiculated and smooth lesions, CNN-denoised images result in a much larger improvement up to 50%. The performance assessment framework propose in this work can systematically map out the nonlinear transfer functions for deep learning algorithms and can potentially enable robust deployment of such algorithms in medical imaging applications.

PixelPrint: Three-dimensional printing of realistic patient-specific lung phantoms for CT imaging

Phantoms are essential tools for assessing and verifying performance in computed tomography (CT). Realistic patient-based lung phantoms that accurately represent textures and densities are essential in developing and evaluating novel CT hardware and software. This study introduces PixelPrint, a 3D-printing solution to create patient-specific lung phantoms with accurate contrast and textures. PixelPrint converts patient images directly into printer instructions, where density is modeled as the ratio of filament to voxel volume to emulate local attenuation values. For evaluation of PixelPrint, phantoms based on four COVID-19 pneumonia patients were manufactured and scanned with the original (clinical) CT scanners and protocols. Density and geometrical accuracies between phantom and patient images were evaluated for various anatomical features in the lung, and a radiomic feature comparison was performed for mild, moderate, and severe COVID-19 pneumonia patient-based phantoms. Qualitatively, CT images of the patient-based phantoms closely resemble the original CT images, both in texture and contrast levels, with clearly visible vascular and parenchymal structures. Regions-of-interest (ROIs) comparing attenuation demonstrated differences below 15 HU. Manual size measurements performed by an experienced thoracic radiologist revealed a high degree of geometrical correlation between identical patient and phantom features, with differences smaller than the intrinsic spatial resolution of the images. Radiomic feature analysis revealed high correspondence, with correlations of 0.95-0.99 between patient and phantom images. Our study demonstrates the feasibility of 3D-printed patient-based lung phantoms with accurate geometry, texture, and contrast that will enable protocol optimization, CT research and development advancements, and generation of ground-truth datasets for radiomic evaluations.

Non-circular CBCT orbit design and realization on a clinical robotic C-arm for metal artifact reduction

Metal artifacts have been a difficult challenge for cone-beam CT (CBCT), especially for intraoperative imaging. Metal surgical tools and implants are often present in the field of view and can attenuate X-rays so heavily that they essentially create a missing-data problem. Recently, an increasing number of intra-operative imaging systems such as robotic C-arms are capable of non-circular orbits for data acquisition. Such trajectories can potentially improve sampling and the degree of data completeness to solve the metal-induced missing-data problem, thereby reducing or eliminating the associated image artifacts. In this work, we extend our prior theoretical and experimental work and implement non-circular orbits for metal artifact reduction on a clinical robotic C-arm (Siemens Artis zeego). To maximize the potential for clinical translation, we restrict our implementation to standard built-in motion and data collection functions, also available on other zeego systems, and work within the physical constraints and limitations on positioning and motion. Customized software tools for data extraction, processing, calibration, and reconstruction are used. We demonstrate example non-circular orbits and the resulting image quality using a phantom containing pedicle screws for spine fixation. As compared with a standard circular CBCT orbit, these non-circular orbits exhibit significantly reduced metal artifacts. These results suggest a high potential for image quality improvements for intraoperative CBCT imaging when metal tools or implants are present in the field-of-view.

Data-dependent Nonlinearity Analysis in CT Denoising CNNs

Recent years have seen the increasing application of deep learning methods in medical imaging formation, processing, and analysis. These methods take advantage of the flexibility of nonlinear neural network models to encode information and features in ways that can outperform conventional approaches. However, because of the nonlinear nature of this processing, images formed by neural networks have properties that are highly data-dependent and difficult to analyze. In particular, the generalizability and robustness of these approaches can be difficult to ascertain. In this work, we analyze a class of neural networks that use only piece-wise linear activation functions. This class of networks can be represented by locally linear systems where the linear properties are highly data-dependent - allowing, for example, estimation of noise in image output via standard propagation methods. We propose a nonlinearity index metric that quantifies the fidelity of a local linear approximation of trained models based on specific input data. We applied this analysis to three example CT denoising CNNs to analytically predict the noise properties in the output images. We found that the proposed nonlinearity metric highly correlates with the accuracy of noise predictions. The analysis proposed in this work provides theoretical understanding of the nonlinear behavior of neural networks and enables performance prediction and quantitation under certain conditions.

Control of Variance and Bias in CT Image Processing with Variational Training of Deep Neural Networks

Optimization of CT image quality typically involves balancing noise and bias. In filtered back-projection, this trade-off is controlled by the particular filter and cutoff frequency. In penalized-likelihood iterative reconstruction, the penalty weight serves the same function. Deep neural networks typically do not provide this tuneable control over output image properties. Models are often trained to minimize mean squared error which penalizes both variance and bias in image outputs but does not offer any control over the trade-off between the two. In this work, we propose a method for controlling the output image properties of neural networks with a new loss function called weighted covariance and bias (WCB). Our proposed method includes separate weighting parameters to control the relative importance of noise or bias reduction. Moreover, we show that tuning these weights enables targeted penalization of specific image features (e.g. spatial frequencies). To evaluate our method, we present a simulation study using digital anthropormorphic phantoms, physical simulation of non-ideal CT data, and image formation with various algorithms. We show that WCB offers a greater degree of control over trade-offs between variance and bias whereas MSE has only one configuration. We also show that WCB can be used to control specific image properties including variance, bias, spatial resolution, and the noise correlation of neural network outputs. Finally, we present a method to optimize the proposed weights for stimulus detectability. Our results demonstrate the potential for this new capability to control the image properties of DNN outputs and optimize image quality for the task-specific applications.

Fast CBCT Reconstruction using Convolutional Neural Networks for Arbitrary Robotic C-arm Orbits

Cone-beam CT (CBCT) with non-circular acquisition orbits has the potential to improve image quality, increase the field-of view, and facilitate minimal interference within an interventional imaging setting. Because time is of the essence in interventional imaging scenarios, rapid reconstruction methods are advantageous. Model-Based Iterative Reconstruction (MBIR) techniques implicitly handle arbitrary geometries; however, the computational burden for these approaches is particularly high. The aim of this work is to extend a previously proposed framework for fast reconstruction of non-circular CBCT trajectories. The pipeline combines a deconvolution operation on the backprojected measurements using an approximate, shift-invariant system response prior to processing with a Convolutional Neural Network (CNN). We trained and evaluated the CNN for this approach using 1800 randomized arbitrary orbits. Noisy projection data were formed from 1000 procedurally generated tetrahedral phantoms as well as anthropomorphic data in the form of 800 CT and CBCT images from the Lung Image Database Consortium Image Collection (LIDC). Using this proposed reconstruction pipeline, computation time was reduced by 90% as compared to MBIR with only minor differences in performance. Quantitative comparisons of nRMSE, FSIM and SSIM are reported. Performance was consistent for projection data simulated with acquisition orbits the network has not previously been trained on. These results suggest the potential for fast processing of arbitrary CBCT trajectory data with reconstruction times that are clinically relevant and applicable - facilitating the application of non-circular orbits in CT image-guided interventions and intraoperative imaging.

Three-dimensional printing of patient-specific lung phantoms for CT imaging: Emulating lung tissue with accurate attenuation profiles and textures

PURPOSE

Phantoms are a basic tool for assessing and verifying performance in CT research and clinical practice. Patient-based realistic lung phantoms accurately representing textures and densities are essential in developing and evaluating novel CT hardware and software. This study introduces PixelPrint, a 3D printing solution to create patient-based lung phantoms with accurate attenuation profiles and textures.

METHODS

PixelPrint, a software tool, was developed to convert patient digital imaging and communications in medicine (DICOM) images directly into FDM printer instructions (G-code). Density was modeled as the ratio of filament to voxel volume to emulate attenuation profiles for each voxel, with the filament ratio controlled through continuous modification of the printing speed. A calibration phantom was designed to determine the mapping between filament line width and Hounsfield units (HU) within the range of human lungs. For evaluation of PixelPrint, a phantom based on a single human lung slice was manufactured and scanned with the same CT scanner and protocol used for the patient scan. Density and geometrical accuracy between phantom and patient CT data were evaluated for various anatomical features in the lung.

RESULTS

For the calibration phantom, measured mean HU show a very high level of linear correlation with respect to the utilized filament line widths, (r > 0.999). Qualitatively, the CT image of the patient-based phantom closely resembles the original CT image both in texture and contrast levels (from -800 to 0 HU), with clearly visible vascular and parenchymal structures. Regions of interest comparing attenuation illustrated differences below 15 HU. Manual size measurements performed by an experienced thoracic radiologist reveal a high degree of geometrical correlation of details between identical patient and phantom features, with differences smaller than the intrinsic spatial resolution of the scans.

CONCLUSION

The present study demonstrates the feasibility of 3D-printed patient-based lung phantoms with accurate organ geometry, image texture, and attenuation profiles. PixelPrint will enable applications in the research and development of CT technology, including further development in radiomics.

Flat-panel conebeam CT in the clinic: history and current state

Research into conebeam CT concepts began as soon as the first clinical single-slice CT scanner was conceived. Early implementations of conebeam CT in the 1980s focused on high-contrast applications where concurrent high resolution ( < 200    μ m ), for visualization of small contrast-filled vessels, bones, or teeth, was an imaging requirement that could not be met by the contemporaneous CT scanners. However, the use of nonlinear imagers, e.g., x-ray image intensifiers, limited the clinical utility of the earliest diagnostic conebeam CT systems. The development of consumer-electronics large-area displays provided a technical foundation that was leveraged in the 1990s to first produce large-area digital x-ray detectors for use in radiography and then compact flat panels suitable for high-resolution and high-frame-rate conebeam CT. In this review, we show the concurrent evolution of digital flat panel (DFP) technology and clinical conebeam CT. We give a brief summary of conebeam CT reconstruction, followed by a brief review of the correction approaches for DFP-specific artifacts. The historical development and current status of flat-panel conebeam CT in four clinical areas-breast, fixed C-arm, image-guided radiation therapy, and extremity/head-is presented. Advances in DFP technology over the past two decades have led to improved visualization of high-contrast, high-resolution clinical tasks, and image quality now approaches the soft-tissue contrast resolution that is the standard in clinical CT. Future technical developments in DFPs will enable an even broader range of clinical applications; research in the arena of flat-panel CT shows no signs of slowing down.

Generative Adversarial Networks and Radiomics Supervision for Lung Lesion Synthesis

Realistic lesion generation is a useful tool for system evaluation and optimization. In this work, we investigate a data-driven approach for categorical lung lesion generation using public lung CT databases. We propose a generative adversarial network with a Wasserstein discrimination and gradient penalty to stabilize training. We further included conditional inputs such that the network can generate user-specified lesion categories. Novel to our network, we directly incorporated radiomic features in an intermediate supervision step to encourage similar textures between generated and real lesions. We evaluated the network using lung lesions from the Lung Image Database Consortium (LIDC) database. The lesions are divided into two categories: solid vs. non-solid. We performed quantitative evaluation of network performance base on four criteria: 1) overfitting in terms of structural and morphological similarity to the training data, 2) diversity of generated lesions in terms of similarity to other generated data, 3) similarity to real lesions in terms of distribution of example radiomics features, and 4) conditional consistency in terms of classification accuracy using a classifier trained on the training lesions. We imposed a quantitative threshold for similarity based on visual inspection. The percentage of non-solid and solid lesions that satisfy low overfitting and high diversity is 96.9% and 88.6% of non-solid and solid lesions respectively. The distribution of example radiomics features are similar in the generated and real lesions indicated by a low Kullback-Leibler divergence score. Classification accuracy for the generated lesions are comparable with that for the real lesions. The proposed network is a promising approach for data-driven generation of realistic lung lesions.

Manifold Reconstruction of Differences: A Model-Based Iterative Statistical Estimation Algorithm With a Data-Driven Prior

Manifold learning using deep neural networks been shown to be an effective tool for building sophisticated prior image models that can be applied to noise reduction in low-close CT. A manifold is a low-dimensional space that captures most of the variation in a class of data (e.g. chest CT images). This nonlinear reduction in dimensionality is one way to build up a sophisticated model of the features and structures present in image data. This nonlinear dimensionality reduction tends to learn features associated with the signal rather than the noise when provided with a large training dataset. However, the internal workings operation are typically not easy to understand. The results can be highly nonlinear and object-dependent. After training the model is fixed and during reconstruction is typically no check for fitness between the image estimates and the measured data. We propose a new iterative CT reconstruction algorithm, called Manifold Reconstruction of Differences (MRoD), which combines physical and statistical models with a data-driven prior based on manifold learning. The MRoD algorithm involves estimating a manifold component, approximating common features among all patients, and the difference component which has the freedom to fit the measured data. By applying a sparsity-promoting penalty to the difference image rather than a hard constraint to the manifold, the MRoD algorithm is able to reconstruct features which are not present in the training data. The difference component itself may be independently useful. While the manifold captures typical patient features (e.g. healthy anatomy), the difference image highlights patient-specific elements (e.g. pathology). In this work, we present a description of an optimization framework which combines trained manifold-based modules with physical modules. We present a simulation study using anthropomorphic lung data showing that the MRoD algorithm can both isolate differences between a particular patient and the typical distribution, but also provide significant noise reduction with less bias than a typical penalized likelihood estimator in composite manifold plus difference reconstructions.

Spectral CT using a fine grid structure and varying x-ray incidence angle

PURPOSE

Interest in spectral computed tomography (CT) for diagnostics and therapy evaluation has been growing. Data acquisitions with distinct spectral sensitivities provide the ability to discriminate multiple materials, quantitative density estimates, and reduced artifacts due to energy dependencies. We introduce a novel spectral CT concept that includes a fine-pitch grid structure for prefiltration of the x-ray beam.

METHODS

We develop physical models for grid designs and illustrate the basic operating principles wherein small angulations of the incident x rays results significant filtration and spectral shaping of the beam. We fabricate a prototype grid with tungsten lamellae. We compare x-ray spectra induced by this filter as a function of incidence angle in both simulation students and in physical measurements. The grid is also integrated onto a CT test bench where we scanned an iodinated phantom with clinically relevant concentrations (5, 10, 20, and 50 mgI/mL) to demonstrate the ability to perform spectral CT acquisitions and material decomposition.

RESULTS

X-ray spectrometer measurements reveal diverse and controllable spectral shaping with small angle changes that are in agreement with simulation studies. Critical angles where the characteristics of the induced spectrum changes dramatically are identified. Reconstructions of projection data for two angulations separated by 2° was reconstructed and material decomposition into iodine and water images shows good agreement with the known iodine concentrations.

CONCLUSIONS

This work demonstrates the feasibility of the grid-based approach to enable spectral CT data acquisitions and accurate material decompositions. On-going and future studies will investigate the potential of this novel concept as a relatively simple upgrade to standard energy-integrating CT.

High-resolution model-based material decomposition in dual-layer flat-panel CBCT

PURPOSE

Spectral CT uses energy-dependent measurements that enable material discrimination in addition to reconstruction of structural information. Flat-panel detectors (FPDs) have been widely used in dedicated and interventional systems to deliver high spatial resolution, volumetric cone-beam CT (CBCT) in compact and OR-friendly designs. In this work, we derive a model-based method that facilitates high-resolution material decomposition in a spectral CBCT system equipped with a prototype dual-layer FPD. Through high-fidelity modeling of multilayer detector, we seek to avoid resolution loss that is present in more traditional processing and decomposition approaches.

METHOD

A physical model for spectral measurements in dual-layer flat-panel CBCT is developed including layer-dependent differences in system geometry, spectral sensitivities, and detector blur (e.g., due to varied scintillator thicknesses). This forward model is integrated into a model-based material decomposition (MBMD) method based on minimization of a penalized weighted least-squared (PWLS) objective function. The noise and resolution performance of this approach was compared with traditional projection-domain decomposition (PDD) and image-domain decomposition (IDD) approaches as well as one-step MBMD with lower-fidelity models that use approximated geometry, projection interpolation, or an idealized system geometry without system blur model. Physical studies using high-resolution three-dimensional (3D)-printed water-iodine phantoms were conducted to demonstrate the high-resolution imaging performance of the compared decomposition methods in iodine basis images and synthetic monoenergetic images.

RESULTS

Physical experiments demonstrate that the MBMD methods incorporating an accurate geometry model can yield higher spatial resolution iodine basis images and synthetic monoenergetic images than PDD and IDD results at the same noise level. MBMD with blur modeling can further improve the spatial-resolution compared with the decomposition results obtained with IDD, PDD, and MBMD methods with lower-fidelity models. Using the MBMD without or with blur model can increase the absolute modulation at 1.75 lp/mm by 10% and 22% compared with IDD at the same noise level.

CONCLUSION

The proposed model-based material decomposition method for a dual-layer flat-panel CBCT system has demonstrated an ability to extend high-resolution performance through sophisticated detector modeling including the layer-dependent blur. The proposed work has the potential to not only facilitate high-resolution spectral CT in interventional and dedicated CBCT systems, but may also provide the opportunity to evaluate different flat-panel design trade-offs including multilayer FPDs with mismatched geometries, scintillator thicknesses, and spectral sensitivities.

A prototype spatial-spectral CT system for material decomposition with energy-integrating detectors

PURPOSE

Spectral CT has great potential for a variety of clinical applications due to improved tissue and material discrimination over conventional single-energy CT. Many clinical and preclinical spectral CT systems have two spectral channels enabling dual-energy CT. Strategies include split filtration, dual-layer detectors, photon-counting detectors, and kVp switching. The motivation for this work is the development of an x-ray source spectral modulation device with three or more spectral channels to enable high-sensitivity multi-material decomposition with energy-integrating detectors.

MATERIALS AND METHODS

We present spatial-spectral filters which are a new x-ray source modulation technology with the potential for additional channel diversity. The filtering device consists of an array of K-edge materials which divide the x-ray beam into spectrally varied beamlets. This design allows for an arbitrary number of spectral channels-trading off spatial and spectral information. We use a one-step model-based material decomposition (MBMD) algorithm to iteratively estimate material density images directly from the spatial-spectral CT data. In this work, we present a prototype spatial-spectral filter integrated with an x-ray CT test bench. The filter is composed of an array of tin, erbium, tantalum, and lead filter tiles which spatially modulate the system spectral sensitivity pattern. In a simulation study, we investigate the particular problem of mis-calibration between the data acquisition and the reconstruction model. With an understanding of the required model accuracy, we present a spectral calibration method to estimate the critical model parameters. To demonstrate feasibility of the spatial-spectral filter with a calibrated beamlet model, we collected a spatial-spectral CT scan of a multicontrast-enhanced phantom containing water, iodine, and gadolinium solutions.

RESULTS

With simulations, we show that material decomposition is possible with spatial-spectral-filtered CT data, and we demonstrate the importance of a well-calibrated physical model. We find a 50% increase in error for focal spot model mismatch of 0.27mm and gap width model mismatch of 16 mμ. With physical results, we demonstrate that the calibrated system model is in close agreement with the measured data, and that the reconstructed material density images match the ground truth concentrations for the multicontrast phantom. Empirical results indicate gadolinium density estimation had an error of 17-58% mostly due to a systematic constant bias of 0.30-0.60 mg/ml. Water density estimates are within 1% and iodine estimates are within 10% of ground truth.

CONCLUSION

These preliminary results demonstrate the potential of spatial-spectral filters to enable multicontrast imaging. Moreover, this device is compatible with energy-integrating detectors and so provides a feasible modification to enable spectral CT imaging with existing single-energy systems.

Direct reconstruction of anatomical change in low-dose lung nodule surveillance

Purpose: In sequential imaging studies, there exists rich information from past studies that can be used in prior-image-based reconstruction (PIBR) as a form of improved regularization to yield higher-quality images in subsequent studies. PIBR methods, such as reconstruction of difference (RoD), have demonstrated great improvements in the image quality of subsequent anatomy reconstruction even when CT data are acquired at very low-exposure settings. Approach: However, to effectively use information from past studies, two major elements are required: (1) registration, usually deformable, must be applied between the current and prior scans. Such registration is greatly complicated by potential ambiguity between patient motion and anatomical change-which is often the target of the followup study. (2) One must select regularization parameters for reliable and robust reconstruction of features. Results: We address these two major issues and apply a modified RoD framework to the clinical problem of lung nodule surveillance. Specifically, we develop a modified deformable registration approach that enforces a locally smooth/rigid registration around the change region and extend previous analytic expressions relating reconstructed contrast to the regularization parameter and other system dependencies for reliable representation of image features. We demonstrate the efficacy of this approach using a combination of realistic digital phantoms and clinical projection data. Performance is characterized as a function of the size of the locally smooth registration region of interest as well as x-ray exposure. Conclusions: This modified framework is effectively able to separate patient motion and anatomical change to directly highlight anatomical change in lung nodule surveillance.

Accelerated 3D image reconstruction with a morphological pyramid and noise-power convergence criterion

Model-based iterative reconstruction (MBIR) for cone-beam CT (CBCT) offers better noise-resolution tradeoff and image quality than analytical methods for acquisition protocols with low x-ray dose or limited data, but with increased computational burden that poses a drawback to routine application in clinical scenarios. This work develops a comprehensive framework for acceleration of MBIR in the form of penalized weighted least squares optimized with ordered subsets separable quadratic surrogates. The optimization was scheduled on a set of stages forming a morphological pyramid varying in voxel size. Transition between stages was controlled with a convergence criterion based on the deviation between the mid-band noise power spectrum (NPS) measured on a homogeneous region of the evolving reconstruction and that expected for the converged image, computed with an analytical model that used projection data and the reconstruction parameters. A stochastic backprojector was developed by introducing a random perturbation to the sampling position of each voxel for each ray in the reconstruction within a voxel-based backprojector, breaking the deterministic pattern of sampling artifacts when combined with an unmatched Siddon forward projector. This fast, forward and backprojector pair were included into a multi-resolution reconstruction strategy to provide support for objects partially outside of the field of view. Acceleration from ordered subsets was combined with momentum accumulation stabilized with an adaptive technique that automatically resets the accumulated momentum when it diverges noticeably from the current iteration update. The framework was evaluated with CBCT data of a realistic abdomen phantom acquired on an imaging x-ray bench and with clinical CBCT data from an angiography robotic C-arm (Artis Zeego, Siemens Healthineers, Forchheim, Germany) acquired during a liver embolization procedure. Image fidelity was assessed with the structural similarity index (SSIM) computed with a converged reconstruction. The accelerated framework provided accurate reconstructions in 60 s (SSIM = 0.97) and as little as 27 s (SSIM = 0.94) for soft-tissue evaluation. The use of simple forward and backprojectors resulted in 9.3× acceleration. Accumulation of momentum provided extra ∼3.5× acceleration with stable convergence for 6-30 subsets. The NPS-driven morphological pyramid resulted in initial faster convergence, achieving similar SSIM with 1.5× lower runtime than the single-stage optimization. Acceleration of MBIR to provide reconstruction time compatible with clinical applications is feasible via architectures that integrate algorithmic acceleration with approaches to provide stable convergence, and optimization schedules that maximize convergence speed.

Deformable motion compensation for interventional cone-beam CT

Image-guided therapies in the abdomen and pelvis are often hindered by motion artifacts in cone-beam CT (CBCT) arising from complex, non-periodic, deformable organ motion during long scan times (5-30 s). We propose a deformable image-based motion compensation method to address these challenges and improve CBCT guidance. Motion compensation is achieved by selecting a set of small regions of interest in the uncompensated image to minimize a cost function consisting of an autofocus objective and spatiotemporal regularization penalties. Motion trajectories are estimated using an iterative optimization algorithm (CMA-ES) and used to interpolate a 4D spatiotemporal motion vector field. The motion-compensated image is reconstructed using a modified filtered backprojection approach. Being image-based, the method does not require additional input besides the raw CBCT projection data and system geometry that are used for image reconstruction. Experimental studies investigated: (1) various autofocus objective functions, analyzed using a digital phantom with a range of sinusoidal motion magnitude (4, 8, 12, 16, 20 mm); (2) spatiotemporal regularization, studied using a CT dataset from The Cancer Imaging Archive with deformable sinusoidal motion of variable magnitude (10, 15, 20, 25 mm); and (3) performance in complex anatomy, evaluated in cadavers undergoing simple and complex motion imaged on a CBCT-capable mobile C-arm system (Cios Spin 3D, Siemens Healthineers, Forchheim, Germany). Gradient entropy was found to be the best autofocus objective for soft-tissue CBCT, increasing structural similarity (SSIM) by 42%-92% over the range of motion magnitudes investigated. The optimal temporal regularization strength was found to vary widely (0.5-5 mm^-2) over the range of motion magnitudes investigated, whereas optimal spatial regularization strength was relatively constant (0.1). In cadaver studies, deformable motion compensation was shown to improve local SSIM by ∼17% for simple motion and ∼21% for complex motion and provided strong visual improvement of motion artifacts (reduction of blurring and streaks and improved visibility of soft-tissue edges). The studies demonstrate the robustness of deformable motion compensation to a range of motion magnitudes, frequencies, and other factors (e.g. truncation and scatter).

A CT Denoising Neural Network with Image Properties Parameterization and Control

A wide range of dose reduction strategies for x-ray computed tomography (CT) have been investigated. Recently, denoising strategies based on machine learning have been widely applied, often with impressive results, and breaking free from traditional noise-resolution trade-offs. However, since typical machine learning strategies provide a single denoised image volume, there is no user-tunable control of a particular trade-off between noise reduction and image properties (biases) of the denoised image. This is in contrast to traditional filtering and model-based processing that permits tuning of parameters for a level of noise control appropriate for the specific diagnostic task. In this work, we propose a novel neural network that includes a spatial-resolution parameter as additional input permits explicit control of the noise-bias trade-off. Preliminary results show the ability to control image properties through such parameterization as well as the possibility to tune such parameters for increased detectability in task-based evaluation.

End-to-end Modeling for Predicting and Estimating Radiomics: Application to Gray Level Co-occurrence Matrices in CT

While radiomics models are finding increased use in computer-aided diagnostics and as imaging biomarkers for inference and discovery, their utility in computed tomography (CT) is limited by variability of the image properties produced by different CT scanners, imaging protocols, patient anatomy, and an increasingly diverse range of reconstruction and post-processing software. While these effects can be mitigated with careful data curation and standardization of protocols, this is impractical for diverse sources of image data. In this work, we propose to generalize traditional end-to-end imaging system models to include radiomics calculation as an explicit stage. Such a model permits both prediction of the undesirable variability of radiomics, but also forms a basis for inverting the process to estimate the true underlying radiomics. This framework has the potential to provide for standardization of radiomics across imaging conditions permitting more widespread application of radiomics models; larger, more diverse image databases; and improved diagnoses and inferences based on those standardized metrics. We apply this framework to a large class of popular radiomics based on the Gray Level Co-occurrence matrix under conditions of imaging system that are well describe by traditional linear systems approaches as well as nonlinear systems for which traditional analytic models do not apply.

Model-based dual-energy tomographic image reconstruction of objects containing known metal components

Dual-energy (DE) decomposition has been adopted in orthopedic imaging to measure bone composition and visualize intraarticular contrast enhancement. One of the potential applications involves monitoring of callus mineralization for longitudinal assessment of fracture healing. However, fracture repair usually involves internal fixation hardware that can generate significant artifacts in reconstructed images. To address this challenge, we develop a novel algorithm that combines simultaneous reconstruction-decomposition using a previously reported method for model-based material decomposition (MBMD) augmented by the known-component (KC) reconstruction framework to mitigate metal artifacts. We apply the proposed algorithm to simulated DE data representative of a dedicated extremity cone-beam CT (CBCT) employing an x-ray unit with three vertically arranged sources. The scanner generates DE data with non-coinciding high- and low-energy projection rays when the central source is operated at high tube potential and the peripheral sources at low potential. The proposed algorithm was validated using a digital extremity phantom containing varying concentrations of Ca-water mixtures and Ti implants. Decomposition accuracy was compared to MBMD without the KC model. The proposed method suppressed metal artifacts and yielded estimated Ca concentrations that approached the reconstructions of an implant-free phantom for most mixture regions. In the vicinity of simple components, the errors of Ca density estimates obtained by incorporating KC in MBMD were ∼1.5-5× lower than the errors of conventional MBMD; for cases with complex implants, the errors were ∼3-5× lower. In conclusion, the proposed method can achieve accurate bone mineral density measurements in the presence of metal implants using non-coinciding DE projections acquired on a multisource CBCT system.

Three-dimensional regions-of-interest-based intra-operative four-dimensional soft tissue perfusion imaging using a standard x-ray system with no gantry rotation: A simulation study for a proof of concept

PURPOSE

Many interventional procedures aim at changing soft tissue perfusion or blood flow. One problem at present is that soft tissue perfusion and its changes cannot be assessed in an interventional suite because cone-beam computed tomography is too slow (it takes 4-10 s per volume scan). In order to address the problem, we propose a novel method called IPEN for Intra-operative four-dimensional soft tissue PErfusion using a standard x-ray system with No gantry rotation.

METHODS

IPEN uses two input datasets: (a) the contours and locations of three-dimensional regions-of-interest (ROIs) such as arteries and sub-sections of cancerous lesions, and (b) a series of x-ray projection data obtained from an intra-arterial contrast injection to contrast enhancement to wash-out. IPEN then estimates a time-enhancement curve (TEC) for each ROI directly from projections without reconstructing cross-sectional images by maximizing the agreement between synthesized and measured projections with a temporal roughness penalty. When path lengths through ROIs are known for each x-ray beam, the ROI-specific enhancement can be accurately estimated from projections. Computer simulations are performed to assess the performance of the IPEN algorithm. Intra-arterial contrast-enhanced liver scans over 25 s were simulated using XCAT phantom version 2.0 with heterogeneous tissue textures and cancerous lesions. The following four sub-studies were performed: (a) The accuracy of the estimated TECs with overlapped lesions was evaluated at various noise (dose) levels with either homogeneous or heterogeneous lesion enhancement patterns; (b) the accuracy of IPEN with inaccurate ROI contours was assessed; (c) we investigated how overlapping ROIs and noise in projections affected the accuracy of the IPEN algorithm; and (d) the accuracy of the perfusion indices was assessed.

RESULTS

The TECs estimated by IPEN were sufficiently accurate at a reference dose level with the root-mean-square deviation (RMSD) of 0.0027 ± 0.0001 cm^-1 or 13 ± 1 Hounsfield unit (mean ± standard deviation) for the homogeneous lesion enhancement and 0.0032 ± 0.0005 cm^-1 for the heterogeneous enhancement (N = 20 each). The accuracy was degraded with decreasing doses: The RMSD with homogeneous enhancement was 0.0220 ± 0.0003 cm^-1 for 20% of the reference dose level. Performing 3 × 3 pixel averaging on projection data improved the RMSDs to 0.0051 ± 0.0002 cm^-1 for 20% dose. When the ROI contours were inaccurate, smaller ROI contours resulted in positive biases in TECs, whereas larger ROI contours produced negative biases. The bias remained small, within ± 0.0070 cm^-1 , when the Sorenson-Dice coefficients (SDCs) were larger than 0.81. The RMSD of the TEC estimation was strongly associated with the condition of the problem, which can be empirically quantified using the condition number of a matrix A z that maps a vector of ROI enhancement values z to projection data and a weighted variance of projection data: a linear correlation coefficient (R) was 0.794 (P < 0.001). The perfusion index values computed from the estimated TECs agreed well with the true values (R ≥ 0.985, P < 0.0001).

CONCLUSION

The IPEN algorithm can estimate ROI-specific TECs with high accuracy especially when 3 × 3 pixel averaging is applied, even when lesion enhancement is heterogeneous, or ROI contours are inaccurate but the SDC is at least 0.81.

Grating-based Spectral CT using Small Angle X-ray Beam Deflections

Interest in spectral CT for diagnostics and therapy evaluation has been growing. Acquisitions of data from distinct energy spectra provide, among other advantages, quantitative density estimations for multiple materials. We introduce a novel spectral CT concept that includes a fine-pitch grating for prefiltration of the x-ray beam. The attenuation behavior of this grating changes significantly if x-rays are slightly angled in relation to the grating structures. To apply such an angle (i.e. switch between the different filtrations) we propose a fast, controllable, and precise solution by moving the focal spot of the x-ray tube. In this work, we performed preliminary evaluations with a grating prototype on a CT test bench. Our results include x-ray spectrometer measurements that reveal diverse and controllable spectral shaping between 4° and 6° for a specific grating design. Additional experiments with a contrast agent phantom illustrated the capability to decompose clinically relevant iodine concentrations (5, 10, 20, and 50mg/mL) - demonstrating the feasibility of the grating-based approach. Ongoing and future studies will investigate the potential of this novel concept as a relatively simple upgrade to standard energy-integrating CT.

Metal-Tolerant Noncircular Orbit Design and Implementation on Robotic C-Arm Systems

Metal artifacts are a major confounding factor for image quality in CT, especially in image-guided surgery scenarios where surgical tools and implants frequently occur in the field-of-view. Traditional metal artifact correction methods typically use algorithmic solutions to interpolate over the highly attenuated projection measurements where metal is present but cannot recover the missing information obstructed by the metal. In this work, we treat metal artifacts as a missing data problem and employ noncircular orbits to maximize data completeness in the presence of metal. We first implement a local data completeness metric based on Tuy's condition as the percentage of great circles sampled by a particular orbit and accounted for the presence of metal by discounting any rays that pass through metal. We then compute the metric over many locations and many possible metal locations to reflect data completeness for arbitrary metal placements within a volume of interest. We used this metric to evaluate the effectiveness of sinusoidal orbits of different magnitudes and frequencies in metal artifact reduction. We also evaluated noncircular orbits in two imaging systems for phantoms with different metal objects and metal arrangements. Among a circular, tilted circular, and a sinusoidal orbit of two cycles per rotation, the latter is shown to most effectively remove metal artifacts. The noncircular orbit not only reduce the extent of streaks, but allows better visualization of spatial frequencies that cannot be recovered by metal artifact correction algorithms. These results illustrate the potential of relatively simple noncircular orbits to be robust against metal implants which ordinarily present significant challenges in interventional imaging.

Perturbation Response of Model-based Material Decomposition with Edge-Preserving Penalties

Spectral CT permits material discrimination beyond the structural information in conventional single-energy CT. Model-based material decomposition facilitates direct estimation of material density from spectral measurements, incorporating a general forward model for arbitrary spectral CT system, a statistical model of spectral CT measurements, and flexible regularization schemes. Such one-step approaches are promising for superior image quality, but the relationship between regularization parameters, imaging conditions, and reconstructed image properties is complicated. More specifically, the estimator is inherently nonlinear and may include additional nonlinearities like edge-preserving regularization, making image quality metrics intended for linear system evaluation difficult to apply. In this work, we seek approaches to quantify the image properties of this inherently nonlinear process through an investigation of perturbation response - the generalized system response to a local perturbation of arbitrary shape, location, and contrast. Such responses include cross-talk between material density channels, and we investigate the application of this metric in a sample spectral CT system. Inspired by the prior work under assumptions of local linearity and shift-invariant we also propose a prediction framework for perturbation response using a perceptron neural network. The proposed prediction framework offers an alternative to exhaustive evaluation and is a potential tool that can be used to prospectively choose optimal regularization parameters based on imaging conditions and diagnostic task.

Multi-Contrast CT Imaging with a Prototype Spatial-Spectral Filter

Spectral CT has great potential for a variety of clinical applications due to the improved material discrimination with respect to conventional CT. Many clinical and preclinical spectral CT systems have two spectral channels for dual-energy CT using strategies such as split-filtration, dual-layer detectors, or kVp-switching. However, there are emerging clinical imaging applications which would require three or more spectral sensitivity channels, for example, multiple exogenous contrast agents in a single scan. Spatial-spectral filters are a new spectral CT technology which use x-ray beam modulation to offer greater spectral diversity. The device consists of an array of k-edge filters which divide the x-ray beam into spectrally varied beamlets. This design allows for an arbitrary number of spectral channels; however, traditional two-step reconstruction-decomposition schemes are typically not effective because the measured data for any individual spectral channel is sparse in the projection domain. Instead, we use a one-step model-based material decomposition algorithm to iteratively estimate material density images directly from spectral CT data. In this work, we present a prototype spatial-spectral filter integrated with an x-ray CT test-bench. The filter is composed of an array of tin, erbium, tantalum, and lead filter tiles which spatially modulate the system spectral sensitivity pattern. After the system was characterized and modeled, we conducted a spectral CT scan of a multi-contrast-enhanced phantom containing water, iodine, and gadolinium solutions. We present the resulting spectral CT data as well as the material density images estimated by model-based material decomposition. The calibrated system model is in close agreement with the measured data, and the reconstructed material density images match the ground truth concentrations for the multi-contrast phantom. These preliminary results demonstrate the potential of spatial-spectral filters to enable multi-contrast imaging and other new clinical applications of spectral CT.

High-Resolution Model-based Material Decomposition for Multi-Layer Flat-Panel Detectors

In this work we compare a novel model-based material decomposition (MBMD) approach against a standard approach in high-resolution spectral CT using multi-layer flat-panel detectors. Physical experiments were conducted using a prototype dual-layer detector and a custom high-resolution iodine-enhanced line-pair phantom. Reconstructions were performed using three methods: traditional filtered back-projection (FBP) followed by image-domain decomposition, idealized MBMD with no blur modeling (iMBMD), and MBMD with system blur modeling (bMBMD). We find that both MBMD methods yielded higher resolution decompositions with lower noise than the FBP method, and that bMBMD further improves spatial resolution over iMBMD due to the additional blur modeling. These results demonstrate the advantages of MBMD in resolution performance and noise control over traditional methods for spectral CT. Model-based material decomposition hence has great potential in high-resolution spectral CT applications.

Special Section Guest Editorial: Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine

Guest editors Scott D. Metzler, Samuel Matej, and J. Webster Stayman provide an introduction to the Special Section on Three-Dimensional Image Reconstruction in Nuclear Medicine, PET, and CT.

Cone-beam CT for imaging of the head/brain: Development and assessment of scanner prototype and reconstruction algorithms

PURPOSE

Our aim was to develop a high-quality, mobile cone-beam computed tomography (CBCT) scanner for point-of-care detection and monitoring of low-contrast, soft-tissue abnormalities in the head/brain, such as acute intracranial hemorrhage (ICH). This work presents an integrated framework of hardware and algorithmic advances for improving soft-tissue contrast resolution and evaluation of its technical performance with human subjects.

METHODS

Four configurations of a CBCT scanner prototype were designed and implemented to investigate key aspects of hardware (including system geometry, antiscatter grid, bowtie filter) and technique protocols. An integrated software pipeline (c.f., a serial cascade of algorithms) was developed for artifact correction (image lag, glare, beam hardening and x-ray scatter), motion compensation, and three-dimensional image (3D) reconstruction [penalized weighted least squares (PWLS), with a hardware-specific statistical noise model]. The PWLS method was extended in this work to accommodate multiple, independently moving regions with different resolution (to address both motion compensation and image truncation). Imaging performance was evaluated quantitatively and qualitatively with 41 human subjects in the neurosciences critical care unit (NCCU) at our institution.

RESULTS

The progression of four scanner configurations exhibited systematic improvement in the quality of raw data by variations in system geometry (source-detector distance), antiscatter grid, and bowtie filter. Quantitative assessment of CBCT images in 41 subjects demonstrated: ~70% reduction in image nonuniformity with artifact correction methods (lag, glare, beam hardening, and scatter); ~40% reduction in motion-induced streak artifacts via the multi-motion compensation method; and ~15% improvement in soft-tissue contrast-to-noise ratio (CNR) for PWLS compared to filtered backprojection (FBP) at matched resolution. Each of these components was important to improve contrast resolution for point-of-care cranial imaging.

CONCLUSIONS

This work presents the first application of a high-quality, point-of-care CBCT system for imaging of the head/ brain in a neurological critical care setting. Hardware configuration iterations and an integrated software pipeline for artifacts correction and PWLS reconstruction mitigated artifacts and noise to achieve image quality that could be valuable for point-of-care detection and monitoring of a variety of intracranial abnormalities, including ICH and hydrocephalus.