Deep learning based synthetic-CT generation in radiotherapy and PET: A review

Streaking artifact reduction for CBCT-based synthetic CT generation in adaptive radiotherapy

BACKGROUND

Cone-beam computed tomography (CBCT) is widely used for daily image guidance in radiation therapy, enhancing the reproducibility of patient setup. However, its application in adaptive radiotherapy (ART) is limited by many imaging artifacts and inaccurate Hounsfield units (HUs). The correction of CBCT image is necessary and of great value for CBCT-based ART.

PURPOSE

To explore the synthetic CT (sCT) generation from CBCT images of thorax and abdomen patients, which usually surfer from serious artifacts duo to organ state changes. In this study, a streaking artifact reduction network (SARN) is proposed to reduce artifacts and combine with cycleGAN to generate high-quality sCT images from CBCT and achieve an accurate dose calculation.

METHODS

The proposed SARN was trained in a self-supervised manner. Artifact-CT images were generated from planning CT by random deformation and projection replacement, and SARN was trained based on paired artifact-CT and CT images. The planning CT and CBCT images of 260 patients with cancer, including 120 thoracic and 140 abdominal CT scans, were used to train and evaluate neural networks. The CBCT images of another 12 patients in late treatment fractions, which contained large anatomy changes, were also tested by trained models. The trained models include commonly used U-Net, cycleGAN, attention-gated cycleGAN (cycAT), and cascade models combined SARN with cycleGAN or cycAT. The generated sCT images were compared in terms of image quality and dose calculation accuracy.

RESULTS

The sCT images generated by SARN combined with cycleGAN and cycAT showed the best image quality, removed the most artifacts, and retained the normal anatomical structure. The SARN+cycleGAN performed best in streaking artifacts removal with the maximum percent integrity uniformity (PIU_m ) of 91.0% and minimum standard deviation (SD) of 35.4 HU for delineated artifact regions among all models. The mean absolute error (MAE) of CBCT images in the thorax and abdomen were 71.6 and 55.2 HU, respectively, using planning CT images after deformable registration as ground truth. Compared with CBCT, the thoracic and abdominal sCT images generated by each model had significantly improved image quality with smaller MAE (p < 0.05). The SARN+cycAT obtained the minimum MAEs of 42.5 HU in the thorax while SARN+cycleGAN got the minimum MAEs of 32.0 HU in the abdomen. The sCT generated by U-Net had a remarkably lower anatomical structure accuracy compared with the other models. The thoracic and abdominal sCT images generated by SARN+cycleGAN showed optimal dose calculation accuracy with gamma passing rates (2 mm/2%) of 98.2% and 96.9%, respectively.

CONCLUSIONS

The proposed SARN can reduce serious streaking artifacts in CBCT images. The SARN combined with cycleGAN can generate high-quality sCT images with fewer artifacts, high-accuracy HU values, and accurate anatomical structures, thus providing reliable dose calculation in ART.

Synthetic computed tomography generation for abdominal adaptive radiotherapy using low-field magnetic resonance imaging

Background and Purpose

Magnetic Resonance guided Radiotherapy (MRgRT) still needs the acquisition of Computed Tomography (CT) images and co-registration between CT and Magnetic Resonance Imaging (MRI). The generation of synthetic CT (sCT) images from the MR data can overcome this limitation. In this study we aim to propose a Deep Learning (DL) based approach for sCT image generation for abdominal Radiotherapy using low field MR images.

Materials and methods

CT and MR images were collected from 76 patients treated on abdominal sites. U-Net and conditional Generative Adversarial Network (cGAN) architectures were used to generate sCT images. Additionally, sCT images composed of only six bulk densities were generated with the aim of having a Simplified sCT.Radiotherapy plans calculated using the generated images were compared to the original plan in terms of gamma pass rate and Dose Volume Histogram (DVH) parameters.

Results

sCT images were generated in 2 s and 2.5 s with U-Net and cGAN architectures respectively.Gamma pass rates for 2%/2mm and 3%/3mm criteria were 91% and 95% respectively. Dose differences within 1% for DVH parameters on the target volume and organs at risk were obtained.

Conclusion

U-Net and cGAN architectures are able to generate abdominal sCT images fast and accurately from low field MRI.

Anatomical evaluation of deep-learning synthetic computed tomography images generated from male pelvis cone-beam computed tomography

Background and purpose

To improve cone-beam computed tomography (CBCT), deep-learning (DL)-models are being explored to generate synthetic CTs (sCT). The sCT evaluation is mainly focused on image quality and CT number accuracy. However, correct representation of daily anatomy of the CBCT is also important for sCTs in adaptive radiotherapy. The aim of this study was to emphasize the importance of anatomical correctness by quantitatively assessing sCT scans generated from CBCT scans using different paired and unpaired dl-models.

Materials and methods

Planning CTs (pCT) and CBCTs of 56 prostate cancer patients were included to generate sCTs. Three different dl-models, Dual-UNet, Single-UNet and Cycle-consistent Generative Adversarial Network (CycleGAN), were evaluated on image quality and anatomical correctness. The image quality was assessed using image metrics, such as Mean Absolute Error (MAE). The anatomical correctness between sCT and CBCT was quantified using organs-at-risk volumes and average surface distances (ASD).

Results

MAE was 24 Hounsfield Unit (HU) [range:19-30 HU] for Dual-UNet, 40 HU [range:34-56 HU] for Single-UNet and 41HU [range:37-46 HU] for CycleGAN. Bladder ASD was 4.5 mm [range:1.6-12.3 mm] for Dual-UNet, 0.7 mm [range:0.4-1.2 mm] for Single-UNet and 0.9 mm [range:0.4-1.1 mm] CycleGAN.

Conclusions

Although Dual-UNet performed best in standard image quality measures, such as MAE, the contour based anatomical feature comparison with the CBCT showed that Dual-UNet performed worst on anatomical comparison. This emphasizes the importance of adding anatomy based evaluation of sCTs generated by dl-models. For applications in the pelvic area, direct anatomical comparison with the CBCT may provide a useful method to assess the clinical applicability of dl-based sCT generation methods.

The future of MRI in radiation therapy: Challenges and opportunities for the MR community

Radiation therapy is a major component of cancer treatment pathways worldwide. The main aim of this treatment is to achieve tumor control through the delivery of ionizing radiation while preserving healthy tissues for minimal radiation toxicity. Because radiation therapy relies on accurate localization of the target and surrounding tissues, imaging plays a crucial role throughout the treatment chain. In the treatment planning phase, radiological images are essential for defining target volumes and organs-at-risk, as well as providing elemental composition (e.g., electron density) information for radiation dose calculations. At treatment, onboard imaging informs patient setup and could be used to guide radiation dose placement for sites affected by motion. Imaging is also an important tool for treatment response assessment and treatment plan adaptation. MRI, with its excellent soft tissue contrast and capacity to probe functional tissue properties, holds great untapped potential for transforming treatment paradigms in radiation therapy. The MR in Radiation Therapy ISMRM Study Group was established to provide a forum within the MR community to discuss the unmet needs and fuel opportunities for further advancement of MRI for radiation therapy applications. During the summer of 2021, the study group organized its first virtual workshop, attended by a diverse international group of clinicians, scientists, and clinical physicists, to explore our predictions for the future of MRI in radiation therapy for the next 25 years. This article reviews the main findings from the event and considers the opportunities and challenges of reaching our vision for the future in this expanding field.

Deep learning-based segmentation in prostate radiation therapy using Monte Carlo simulated cone-beam computed tomography

PURPOSE

Segmenting organs in cone-beam CT (CBCT) images would allow to adapt the radiotherapy based on the organ deformations that may occur between treatment fractions. However, this is a difficult task because of the relative lack of contrast in CBCT images, leading to high inter-observer variability. Deformable image registration (DIR) and deep-learning based automatic segmentation approaches have shown interesting results for this task in the past years. However, they are either sensitive to large organ deformations, or require to train a convolutional neural network (CNN) from a database of delineated CBCT images, which is difficult to do without improvement of image quality. In this work, we propose an alternative approach: to train a CNN (using a deep learning-based segmentation tool called nnU-Net) from a database of artificial CBCT images simulated from planning CT, for which it is easier to obtain the organ contours.

METHODS

Pseudo-CBCT (pCBCT) images were simulated from readily available segmented planning CT images, using the GATE Monte Carlo simulation. CT reference delineations were copied onto the pCBCT, resulting in a database of segmented images used to train the neural network. The studied segmentation contours were: bladder, rectum, and prostate contours. We trained multiple nnU-Net models using different training: (1) segmented real CBCT, (2) pCBCT, (3) segmented real CT and tested on pseudo-CT (pCT) generated from CBCT with cycleGAN, and (4) a combination of (2) and (3). The evaluation was performed on different datasets of segmented CBCT or pCT by comparing predicted segmentations with reference ones thanks to Dice similarity score and Hausdorff distance. A qualitative evaluation was also performed to compare DIR-based and nnU-Net-based segmentations.

RESULTS

Training with pCBCT was found to lead to comparable results to using real CBCT images. When evaluated on CBCT obtained from the same hospital as the CT images used in the simulation of the pCBCT, the model trained with pCBCT scored mean DSCs of 0.92 ± 0.05, 0.87 ± 0.02, and 0.85 ± 0.04 and mean Hausdorff distance 4.67 ± 3.01, 3.91 ± 0.98, and 5.00 ± 1.32 for the bladder, rectum, and prostate contours respectively, while the model trained with real CBCT scored mean DSCs of 0.91 ± 0.06, 0.83 ± 0.07, and 0.81 ± 0.05 and mean Hausdorff distance 5.62 ± 3.24, 6.43 ± 5.11, and 6.19 ± 1.14 for the bladder, rectum, and prostate contours, respectively. It was also found to outperform models using pCT or a combination of both, except for the prostate contour when tested on a dataset from a different hospital. Moreover, the resulting segmentations demonstrated a clinical acceptability, where 78% of bladder segmentations, 98% of rectum segmentations, and 93% of prostate segmentations required minor or no corrections, and for 76% of the patients, all structures of the patient required minor or no corrections.

CONCLUSION

We proposed to use simulated CBCT images to train a nnU-Net segmentation model, avoiding the need to gather complex and time-consuming reference delineations on CBCT images.

Deep learning-based 4D-synthetic CTs from sparse-view CBCTs for dose calculations in adaptive proton therapy

BACKGROUND

Time-resolved 4D cone beam-computed tomography (4D-CBCT) allows a daily assessment of patient anatomy and respiratory motion. However, 4D-CBCTs suffer from imaging artifacts that affect the CT number accuracy and prevent accurate proton dose calculations. Deep learning can be used to correct CT numbers and generate synthetic CTs (sCTs) that can enable CBCT-based proton dose calculations.

PURPOSE

In this work, sparse view 4D-CBCTs were converted into 4D-sCT utilizing a deep convolutional neural network (DCNN). 4D-sCTs were evaluated in terms of image quality and dosimetric accuracy to determine if accurate proton dose calculations for adaptive proton therapy workflows of lung cancer patients are feasible.

METHODS

A dataset of 45 thoracic cancer patients was utilized to train and evaluate a DCNN to generate 4D-sCTs, based on sparse view 4D-CBCTs reconstructed from projections acquired with a 3D acquisition protocol. Mean absolute error (MAE) and mean error were used as metrics to evaluate the image quality of single phases and average 4D-sCTs against 4D-CTs acquired on the same day. The dosimetric accuracy was checked globally (gamma analysis) and locally for target volumes and organs-at-risk (OARs) (lung, heart, and esophagus). Furthermore, 4D-sCTs were also compared to 3D-sCTs. To evaluate CT number accuracy, proton radiography simulations in 4D-sCT and 4D-CTs were compared in terms of range errors. The clinical suitability of 4D-sCTs was demonstrated by performing a 4D dose reconstruction using patient specific treatment delivery log files and breathing signals.

RESULTS

4D-sCTs resulted in average MAEs of 48.1 ± 6.5 HU (single phase) and 37.7 ± 6.2 HU (average). The global dosimetric evaluation showed gamma pass ratios of 92.3% ± 3.2% (single phase) and 94.4% ± 2.1% (average). The clinical target volume showed high agreement in D₉₈ between 4D-CT and 4D-sCT, with differences below 2.4% for all patients. Larger dose differences were observed in mean doses of OARs (up to 8.4%). The comparison with 3D-sCTs showed no substantial image quality and dosimetric differences for the 4D-sCT average. Individual 4D-sCT phases showed slightly lower dosimetric accuracy. The range error evaluation revealed that lung tissues cause range errors about three times higher than the other tissues.

CONCLUSION

In this study, we have investigated the accuracy of deep learning-based 4D-sCTs for daily dose calculations in adaptive proton therapy. Despite image quality differences between 4D-sCTs and 3D-sCTs, comparable dosimetric accuracy was observed globally and locally. Further improvement of 3D and 4D lung sCTs could be achieved by increasing CT number accuracy in lung tissues.

Evaluation of a New, Highly Flexible Radiofrequency Coil for MR Simulation of Patients Undergoing External Beam Radiation Therapy

PURPOSE

To evaluate the performance of a new, highly flexible radiofrequency (RF) coil system for imaging patients undergoing MR simulation.

METHODS

Volumetric phantom and in vivo images were acquired with a commercially available and prototype RF coil set. Phantom evaluation was performed using a silicone-filled humanoid phantom of the head and shoulders. In vivo assessment was performed in five healthy and six patient subjects. Phantom data included T1-weighted volumetric imaging, while in vivo acquisitions included both T1- and T2-weighted volumetric imaging. Signal to noise ratio (SNR) and uniformity metrics were calculated in the phantom data, while SNR values were calculated in vivo. Statistical significance was tested by means of a non-parametric analysis of variance test.

RESULTS

At a threshold of p = 0.05, differences in measured SNR distributions within the entire phantom volume were statistically different in two of the three paired coil set comparisons. Differences in per slice average SNR between the two coil sets were all statistically significant, as well as differences in per slice image uniformity. For patients, SNRs within the entire imaging volume were statistically significantly different in four of the nine comparisons and seven of the nine comparisons performed on the per slice average SNR values. For healthy subjects, SNRs within the entire imaging volume were statistically significantly different in seven of the nine comparisons and eight of the nine comparisons when per slice average SNR was tested.

CONCLUSIONS

Phantom and in vivo results demonstrate that image quality obtained from the novel flexible RF coil set was similar or improved over the conventional coil system. The results also demonstrate that image quality is impacted by the specific coil configurations used for imaging and should be matched appropriately to the anatomic site imaged to ensure optimal and reproducible image quality.

Quality assurance for MRI-only radiation therapy: A voxel-wise population-based methodology for image and dose assessment of synthetic CT generation methods

The quality assurance of synthetic CT (sCT) is crucial for safe clinical transfer to an MRI-only radiotherapy planning workflow. The aim of this work is to propose a population-based process assessing local errors in the generation of sCTs and their impact on dose distribution. For the analysis to be anatomically meaningful, a customized interpatient registration method brought the population data to the same coordinate system. Then, the voxel-based process was applied on two sCT generation methods: a bulk-density method and a generative adversarial network. The CT and MRI pairs of 39 patients treated by radiotherapy for prostate cancer were used for sCT generation, and 26 of them with delineated structures were selected for analysis. Voxel-wise errors in sCT compared to CT were assessed for image intensities and dose calculation, and a population-based statistical test was applied to identify the regions where discrepancies were significant. The cumulative histograms of the mean absolute dose error per volume of tissue were computed to give a quantitative indication of the error for each generation method. Accurate interpatient registration was achieved, with mean Dice scores higher than 0.91 for all organs. The proposed method produces three-dimensional maps that precisely show the location of the major discrepancies for both sCT generation methods, highlighting the heterogeneity of image and dose errors for sCT generation methods from MRI across the pelvic anatomy. Hence, this method provides additional information that will assist with both sCT development and quality control for MRI-based planning radiotherapy.

Assessment of CBCT-based synthetic CT generation accuracy for adaptive radiotherapy planning

PURPOSE

Cone-beam CT (CBCT)-based synthetic CT (sCT) dose calculation has the potential to make the adaptive radiotherapy (ART) pathway more efficient while removing subjectivity. This study assessed four sCT generation methods using 15 head-and-neck rescanned ART patients. Each patient's planning CT (pCT), rescan CT (rCT), and CBCT post-rCT was acquired with the CBCT deformably registered to the rCT (dCBCT).

METHODS

The four methods investigated were as follows: method 1-deformably registering the pCT to the dCBCT. Method 2-assigning six mass density values to the dCBCT. Method 3-iteratively removing artifacts and correcting the dCBCT Hounsfield units (HU). Method 4-using a cycle general adversarial network machine learning model (trained with 45 paired pCT and CBCT). Treatment plans were created on the rCT and recalculated on each sCT. Planning target volume (PTV) and organ-at-risk (OAR) structures were contoured by clinicians on the rCT (high-dose PTV, low-dose PTV, spinal canal, larynx, brainstem, and parotids) to allow the assessment of dose-volume histogram statistics at clinically relevant points.

RESULTS

The HU mean absolute error (MAE) and minimum dose gamma index pass rate (2%/2 mm) were calculated, and the generation time was measured for 15 patients using the rCT as the comparator. For methods 1-4 the MAE, gamma index analysis, and generation time were as follows: 59.7 HU, 100.0%, and 143 s; 164.2 HU, 95.2%, and 232 s; 75.7 HU, 99.9%, and 153 s; and 79.4 HU, 99.8%, and 112 s, respectively. Dose differences for PTVs and OARs were all <0.3 Gy except for method 2 (<0.5 Gy).

CONCLUSION

All methods were considered clinically viable. The machine learning method was found to be most suitable for clinical implementation due to its high dosimetric accuracy and short generation time. Further investigation is required for larger anatomical changes between the CBCT and pCT and for other anatomical sites.

Synthetic CT generation for MRI-guided adaptive radiotherapy in prostate cancer

Current MRI-guided adaptive radiotherapy (MRgART) workflows require fraction-specific electron and/or mass density maps, which are created by deformable image registration (DIR) between the simulation CT images and daily MR images. Manual density overrides may also be needed where DIR-produced results are inaccurate. This approach slows the adaptive radiotherapy workflow and introduces additional dosimetric uncertainties, especially in the presence of the magnetic field. This study investigated a method based on a conditional generative adversarial network (cGAN) with a multi-planar method to generate synthetic CT images from low-field MR images to improve efficiency in MRgART workflows for prostate cancer. Fifty-seven male patients, who received MRI-guided radiation therapy to the pelvis using the ViewRay MRIdian Linac, were selected. Forty-five cases were randomly assigned to the training cohort with the remaining twelve cases assigned to the validation/testing cohort. All patient datasets had a semi-paired DIR-deformed CT-sim image and 0.35T MR image acquired using a true fast imaging with steady-state precession (TrueFISP) sequence. Synthetic CT images were compared with deformed CT images to evaluate image quality and dosimetric accuracy. To evaluate the dosimetric accuracy of this method, clinical plans were recalculated on synthetic CT images in the MRIdian treatment planning system. Dose volume histograms for planning target volumes (PTVs) and organs-at-risk (OARs) and dose distributions using gamma analyses were evaluated. The mean-absolute-errors (MAEs) in CT numbers were 30.1 ± 4.2 HU, 19.6 ± 2.3 HU and 158.5 ± 26.0 HU for the whole pelvis, soft tissue, and bone, respectively. The peak signal-to-noise ratio was 35.2 ± 1.7 and the structural index similarity measure was 0.9758 ± 0.0035. The dosimetric difference was on average less than 1% for all PTV and OAR metrics. Plans showed good agreement with gamma pass rates of 99% and 99.9% for 1%/1 mm and 2%/2 mm, respectively. Our study demonstrates the potential of using synthetic CT images created with a multi-planar cGAN method from 0.35T MRI TrueFISP images for the MRgART treatment of prostate radiotherapy. Future work will validate the method in a large cohort of patients and investigate the limitations of the method in the adaptive workflow.

Emergence of MR-Linac in Radiation Oncology: Successes and Challenges of Riding on the MRgRT Bandwagon

The special issue of JCM on “Advances of MRI in Radiation Oncology” provides a unique forum for scientific literature related to MR imaging in radiation oncology. This issue covered many aspects, such as MR technology, motion management, economics, soft-tissue–air interface issues, and disease sites such as the pancreas, spine, sarcoma, prostate, head and neck, and rectum from both camps—the Unity and MRIdian systems. This paper provides additional information on the success and challenges of the two systems. A challenging aspect of this technology is low throughput and the monumental task of education and training that hinders its use for the majority of therapy centers. Additionally, the cost of this technology is too high for most institutions, and hence widespread use is still limited. This article highlights some of the difficulties and how to resolve them.

Deep Learning for Synthetic CT from Bone MRI in the Head and Neck

BACKGROUND AND PURPOSE

Bone MR imaging techniques enable visualization of cortical bone without the need for ionizing radiation. Automated conversion of bone MR imaging to synthetic CT is highly desirable for downstream image processing and eventual clinical adoption. Given the complex anatomy and pathology of the head and neck, deep learning models are ideally suited for learning such mapping.

MATERIALS AND METHODS

This was a retrospective study of 39 pediatric and adult patients with bone MR imaging and CT examinations of the head and neck. For each patient, MR imaging and CT data sets were spatially coregistered using multiple-point affine transformation. Paired MR imaging and CT slices were generated for model training, using 4-fold cross-validation. We trained 3 different encoder-decoder models: Light_U-Net (2 million parameters) and VGG-16 U-Net (29 million parameters) without and with transfer learning. Loss functions included mean absolute error, mean squared error, and a weighted average. Performance metrics included Pearson R, mean absolute error, mean squared error, bone precision, and bone recall. We investigated model generalizability by training and validating across different conditions.

RESULTS

The Light_U-Net architecture quantitatively outperformed VGG-16 models. Mean absolute error loss resulted in higher bone precision, while mean squared error yielded higher bone recall. Performance metrics decreased when using training data captured only in a different environment but increased when local training data were augmented with those from different hospitals, vendors, or MR imaging techniques.

CONCLUSIONS

We have optimized a robust deep learning model for conversion of bone MR imaging to synthetic CT, which shows good performance and generalizability when trained on different hospitals, vendors, and MR imaging techniques. This approach shows promise for facilitating downstream image processing and adoption into clinical practice.

Zero-TE MRI: principles and applications in the head and neck

Zero echo-time (ZTE) MRI is a novel imaging technique that utilizes ultrafast readouts to capture signal from short-T2 tissues. Additional sequence advantages include rapid imaging times, silent scanning, and artifact resistance. A robust application of this technology is imaging of cortical bone without the use of ionizing radiation, thus representing a viable alternative to CT for both rapid screening and "one-stop-shop" MRI. Although ZTE is increasingly used in musculoskeletal and body imaging, neuroimaging applications have historically been limited by complex anatomy and pathology. In this article, we review the imaging physics of ZTE including pulse sequence options, practical limitations, and image reconstruction. We then discuss optimization of settings for ZTE bone neuroimaging including acquisition, processing, segmentation, synthetic CT generation, and artifacts. Finally, we examine clinical utility of ZTE in the head and neck with imaging examples including malformations, trauma, tumors, and interventional procedures.

Possibilities and challenges when using synthetic computed tomography in an adaptive carbon-ion treatment workflow

BACKGROUND AND PURPOSE

Anatomical surveillance during ion-beam therapy is the basis for an effective tumor treatment and optimal organ at risk (OAR) sparing. Synthetic computed tomography (sCT) based on magnetic resonance imaging (MRI) can replace the X-ray based planning CT (X-rayCT) in photon radiotherapy and improve the workflow efficiency without additional imaging dose. The extension to carbon-ion radiotherapy is highly challenging; complex patient positioning, unique anatomical situations, distinct horizontal and vertical beam incidence directions, and limited training data are only few problems. This study gives insight into the possibilities and challenges of using sCTs in carbon-ion therapy.

MATERIALS AND METHODS

For head and neck patients immobilised with thermoplastic masks 30 clinically applied actively scanned carbon-ion treatment plans on 15 CTs comprising 60 beams were analyzed. Those treatment plans were re-calculated on MRI based sCTs which were created employing a 3D U-Net. Dose differences and carbon-ion spot displacements between sCT and X-rayCT were evaluated on a patient specific basis.

RESULTS

Spot displacement analysis showed a peak displacement by 0.2 cm caused by the immobilisation mask not measurable with the MRI. 95.7% of all spot displacements were located within 1 cm. For the clinical target volume (CTV) the median D_50% agreed within -0.2% (-1.3 to 1.4%), while the median D_0.01cc differed up to 4.2% (-1.3 to 25.3%) comparing the dose distribution on the X-rayCT and the sCT. OAR deviations depended strongly on the position and the dose gradient. For three patients no deterioration of the OAR parameters was observed. Other patients showed large deteriorations, e.g. for one patient D_2% of the chiasm differed by 28.1%.

CONCLUSION

The usage of sCTs opens several new questions, concluding that we are not ready yet for an MR-only workflow in carbon-ion therapy, as envisaged in photon therapy. Although omitting the X-rayCT seems unfavourable in the case of carbon-ion therapy, an sCT could be advantageous for monitoring, re-planning, and adaptation.

Target Definition in MR-Guided Adaptive Radiotherapy for Head and Neck Cancer

Simple Summary

Adaptive radiotherapy for head and neck cancer has become more routine due to an increase in imaging quality and improvement in radiation techniques. With the availability of faster adaptive workflows, it is possible to adapt more easily to (daily) changes. MRI offers besides great anatomical imaging, also functional information about the tumor and surrounding tissue. The aim of this review is to provide current state of evidence about target definition on MRI for adaptive strategies in the treatment of head and neck cancer.

Abstract

In recent years, MRI-guided radiotherapy (MRgRT) has taken an increasingly important position in image-guided radiotherapy (IGRT). Magnetic resonance imaging (MRI) offers superior soft tissue contrast in anatomical imaging compared to computed tomography (CT), but also provides functional and dynamic information with selected sequences. Due to these benefits, in current clinical practice, MRI is already used for target delineation and response assessment in patients with head and neck squamous cell carcinoma (HNSCC). Because of the close proximity of target areas and radiosensitive organs at risk (OARs) during HNSCC treatment, MRgRT could provide a more accurate treatment in which OARs receive less radiation dose. With the introduction of several new radiotherapy techniques (i.e., adaptive MRgRT, proton therapy, adaptive cone beam computed tomography (CBCT) RT, (daily) adaptive radiotherapy ensures radiation dose is accurately delivered to the target areas. With the integration of a daily adaptive workflow, interfraction changes have become visible, which allows regular and fast adaptation of target areas. In proton therapy, adaptation is even more important in order to obtain high quality dosimetry, due to its susceptibility for density differences in relation to the range uncertainty of the protons. The question is which adaptations during radiotherapy treatment are oncology safe and at the same time provide better sparing of OARs. For an optimal use of all these new tools there is an urgent need for an update of the target definitions in case of adaptive treatment for HNSCC. This review will provide current state of evidence regarding adaptive target definition using MR during radiotherapy for HNSCC. Additionally, future perspectives for adaptive MR-guided radiotherapy will be discussed.

Joint synthesis and registration network for deformable MR-CBCT image registration for neurosurgical guidance

Objective.The accuracy of navigation in minimally invasive neurosurgery is often challenged by deep brain deformations (up to 10 mm due to egress of cerebrospinal fluid during neuroendoscopic approach). We propose a deep learning-based deformable registration method to address such deformations between preoperative MR and intraoperative CBCT.Approach.The registration method uses a joint image synthesis and registration network (denoted JSR) to simultaneously synthesize MR and CBCT images to the CT domain and perform CT domain registration using a multi-resolution pyramid. JSR was first trained using a simulated dataset (simulated CBCT and simulated deformations) and then refined on real clinical images via transfer learning. The performance of the multi-resolution JSR was compared to a single-resolution architecture as well as a series of alternative registration methods (symmetric normalization (SyN), VoxelMorph, and image synthesis-based registration methods).Main results.JSR achieved median Dice coefficient (DSC) of 0.69 in deep brain structures and median target registration error (TRE) of 1.94 mm in the simulation dataset, with improvement from single-resolution architecture (median DSC = 0.68 and median TRE = 2.14 mm). Additionally, JSR achieved superior registration compared to alternative methods-e.g. SyN (median DSC = 0.54, median TRE = 2.77 mm), VoxelMorph (median DSC = 0.52, median TRE = 2.66 mm) and provided registration runtime of less than 3 s. Similarly in the clinical dataset, JSR achieved median DSC = 0.72 and median TRE = 2.05 mm.Significance.The multi-resolution JSR network resolved deep brain deformations between MR and CBCT images with performance superior to other state-of-the-art methods. The accuracy and runtime support translation of the method to further clinical studies in high-precision neurosurgery.

Adaptive Proton Therapy of Pediatric Head and Neck Cases Using MRI-Based Synthetic CTs: Initial Experience of the Prospective KiAPT Study

BACKGROUND AND PURPOSE

Interfractional anatomical changes might affect the outcome of proton therapy (PT). We aimed to prospectively evaluate the role of Magnetic Resonance Imaging (MRI) based adaptive PT for children with tumors of the head and neck and base of skull.

METHODS

MRI verification images were acquired at half of the treatment course. A synthetic computed tomography (CT) image was created using this MRI and a deformable image registration (DIR) to the reference MRI. The methodology was verified with in-silico phantoms and validated using a clinical case with a shrinking cystic hygroma on the basis of dosimetric quantities of contoured structures. The dose distributions on the verification X-ray CT and on the synthetic CT were compared with a gamma-index test using global 2 mm/2% criteria.

RESULTS

Regarding the clinical validation case, the gamma-index pass rate was 98.3%. Eleven patients were included in the clinical study. The most common diagnosis was rhabdomyosarcoma (73%). Craniofacial tumor site was predominant in 64% of patients, followed by base of skull (18%). For one individual case the synthetic CT showed an increase in the median D2 and Dmax dose on the spinal cord from 20.5 GyRBE to 24.8 GyRBE and 14.7 GyRBE to 25.1 GyRBE, respectively. Otherwise, doses received by OARs remained relatively stable. Similarly, the target volume coverage seen by D95% and V95% remained unchanged.

CONCLUSIONS

The method of transferring anatomical changes from MRIs to a synthetic CTs was successfully implemented and validated with simple, commonly available tools. In the frame of our early results on a small cohort, no clinical relevant deterioration for neither PTV coverage nor an increased dose burden to OARs occurred. However, the study will be continued to identify a pediatric patient cohort, which benefits from adaptive treatment planning.

Training of deep cross-modality conversion models with a small dataset, and their application in megavoltage CT to kilovoltage CT conversion

PURPOSE

In recent years, deep-learning-based image processing has emerged as a valuable tool for medical imaging owing to its high performance. However, the quality of deep-learning-based methods heavily relies on the amount of training data; the high cost of acquiring a large dataset is a limitation to their utilization in medical fields. Herein, based on deep learning, we developed a computed tomography (CT) modality conversion method requiring only a few unsupervised images.

METHODS

The proposed method is based on CycleGAN with several extensions tailored for CT images, which aims at preserving the structure in the processed images and reducing the amount of training data. This method was applied to realize the conversion of megavoltage computed tomography (MVCT) to kilovoltage computed tomography (kVCT) images. Training was conducted using several datasets acquired from patients with head and neck cancer. The size of the datasets ranged from 16 slices (two patients) to 2745 slices (137 patients) for MVCT and 2824 slices (98 patients) for kVCT.

RESULTS

The required size of the training data was found to be as small as a few hundred slices. By statistical and visual evaluations, the quality improvement and structure preservation of the MVCT images converted by the proposed model were investigated. As a clinical benefit, it was observed by medical doctors that the converted images enhanced the precision of contouring.

CONCLUSIONS

We developed an MVCT to kVCT conversion model based on deep learning, which can be trained using only a few hundred unpaired images. The stability of the model against changes in data size was demonstrated. This study promotes the reliable use of deep learning in clinical medicine by partially answering commonly asked questions, such as "Is our data sufficient?" and "How much data should we acquire?" This article is protected by copyright. All rights reserved.

Deep learning for Dixon MRI-based attenuation correction in PET/MRI of head and neck cancer patients

Background

Quantitative whole-body PET/MRI relies on accurate patient-specific MRI-based attenuation correction (AC) of PET, which is a non-trivial challenge, especially for the anatomically complex head and neck region. We used a deep learning model developed for dose planning in radiation oncology to derive MRI-based attenuation maps of head and neck cancer patients and evaluated its performance on PET AC.

Methods

Eleven head and neck cancer patients, referred for radiotherapy, underwent CT followed by PET/MRI with acquisition of Dixon MRI. Both scans were performed in radiotherapy position. PET AC was performed with three different patient-specific attenuation maps derived from: (1) Dixon MRI using a deep learning network (PET_Deep). (2) Dixon MRI using the vendor-provided atlas-based method (PET_Atlas). (3) CT, serving as reference (PET_CT). We analyzed the effect of the MRI-based AC methods on PET quantification by assessing the average voxelwise error within the entire body, and the error as a function of distance to bone/air. The error in mean uptake within anatomical regions of interest and the tumor was also assessed.

Results

The average (± standard deviation) PET voxel error was 0.0 ± 11.4% for PET_Deep and −1.3 ± 21.8% for PET_Atlas. The error in mean PET uptake in bone/air was much lower for PET_Deep (−4%/12%) than for PET_Atlas (−15%/84%) and PET_Deep also demonstrated a more rapidly decreasing error with distance to bone/air affecting only the immediate surroundings (less than 1 cm). The regions with the largest error in mean uptake were those containing bone (mandible) and air (larynx) for both methods, and the error in tumor mean uptake was −0.6 ± 2.0% for PET_Deep and −3.5 ± 4.6% for PET_Atlas.

Conclusion

The deep learning network for deriving MRI-based attenuation maps of head and neck cancer patients demonstrated accurate AC and exceeded the performance of the vendor-provided atlas-based method both overall, on a lesion-level, and in vicinity of challenging regions such as bone and air.

Delayed PET imaging using image synthesis network and nonrigid registration without additional CT scan

PURPOSE

Attenuation correction is critical for positron emission tomography (PET) image reconstruction. The standard protocol for obtaining attenuation information in a clinical PET scanner is via the coregistered computed tomography (CT) images. Therefore for delayed PET imaging, the CT scan is repeated twice, which increases the radiation dose for the patient. In this paper, we propose a zero-extra-dose delayed PET imaging method which requires no additional CT scans.

METHODS

A deep learning based synthesis network is designed to convert the PET data into a pseudo CT image for the delayed scan. Then, nonrigid registration is performed between this pseudo CT image and the CT image of the first scan, warping the CT image of the first scan to an estimated CT images for the delayed scan. Finally, the PET image attenuation correction in the delayed scan is obtained from this estimated CT image. Experiments with clinical datasets are implemented to assess the effectiveness of the proposed method with the well-recognized GAN method. The average peak signal-to-noise ratio (PSNR) and the mean absolute percent error (MAPE) are used in comparison. We also use scoring from three experienced radiologists as subjective measurement means, based on the diagnostic consistency of the PET images reconstructed from GAN and the proposed method with respect to the ground truth images.

RESULTS

The experiments show that the average PSNR is 47.04 dB (the proposed method) v.s. 44.41 dB (the traditional GAN method) for the reconstructed delayed PET images in our evaluation dataset. The average MAPEs are 1.59% for the proposed method and 3.32% for the traditional GAN method across five organ Regions of Interest (ROIs). The scores for the GAN and the proposed method rated by three experienced radiologists are 8.08±0.60 and 9.02±0.52, indicating that the proposed method yields more consistent PET images with the ground truth.

CONCLUSIONS

This work proposes a novel method for CT-less delayed PET imaging based on image synthesis network and nonrigid image registration. The PET image reconstructed using the proposed method yields delayed PET images with high image quality without artifacts, and is quantitatively more accurate compared with the traditional GAN method. This article is protected by copyright. All rights reserved.

Magnetic Resonance Imaging Versus Computed Tomography for Three-Dimensional Bone Imaging of Musculoskeletal Pathologies: A Review

Magnetic resonance imaging (MRI) is increasingly utilized as a radiation‐free alternative to computed tomography (CT) for the diagnosis and treatment planning of musculoskeletal pathologies. MR imaging of hard tissues such as cortical bone remains challenging due to their low proton density and short transverse relaxation times, rendering bone tissues as nonspecific low signal structures on MR images obtained from most sequences. Developments in MR image acquisition and post‐processing have opened the path for enhanced MR‐based bone visualization aiming to provide a CT‐like contrast and, as such, ease clinical interpretation. The purpose of this review is to provide an overview of studies comparing MR and CT imaging for diagnostic and treatment planning purposes in orthopedic care, with a special focus on selective bone visualization, bone segmentation, and three‐dimensional (3D) modeling. This review discusses conventional gradient‐echo derived techniques as well as dedicated short echo time acquisition techniques and post‐processing techniques, including the generation of synthetic CT, in the context of 3D and specific bone visualization. Based on the reviewed literature, it may be concluded that the recent developments in MRI‐based bone visualization are promising. MRI alone provides valuable information on both bone and soft tissues for a broad range of applications including diagnostics, 3D modeling, and treatment planning in multiple anatomical regions, including the skull, spine, shoulder, pelvis, and long bones.

Unsupervised Cross-Modality Domain Adaptation Network for CNN-Based X-ray to CT

2D/3D registration that achieves high accuracy and real-time computation is one of the enabling technologies for radiotherapy and image-guided surgeries. Recently, the Convolutional Neural Network(CNN) has been explored to significantly improve the accuracy and efficiency of 2D/3D registration. A pair of intraoperative 2-D x-ray images and synthetic data from pre-operative volume are often required to model the nonconvex mappings between registration parameters and image residual. However, a large clinical dataset collection with accurate poses for x-ray images can be very challenging or even impractical, while exclusive training on synthetic data can frequently cause performance degradation when tested on x-rays. Thus, we propose to train a model on source domain (i.e., synthetic data) to build appearance-pose relationship first and then use an unsupervised cross-modality domain adaptation network (UCMDAN) to adapt the model to target domain (i.e., X-rays) through adversarial learning. We propose to narrow the significant domain gap by alignment in both pixel and feature space. In particular, the image appearance transformation and domain-invariance feature learning by multiple aspects are conducted synergistically. Extensive experiments on CT and CBCT dataset show that the proposed UCMDAN outperforms the existing state-of-the-art domain adaptation approaches.

Minimizing the need for coil attenuation correction in integrated PET/MRI at 1.5 T using low-density MR-linac receive arrays

The simultaneous use of positron emission tomography (PET) and magnetic resonance imaging (MRI) requires attenuation correction (AC) of photon-attenuating objects, such as MRI receive arrays. However, AC of flexible, on-body arrays is complex and therefore often omitted. This can lead to significant, spatially varying PET signal losses when conventional MRI receive arrays are used. Only few dedicated, photon transparent PET/MRI arrays exist, none of which are compatible with our new, wide-bore 1.5 T PET/MRI system dedicated to radiotherapy planning. In this work, we investigated the use of 1.5 T MR-linac (MRL) receive arrays for PET/MRI, as these were designed to have a low photon attenuation for accurate dose delivery and can be connected to the new 1.5 T PET/MRI scanner. Three arrays were assessed: an 8-channel clinically-used MRL array, a 32-channel prototype MRL array, and a conventional MRI receive array. We experimentally determined, simulated, and compared the impact of these arrays on the PET sensitivity and image reconstructions. Furthermore, MRI performance was compared. Overall coil-induced PET sensitivity losses were reduced from 8.5% (conventional) to 1.7% (clinical MRL) and 0.7% (prototype MRL). Phantom measurements showed local signal errors of up to 32.7% (conventional) versus 3.6% (clinical MRL) and 3.5% (prototype MRL). Simulations with data of eight cancer patients showed average signal losses were reduced from 14.3% (conventional) to 1.2% (clinical MRL) and 1.0% (prototype MRL). MRI data showed that the signal-to-noise ratio of the MRL arrays was slightly lower at depth (110 versus 135). The parallel imaging performance of the conventional and prototype MRL arrays was similar, while the clinical MRL array's performance was lower. In conclusion, MRL arrays reducein-vivoPET signal losses >10×, which decreases, or eliminates, the need for coil AC on a new 1.5 T PET/MRI system. The prototype MRL array allows flexible coil positioning without compromising PET or MRI performance. One limitation of MRL arrays is their limited radiolucent PET window (field of view) in the craniocaudal direction.

Artificial Intelligence-Based Data Corrections for Attenuation and Scatter in Position Emission Tomography and Single-Photon Emission Computed Tomography

Recent developments in artificial intelligence (AI) technology have enabled new developments that can improve attenuation and scatter correction in PET and single-photon emission computed tomography (SPECT). These technologies will enable the use of accurate and quantitative imaging without the need to acquire a computed tomography image, greatly expanding the capability of PET/MR imaging, PET-only, and SPECT-only scanners. The use of AI to aid in scatter correction will lead to improvements in image reconstruction speed, and improve patient throughput. This article outlines the use of these new tools, surveys contemporary implementation, and discusses their limitations.