Quantitative assessment of acquisition imaging parameters on MRI radiomics features: a prospective anthropomorphic phantom study using a 3D-T2W-TSE sequence for MR-guided-radiotherapy

Towards equitable AI in oncology

Artificial intelligence (AI) stands at the threshold of revolutionizing clinical oncology, with considerable potential to improve early cancer detection and risk assessment, and to enable more accurate personalized treatment recommendations. However, a notable imbalance exists in the distribution of the benefits of AI, which disproportionately favour those living in specific geographical locations and in specific populations. In this Perspective, we discuss the need to foster the development of equitable AI tools that are both accurate in and accessible to a diverse range of patient populations, including those in low-income to middle-income countries. We also discuss some of the challenges and potential solutions in attaining equitable AI, including addressing the historically limited representation of diverse populations in existing clinical datasets and the use of inadequate clinical validation methods. Additionally, we focus on extant sources of inequity including the type of model approach (such as deep learning, and feature engineering-based methods), the implications of dataset curation strategies, the need for rigorous validation across a variety of populations and settings, and the risk of introducing contextual bias that comes with developing tools predominantly in high-income countries.

Radiomic profiles improve prognostication and reveal targets for therapy in cervical cancer

Cervical cancer (CC) is a major global health problem with 570,000 new cases and 266,000 deaths annually. Prognosis is poor for advanced stage disease, and few effective treatments exist. Preoperative diagnostic imaging is common in high-income countries and MRI measured tumor size routinely guides treatment allocation of cervical cancer patients. Recently, the role of MRI radiomics has been recognized. However, its potential to independently predict survival and treatment response requires further clarification. This retrospective cohort study demonstrates how non-invasive, preoperative, MRI radiomic profiling may improve prognostication and tailoring of treatments and follow-ups for cervical cancer patients. By unsupervised clustering based on 293 radiomic features from 132 patients, we identify three distinct clusters comprising patients with significantly different risk profiles, also when adjusting for FIGO stage and age. By linking their radiomic profiles to genomic alterations, we identify putative treatment targets for the different patient clusters (e.g., immunotherapy, CDK4/6 and YAP-TEAD inhibitors and p53 pathway targeting treatments).

Development and multicenter validation of a multiparametric imaging model to predict treatment response in rectal cancer

OBJECTIVES

To develop and validate a multiparametric model to predict neoadjuvant treatment response in rectal cancer at baseline using a heterogeneous multicenter MRI dataset.

METHODS

Baseline staging MRIs (T2W (T2-weighted)-MRI, diffusion-weighted imaging (DWI) / apparent diffusion coefficient (ADC)) of 509 patients (9 centres) treated with neoadjuvant chemoradiotherapy (CRT) were collected. Response was defined as (1) complete versus incomplete response, or (2) good (Mandard tumor regression grade (TRG) 1-2) versus poor response (TRG3-5). Prediction models were developed using combinations of the following variable groups: (1) Non-imaging: age/sex/tumor-location/tumor-morphology/CRT-surgery interval (2) Basic staging: cT-stage/cN-stage/mesorectal fascia involvement, derived from (2a) original staging reports, or (2b) expert re-evaluation (3) Advanced staging: variables from 2b combined with cTN-substaging/invasion depth/extramural vascular invasion/tumor length (4) Quantitative imaging: tumour volume + first-order histogram features (from T2W-MRI and DWI/ADC) Models were developed with data from 6 centers (n = 412) using logistic regression with the Least Absolute Shrinkage and Selector Operator (LASSO) feature selection, internally validated using repeated (n = 100) random hold-out validation, and externally validated using data from 3 centers (n = 97).

RESULTS

After external validation, the best model (including non-imaging and advanced staging variables) achieved an area under the curve of 0.60 (95%CI=0.48-0.72) to predict complete response and 0.65 (95%CI=0.53-0.76) to predict a good response. Quantitative variables did not improve model performance. Basic staging variables consistently achieved lower performance compared to advanced staging variables.

CONCLUSIONS

Overall model performance was moderate. Best results were obtained using advanced staging variables, highlighting the importance of good-quality staging according to current guidelines. Quantitative imaging features had no added value (in this heterogeneous dataset).

CLINICAL RELEVANCE STATEMENT

Predicting tumour response at baseline could aid in tailoring neoadjuvant therapies for rectal cancer. This study shows that image-based prediction models are promising, though are negatively affected by variations in staging quality and MRI acquisition, urging the need for harmonization.

KEY POINTS

This multicenter study combining clinical information and features derived from MRI rendered disappointing performance to predict response to neoadjuvant treatment in rectal cancer. Best results were obtained with the combination of clinical baseline information and state-of-the-art image-based staging variables, highlighting the importance of good quality staging according to current guidelines and staging templates. No added value was found for quantitative imaging features in this multicenter retrospective study. This is likely related to acquisition variations, which is a major problem for feature reproducibility and thus model generalizability.

A multimodal radiomic machine learning approach to predict the LCK expression and clinical prognosis in high-grade serous ovarian cancer

We developed and validated a multimodal radiomic machine learning approach to noninvasively predict the expression of lymphocyte cell-specific protein-tyrosine kinase (LCK) expression and clinical prognosis of patients with high-grade serous ovarian cancer (HGSOC). We analyzed gene enrichment using 343 HGSOC cases extracted from The Cancer Genome Atlas. The corresponding biomedical computed tomography images accessed from The Cancer Imaging Archive were used to construct the radiomic signature (Radscore). A radiomic nomogram was built by combining the Radscore and clinical and genetic information based on multimodal analysis. We compared the model performances and clinical practicability via area under the curve (AUC), Kaplan-Meier survival, and decision curve analyses. LCK mRNA expression was associated with the prognosis of HGSOC patients, serving as a significant prognostic marker of the immune response and immune cells infiltration. Six radiomic characteristics were chosen to predict the expression of LCK and overall survival (OS) in HGSOC patients. The logistic regression (LR) radiomic model exhibited slightly better predictive abilities than the support vector machine model, as assessed by comparing combined results. The performance of the LR radiomic model for predicting the level of LCK expression with five-fold cross-validation achieved AUCs of 0.879 and 0.834, respectively, in the training and validation sets. Decision curve analysis at 60 months demonstrated the high clinical utility of our model within thresholds of 0.25 and 0.7. The radiomic nomograms were robust and displayed effective calibration. Abnormally high expression of LCK in HGSOC patients is significantly correlated with the tumor immune microenvironment and can be used as an essential indicator for predicting the prognosis of HGSOC. The multimodal radiomic machine learning approach can capture the heterogeneity of HGSOC, noninvasively predict the expression of LCK, and replace LCK for predictive analysis, providing a new idea for predicting the clinical prognosis of HGSOC and formulating a personalized treatment plan.

RESOLVE-based radiomics in cervical cancer: improved image quality means better feature reproducibility?

AIM

To compare the reproducibility of apparent diffusion coefficient (ADC)-based radiomic features between readout-segmented echo-planar diffusion-weighted imaging (RESOLVE) and single-shot echo-planar diffusion-weighted imaging (SS-EPI DWI) in cervical cancer.

MATERIALS AND METHODS

The RESOLVE and SS-EPI DWI images of 36 patients with histopathologically confirmed cervical cancer were collected retrospectively. Two observers independently delineated the whole tumour on RESOLVE and SS-EPI DWI, and then copied them to the corresponding ADC maps. Shape, first-order, and texture features were extracted from ADC maps in the original and filtered (Laplacian of Gaussian [LoG] and wavelet) images. Thereafter, 1,316 features were generated in each RESOLVE and SS-EPI DWI, respectively. The reproducibility of radiomic features was assessed using intraclass correlation coefficient (ICC).

RESULTS

In the original images, RESOLVE showed 92.86%, 66.67%, and 86.67% of features with excellent reproducibility in shape, first-order, and texture features, while SS-EPI DWI showed 85.71%, 72.22%, and 60% of features with excellent reproducibility, respectively. In the LoG and wavelet filtered images, RESOLVE had 56.77% and 65.32% of features with excellent reproducibility and SS-EPI DWI had 44.95% and 61.96% of features with excellent reproducibility, respectively.

CONCLUSION

Compared with SS-EPI DWI, the feature reproducibility of RESOLVE was better in cervical cancer, especially for texture features. The filtered images cannot improve the feature reproducibility compared with the original images for both SS-EPI DWI and RESOLVE.

Determining the reliable feature change in longitudinal radiomics studies: A methodological approach using the reliable change index

PURPOSE

Determination of reliable change of radiomics feature over time is essential and vital in delta-radiomics, but has not yet been rigorously examined. This study attempts to propose a methodological approach using reliable change index (RCI), a statistical metric to determine the reliability of quantitative biomarker changes by accounting for the baseline measurement standard error, in delta-radiomics. The use of RCI was demonstrated with the MRI data acquired from a group of prostate cancer (PCa) patients treated by 1.5 T MRI-guided radiotherapy (MRgRT).

METHODS

Fifty consecutive PCa patients who underwent five-fractionated MRgRT were retrospectively included, and 1023 radiomics features were extracted from the clinical target volume (CTV) and planning target volume (PTV). The two MRI datasets acquired at the first fraction (MRI11 and MRI21) were used to calculate the baseline feature reliability against image acquisition using intraclass correlation coefficient (ICC). The RCI was constructed based on the baseline feature measurement standard deviation, ICC, and feature value differences at two time points between the fifth (MRI51) and the first fraction MRI (MRI11). The reliable change of features was determined in each patient only if the calculated RCI was over 1.96 or smaller than -1.96. The feature changes between MRI51 and MRI11 were correlated to two patient-reported quality-of-life clinical endpoints of urinary domain summary score (UDSS) and bowel domain summary score (BDSS) in 35 patients using the Spearman correlation test. Only the significant correlations between a feature that was reliably changed in ≥7 patients (20%) by RCI and an endpoint were considered as true significant correlations.

RESULTS

The 352 (34.4%) and 386 (37.7%) features among all 1023 features were determined by RCI to be reliably changed in more than five (10%) patients in the CTV and PTV, respectively. Nineteen features were found reliably changed in the CTV and 31 features in the PTV, respectively, in 10 (20%) or more patients. These features were not necessarily associated with significantly different longitudinal feature values (group p-value < 0.05). Most reliably changed features in more than 10 patients had excellent or good baseline test-retest reliability ICC, while none showed poor reliability. The RCI method ruled out the features to be reliably changed when substantial feature measurement bias was presented. After applying the RCI criterion, only four and five true significant correlations were confirmed with UDSS and BDSS in the CTV, respectively, with low true significance correlation rates of 10.8% (4/37) and 17.9% (5/28). No true significant correlations were found in the PTV.

CONCLUSIONS

The RCI method was proposed for delta-radiomics and demonstrated using PCa MRgRT data. The RCI has advantages over some other statistical metrics commonly used in the previous delta-radiomics studies, and is useful to reliably identify the longitudinal radiomics feature change on an individual basis. This proposed RCI method should be helpful for the development of essential feature selection methodology in delta-radiomics.

Multimodal investigation of bladder cancer data based on computed tomography, whole slide imaging, and transcriptomics

Background

Multimodal analysis has shown great potential in the diagnosis and management of cancer. This study aimed to determine the multimodal data associations between radiological, pathologic, and molecular characteristics in bladder cancer.

Methods

A retrospective study of computed tomography (CT), pathologic slice, and RNA sequencing data from 127 consecutive adult patients in China who underwent bladder surgery and were pathologically diagnosed with bladder cancer was conducted. A total of 200 radiological and 1,029 pathologic features were extracted by radiomics and pathomics. Multimodal associations analysis and structural equation modeling were used to measure the cross-modal associations and structural relationships between CT and pathologic slice. A convolutional neural network was constructed for molecular subtyping based on multimodal imaging features. Class activation maps were used to examine the feature contribution in model decision-making. Cox regression and Kaplan-Meier survival analysis were used to explore the relevance of multimodal features to the prognosis of patients with bladder cancer.

Results

A total of 77 densely associated blocks of feature pairs were identified between CT and whole slide images. The largest cross-modal associated block reflected the tumor-grade properties. A significant relation was found between pathological features and molecular subtypes (β=0.396; P<0.001). High-grade bladder cancer showed heterogeneity of significance across different scales and higher disorders at the microscopic level. The fused radiological and pathologic features achieved higher accuracy (area under the curve: 0.89; 95% CI: 0.75-1.0) than the unimodal method. Thirteen prognosis-related features from CT and whole slide images were identified.

Conclusions

Our work demonstrated the associations between CT, pathologic slices, and molecular signatures, and the potential to use multimodal data analysis in related clinical applications. Multimodal data analysis showed the potential of cross-inference of modal data and had higher diagnostic accuracy than the unimodal method.

Predictive value of magnetic resonance imaging radiomics-based machine learning for disease progression in patients with high-grade glioma

Background

Accurately predicting the prognosis of patients with high-grade glioma (HGG) is potentially important for treatment. However, the predictive value of images of various magnetic resonance imaging (MRI) sequences for prognosis at different time points is unknown. We established predictive machine learning models of HGG disease progression and recurrence using MRI radiomics and explored the factors influencing prediction accuracy.

Methods

Radiomics features were extracted from T1-weighted (T1WI), contrast-enhanced T1-weighted (CE-T1WI), T2-weighted (T2WI), and fluid-attenuated inversion recovery (FLAIR) images (postoperative radiotherapy planning MRI images) obtained from 162 patients with HGG. The Mann-Whitney U test and least absolute shrinkage and selection operator (LASSO) algorithm were used for feature selection. Machine learning models were used to build prediction models to estimate disease progression or recurrence. The influence of different MRI sequences, regions of interest (ROIs), and prediction time points was also explored. The receiver operating characteristic (ROC) curve was used to evaluate the discriminative performance of each model, and the DeLong test was employed to compare the ROC curves.

Results

Radiomics features from T2WI and FLAIR demonstrated greater predictive value for disease progression compared with T1WI or CE-TIWI. The best predictive models, with areas under the ROC curves (AUCs) of 0.70, 0.68, 0.78, 0.78, and 0.78 for predicting disease progression at the 6th, 9th, 12th, 15th, and 18th month after radiotherapy, respectively, were obtained by combining clinical features with gross tumor volume (GTV) and clinical target volume (CTV) features extracted from T2WI and FLAIR.

Conclusions

Structural MRI obtained before radiotherapy can be used to predict the disease progression or posttreatment recurrence of HGG. When using MRI radiomics to predict long-term outcomes as opposed to short-term outcomes, better predictive results may be obtained.

Radiomics in clinical trials: perspectives on standardization

The term biomarker is used to describe a biological measure of the disease behavior. The existing imaging biomarkers are associated with the known tissue biological characteristics and follow a well-established roadmap to be implemented in routine clinical practice. Recently, a new quantitative imaging analysis approach named radiomics has emerged. It refers to the extraction of a large number of advanced imaging features with high-throughput computing. Extensive research has demonstrated its value in predicting disease behavior, progression, and response to therapeutic options. However, there are numerous challenges to establishing it as a clinically viable solution, including lack of reproducibility and transparency. The data-driven nature also does not offer insights into the underpinning biology of the observed relationships. As such, additional effort is needed to establish it as a qualified biomarker to inform clinical decisions. Here we review the technical difficulties encountered in the clinical applications of radiomics and current effort in addressing some of these challenges in clinical trial designs. By addressing these challenges, the true potential of radiomics can be unleashed.

Repeatability and reproducibility of magnetic resonance imaging-based radiomic features in rectal cancer

Purpose: Radiomics of magnetic resonance images (MRIs) in rectal cancer can non-invasively characterize tumor heterogeneity with potential to discover new imaging biomarkers. However, for radiomics to be reliable, the imaging features measured must be stable and reproducible. The aim of this study is to quantify the repeatability and reproducibility of MRI-based radiomic features in rectal cancer. Approach: An MRI radiomics phantom was used to measure the longitudinal repeatability of radiomic features and the impact of post-processing changes related to image resolution and noise. Repeatability measurements in rectal cancers were also quantified in a cohort of 10 patients with test-retest imaging among two observers. Results: We found that many radiomic features, particularly from texture classes, were highly sensitive to changes in image resolution and noise. About 49% of features had coefficient of variations ≤ 10 % in longitudinal phantom measurements. About 75% of radiomic features in in vivo test-retest measurements had an intraclass correlation coefficient of ≥ 0.8 . We saw excellent interobserver agreement with mean Dice similarity coefficient of 0.95 ± 0.04 for test and retest scans. Conclusions: The results of this study show that even when using a consistent imaging protocol many radiomic features were unstable. Therefore, caution must be taken when selecting features for potential imaging biomarkers.

The stability of oncologic MRI radiomic features and the potential role of deep learning: a review

The use of MRI radiomic models for the diagnosis, prognosis and treatment response prediction of tumors has been increasingly reported in literature. However, its widespread adoption in clinics is hampered by issues related to features stability. In the MRI radiomic workflow, the main factors that affect radiomic features computation can be found in the image acquisition and reconstruction phase, in the image pre-processing steps, and in the segmentation of the region of interest on which radiomic indices are extracted. Deep Neural Networks (DNNs), having shown their potentiality in the medical image processing and analysis field, can be seen as an attractive strategy to partially overcome the issues related to radiomic stability and mitigate their impact. In fact, DNN approaches can be prospectively integrated in the MRI radiomic workflow to improve image quality, obtain accurate and reproducible segmentations and generate standardized images. In this review, DNN methods that can be included in the image processing steps of the radiomic workflow are described and discussed, in the light of a detailed analysis of the literature in the context of MRI radiomic reliability.

Acquisition repeatability of MRI radiomics features in the head and neck: a dual-3D-sequence multi-scan study

Radiomics has increasingly been investigated as a potential biomarker in quantitative imaging to facilitate personalized diagnosis and treatment of head and neck cancer (HNC), a group of malignancies associated with high heterogeneity. However, the feature reliability of radiomics is a major obstacle to its broad validity and generality in application to the highly heterogeneous head and neck (HN) tissues. In particular, feature repeatability of radiomics in magnetic resonance imaging (MRI) acquisition, which is considered a crucial confounding factor of radiomics feature reliability, is still sparsely investigated. This study prospectively investigated the acquisition repeatability of 93 MRI radiomics features in ten HN tissues of 15 healthy volunteers, aiming for potential magnetic resonance-guided radiotherapy (MRgRT) treatment of HNC. Each subject underwent four MRI acquisitions with MRgRT treatment position and immobilization using two pulse sequences of 3D T1-weighed turbo spin-echo and 3D T2-weighed turbo spin-echo on a 1.5 T MRI simulator. The repeatability of radiomics feature acquisition was evaluated in terms of the intraclass correlation coefficient (ICC), whereas within-subject acquisition variability was evaluated in terms of the coefficient of variation (CV). The results showed that MRI radiomics features exhibited heterogeneous acquisition variability and uncertainty dependent on feature types, tissues, and pulse sequences. Only a small fraction of features showed excellent acquisition repeatability (ICC > 0.9) and low within-subject variability. Multiple MRI scans improved the accuracy and confidence of the identification of reliable features concerning MRI acquisition compared to simple test-retest repeated scans. This study contributes to the literature on the reliability of radiomics features with respect to MRI acquisition and the selection of reliable radiomics features for use in modeling in future HNC MRgRT applications.

Sources of variation in multicenter rectal MRI data and their effect on radiomics feature reproducibility

OBJECTIVES

To investigate sources of variation in a multicenter rectal cancer MRI dataset focusing on hardware and image acquisition, segmentation methodology, and radiomics feature extraction software.

METHODS

T2W and DWI/ADC MRIs from 649 rectal cancer patients were retrospectively acquired in 9 centers. Fifty-two imaging features (14 first-order/6 shape/32 higher-order) were extracted from each scan using whole-volume (expert/non-expert) and single-slice segmentations using two different software packages (PyRadiomics/CapTk). Influence of hardware, acquisition, and patient-intrinsic factors (age/gender/cTN-stage) on ADC was assessed using linear regression. Feature reproducibility was assessed between segmentation methods and software packages using the intraclass correlation coefficient.

RESULTS

Image features differed significantly (p < 0.001) between centers with more substantial variations in ADC compared to T2W-MRI. In total, 64.3% of the variation in mean ADC was explained by differences in hardware and acquisition, compared to 0.4% by patient-intrinsic factors. Feature reproducibility between expert and non-expert segmentations was good to excellent (median ICC 0.89-0.90). Reproducibility for single-slice versus whole-volume segmentations was substantially poorer (median ICC 0.40-0.58). Between software packages, reproducibility was good to excellent (median ICC 0.99) for most features (first-order/shape/GLCM/GLRLM) but poor for higher-order (GLSZM/NGTDM) features (median ICC 0.00-0.41).

CONCLUSIONS

Significant variations are present in multicenter MRI data, particularly related to differences in hardware and acquisition, which will likely negatively influence subsequent analysis if not corrected for. Segmentation variations had a minor impact when using whole volume segmentations. Between software packages, higher-order features were less reproducible and caution is warranted when implementing these in prediction models.

KEY POINTS

• Features derived from T2W-MRI and in particular ADC differ significantly between centers when performing multicenter data analysis. • Variations in ADC are mainly (> 60%) caused by hardware and image acquisition differences and less so (< 1%) by patient- or tumor-intrinsic variations. • Features derived using different image segmentations (expert/non-expert) were reproducible, provided that whole-volume segmentations were used. When using different feature extraction software packages with similar settings, higher-order features were less reproducible.

Reliability of MRI radiomics features in MR-guided radiotherapy for prostate cancer: Repeatability, reproducibility, and within-subject agreement

PURPOSE

The MR-guided radiotherapy (MRgRT) images on the integrated MRI and linear accelerator (MR-LINAC) might facilitate radiomics analysis for longitudinal treatment response assessment. However, the reliability of MRgRT radiomics features is largely unknown. This study aims to investigate MRgRT radiomics feature reliability acquired using a standardized 3D-T2W-TSE sequence in terms of repeatability, reproducibility, and within-subject feature agreement on a 1.5T MR-simulator and a 1.5T MR-LINAC for prostate cancer (PC).

METHODS

Twenty-six consecutive PC patients who underwent one MRI-simulator scan and two MR-LINAC scans before dose delivery were retrospectively included. The three MRI datasets were rigidly co-registered. 1023 first-order and texture radiomics features were extracted with different intensity bin widths for each scan in the manually segmented clinical target volume (CTV) and planning target volume (PTV) by an experienced radiation oncologist. Intraclass correlation coefficient (ICC) was used to evaluate feature repeatability between MR-LINAC scans and reproducibility between MRI-simulator and MR-LINAC scans. The within-subject feature value agreements were evaluated using Bland-Altman analysis. The impact of inter-observer segmentation on the radiomics feature reliability was also examined based on the second manual segmentation of CTV and PTV by an MRI researcher.

RESULTS

Based on the segmentation by the radiation oncologist and the default bin width of 25, 9.6%, 24.1%, 49.6%, and 16.8% of the total 1023 features exhibited excellent (ICC > 0.9), good (0.9 > ICC > 0.75), moderate (0.75 > ICC > 0.5), and poor (ICC < 0.5) repeatability in the CTV, and 9.2%, 26.8%, 50.5%, and 13.5% in the PTV, respectively. For reproducibility, the corresponding feature percentages were 8.9%, 19.7%, 41.9%, and 29.6% in the CTV, and 8.4%, 17.8%, 47.9%, and 26% in the PTV. Feature reliability was not notably influenced by intensity bin width for discretization. BA analysis revealed wide 95% limit-of-agreements and substantial biases of feature values between CTV and PTV and between any two MRI scans. The features even with excellent ICC were still subjected to considerable inter-scan feature variations in each individual subject. The analysis on the second segmentation by the MRI researcher showed insignificantly different feature repeatability and reproducibility in terms of ICC values.

CONCLUSIONS

Only a small proportion of features exhibited excellent/good repeatability and reproducibility, highlighting the importance of reliable MRgRT feature selection. The within-subject feature values were subjected to considerable inter-scan variations, imposing a challenge on the determination of the smallest detectable change in future MRgRT delta-radiomics studies.