Geometric distortions in clinical MRI sequences for radiotherapy: insights gained from a multicenter investigation.

BACKGROUND: As magnetic resonance imaging (MRI) becomes increasingly integrated into radiotherapy (RT) for enhanced treatment planning and adaptation, the inherent geometric distortion in acquired MR images pose a potential challenge to treatment accuracy. This study aimed to evaluate the geometric distortion levels in the clinical MRI protocols used across Danish RT centers and discuss influence of specific sequence parameters. Based on the variety in geometric performance across centers, we assess if harmonization of MRI sequences is a relevant measure. MATERIALS AND METHODS: Nine centers participated with 12 MRI scanners and MRI-Linacs (MRL). Using a travelling phantom approach, a reference MRI sequence was used to assess variation in baseline distortion level between scanners. The phantom was also scanned with local clinical MRI sequences for brain, head/neck (H/N), abdomen, and pelvis. The influence of echo time, receiver bandwidth, image weighting, and 2D/3D acquisition was investigated. RESULTS: We found a large variation in geometric accuracy across 93 clinical sequences examined, exceeding the baseline variation found between MRI scanners (σ = 0.22 mm), except for abdominal sequences where the variation was lower. Brain and abdominal sequences showed lowest distortion levels ([0.22, 2.26] mm), and a large variation in performance was found for H/N and pelvic sequences ([0.19, 4.07] mm). Post hoc analyses revealed that distortion levels decreased with increasing bandwidth and a less clear increase in distortion levels with increasing echo time. 3D MRI sequences had lower distortion levels than 2D (median of 1.10 and 2.10 mm, respectively), and in DWI sequences, the echo-planar imaging read-out resulted in highest distortion levels. CONCLUSION: There is a large variation in the geometric distortion levels of clinical MRI sequences across Danish RT centers, and between anatomical sites. The large variation observed makes harmonization of MRI sequences across institutions and adoption of practices from well-performing anatomical sites, a relevant measure within RT.

Evaluation of MRI-only based online adaptive radiotherapy of abdominal region on MR-linac.

PURPOSE: A hybrid magnetic resonance linear accelerator (MRL) can perform magnetic resonance imaging (MRI) with high soft-tissue contrast to be used for online adaptive radiotherapy (oART). To obtain electron densities needed for the oART dose calculation, a computed tomography (CT) is often deformably registered to MRI. Our aim was to evaluate an MRI-only based synthetic CT (sCT) generation as an alternative to the deformed CT (dCT)-based oART in the abdominal region. METHODS: The study data consisted of 57 patients who were treated on a 0.35 T MRL system mainly for abdominal tumors. Simulation MRI-CT pairs of 43 patients were used for training and validation of a prototype convolutional neural network sCT-generation algorithm, based on HighRes3DNet, for the abdominal region. For remaining test patients, sCT images were produced from simulation MRIs and daily MRIs. The dCT-based plans were re-calculated on sCT with identical calculation parameters. The sCT and dCT were compared in terms of geometric agreement and calculated dose. RESULTS: The mean and one standard deviation of the geometric agreement metrics over dCT-sCT-pairs were: mean error of 8 ± 10 HU, mean absolute error of 49 ± 10 HU, and Dice similarity coefficient of 55 ± 12%, 60 ± 5%, and 82 ± 15% for bone, fat, and lung tissues, respectively. The dose differences between the sCT and dCT-based dose for planning target volumes were 0.5 ± 0.9%, 0.6 ± 0.8%, and 0.5 ± 0.8% at D2% , D50% , and D98% in physical dose and 0.8 ± 1.4%, 0.8 ± 1.2%, and 0.6 ± 1.1% in biologically effective dose (BED). For organs-at-risk, the dose differences of all evaluated dose-volume histogram points were within [-4.5%, 7.8%] and [-1.1 Gy, 3.5 Gy] in both physical dose and BED. CONCLUSIONS: The geometric agreement metrics were within typically reported values and most average relative dose differences were within 1%. Thus, an MRI-only sCT-based approach is a promising alternative to the current clinical practice of the abdominal oART on MRL.

Dual-energy material decomposition for cone-beam computed tomography in image-guided radiotherapy.

Background: Dual-energy (DE) diagnostic computed tomography (CT) combines two scans of different photon energy spectra which can provide additional image information as compared to standard CT. We developed a DE material decomposition scan protocol for daily cone-beam CT (CBCT) of head-and-neck patients receiving radiotherapy and tested it in a clinical trial. Material and methods: Our DE CBCT protocol consisted of an 80 and 140 kVp scan. The material decomposition algorithm split the low and high energy scan into components of two basis materials, aluminum and acrylic. Scans of different thicknesses and overlap of the basis materials were acquired to calibrate the model which decomposed the CBCT projections into thicknesses of aluminum and acrylic on a per-pixel basis. Pseudo monochromatic projections were created from these thicknesses and the known energy dependence of the attenuation coefficient of the basis materials. A frequency selective de-noising method was further applied to the basis material projections. The DE CBCT protocol was tested on seven patients. Two DE images were chosen, one at low (50-60) keV to evaluate soft tissue image quality and one at 150 keV to assess metal artifact reduction as compared to standard CBCT. Results: The de-noising algorithm reduced noise by 41% and 69% in the 60 and 150 keV images, respectively, compared to images without the de-noising. The low keV image showed an increase in soft tissue contrast-to-noise ratio of 7-43% compared to the standard clinical CBCT for six of the seven patients. The 150 keV DE CBCT image reduced metal artifacts. Enhanced streaking from metal artifacts were observed in some of the DE CBCT images. Conclusion: Monochromatic DE images from material decomposition can improve soft tissue contrast-to-noise ratio and metal artifact reduction. Improvements are limited, however, and new artifacts were also introduced by the DE algorithm.

Cone beam computed tomography guided treatment delivery and planning verification for magnetic resonance imaging only radiotherapy of the brain.

BACKGROUND: Radiotherapy based on MRI only (MRI-only RT) shows a promising potential for the brain. Much research focuses on creating a pseudo computed tomography (pCT) from MRI for treatment planning while little attention is often paid to the treatment delivery. Here, we investigate if cone beam CT (CBCT) can be used for MRI-only image-guided radiotherapy (IGRT) and for verifying the correctness of the corresponding pCT. MATERIAL AND METHODS: Six patients receiving palliative cranial RT were included in the study. Each patient had three-dimensional (3D) T1W MRI, a CBCT and a CT for reference. Further, a pCT was generated using a patch-based approach. MRI, pCT and CT were placed in the same frame of reference, matched to CBCT and the differences noted. Paired pCT-CT and pCT-CBCT data were created in bins of 10 HU and the absolute difference calculated. The data were converted to relative electron densities (RED) using the CT or a CBCT calibration curve. The latter was either based on a CBCT phantom (phan) or a paired CT-CBCT population (pop) of the five other patients. RESULTS: Non-significant (NS) differences in the pooled CT-CBCT, MRI-CBCT and pCT-CBCT transformations were noted. The largest deviations from the CT-CBCT reference were < 1 mm and 1°. The average median absolute error (MeAE) in HU was 184 ± 34 and 299 ± 34 on average for pCT-CT and pCT-CBCT, respectively, and was significantly different (p < 0.01) in each patient. The average MeAE in RED was 0.108 ± 0.025, 0.104 ± 0.011 and 0.099 ± 0.017 for pCT-CT, pCT-CBCT phan (p < 0.01 on 2 patients) and pCT-CBCT pop (NS), respectively. CONCLUSIONS: CBCT can be used for patient setup with either MRI or pCT as reference. The correctness of pCT can be verified from CBCT using a population-based calibration curve in the treatment geometry.

Cone beam computed tomography based image guidance and quality assessment of prostate cancer for magnetic resonance imaging-only radiotherapy in the pelvis.

BACKGROUND AND PURPOSE: Radiotherapy (RT) based on magentic resonance imaging (MRI) only is currently used clinically in the pelvis. A synthetic computed tomography (sCT) is needed for dose planning. Here, we investigate the accuracy of cone beam CT (CBCT) based MRI-only image guided RT (IGRT) and sCT image quality. MATERIALS AND METHODS: CT, MRI and CBCT scans of ten prostate cancer patients were included. The MRI was converted to a sCT using a multi-atlas approach. The sCT, CT and MR images were auto-matched with the CBCT on the bony anatomy. Paired sCT-CT and sCT-CBCT data were created. CT numbers were converted to relative electron (RED) and mass densities (DES) using a standard calibration curve for the CT and sCT. For the CBCT RED/DES conversion, a phantom and paired CT-CBCT population based calibration curve was used. For the latter, the CBCT numbers were averaged in 100 HU bins and the known RED/DES of the CT were assigned. The paired sCT-CT and sCT-CBCT data were averaged in bins of 10 HU or 0.01 RED/DES. The median absolute error (MeAE) between the sCT-CT and sCT-CBCT bins was calculated. Wilcoxon rank-sum tests were carried out for the IGRT and MeAE study. RESULTS: The mean sCT or MR IGRT difference from CT was ≤ 2 mm but significant differences were observed. A CBCT HU or phantom-based RED/DES MeAE did not estimate the sCT quality similar to a CT based MeAE but the CBCT population-based RED/DES MeAE did. CONCLUSIONS: MRI-only CBCT-based IGRT seems feasible but caution is advised. A MeAE around 0.1 DES could call for sCT quality inspection.

A review of substitute CT generation for MRI-only radiation therapy.

Radiotherapy based on magnetic resonance imaging as the sole modality (MRI-only RT) is an area of growing scientific interest due to the increasing use of MRI for both target and normal tissue delineation and the development of MR based delivery systems. One major issue in MRI-only RT is the assignment of electron densities (ED) to MRI scans for dose calculation and a similar need for attenuation correction can be found for hybrid PET/MR systems. The ED assigned MRI scan is here named a substitute CT (sCT). In this review, we report on a collection of typical performance values for a number of main approaches encountered in the literature for sCT generation as compared to CT. A literature search in the Scopus database resulted in 254 papers which were included in this investigation. A final number of 50 contributions which fulfilled all inclusion criteria were categorized according to applied method, MRI sequence/contrast involved, number of subjects included and anatomical site investigated. The latter included brain, torso, prostate and phantoms. The contributions geometric and/or dosimetric performance metrics were also noted. The majority of studies are carried out on the brain for 5-10 patients with PET/MR applications in mind using a voxel based method. T1 weighted images are most commonly applied. The overall dosimetric agreement is in the order of 0.3-2.5%. A strict gamma criterion of 1% and 1mm has a range of passing rates from 68 to 94% while less strict criteria show pass rates > 98%. The mean absolute error (MAE) is between 80 and 200 HU for the brain and around 40 HU for the prostate. The Dice score for bone is between 0.5 and 0.95. The specificity and sensitivity is reported in the upper 80s% for both quantities and correctly classified voxels average around 84%. The review shows that a variety of promising approaches exist that seem clinical acceptable even with standard clinical MRI sequences. A consistent reference frame for method benchmarking is probably necessary to move the field further towards a widespread clinical implementation.

A patch-based pseudo-CT approach for MRI-only radiotherapy in the pelvis.

PURPOSE: In radiotherapy based only on magnetic resonance imaging (MRI), knowledge about tissue electron densities must be derived from the MRI. This can be achieved by converting the MRI scan to the so-called pseudo-computed tomography (pCT). An obstacle is that the voxel intensities in conventional MRI scans are not uniquely related to electron density. The authors previously demonstrated that a patch-based method could produce accurate pCTs of the brain using conventional T1-weighted MRI scans. The method was driven mainly by local patch similarities and relied on simple affine registrations between an atlas database of the co-registered MRI/CT scan pairs and the MRI scan to be converted. In this study, the authors investigate the applicability of the patch-based approach in the pelvis. This region is challenging for a method based on local similarities due to the greater inter-patient variation. The authors benchmark the method against a baseline pCT strategy where all voxels inside the body contour are assigned a water-equivalent bulk density. Furthermore, the authors implement a parallelized approximate patch search strategy to speed up the pCT generation time to a more clinically relevant level. METHODS: The data consisted of CT and T1-weighted MRI scans of 10 prostate patients. pCTs were generated using an approximate patch search algorithm in a leave-one-out fashion and compared with the CT using frequently described metrics such as the voxel-wise mean absolute error (MAEvox) and the deviation in water-equivalent path lengths. Furthermore, the dosimetric accuracy was tested for a volumetric modulated arc therapy plan using dose-volume histogram (DVH) point deviations and γ-index analysis. RESULTS: The patch-based approach had an average MAEvox of 54 HU; median deviations of less than 0.4% in relevant DVH points and a γ-index pass rate of 0.97 using a 1%/1 mm criterion. The patch-based approach showed a significantly better performance than the baseline water pCT in almost all metrics. The approximate patch search strategy was 70x faster than a brute-force search, with an average prediction time of 20.8 min. CONCLUSIONS: The authors showed that a patch-based method based on affine registrations and T1-weighted MRI could generate accurate pCTs of the pelvis. The main source of differences between pCT and CT was positional changes of air pockets and body outline.

Patch-based generation of a pseudo CT from conventional MRI sequences for MRI-only radiotherapy of the brain.

PURPOSE: In radiotherapy (RT) based on magnetic resonance imaging (MRI) as the only modality, the information on electron density must be derived from the MRI scan by creating a so-called pseudo computed tomography (pCT). This is a nontrivial task, since the voxel-intensities in an MRI scan are not uniquely related to electron density. To solve the task, voxel-based or atlas-based models have typically been used. The voxel-based models require a specialized dual ultrashort echo time MRI sequence for bone visualization and the atlas-based models require deformable registrations of conventional MRI scans. In this study, we investigate the potential of a patch-based method for creating a pCT based on conventional T1-weighted MRI scans without using deformable registrations. We compare this method against two state-of-the-art methods within the voxel-based and atlas-based categories. METHODS: The data consisted of CT and MRI scans of five cranial RT patients. To compare the performance of the different methods, a nested cross validation was done to find optimal model parameters for all the methods. Voxel-wise and geometric evaluations of the pCTs were done. Furthermore, a radiologic evaluation based on water equivalent path lengths was carried out, comparing the upper hemisphere of the head in the pCT and the real CT. Finally, the dosimetric accuracy was tested and compared for a photon treatment plan. RESULTS: The pCTs produced with the patch-based method had the best voxel-wise, geometric, and radiologic agreement with the real CT, closely followed by the atlas-based method. In terms of the dosimetric accuracy, the patch-based method had average deviations of less than 0.5% in measures related to target coverage. CONCLUSIONS: We showed that a patch-based method could generate an accurate pCT based on conventional T1-weighted MRI sequences and without deformable registrations. In our evaluations, the method performed better than existing voxel-based and atlas-based methods and showed a promising potential for RT of the brain based only on MRI.

A criterion for the reliable use of MRI-only radiotherapy.

BACKGROUND: MRI-only radiotherapy will eliminate the systematic registration errors introduced when transferring MRI information to the CT. However, challenges concerning the missing information on electron density, necessary for dose calculation and patient setup on bony anatomy are introduced. This study presents a possible statistical approach to evaluate, if deviations based on MRI-only radiotherapy as compared to the CT based radiotherapy are acceptable. METHODS: 18 head-and-neck, 21 prostate, 10 vesica and 8 pelvic patients were included in the study. Data from each patient contained a CT and a T2-weighted MRI scan, a structure set and a clinically approved CT based treatment plan, which was re-calculated with identical parameters on the density corrected MRI scans. A statistical analysis including a 95% confidence interval was performed in clinically relevant DVH points. RESULTS: The mean differences in the investigated DVH points were in the order of 1.5% for the PTV and up to 4.2% for organs at risk. In addition, a proposed criterion of 2% dose difference in the PTV coverage for 95% of the patients was fulfilled for all diagnostic groups for a bulk segmented MRI in the DVH points, D(median) and D2%, while only head-and-neck and prostate further fulfilled the criterion in D98%. CONCLUSION: Here, we suggested a method for establishing a reliable use of MRI-only radiotherapy. A population-based study comparing CT based dose calculations with those obtained on a suggested segmentation of MRI should be initiated and acceptable deviations in clinically relevant DVH points should be established. Such a population-based approach could form a part of the clinical commissioning of MRI-only radiotherapy.

A voxel-based investigation for MRI-only radiotherapy of the brain using ultra short echo times.

Radiotherapy (RT) based on magnetic resonance imaging (MRI) as the only modality, so-called MRI-only RT, would remove the systematic registration error between MR and computed tomography (CT), and provide co-registered MRI for assessment of treatment response and adaptive RT. Electron densities, however, need to be assigned to the MRI images for dose calculation and patient setup based on digitally reconstructed radiographs (DRRs). Here, we investigate the geometric and dosimetric performance for a number of popular voxel-based methods to generate a so-called pseudo CT (pCT). Five patients receiving cranial irradiation, each containing a co-registered MRI and CT scan, were included. An ultra short echo time MRI sequence for bone visualization was used. Six methods were investigated for three popular types of voxel-based approaches; (1) threshold-based segmentation, (2) Bayesian segmentation and (3) statistical regression. Each approach contained two methods. Approach 1 used bulk density assignment of MRI voxels into air, soft tissue and bone based on logical masks and the transverse relaxation time T2 of the bone. Approach 2 used similar bulk density assignments with Bayesian statistics including or excluding additional spatial information. Approach 3 used a statistical regression correlating MRI voxels with their corresponding CT voxels. A similar photon and proton treatment plan was generated for a target positioned between the nasal cavity and the brainstem for all patients. The CT agreement with the pCT of each method was quantified and compared with the other methods geometrically and dosimetrically using both a number of reported metrics and introducing some novel metrics. The best geometrical agreement with CT was obtained with the statistical regression methods which performed significantly better than the threshold and Bayesian segmentation methods (excluding spatial information). All methods agreed significantly better with CT than a reference water MRI comparison. The mean dosimetric deviation for photons and protons compared to the CT was about 2% and highest in the gradient dose region of the brainstem. Both the threshold based method and the statistical regression methods showed the highest dosimetrical agreement.Generation of pCTs using statistical regression seems to be the most promising candidate for MRI-only RT of the brain. Further, the total amount of different tissues needs to be taken into account for dosimetric considerations regardless of their correct geometrical position.