Automatic lung segmentation of magnetic resonance images: A new approach applied to healthy volunteers undergoing enhanced Deep-Inspiration-Breath-Hold for motion-mitigated 4D proton therapy of lung tumors

Background and purpose

Respiratory suppression techniques represent an effective motion mitigation strategy for 4D-irradiation of lung tumors with protons. A magnetic resonance imaging (MRI)-based study applied and analyzed methods for this purpose, including enhanced Deep-Inspiration-Breath-Hold (eDIBH). Twenty-one healthy volunteers (41-58 years) underwent thoracic MR scans in four imaging sessions containing two eDIBH-guided MRIs per session to simulate motion-dependent irradiation conditions. The automated MRI segmentation algorithm presented here was critical in determining the lung volumes (LVs) achieved during eDIBH.

Materials and methods

The study included 168 MRIs acquired under eDIBH conditions. The lung segmentation algorithm consisted of four analysis steps: (i) image preprocessing, (ii) MRI histogram analysis with thresholding, (iii) automatic segmentation, (iv) 3D-clustering. To validate the algorithm, 46 eDIBH-MRIs were manually contoured. Sørensen-Dice similarity coefficients (DSCs) and relative deviations of LVs were determined as similarity measures. Assessment of intrasessional and intersessional LV variations and their differences provided estimates of statistical and systematic errors.

Results

Lung segmentation time for 100 2D-MRI planes was ∼ 10 s. Compared to manual lung contouring, the median DSC was 0.94 with a lower 95 % confidence level (CL) of 0.92. The relative volume deviations yielded a median value of 0.059 and 95 % CLs of -0.013 and 0.13. Artifact-based volume errors, mainly of the trachea, were estimated. Estimated statistical and systematic errors ranged between 6 and 8 %.

Conclusions

The presented analytical algorithm is fast, precise, and readily available. The results are comparable to time-consuming, manual segmentations and other automatic segmentation approaches. Post-processing to remove image artifacts is under development.

Review and recommendations on deformable image registration uncertainties for radiotherapy applications

Deformable image registration (DIR) is a versatile tool used in many applications in radiotherapy (RT). DIR algorithms have been implemented in many commercial treatment planning systems providing accessible and easy-to-use solutions. However, the geometric uncertainty of DIR can be large and difficult to quantify, resulting in barriers to clinical practice. Currently, there is no agreement in the RT community on how to quantify these uncertainties and determine thresholds that distinguish a good DIR result from a poor one. This review summarises the current literature on sources of DIR uncertainties and their impact on RT applications. Recommendations are provided on how to handle these uncertainties for patient-specific use, commissioning, and research. Recommendations are also provided for developers and vendors to help users to understand DIR uncertainties and make the application of DIR in RT safer and more reliable.

Evaluation of DIR algorithm performance in real patients for radiotherapy treatments: A systematic review of operator-dependent strategies

PURPOSE

The performance of deformable medical image registration (DIR) algorithms has become a major concern.

METHODS

We aimed to obtain updated information on DIR algorithm performance quantification through a literature review of articles published between 2010 and 2022. We focused only on studies using operator-based methods to treat real patients. The PubMed, Google Scholar and Embase databases were searched following PRISMA guidelines.

RESULTS

One hundred and seven articles were identified. The mean number of patients and registrations per publication was 20 and 63, respectively. We found 23 different geometric metrics appearing at least twice, and the dosimetric impact of DIR was quantified in 32 articles. Forty-eight different at-risk organs were described, and target volumes were studied in 43 publications. Prostate, head-and-neck and thoracic locations represented more than ¾ of the studied locations. We summarized the type of DIR and the images used, and other key elements. Intra/interobserver variability, threshold values and the correlation between metrics were also discussed.

CONCLUSIONS

This literature review covers the past decade and should facilitate the implementation of DIR algorithms in clinical practice by providing practical and pertinent information to quantify their performance on real patients.

Quantitative assessment of intra- and inter-modality deformable image registration of the heart, left ventricle, and thoracic aorta on longitudinal 4D-CT and MR images

Purpose

Magnetic resonance imaging (MRI)‐based investigations into radiotherapy (RT)‐induced cardiotoxicity require reliable registrations of magnetic resonance (MR) imaging to planning computed tomography (CT) for correlation to regional dose. In this study, the accuracy of intra‐ and inter‐modality deformable image registration (DIR) of longitudinal four‐dimensional CT (4D‐CT) and MR images were evaluated for heart, left ventricle (LV), and thoracic aorta (TA).

Methods and materials

Non‐cardiac‐gated 4D‐CT and T1 volumetric interpolated breath‐hold examination (T1‐VIBE) MRI datasets from five lung cancer patients were obtained at two breathing phases (inspiration/expiration) and two time points (before treatment and 5 weeks after initiating RT). Heart, LV, and TA were manually contoured. Each organ underwent three intramodal DIRs ((A) CT modality over time, (B) MR modality over time, and (C) MR contrast effect at the same time) and two intermodal DIRs ((D) CT/MR multimodality at same time and (E) CT/MR multimodality over time). Hausdorff distance (HD), mean distance to agreement (MDA), and Dice were evaluated and assessed for compliance with American Association of Physicists in Medicine (AAPM) Task Group (TG)‐132 recommendations.

Results

Mean values of HD, MDA, and Dice under all registration scenarios for each region of interest ranged between 8.7 and 16.8 mm, 1.0 and 2.6 mm, and 0.85 and 0.95, respectively, and were within the TG‐132 recommended range (MDA < 3 mm, Dice > 0.8). Intramodal DIR showed slightly better results compared to intermodal DIR. Heart and TA demonstrated higher registration accuracy compared to LV for all scenarios except for HD and Dice values in Group A. Significant differences for each metric and tissue of interest were noted between Groups B and D and between Groups B and E. MDA and Dice significantly differed between LV and heart in all registrations except for MDA in Group E.

Conclusions

DIR of the heart, LV, and TA between non‐cardiac‐gated longitudinal 4D‐CT and MRI across two modalities, breathing phases, and pre/post‐contrast is acceptably accurate per AAPM TG‐132 guidelines. This study paves the way for future evaluation of RT‐induced cardiotoxicity and its related factors using multimodality DIR.

Automated atlas-based segmentation for skull base surgical planning

PURPOSE

Computational surgical planning tools could help develop novel skull base surgical approaches that improve safety and patient outcomes. This defines a need for automated skull base segmentation to improve the usability of surgical planning software. The objective of this work was to design and validate an algorithm for atlas-based automated segmentation of skull base structures in individual image sets for skull base surgical planning.

METHODS

Advanced Normalization Tools software was used to construct a synthetic CT template from 6 subjects, and skull base structures were manually segmented to create a reference atlas. Landmark registration followed by Elastix deformable registration was applied to the template to register it to each of the 30 trusted reference image sets. Dice coefficient, average Hausdorff distance, and clinical usability scoring were used to compare the atlas segmentations to those of the trusted reference image sets.

RESULTS

The mean for average Hausdorff distance for all structures was less than 2 mm (mean for 95th percentile Hausdorff distance was less than 5 mm). For structures greater than 2.5 mL in volume, the average Dice coefficient was 0.73 (range 0.59-0.82), and for structures less than 2.5 mL in volume the Dice coefficient was less than 0.7. The usability scoring survey was completed by three experts, and all structures met the criteria for acceptable effort except for the foramen spinosum, rotundum, and carotid artery, which required more than minor corrections.

CONCLUSION

Currently available open-source algorithms, such as the Elastix deformable algorithm, can be used for automated atlas-based segmentation of skull base structures with acceptable clinical accuracy and minimal corrections with the use of the proposed atlas. The first publicly available CT template and anterior skull base segmentation atlas being released (available at this link: http://hdl.handle.net/1773/46259 ) with this paper will allow for general use of automated atlas-based segmentation of the skull base.

Evaluation of Varian's SmartAdapt for clinical use in radiation therapy for patients with thoracic lesions

INTRODUCTION

Deformable image registration (DIR) is a required tool in any adaptive radiotherapy program to help account for anatomical changes that occur during a multifraction treatment. SmartAdapt is a DIR tool from Varian incorporated within the eclipse treatment planning system, that can be used for contour propagation and transfer of PET, MRI, or computed tomography (CT) data. The purpose of this work is to evaluate the registration and contour propagation accuracy of SmartAdapt for thoracic CT studies using the guidelines from AAPM TG 132.

METHODS

To evaluate the registration accuracy of SmartAdapt the mean target registration error (TRE) was measured for ten landmarked 4DCT images from the https://www.dir-labs.com/ which included 300 landmarks matching the inspiration and expiration phase images. To further characterize the registration accuracy, the magnitude of deformation for each 4DCT was measured and compared against the mean TRE for each study. Contour propagation accuracy was evaluated using 22 randomly selected lung cancer cases from our center where there was either a replan, or the patient was treated for a new lesion within the lung. Contours evaluated included the right and left lung, esophagus, spinal canal, heart and the GTV and the results were quantified using the DICE similarity coefficient.

RESULTS

The mean TRE from all ten cases was 1.89 mm, the maximum mean TRE per case was 3.8 mm from case #8, which also had the most landmark pairs with displacements >2 cm. For contour propagation accuracy, the DICE coefficient results for left lung, right lung, heart, esophagus, and spinal canal were 0.93, 0.94, 0.90, 0.61, and 0.82 respectively.

CONCLUSION

The results from our study demonstrate that for thoracic images SmartAdapt in most cases will be accurate to below 2 mm in registration error unless there is deformation greater than 2 cm.

Fully automatic catheter segmentation in MRI with 3D convolutional neural networks: application to MRI-guided gynecologic brachytherapy

External-beam radiotherapy followed by high dose rate (HDR) brachytherapy is the standard-of-care for treating gynecologic cancers. The enhanced soft-tissue contrast provided by magnetic resonance imaging (MRI) makes it a valuable imaging modality for diagnosing and treating these cancers. However, in contrast to computed tomography (CT) imaging, the appearance of the brachytherapy catheters, through which radiation sources are inserted to reach the cancerous tissue later on, is often variable across images. This paper reports, for the first time, a new deep-learning-based method for fully automatic segmentation of multiple closely spaced brachytherapy catheters in intraoperative MRI. Represented in the data are 50 gynecologic cancer patients treated by MRI-guided HDR brachytherapy. For each patient, a single intraoperative MRI was used. 826 catheters in the images were manually segmented by an expert radiation physicist who is also a trained radiation oncologist. The number of catheters in a patient ranged between 10 and 35. A deep 3D convolutional neural network (CNN) model was developed and trained. In order to make the learning process more robust, the network was trained 5 times, each time using a different combination of shown patients. Finally, each test case was processed by the five networks and the final segmentation was generated by voting on the obtained five candidate segmentations. 4-fold validation was executed and all the patients were segmented. An average distance error of 2.0  ±  3.4 mm was achieved. False positive and false negative catheters were 6.7% and 1.5% respectively. Average Dice score was equal to 0.60  ±  0.17. The algorithm is available for use in the open source software platform 3D Slicer allowing for wide scale testing and research discussion. In conclusion, to the best of our knowledge, fully automatic segmentation of multiple closely spaced catheters from intraoperative MR images was achieved for the first time in gynecological brachytherapy.

Evaluation of Image Registration Accuracy for Tumor and Organs at Risk in the Thorax for Compliance With TG 132 Recommendations

Purpose

To evaluate accuracy for 2 deformable image registration methods (in-house B-spline and MIM freeform) using image pairs exhibiting changes in patient orientation and lung volume and to assess the appropriateness of registration accuracy tolerances proposed by the American Association of Physicists in Medicine Task Group 132 under such challenging conditions via assessment by expert observers.

Methods and Materials

Four-dimensional computed tomography scans for 12 patients with lung cancer were acquired with patients in prone and supine positions. Tumor and organs at risk were delineated by a physician on all data sets: supine inhale (SI), supine exhale, prone inhale, and prone exhale. The SI image was registered to the other images using both registration methods. All SI contours were propagated using the resulting transformations and compared with physician delineations using Dice similarity coefficient, mean distance to agreement, and Hausdorff distance. Additionally, propagated contours were anonymized along with ground-truth contours and rated for quality by physician-observers.

Results

Averaged across all patients, the accuracy metrics investigated remained within tolerances recommended by Task Group 132 (Dice similarity coefficient >0.8, mean distance to agreement <3 mm). MIM performed better with both complex (vertebrae) and low-contrast (esophagus) structures, whereas the in-house method performed better with lungs (whole and individual lobes). Accuracy metrics worsened but remained within tolerances when propagating from supine to prone; however, the Jacobian determinant contained regions with negative values, indicating localized nonphysiologic deformations. For MIM and in-house registrations, 50% and 43.8%, respectively, of propagated contours were rated acceptable as is and 8.2% and 11.0% as clinically unacceptable.

Conclusions

The deformable image registration methods performed reliably and met recommended tolerances despite anatomically challenging cases exceeding typical interfraction variability. However, additional quality assurance measures are necessary for complex applications (eg, dose propagation). Human review rather than unsupervised implementation should always be part of the clinical registration workflow.

Evaluation of automatic contour propagation in T2-weighted 4DMRI for normal-tissue motion assessment using internal organ-at-risk volume (IRV)

Purpose

The purpose of this study was to evaluate the quality of automatically propagated contours of organs at risk (OARs) based on respiratory‐correlated navigator‐triggered four‐dimensional magnetic resonance imaging (RC‐4DMRI) for calculation of internal organ‐at‐risk volume (IRV) to account for intra‐fractional OAR motion.

Methods and Materials

T2‐weighted RC‐4DMRI images were of 10 volunteers acquired and reconstructed using an internal navigator‐echo surrogate and concurrent external bellows under an IRB‐approved protocol. Four major OARs (lungs, heart, liver, and stomach) were delineated in the 10‐phase 4DMRI. Two manual‐contour sets were delineated by two clinical personnel and two automatic‐contour sets were propagated using free‐form deformable image registration. The OAR volume variation within the 10‐phase cycle was assessed and the IRV was calculated as the union of all OAR contours. The OAR contour similarity between the navigator‐triggered and bellows‐rebinned 4DMRI was compared. A total of 2400 contours were compared to the most probable ground truth with a 95% confidence level (S95) in similarity, sensitivity, and specificity using the simultaneous truth and performance level estimation (STAPLE) algorithm.

Results

Visual inspection of automatically propagated contours finds that approximately 5–10% require manual correction. The similarity, sensitivity, and specificity between manual and automatic contours are indistinguishable (P > 0.05). The Jaccard similarity indexes are 0.92 ± 0.02 (lungs), 0.89 ± 0.03 (heart), 0.92 ± 0.02 (liver), and 0.83 ± 0.04 (stomach). Volume variations within the breathing cycle are small for the heart (2.6 ± 1.5%), liver (1.2 ± 0.6%), and stomach (2.6 ± 0.8%), whereas the IRV is much larger than the OAR volume by: 20.3 ± 8.6% (heart), 24.0 ± 8.6% (liver), and 47.6 ± 20.2% (stomach). The Jaccard index is higher in navigator‐triggered than bellows‐rebinned 4DMRI by 4% (P < 0.05), due to the higher image quality of navigator‐based 4DMRI.

Conclusion

Automatic and manual OAR contours from Navigator‐triggered 4DMRI are not statistically distinguishable. The navigator‐triggered 4DMRI image provides higher contour quality than bellows‐rebinned 4DMRI. The IRVs are 20–50% larger than OAR volumes and should be considered in dose estimation.

Prognostic factors associated with the accuracy of deformable image registration in lung cancer patients treated with stereotactic body radiotherapy

We evaluated the accuracy of an in-house program in lung stereotactic body radiation therapy (SBRT) cancer patients, and explored the prognostic factors associated with the accuracy of deformable image registrations (DIRs). The accuracy of the 3 programs which implement the free-form deformation and the B-spline algorithm was compared regarding the structures on 4-dimensional computed tomography (4DCT) image datasets between the peak-inhale and peak-exhale phases. The dice similarity coefficient (DSC) and normalized DSC (NDSC) were measured for the gross tumor volumes from 19 lung SBRT patients. We evaluated the accuracy of DIR using gross tumor volume, magnitude of displacement from 0% phase to 50% phase, whole lung volume in the 50% phase image, and status of tumor pleural attachment. The median NDSC values using the NiftyReg, MIM Maestro and Velocity AI programs were 1.027, 1.005, and 0.946, respectively, indicating that NiftyReg and MIM Maestro programs had similar accuracy with an uncertainty of < 1 mm. Larger uncertainty of 1 to 2 mm was observed using the Velocity AI program. The NiftyReg and the MIM programs provided higher NDSC values than the median values when the gross tumor volume was attached to the pleura (p <0.05). However, it showed a different trend in using the Velocity AI program. All software programs provided unexpected results, and there is a possibility that such results would reduce the accuracy of 4D treatment planning and adaptive radiotherapy. The unexpected results may be because the tumors are surrounded by other tissues, and there are differences regarding the region of interest for rigid and nonrigid registration. Furthermore, our results indicated that the pleural attachment status might be an important predictor of DIR accuracy for thoracic images, indicating that there is a potentially large dose distribution discrepancy concerning 4D treatment planning and adaptive radiotherapy.

Automatic Segmentation of the Eye in 3D Magnetic Resonance Imaging: A Novel Statistical Shape Model for Treatment Planning of Retinoblastoma

PURPOSE

Proper delineation of ocular anatomy in 3-dimensional (3D) imaging is a big challenge, particularly when developing treatment plans for ocular diseases. Magnetic resonance imaging (MRI) is presently used in clinical practice for diagnosis confirmation and treatment planning for treatment of retinoblastoma in infants, where it serves as a source of information, complementary to the fundus or ultrasonographic imaging. Here we present a framework to fully automatically segment the eye anatomy for MRI based on 3D active shape models (ASM), and we validate the results and present a proof of concept to automatically segment pathological eyes.

METHODS AND MATERIALS

Manual and automatic segmentation were performed in 24 images of healthy children's eyes (3.29 ± 2.15 years of age). Imaging was performed using a 3-T MRI scanner. The ASM consists of the lens, the vitreous humor, the sclera, and the cornea. The model was fitted by first automatically detecting the position of the eye center, the lens, and the optic nerve, and then aligning the model and fitting it to the patient. We validated our segmentation method by using a leave-one-out cross-validation. The segmentation results were evaluated by measuring the overlap, using the Dice similarity coefficient (DSC) and the mean distance error.

RESULTS

We obtained a DSC of 94.90 ± 2.12% for the sclera and the cornea, 94.72 ± 1.89% for the vitreous humor, and 85.16 ± 4.91% for the lens. The mean distance error was 0.26 ± 0.09 mm. The entire process took 14 seconds on average per eye.

CONCLUSION

We provide a reliable and accurate tool that enables clinicians to automatically segment the sclera, the cornea, the vitreous humor, and the lens, using MRI. We additionally present a proof of concept for fully automatically segmenting eye pathology. This tool reduces the time needed for eye shape delineation and thus can help clinicians when planning eye treatment and confirming the extent of the tumor.