Review of CT image reconstruction open source toolkits

MCR toolkit: A GPU-based toolkit for multi-channel reconstruction of preclinical and clinical x-ray CT data

BACKGROUND

The advancement of x-ray CT into the domains of photon counting spectral imaging and dynamic cardiac and perfusion imaging has created many new challenges and opportunities for clinicians and researchers. To address challenges such as dose constraints and scanning times while capitalizing on opportunities such as multi-contrast imaging and low-dose coronary angiography, these multi-channel imaging applications require a new generation of CT reconstruction tools. These new tools should exploit the relationships between imaging channels during reconstruction to set new image quality standards while serving as a platform for direct translation between the preclinical and clinical domains.

PURPOSE

We outline and demonstrate a new Multi-Channel Reconstruction (MCR) Toolkit for GPU-based analytical and iterative reconstruction of preclinical and clinical multi-energy and dynamic x-ray CT data. To promote open science, open-source distribution of the Toolkit will coincide with the release of this publication (GPL v3; gitlab.oit.duke.edu/dpc18/mcr-toolkit-public).

METHODS

The MCR Toolkit source code is implemented in C/C++ and NVIDIA's CUDA GPU programming interface, with scripting support from MATLAB and Python. The Toolkit implements matched, separable footprint CT reconstruction operators for projection and backprojection in two geometries: planar, cone-beam CT (CBCT) and 3rd generation, cylindrical multi-detector row CT (MDCT). Analytical reconstruction is performed using filtered backprojection (FBP) for circular CBCT, weighted FBP (WFBP) for helical CBCT, and cone-parallel projection rebinning followed by WFBP for MDCT. Arbitrary combinations of energy and temporal channels are iteratively reconstructed under a generalized multi-channel signal model for joint reconstruction. We solve this generalized model algebraically using the split Bregman optimization method and the BiCGSTAB(l) linear solver interchangeably for both CBCT and MDCT data. Rank-sparse kernel regression (RSKR) and patch-based singular value thresholding (pSVT) are used to regularize the energy and time dimensions, respectively. Under a Gaussian noise model, regularization parameters are estimated automatically from the input data, dramatically reducing algorithm complexity for end users. Multi-GPU parallelization of the reconstruction operators is supported to manage reconstruction times.

RESULTS

Denoising with RSKR and pSVT and post-reconstruction material decomposition are illustrated with preclinical and clinical cardiac photon-counting (PC)CT data. A digital MOBY mouse phantom with cardiac motion is used to illustrate single energy (SE), multi-energy (ME), time resolved (TR), and combined multi-energy and time-resolved (METR) helical, CBCT reconstruction. A fixed set of projection data is used across all reconstruction cases to demonstrate the Toolkit's robustness to increasing data dimensionality. Identical reconstruction code is applied to in vivo cardiac PCCT data acquired in a mouse model of atherosclerosis (METR). Clinical cardiac CT reconstruction is illustrated using the XCAT phantom and the DukeSim CT simulator, while dual-source, dual-energy CT reconstruction is illustrated for data acquired with a Siemens Flash scanner. Benchmarking results with NVIDIA RTX 8000 GPU hardware demonstrate 61%-99% efficiency in scaling computation from one to four GPUs for these reconstruction problems.

CONCLUSIONS

The MCR Toolkit provides a robust solution for temporal and spectral x-ray CT reconstruction problems and was built from the ground up to facilitate translation of CT research and development between preclinical and clinical applications.

Angle prediction model when the imaging plane is tilted about z-axis

Computer Tomography (CT) is a complicated imaging system, requiring highly geometric positioning. We found a special artifact caused by detection plane tilted around z-axis. In short scan cone-beam reconstruction, this kind of geometric deviation result in half circle shaped fuzzy around highlighted particles in reconstructed slices. This artifact is distinct near the slice periphery, but deficient around the slice center. We generated mathematical models, and InceptionV3-R deep network to study the slice artifact features to estimate the detector z-axis tilt angle. The testing results are: mean absolute error of 0.08819 degree, the Root mean square error of 0.15221 degree and R-square of 0.99944. A geometric deviation recover formula was deduced, which can eliminate this artifact efficiently. This research enlarges the CT artifact knowledge hierarchy, and verifies the capability of machine learning in CT geometric deviation artifact recoveries.

Reconstruction Algorithm-Based CT Imaging for the Diagnosis of Hepatic Ascites

The study was aimed at exploring the diagnostic value of artificial intelligence reconstruction algorithm combined with CT image parameters on hepatic ascites, expected to provide a reference for the etiological evaluation of clinical abdominal effusion. Specifically, the adaptive iterative hard threshold (AIHT) algorithm for CT image reconstruction was proposed. Then, 100 patients with peritoneal effusion were selected as the research subjects. After 8 cases were excluded, the remaining was divided into 50 cases of the S1 group (hepatic ascites) and 42 cases of the D0 group (cancerous peritoneal effusion). Gemstone energy spectrum CT scanning was performed on all patients, and CT image parameters of the two groups were compared. It was found that CT value of mixed energy, CT value of 60-100 KeV single energy, concentration value of water (calcium), concentration value of water (iodine), and slope of energy spectrum curve in the S1 group were significantly lower than those in the D0 group ( $P<0.05$ ). The effective atomic number in the S1 group was significantly higher than that in the D0 group ( $P<0.05$ ). Of the 50 patients in the S1 group, 3 (6%) had an ascending and 47 (94%) had a descending spectral curve. Of the 42 patients in the D0 group, 37 (88.1%) had an ascending and 5 (11.9%) had a descending spectral curve. The sensitivity and specificity of water (iodine) were 0.927 and 0.836, respectively. The sensitivity and specificity of water (calcium) were 0.863 and 0.887, respectively. For different scan ranges ([0,90]; [0,120]), root mean square error (RMSE) of AIHT reconstructed image was significantly smaller than that of traditional algorithm, while peak signal-to-noise ratio (PSNR) was opposite. The differences were statistically significant ( $P<0.05$ ). In conclusion, AIHT-based CT images can better display the distribution of hepatic ascites, and the parameters of CT value, effective atomic number, water (iodine), water (calcium), and spectral curve can all provide help for the identification of hepatic ascites. Especially, water (iodine) and water (calcium) demonstrated high diagnostic performance of hepatic ascites.

A new weighting scheme for arc based circle cone-beam CT reconstruction

In this paper, we present an arc based fan-beam computed tomography (CT) reconstruction algorithm by applying Katsevich's helical CT image reconstruction formula to 2D fan-beam CT scanning data. Specifically, we propose a new weighting function to deal with the redundant data. Our weighting function ϖ(x_,λ) is an average of two characteristic functions, where each characteristic function indicates whether the projection data of the scanning angle contributes to the intensity of the pixel x_. In fact, for every pixel x_, our method uses the projection data of two scanning angle intervals to reconstruct its intensity, where one interval contains the starting angle and another contains the end angle. Each interval corresponds to a characteristic function. By extending the fan-beam algorithm to the circle cone-beam geometry, we also obtain a new circle cone-beam CT reconstruction algorithm. To verify the effectiveness of our method, the simulated experiments are performed for 2D fan-beam geometry with straight line detectors and 3D circle cone-beam geometry with flat-plan detectors, where the simulated sinograms are generated by the open-source software "ASTRA toolbox." We compare our method with the other existing algorithms. Our experimental results show that our new method yields the lowest root-mean-square-error (RMSE) and the highest structural-similarity (SSIM) for both reconstructed 2D and 3D fan-beam CT images.

Reconstruction Algorithm-Based Ultrasonic and Spiral CT Images in Evaluating the Effects of Dexmedetomidine Anesthesia for Acute Abdomen

OBJECTIVE

The study focused on the application value of iteration reconstruction algorithm-based ultrasound and spiral computed tomography (CT) examinations, and the safety of dexmedetomidine anesthesia in acute abdominal surgery.

METHODS

80 cases having the acute abdomen surgery were selected as the research subjects. They were divided into group A (40 cases) and group B (40 cases) according to the anesthetic drugs used in the later period. The experimental group was injected with propofol, remifentanil, and atracurium combined with dexmedetomidine; the control group was injected with propofol, remifentanil, and atracurium only. After the operation, the patient was for observed for the pain, agitation, adverse reactions, heart rate (HR), and blood pressure. All patients received ultrasound and spiral CT examinations, and based on the characteristics of the back-projection algorithm, an accelerated algorithm was established and used to process the image, and according to which, the patient's condition and curative effects were evaluated.

RESULTS

After image reconstruction, the ultrasound and spiral CT images were clearer with less noise and more prominent lesions than before reconstruction. Before image reconstruction, the accuracy rates of ultrasound and spiral CT in diagnosing acute abdomen were 92.3% and 91.1%, respectively. After reconstruction, the corresponding numbers were 96.3% and 98.1%, respectively. After reconstruction, the accuracy of the two methods in diagnosing acute abdomen was significantly improved compared with that before reconstruction, and the difference was statistically significant (P < 0.05). The Ramsay score of the experimental group was significantly higher than that of the control group at each time period, P < 0.05; the agitation score and visual analogue scale (VAS) score of the experimental group were significantly lower than the control group at each time period after waking up, P < 0.05.

CONCLUSION

Reconstruction algorithm-based ultrasound and spiral CT images have high application value in the diagnosis of patients with acute abdomen, and dexmedetomidine has good safety in anesthesia surgery.

Learning a Deep CNN Denoising Approach Using Anatomical Prior Information Implemented With Attention Mechanism for Low-Dose CT Imaging on Clinical Patient Data From Multiple Anatomical Sites

Dose reduction in computed tomography (CT) has gained considerable attention in clinical applications because it decreases radiation risks. However, a lower dose generates noise in low-dose computed tomography (LDCT) images. Previous deep learning (DL)-based works have investigated ways to improve diagnostic performance to address this ill-posed problem. However, most of them disregard the anatomical differences among different human body sites in constructing the mapping function between LDCT images and their high-resolution normal-dose CT (NDCT) counterparts. In this article, we propose a novel deep convolutional neural network (CNN) denoising approach by introducing information of the anatomical prior. Instead of designing multiple networks for each independent human body anatomical site, a unified network framework is employed to process anatomical information. The anatomical prior is represented as a pattern of weights of the features extracted from the corresponding LDCT image in an anatomical prior fusion module. To promote diversity in the contextual information, a spatial attention fusion mechanism is introduced to capture many local regions of interest in the attention fusion module. Although many network parameters are saved, the experimental results demonstrate that our method, which incorporates anatomical prior information, is effective in denoising LDCT images. Furthermore, the anatomical prior fusion module could be conveniently integrated into other DL-based methods and avails the performance improvement on multiple anatomical data.

Musiré: multimodal simulation and reconstruction framework for the radiological imaging sciences

A software-based workflow is proposed for managing the execution of simulation and image reconstruction for SPECT, PET, CBCT, MRI, BLI and FMI packages in single and multimodal biomedical imaging applications. The workflow is composed of a Bash script, the purpose of which is to provide an interface to the user, and to organize data flow between dedicated programs for simulation and reconstruction. The currently incorporated simulation programs comprise GATE for Monte Carlo simulation of SPECT, PET and CBCT, SpinScenario for simulating MRI, and Lipros for Monte Carlo simulation of BLI and FMI. Currently incorporated image reconstruction programs include CASToR for SPECT and PET as well as RTK for CBCT. MetaImage (mhd) standard is used for voxelized phantom and image data format. Meshlab project (mlp) containers incorporating polygon meshes and point clouds defined by the Stanford triangle format (ply) are employed to represent anatomical structures for optical simulation, and to represent tumour cell inserts. A number of auxiliary programs have been developed for data transformation and adaptive parameter assignment. The software workflow uses fully automatic distribution to, and consolidation from, any number of Linux workstations and CPU cores. Example data are presented for clinical SPECT, PET and MRI systems using the Mida head phantom and for preclinical X-ray, PET and BLI systems employing the Digimouse phantom. The presented method unifies and simplifies multimodal simulation setup and image reconstruction management and might be of value for synergistic image research. This article is part of the theme issue 'Synergistic tomographic image reconstruction: part 2'.

Computed Tomography- (CT-) Based Virtual Surgery Planning for Spinal Intervertebral Foraminal Assisted Clinical Treatment

With the development of minimally invasive spine concepts and the introduction of new minimally invasive instruments, minimally invasive spine technology, represented by foraminoscopy, has flourished, and percutaneous foraminoscopy has become one of the most reliable minimally invasive procedures for the treatment of lumbar disc herniation. Percutaneous foraminoscopy is a safe and effective minimally invasive spinal endoscopic surgical technique. It fully protects the paravertebral muscles and soft tissues as well as the posterior column structure of the spine, provides precise treatment of the target nucleus pulposus tissue, with the advantages of less surgical trauma, fewer postoperative complications, and rapid postoperative recovery, and is widely promoted and used in clinical practice. In this paper, we can view the location, morphology, structure, alignment, and adjacency relationships by performing coronary, CT, and diagonal reconstruction along the attachment of the yellow ligaments and performing 3D reconstruction or processing techniques after performing CT scans. This allows clinicians to observe the laminoplasty and the stenosis of the vertebral canal in a more intuitive and overall manner. It has clinical significance for the display of the sublaminar spine as well as the physician's judgment of the disease and the choice of surgery.

DaNet: dose-aware network embedded with dose-level estimation for low-dose CT imaging

Many deep learning (DL)-based image restoration methods for low-dose CT (LDCT) problems directly employ the end-to-end networks on low-dose training data without considering dose differences. However, the radiation dose difference has a great impact on the ultimate results, and lower doses increase the difficulty of restoration. Moreover, there is increasing demand to design and estimate acceptable scanning doses for patients in clinical practice, necessitating dose-aware networks embedded with adaptive dose estimation. In this paper, we consider these dose differences of input LDCT images and propose an adaptive dose-aware network. First, considering a large dose distribution range for simulation convenience, we coarsely define five dose levels in advance as lowest, lower, mild, higher and highest radiation dose levels. Instead of directly building the end-to-end mapping function between LDCT images and high-dose CT counterparts, the dose level is primarily estimated in the first stage. In the second stage, the adaptively learned low-dose level is used to guide the image restoration process as the pattern of prior information through the channel feature transform. We conduct experiments on a simulated dataset based on original high dose parts of American Association of Physicists in Medicine challenge datasets from the Mayo Clinic. Ablation studies validate the effectiveness of the dose-level estimation, and the experimental results show that our method is superior to several other DL-based methods. Specifically, our method provides obviously better performance in terms of the peak signal-to-noise ratio and visual quality reflected in subjective scores. Due to the dual-stage process, our method may suffer limitations under more parameters and coarse dose-level definitions, and thus, further improvements in clinical practical applications with different CT equipment vendors are planned in future work.

A TV-minimization image-reconstruction algorithm without system matrix

PURPOSE

Total Variation (TV) minimization algorithm is a classical compressed sensing (CS) based iterative image reconstruction algorithm that can accurately reconstruct images from sparse-view projections in computed tomography (CT). However, the system matrix used in the algorithm is often too large to be stored in computer memory. The purpose of this study is to investigate a new TV algorithm based on image rotation and without system matrix to avoid the memory requirement of system matrix.

METHODS

Without loss of generality, a rotation-based adaptive steepest descent-projection onto convex sets (R-ASD-POCS) algorithm is proposed and tested to solve the TV model in parallel beam CT. Specifically, simulation experiments are performed via the Shepp-Logan, FORBILD and real CT image phantoms are used to verify the inverse-crime capability of the algorithm and evaluate the sparse reconstruction capability and the noise suppression performance of the algorithm.

RESULTS

Experimental results show that the algorithm can achieve inverse-crime, accurate sparse reconstruction and thus accurately reconstruct images from noisy projections. Compared with the classical ASD-POCS algorithm, the new algorithm may yield the similar image reconstruction accuracy without use of the huge system matrix, which saves the computational memory space significantly. Additionally, the results also show that R-ASD-POCS algorithm is faster than ASD-POCS.

CONCLUSIONS

The proposed new algorithm can effectively solve the problem of using huge memory in large scale and iterative image reconstruction. Integrating with ASD-POCS frame, this no-system-matrix based scheme may be readily extended and applied to any iterative image reconstructions.