MRI texture analysis on texture test objects, normal brain and intracranial tumors

Persistent fatigue in post-acute COVID syndrome is associated with altered T1 MRI texture in subcortical structures: a preliminary investigation

Post-acute COVID syndrome (PACS) is a global health concern and is often associated with debilitating symptoms. Post-COVID fatigue is a particularly frequent and troubling issue, and its underlying mechanisms remain incompletely understood. One potential contributor is micropathological injury of subcortical and brainstem structures, as has been identified in other patient populations. Texture-based analysis (TA) may be used to measure such changes in anatomical MRI data. The present study develops a methodology of voxel-wise TA mapping in subcortical and brainstem regions, which is then applied to T1-weighted MRI data from a cohort of 48 individuals who had PACS (32 with and 16 without ongoing fatigue symptoms) and 15 controls who had cold and flu-like symptoms but tested negative for COVID-19. Both groups were assessed an average of 4-5 months post-infection. There were no significant differences between PACS and control groups, but significant differences were observed within the PACS groups, between those with and without fatigue symptoms. This included reduced texture energy and increased entropy, along with reduced texture correlation, cluster shade and profile in the putamen, pallidum, thalamus and brainstem. These findings provide new insights into the neurophysiological mechanisms that underlie PACS, with altered tissue texture as a potential biomarker of this debilitating condition.

Performance of convolutional neural networks for the classification of brain tumors using magnetic resonance imaging

Brain tumors are a diverse group of neoplasms that are challenging to detect and classify due to their varying characteristics. Deep learning techniques have proven to be effective in tumor classification. However, there is a lack of studies that compare these techniques using a common methodology. This work aims to analyze the performance of convolutional neural networks in the classification of brain tumors. We propose a network consisting of a few convolutional layers, batch normalization, and max-pooling. Then, we explore recent deep architectures, such as VGG, ResNet, EfficientNet, or ConvNeXt. The study relies on two magnetic resonance imaging datasets with over 3000 images of three types of tumors -gliomas, meningiomas, and pituitary tumors-, as well as images without tumors. We determine the optimal hyperparameters of the networks using the training and validation sets. The training and test sets are used to assess the performance of the models from different perspectives, including training from scratch, data augmentation, transfer learning, and fine-tuning. The experiments are performed using the TensorFlow and Keras libraries in Python. We compare the accuracy of the models and analyze their complexity based on the capacity of the networks, their training times, and image throughput. Several networks achieve high accuracy rates on both datasets, with the best model achieving 98.7% accuracy, which is on par with state-of-the-art methods. The average precision for each type of tumor is 94.3% for gliomas, 93.8% for meningiomas, 97.9% for pituitary tumors, and 95.3% for images without tumors. VGG is the largest model with over 171 million parameters, whereas MobileNet and EfficientNetB0 are the smallest ones with 3.2 and 5.9 million parameters, respectively. These two neural networks are also the fastest to train with 23.7 and 25.4 seconds per epoch, respectively. On the other hand, ConvNext is the slowest model with 58.2 seconds per epoch. Our custom model obtained the highest image throughput with 234.37 images per second, followed by MobileNet with 226 images per second. ConvNext obtained the smallest throughput with 97.35 images per second. ResNet, MobileNet, and EfficientNet are the most accurate networks, with MobileNet and EfficientNet demonstrating superior performance in terms of complexity. Most models achieve the best accuracy using transfer learning followed by a fine-tuning step. However, data augmentation does not contribute to increasing the accuracy of the models in general.

Influence of contrast and texture based image modifications on the performance and attention shift of U-Net models for brain tissue segmentation

Contrast and texture modifications applied during training or test-time have recently shown promising results to enhance the generalization performance of deep learning segmentation methods in medical image analysis. However, a deeper understanding of this phenomenon has not been investigated. In this study, we investigated this phenomenon using a controlled experimental setting, using datasets from the Human Connectome Project and a large set of simulated MR protocols, in order to mitigate data confounders and investigate possible explanations as to why model performance changes when applying different levels of contrast and texture-based modifications. Our experiments confirm previous findings regarding the improved performance of models subjected to contrast and texture modifications employed during training and/or testing time, but further show the interplay when these operations are combined, as well as the regimes of model improvement/worsening across scanning parameters. Furthermore, our findings demonstrate a spatial attention shift phenomenon of trained models, occurring for different levels of model performance, and varying in relation to the type of applied image modification.

Bayesian dynamic profiling and optimization of important ranked energy from gray level co-occurrence (GLCM) features for empirical analysis of brain MRI

Accurate classification of brain tumor subtypes is important for prognosis and treatment. Researchers are developing tools based on static and dynamic feature extraction and applying machine learning and deep learning. However, static feature requires further analysis to compute the relevance, strength, and types of association. Recently Bayesian inference approach gains attraction for deeper analysis of static (hand-crafted) features to unfold hidden dynamics and relationships among features. We computed the gray level co-occurrence (GLCM) features from brain tumor meningioma and pituitary MRIs and then ranked based on entropy methods. The highly ranked Energy feature was chosen as our target variable for further empirical analysis of dynamic profiling and optimization to unfold the nonlinear intrinsic dynamics of GLCM features extracted from brain MRIs. The proposed method further unfolds the dynamics and to detailed analysis of computed features based on GLCM features for better understanding of the hidden dynamics for proper diagnosis and prognosis of tumor types leading to brain stroke.

Brain tumor detection and classification using machine learning: a comprehensive survey

Brain tumor occurs owing to uncontrolled and rapid growth of cells. If not treated at an initial phase, it may lead to death. Despite many significant efforts and promising outcomes in this domain, accurate segmentation and classification remain a challenging task. A major challenge for brain tumor detection arises from the variations in tumor location, shape, and size. The objective of this survey is to deliver a comprehensive literature on brain tumor detection through magnetic resonance imaging to help the researchers. This survey covered the anatomy of brain tumors, publicly available datasets, enhancement techniques, segmentation, feature extraction, classification, and deep learning, transfer learning and quantum machine learning for brain tumors analysis. Finally, this survey provides all important literature for the detection of brain tumors with their advantages, limitations, developments, and future trends.

Use of machine learning to select texture features in investigating the effects of axial loading on T2-maps from magnetic resonance imaging of the lumbar discs

BACKGROUND

Recent advances in texture analysis and machine learning offer new opportunities to improve the application of imaging to intervertebral disc biomechanics. This study employed texture analysis and machine learning on MRIs to investigate the lumbar disc's response to loading.

METHODS

Thirty-five volunteers (30 (SD 11) yrs.) with and without chronic back pain spent 20 min lying in a relaxed unloaded supine position, followed by 20 min loaded in compression, and then 20 min with traction applied. T₂-weighted MR images were acquired during the last 5 min of each loading condition. Custom image analysis software was used to segment discs from adjacent tissues semi-automatically and segment each disc into the nucleus, anterior and posterior annulus automatically. A grey-level, co-occurrence matrix with one to four pixels offset in four directions (0°, 45°, 90° and 135°) was then constructed (320 feature/tissue). The Random Forest Algorithm was used to select the most promising classifiers. Linear mixed-effect models and Cohen's d compared loading conditions.

FINDINGS

All statistically significant differences (p < 0.001) were observed in the nucleus and posterior annulus in the 135° offset direction at the L4-5 level between lumbar compression and traction. Correlation (P_2-Offset, P_4-Offset) and information measure of correlation 1 (P_3-Offset, P_4-Offset) detected significant changes in the nucleus. Statistically significant changes were also observed for homogeneity (P_2-Offset, P_3-Offset), contrast (P_2-Offset), and difference variance (P_4-Offset) of the posterior annulus.

INTERPRETATION

MRI textural features may have the potential of identifying the disc's response to loading, particularly in the nucleus and posterior annulus, which appear most sensitive to loading.

LEVEL OF EVIDENCE

Diagnostic: individual cross-sectional studies with consistently applied reference standard and blinding.

Establishing ADC-Based Histogram and Texture Features for Early Treatment-Induced Changes in Head and Neck Squamous Cell Carcinoma

The purpose of this study was to assess baseline variability in histogram and texture features derived from apparent diffusion coefficient (ADC) maps from diffusion-weighted MRI (DW-MRI) examinations and to identify early treatment-induced changes to these features in patients with head and neck squamous cell carcinoma (HNSCC) undergoing definitive chemoradiation. Patients with American Joint Committee on Cancer Stage III–IV (7^th edition) HNSCC were prospectively enrolled on an IRB-approved study to undergo two pre-treatment baseline DW-MRI examinations, performed 1 week apart, and a third early intra-treatment DW-MRI examination during the second week of chemoradiation. Forty texture and six histogram features were derived from ADC maps. Repeatability of the features from the baseline ADC maps was assessed with the intra-class correlation coefficient (ICC). A Wilcoxon signed-rank test compared average baseline and early treatment feature changes. Data from nine patients were used for this study. Comparison of the two baseline ADC maps yielded 11 features with an ICC ≥ 0.80, indicating that these features had excellent repeatability: Run Gray-Level Non-Uniformity, Coarseness, Long Zone High Gray-Level, Variance (Histogram Feature), Cluster Shade, Long Zone, Variance (Texture Feature), Run Length Non-Uniformity, Correlation, Cluster Tendency, and ADC Median. The Wilcoxon signed-rank test resulted in four features with significantly different early treatment-induced changes compared to the baseline values: Run Gray-Level Non-Uniformity (p = 0.005), Run Length Non-Uniformity (p = 0.005), Coarseness (p = 0.006), and Variance (Histogram) (p = 0.006). The feasibility of histogram and texture analysis as a potential biomarker is dependent on the baseline variability of each metric, which disqualifies many features.

Magnetic resonance imaging texture analysis for the evaluation of viable ovarian tissue in patients with ovarian endometriosis

Background

Texture analysis has been used as a method for quantifying image properties based on textural features. The aim of the present study was to evaluate the usefulness of magnetic resonance imaging (MRI) texture analysis for the evaluation of viable ovarian tissue on the perfusion map of ovarian endometriosis.

Methods

To generate a normalized perfusion map, subtracted T1-weighted imaging (T1WI), T1WI and contrast-enhanced T1W1 with sequences were performed using the same parameters in 25 patients with surgically confirmed ovarian endometriosis. Integrated density is defined as the sum of the values of the pixels in the image or selection. We investigated the parameters for texture analysis in ovarian endometriosis, including angular second moment (ASM), contrast, correlation, inverse difference moment (IDM), and entropy, which is equivalent to the product of area and mean gray value.

Results

The perfusion ratio and integrated density of normal ovary were 0.52±0.05 and 238.72±136.21, respectively. Compared with the normal ovary, the affected ovary showed significant differences in total size (p<0.001), fractional area ratio (p<0.001), and perfusion ratio (p=0.010) but no significant differences in perfused tissue area (p=0.158) and integrated density (p=0.112). In comparison of parameters for texture analysis between the ovary with endometriosis and the contralateral normal ovary, ASM (p=0.004), contrast (p=0.002), IDM (p<0.001), and entropy (p=0.028) showed significant differences. A linear regression analysis revealed that fractional area had significant correlations with ASM (r²=0.211), IDM (r²=0.332), and entropy (r²=0.289).

Conclusion

MRI texture analysis could be useful for the evaluation of viable ovarian tissues in patients with ovarian endometriosis.

Classification of neoplastic and inflammatory brain disease using MRI texture analysis in 119 dogs

Magnetic resonance imaging is the primary method used to diagnose canine glial cell neoplasia and noninfectious inflammatory meningoencephalitis. Subjective differentiation of these diseases can be difficult due to overlapping imaging characteristics. This study utilizes texture analysis (TA) of intra-axial lesions both as a means to quantitatively differentiate these broad categories of disease and to help identify glial tumor grade/cell type and specific meningoencephalitis subtype in a group of 119 dogs with histologically confirmed diagnoses. Fifty-nine dogs with gliomas and 60 dogs with noninfectious inflammatory meningoencephalitis were retrospectively recruited and randomly split into training (n = 80) and test (n = 39) cohorts. Forty-five of 120 texture metrics differed significantly between cohorts after correcting for multiple testing (false discovery rate < 0.05). After training the random forest algorithm, the classification accuracy for the test set was 85% (sensitivity 89%, specificity 81%). TA was only partially able to differentiate the inflammatory subtypes (granulomatous meningoencephalitis [GME], necrotizing meningoencephalitis [NME], and necrotizing leukoencephalitis [NLE]) (out-of-bag error rate of 35.0%) and was unable to identify metrics that could correctly classify glioma grade or cell type (out-of-bag error rate of 59.6% and 47.5%, respectively). Multiple demographic differences, such as patient age, sex, weight, and breed were identified between disease cohorts and subtypes which may be useful in prioritizing differential diagnoses. TA of MR images with a random forest algorithm provided classification accuracy of inflammatory and neoplastic brain disease approaching the accuracy of previously reported subjective radiologist evaluation.

Automated multi-class brain tumor types detection by extracting RICA based features and employing machine learning techniques

Among the other cancer types, the brain tumor is one the leading cause of cancer across globe. If the tumor is properly identified at an earlier stage, then the chances of the survival can be increased. To categorize the brain tumor there are several factors including texture, type and location of brain tumor. We proposed a novel reconstruction independent component analysis (RICA) feature extraction method to detect multi-class brain tumor types (pituitary, meningioma, and glioma). We then employed the robust machine learning techniques as support vector machine (SVM) with quadratic and linear kernels and linear discriminant analysis (LDA). For training and testing of the data validation, a 10-fold cross validation was employed. For the multi-class classification, the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), accuracy and AUC were, respectively, 97.78%, 100%, 100%, 99.07, 99.34% and 0.9892 to detect pituitary using SVM Cubic followed by meningioma with accuracy (96.96%0, AUC (0.9348) and glioma with accuracy (95.88%), AUC (0.9635). The findings indicates that RICA feature based proposed methodology has more potential to detect the multiclass brain tumor types for improving diagnostic efficiency and can further improve the prediction accuracy to achieve the clinical outcomes.

Development of a predictive model of growth hormone deficiency and idiopathic short stature in children

The aim of the present study was to develop predictive models using clinical features and MRI texture features for distinguishing between growth hormone deficiency (GHD) and idiopathic short stature (ISS) in children with short stature. This retrospective study included 362 children with short stature from Children's Hospital of Hebei Province. GHD and ISS were identified via the GH stimulation test using arginine. Overall, there were 190 children with GHD and 172 with ISS. A total of 57 MRI texture features were extracted from the pituitary gland region of interest using C++ language and Matlab software. In addition, the laboratory examination data were collected. Receiver operating characteristic (ROC) regression curves were generated for the predictive performance of clinical features and MRI texture features. Logistic regression models based on clinical and texture features were established for discriminating children with GHD and ISS. Two clinical features [IGF-1 (insulin growth factor-1) and IGFBP-3 (IGF binding protein-3) levels] were used to build the clinical predictive model, whereas the three best MRI textures were used to establish the MRI texture predictive model. The ROC analysis of the two models revealed predictive performance for distinguishing GHD from ISS. The accuracy of predicting ISS from GHD was 64.5% in ROC analysis [area under the curve (AUC), 0.607; sensitivity, 57.6%; specificity, 72.1%] of the clinical model. The accuracy of predicting ISS from GHD was 80.4% in ROC analysis (AUC, 0.852; sensitivity, 93.6%; specificity, 65.8%) of the MRI texture predictive model. In conclusion, these findings indicated that a texture predictive model using MRI texture features was superior for distinguishing children with GHD from those with ISS compared with the model developed using clinical features.

Noninvasive radiomics-based method for evaluating idiopathic central precocious puberty in girls

Objective

Traditional approaches that involve measuring the height and volume of the pituitary by magnetic resonance imaging (MRI) are unreliable. We investigated the use of a more accurate method using texture analysis to evaluate idiopathic central precocious puberty (ICPP) by MRI.

Methods

In total, 352 texture features of the pituitary were extracted from 12 healthy girls and 18 girls with ICPP. A LASSO regression model and linear regression model were used to create the prediction model. Pearson’s correlation analysis and receiver operating characteristic curves were used to evaluate the predictive performance.

Results

The radiomics score had a significant linear relationship with the luteinizing hormone concentration and the luteinizing hormone/follicle-stimulating hormone ratio. The radiomics score showed better predictive performance than traditional pituitary measurements. The area under the curve of the radiomics score, pituitary height, and variable combinations was 0.759 (95% confidence interval [CI], 0.583–0.936), 0.681 (95% CI, 0.483–0.878), and 0.829 (95% CI, 0.681–0.976), respectively.

Conclusion

Combination of the radiomics score with pituitary height measurements allows for better evaluation of the pituitary during diagnostic imaging, indicating satisfactory potential for efficacy assessments.

Radiomics signature of brain metastasis: prediction of EGFR mutation status

OBJECTIVES

To predict epidermal growth factor receptor (EGFR) mutation status in lung adenocarcinoma using MR-based radiomics signature of brain metastasis and explore the optimal MR sequence for prediction.

METHODS

Data from 52 patients with brain metastasis from lung adenocarcinoma (28 with mutant EGFR, 24 with wild-type EGFR) were retrospectively reviewed. Contrast-enhanced T1-weighted imaging (T1-CE), T2 fluid-attenuated inversion recovery (T2-FLAIR), T2WI, and DWI sequences were selected for radiomics features extraction. A total of 438 radiomics features were extracted from each MR sequence. All sequences were randomly divided into training and validation cohorts. The least absolute shrinkage selection operator was used to select informative features, a radiomics signature was built with the logistic regression model of the training cohort, and the radiomics signature performance was evaluated using the validation cohort and an independent testing data set.

RESULTS

The radiomics signature built on 9 selected features showed good discrimination in both the training and validation cohorts for T2-FLAIR. The radiomics signature of T2-FLAIR yielded an AUC of 0.987, a classification accuracy of 0.991, sensitivity of 1.000, and specificity of 0.980 in the validation cohort. The AUC was 0.871 in the independent testing data set. The AUCs of our radiomics signature to differentiate exon 19 and exon 21 mutations were 0.529, 0.580, 0.645, and 0.406 for T1-CE, T2-FLAIR, T2WI, and DWI, respectively.

CONCLUSIONS

We developed a T2-FLAIR radiomics signature that can be used as a noninvasive auxiliary tool for predicting EGFR mutation status in lung adenocarcinoma, which is helpful to guide therapeutic strategies.

KEY POINTS

• MR-based radiomics signature of brain metastasis may help predict EGFR mutation status in lung adenocarcinoma, especially using T2-FLAIR. • Nine radiomics features extracted from T2-FLAIR sequence strongly correlate with EGFR mutation status. • Radiomics features reflect tumor heterogeneity through potential changes in tissue morphology caused by EGFR mutation.

Prediction of the Ki-67 marker index in hepatocellular carcinoma based on CT radiomics features

The noninvasive detection of tumor proliferation is of great value and the Ki-67 is a biomarker of tumor proliferation. We hypothesized that radiomics characteristics may be related to tumor proliferation. To evaluate whether computed tomography (CT) radiomics feature analyses could aid in assessing the Ki-67 marker index in hepatocellular carcinoma (HCC), we retrospectively analyzed preoperative CT findings of 74 patients with HCC. The texture feature calculations were computed from MaZda 4.6 software, and the sequential forward selection algorithm was used as the selection method. The correlation between radiomics features and the Ki-67 marker index, as well as the difference between low Ki-67 (<10%) and high Ki-67 (≥10%) groups were evaluated. A simple logistic regression model was used to evaluate the associations between texture features and high Ki-67, and receiver operating characteristic analysis was performed on important parameters to assess the ability of radiomics characteristics to distinguish the high Ki-67 group from the low Ki-67 group. Contrast, correlation, and inverse difference moment (IDM) were significantly different (P < 0.001) between the low and high Ki-67 groups. Contrast (odds ratio [OR] = 0.957; 95% confidence interval [CI]: 0.926-0.990, P = 0.01) and correlation (OR = 2.5☆105; 95% CI: 7.560-8.9☆109; P = 0.019) were considered independent risk factors for combined model building with logistic regression. Angular second moment (r = -0.285, P = 0.014), contrast (r = -0.449, P < 0.001), correlation (r = 0.552, P < 0.001), IDM (r = 0.458, P < 0.001), and entropy (r = 0.285, P = 0.014) strongly correlated with the Ki-67 scores. Contrast, correlation, and the combined predictor were predictive of Ki-67 status (P < 0.001), with areas under the curve ranging from 0.777 to 0.836. The radiomics characteristics of CT have potential as biomarkers for predicting Ki-67 status in patients with HCC. These findings suggest that the radiomics features of CT might be used as a noninvasive measure of cellular proliferation in HCC.

Impact of quantization algorithm and number of gray level intensities on variability and repeatability of low field strength magnetic resonance image-based radiomics texture features

PURPOSE

The purpose of this work was to investigate the impact of quantization preprocessing parameter selection on variability and repeatability of texture features derived from low field strength magnetic resonance (MR) images.

METHODS

Texture features were extracted from low field strength images of a daily image QA phantom with four texture inserts. Feature variability over time was quantified using all combinations of three quantization algorithms and four different numbers of gray level intensities. In addition, texture features were extracted using the same combinations from the low field strength MR images of the gross tumor volume (GTV) and left kidney of patients with repeated set up scans. The impact of region of interest (ROI) preprocessing on repeatability was investigated with a test-retest study design.

RESULTS

The phantom ROIs quantized to 64 Gy level intensities using the histogram equalization method resulted in the greatest number of features with the least variability. There was no clear method that resulted in the highest repeatability in the GTV or left kidney. However, eight texture features extracted from the GTV were repeatable regardless of ROI processing combination.

CONCLUSION

Low field strength MR images can provide a stable basis for texture analysis with ROIs quantized to 64 Gy levels using histogram equalization, but there is no clear optimal combination for repeatability.

Exploring MRI based radiomics analysis of intratumoral spatial heterogeneity in locally advanced nasopharyngeal carcinoma treated with intensity modulated radiotherapy

Background

We hypothesized that spatial heterogeneity exists between recurrent and non-recurrent regions within a tumor. The aim of this study was to determine if there is a difference between radiomics features derived from recurrent versus non recurrent regions within the tumor based on pre-treatment MRI.

Methods

A total of 14 T4NxM0 NPC patients with histologically proven “in field” recurrence in the post nasal space following curative intent IMRT were included in this study. Pretreatment MRI were co-registered with MRI at the time of recurrence for the delineation of gross tumor volume at diagnosis(GTV) and at recurrence(GTVr). A total of 7 histogram features and 40 texture features were computed from the recurrent(GTVr) and non-recurrent region(GTV-GTVr). Paired t-tests and Wilcoxon signed-rank tests were carried out on the 47 quantified radiomics features.

Results

A total of 7 features were significantly different between recurrent and non-recurrent regions. Other than the variance from intensity-based histogram, the remaining six significant features were either from the gray-level size zone matrix (GLSZM) or the neighbourhood gray-tone difference matrix (NGTDM).

Conclusions

The radiomic features extracted from pre-treatment MRI can potentially reflect the difference between recurrent and non-recurrent regions within a tumor and has a potential role in pre-treatment identification of intra-tumoral radio-resistance for selective dose escalation.

Differentiation of Endometriomas from Ovarian Hemorrhagic Cysts at Magnetic Resonance: The Role of Texture Analysis

Background and Objectives: To assess ovarian cysts with texture analysis (TA) in magnetic resonance (MRI) images for establishing a differentiation criterion for endometriomas and functional hemorrhagic cysts (HCs) that could potentially outperform their classic MRI diagnostic features. Materials and Methods: Forty-three patients with known ovarian cysts who underwent MRI were retrospectively included (endometriomas, n = 29; HCs, n = 14). TA was performed using dedicated software based on T2-weighted images, by incorporating the whole lesions in a three-dimensional region of interest. The most discriminative texture features were highlighted by three selection methods (Fisher, probability of classification error and average correlation coefficients, and mutual information). The absolute values of these parameters were compared through univariate, multivariate, and receiver operating characteristic analyses. The ability of the two classic diagnostic signs ("T2 shading" and "T2 dark spots") to diagnose endometriomas was assessed by quantifying their sensitivity (Se) and specificity (Sp), following their conventional assessment on T1-and T2-weighted images by two radiologists. Results: The diagnostic power of the one texture parameter that was an independent predictor of endometriomas (entropy, 75% Se and 100% Sp) and of the predictive model composed of all parameters that showed statistically significant results at the univariate analysis (100% Se, 100% Sp) outperformed the ones shown by the classic MRI endometrioma features ("T2 shading", 75.86% Se and 35.71% Sp; "T2 dark spots", 55.17% Se and 64.29% Sp). Conclusion: Whole-lesion MRI TA has the potential to offer a superior discrimination criterion between endometriomas and HCs compared to the classic evaluation of the two lesions' MRI signal behaviors.

Differentiating High-Grade Gliomas from Brain Metastases at Magnetic Resonance: The Role of Texture Analysis of the Peritumoral Zone

High-grade gliomas (HGGs) and solitary brain metastases (BMs) have similar imaging appearances, which often leads to misclassification. In HGGs, the surrounding tissues show malignant invasion, while BMs tend to displace the adjacent area. The surrounding edema produced by the two cannot be differentiated by conventional magnetic resonance (MRI) examinations. Forty-two patients with pathology-proven brain tumors who underwent conventional pretreatment MRIs were retrospectively included (HGGs, n = 16; BMs, n = 26). Texture analysis of the peritumoral zone was performed on the T2-weighted sequence using dedicated software. The most discriminative texture features were selected using the Fisher and the probability of classification error and average correlation coefficients. The ability of texture parameters to distinguish between HGGs and BMs was evaluated through univariate, receiver operating, and multivariate analyses. The first percentile and wavelet energy texture parameters were independent predictors of HGGs (75–87.5% sensitivity, 53.85–88.46% specificity). The prediction model consisting of all parameters that showed statistically significant results at the univariate analysis was able to identify HGGs with 100% sensitivity and 66.7% specificity. Texture analysis can provide a quantitative description of the peritumoral zone encountered in solitary brain tumors, that can provide adequate differentiation between HGGs and BMs.

Normal appearing brain white matter changes in relapsing multiple sclerosis: Texture image and classification analysis in serial MRI scans

OBJECTIVE

There is a clinical interest in identifying normal appearing white matter (NAWM) areas in brain T2-weighted (T₂W) MRI scans in multiple sclerosis (MS) subjects. These areas are susceptible to disease development and areas need to be studied in order to find potential associations between texture feature changes and disease progression.

METHODS

The subjects investigated had a first demyelinating event (Clinically Isolated Syndrome-CIS) at baseline (Time₀), and the NAWM₀ (i.e. NAWM at Time₀) of the brain tissue was subsequently converted to demyelinating plaques (as evaluated in a follow up MRI at Time_6-12). 38 untreated subjects that had developed a CIS, had brain MRI scans within an interval of 6-12 months (Time_6-12 at follow-up). An experienced MS neurologist manually delineated the demyelinating lesions at Time₀ (L₀) and at Time_6-12 (L_6-12). Areas in the Time_6-12 MRI scans, where new lesions had been developed, were mapped back to their corresponding NAWM areas on the Time₀ MR scans (ROIS₀). In addition, contralateral ROIs of similar size and shape were segmented on the same images at Time₀ (ROIS_C0) to form an intra-subject control group. Following that, texture features were extracted from all prescribed areas and MS lesions.

RESULTS

Texture features were used as input into Support Vector Machine (SVM) models to differentiate between the following: NAWM₀ vs ROIS_C0, NAWM₀ vs NAWM_6-12, NAWM₀ vs L₀, NAWM_6-12 vs L_6-12, ROIS₀ vs L₀, ROIS₀ vs L_6-12 and ROIS₀ vs ROIS_C0, where the corresponding % correct classifications scores were 89%, 95%, 98%, 92%, 85%, 90% and 65% respectively.

CONCLUSIONS

Texture features may provide complementary information for following up the development and progression of MS disease. Future work will investigate the proposed method on more subjects.

Preliminary study on discriminating HER2 2+ amplification status of breast cancers based on texture features semi-automatically derived from pre-, post-contrast, and subtraction images of DCE-MRI

Objective

To investigate whether texture features extracted from dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) are associated with human epidermal growth factor receptor type 2 (HER2) 2+ status of breast cancer.

Materials and methods

92 MRI cases including 52 HER2 2+ positive and 40 negative patients confirmed by fluorescence in situ hybridization were retrospectively selected. The lesion area was semi-automatically delineated, and a total of 488 texture features were respectively extracted from precontrast, postcontrast, and subtraction images. The Student’s t-test or Mann-Whitney U test was performed to identify statistically significant features between different HER2 2+ amplification groups. Least absolute shrinkage and selection operator (LASSO) was used to search for the optimal feature subsets. Three machine learning classifiers, logistic regression analysis (LRA), quadratic discriminant analysis (QDA), and support vector machine (SVM), were used with a leave-one-out cross validation method to establish the classification models of HER2 2+ status. Classification performance was evaluated by receiver operating characteristic (ROC) analysis.

Results

Based on the texture analysis with SVM model, the areas under the ROC curve (AUCs) were 0.890 for subtraction images, 0.736 for postcontrast images, and 0.672 for precontrast images, respectively. For LRA model, the AUCs were 0.884, 0.733, and 0.623, respectively. For QDA model, the AUCs were 0.831, 0.726, and 0.568, respectively. LRA and the SVM model with subtraction images reached significantly better performance than the QDA model (P = 0.0227 and P = 0.0088, respectively).

Conclusion

Texture features of breast cancer extracted from DCE-MRI are associated with HER2 2+ status. Additional studies are necessary to confirm the present preliminary findings.

Texture analysis of early cerebral tissue damage in magnetic resonance imaging of patients with lung cancer

Primary tumors can secrete many cytokines, inducing tissue damage or microstructural changes in distant organs. The purpose of this study was to investigate changes in texture features in the cerebral tissue of patients with lung cancer without brain metastasis. In this study, 50 patients with lung cancers underwent 3.0-T magnetic resonance imaging (MRI) within 2 weeks of being diagnosed with lung cancer. Texture analysis (TA) was carried out in 8 gray matter areas, including bilateral frontal cortices, parietal cortices, occipital cortices and temporal cortices, as well as 2 areas of bilateral frontoparietal white matter. The same procedure was performed for 57 healthy controls. A total of 32 texture parameters were separately compared between the patients and controls in the different cerebral tissue sites. Texture features among patients based on histological type and clinical stage were also compared. Of the 32 texture parameters, 27 showed significant differences between patients with lung cancer and healthy controls. There were significant differences in cerebral tissue, both gray matter and white matter between patients and controls, especially in several wavelet-based parameters. However, there were no significant differences between tissue at homologous sites in bilateral hemispheres, either in patients or controls. TA detected overt changes in the texture features of cerebral tissue in patients with lung cancer without brain metastasis compared with those of healthy controls. TA may be considered as a novel and adjunctive approach to conventional brain MRI to reveal cerebral tissue changes invisible on MRI alone in patients with lung cancer.

MRI-derived radiomics: methodology and clinical applications in the field of pelvic oncology

Personalized medicine aims at offering optimized treatment options and improved survival for cancer patients based on individual variability. The success of precision medicine depends on robust biomarkers. Recently, the requirement for improved non-biologic biomarkers that reflect tumor biology has emerged and there has been a growing interest in the automatic extraction of quantitative features from medical images, denoted as radiomics. Radiomics as a methodological approach can be applied to any image and most studies have focused on PET, CT, ultrasound, and MRI. Here, we aim to present an overview of the radiomics workflow as well as the major challenges with special emphasis on the use of multiparametric MRI datasets. We then reviewed recent studies on radiomics in the field of pelvic oncology including prostate, cervical, and colorectal cancer.

Texture analysis of placental MRI: can it aid in the prenatal diagnosis of placenta accreta spectrum?

PURPOSE

To determine if texture analysis can differentiate placenta accreta spectrum (PAS) from normal placenta on MRI.

METHODS

We performed retrospective image analysis of 80 patients, comprised of 46 patients with PAS and 34 patients without PAS. Histopathology was used as the reference standard. Sagittal single shot fast spin echo T2-weighted MRI sequences acquired from a single institution were analyzed. Placental heterogeneity was quantified using in-house software on a Matlab platform, including the standard deviation of pixel intensity, coefficient of variation, gray-level co-occurrence matrices (GLCM), histogram-oriented gradients (HOG), and fractal analysis with box sizes from 2 to 512. Two-tailed unpaired Student's t test was used with statistical significance of p < 0.05.

RESULTS

PAS was associated with higher values for standard deviation of pixel intensity and fractal analysis at every box size. Fractal analysis at box sizes 256 (p = 0.011) and 32 (p = 0.021), and standard deviation of pixel intensity (p = 0.023) were the most statistically significant. Fractal values at box size 256 for PAS was 0.13 versus 0.090 for patients without PAS, while standard deviation of pixel intensity was 3.7 for PAS versus 2.5 for patients without PAS. No statistically significant association between PAS and GLCM, coefficient of variation, and HOG was found.

CONCLUSION

Statistically significant differences were found between normal and abnormal groups using standard deviation of pixel intensity and fractal analysis.

The Transition from Metal-Based to Metal-Free Contrast Agents for T1 Magnetic Resonance Imaging Enhancement

Magnetic resonance imaging (MRI) has received significant attention as the noninvasive diagnostic technique for complex diseases. Image-guided therapeutic strategy for diseases such as cancer has also been at the front line of biomedical research, thanks to the innovative MRI, enhanced by the prior delivery of contrast agents (CAs) into patients' bodies through injection. These CAs have contributed a great deal to the clinical utility of MRI but have been based on metal-containing compounds such as gadolinium, manganese, and iron oxide. Some of these CAs have led to cytotoxicities such as the incurable Nephrogenic Systemic Fibrosis (NSF), resulting in their removal from the market. On the other hand, CAs based on organic nitroxide radicals, by virtue of their structural composition, are metal free and without the aforementioned drawbacks. They also have improved biocompatibility, ease of functionalization, and long blood circulation times, and have been proven to offer tissue contrast enhancement with longitudinal relaxivities comparable with those for the metal-containing CAs. Thus, this Review highlights the recent progress in metal-based CAs and their shortcomings. In addition, the remarkable goals achieved by the organic nitroxide radical CAs in the enhancement of MR images have also been discussed extensively. The focal point of this Review is to emphasize or demonstrate the crucial need for transition into the use of organic nitroxide radicals-metal-free CAs-as against the metal-containing CAs, with the aim of achieving safer application of MRI for early disease diagnosis and image-guided therapy.

Use of Precision Imaging in the Evaluation of Pancreas Cancer

Pancreas cancer is an aggressive and fatal disease that will become one of the leading causes of cancer mortality by 2030. An all-out effort is underway to better understand the basic biologic mechanisms of this disease ranging from early development to metastatic disease. In order to change the course of this disease, diagnostic radiology imaging may play a vital role in providing a precise, noninvasive method for early diagnosis and assessment of treatment response. Recent progress in combining medical imaging, advanced image analysis and artificial intelligence, termed radiomics, can offer an innovate approach in detecting the earliest changes of tumor development as well as a rapid method for the detection of response. In this chapter, we introduce the principles of radiomics and demonstrate how it can provide additional information into tumor biology, early detection, and response assessments advancing the goals of precision imaging to deliver the right treatment to the right person at the right time.

Repeatability of texture features derived from magnetic resonance and computed tomography imaging and use in predictive models for non-small cell lung cancer outcome

PURPOSE

To evaluate the repeatability of MRI and CT derived texture features and to investigate the feasibility of use in predictive single and multi-modality models for radiotherapy of non-small cell lung cancer. Methods: Fifty-nine texture features were extracted from unfiltered and wavelet filtered images. Repeatability of test-retest features from helical 4D CT scans, true fast MRI with steady state precession (TRUFISP), and volumetric interpolation breath-hold examination (VIBE) was determined by the concordance correlation coefficient (CCC). A workflow was developed to predict overall survival at 12, 18, and 24 months and tumour response at end of treatment for tumour features, and normal muscle tissue features as a control. Texture features were reduced to repeatable and stable features before clustering. Cluster representative feature selection was performed by univariate or medoid analysis before model selection. P-values were corrected for false discovery rate. Results: Repeatable (CCC ≥ 0.9) features were found for both tumour and normal muscle tissue: CT: 54.4% for tumour and 78.5% for normal tissue, TRUFISP: 64.4% for tumour and 67.8% for normal tissue, and VIBE: 52.6% for tumour and 72.9% for normal muscle tissue. Muscle tissue control analysis found 7 significant models with 6 of 7 models utilizing the univariate representative feature selection technique. Tumour analysis revealed 12 significant models for overall survival and none for tumour response at end of treatment. The accuracy of significant single modality was about the same for MR and CT. Multi-modality tumour models had comparable performance to single modality models. Conclusion: MR derived texture features may add value to predictive models and should be investigated in a larger cohort. Control analysis demonstrated that the medoid representative feature selection method may result in more robust models. .

Pancreatic neuroendocrine tumor: prediction of the tumor grade using magnetic resonance imaging findings and texture analysis with 3-T magnetic resonance

Purpose

The purpose of this study was to evaluate the performance of magnetic resonance imaging (MRI) findings and texture parameters for prediction of the histopathologic grade of pancreatic neuroendocrine tumors (PNETs) with 3-T magnetic resonance.

Patients and methods

PNETs are classified into Grade 1 (G1), Grade 2 (G2), and Grade 3 (G3) tumors based on the Ki-67 proliferation index and the mitotic activity. A total of 77 patients with pathologically confirmed PNETs met the inclusion criteria. Texture analysis (TA) was applied to T2-weighted imaging (T2WI) and diffusion-weighted imaging (DWI) maps. Patient demographics, MRI findings, and texture parameters were compared among three different histopathologic subtypes by using Fisher’s exact tests or Kruskal–Wallis test. Then, logistic regression analysis was adopted to predict tumor grades. ROC curves and AUCs were calculated to assess the diagnostic performance of MRI findings and texture parameters in prediction of tumor grades.

Results

There were 31 G1, 29 G2, and 17 G3 patients. Compared with G1, G2/G3 tumors showed higher frequencies of an ill-defined margin, a predominantly solid tumor type, local invasion or metastases, hypo-enhancement at the arterial phase, and restriction diffusion. Four T2-based (inverse difference moment, energy, correlation, and differenceEntropy) and five DWI-based (correlation, contrast, inverse difference moment, maxintensity, and entropy) TA parameters exhibited statistical significance among PNETs (P<0.001). The AUCs of six predicting models on T2WI and DWI ranged from 0.703–0.989.

Conclusion

Our data indicate that MRI findings, including tumor margin, texture, local invasion or metastases, tumor enhancement, and diffusion restriction, as well as texture parameters can aid the prediction of PNETs grading.

Comparing radiomic classifiers and classifier ensembles for detection of peripheral zone prostate tumors on T2-weighted MRI: a multi-site study

Background

For most computer-aided diagnosis (CAD) problems involving prostate cancer detection via medical imaging data, the choice of classifier has been largely ad hoc, or been motivated by classifier comparison studies that have involved large synthetic datasets. More significantly, it is currently unknown how classifier choices and trends generalize across multiple institutions, due to heterogeneous acquisition and intensity characteristics (especially when considering MR imaging data). In this work, we empirically evaluate and compare a number of different classifiers and classifier ensembles in a multi-site setting, for voxel-wise detection of prostate cancer (PCa) using radiomic texture features derived from high-resolution in vivo T2-weighted (T2w) MRI.

Methods

Twelve different supervised classifier schemes: Quadratic Discriminant Analysis (QDA), Support Vector Machines (SVMs), naïve Bayes, Decision Trees (DTs), and their ensemble variants (bagging, boosting), were compared in terms of classification accuracy as well as execution time. Our study utilized 85 prostate cancer T2w MRI datasets acquired from across 3 different institutions (1 for discovery, 2 for independent validation), from patients who later underwent radical prostatectomy. Surrogate ground truth for disease extent on MRI was established by expert annotation of pre-operative MRI through spatial correlation with corresponding ex vivo whole-mount histology sections. Classifier accuracy in detecting PCa extent on MRI on a per-voxel basis was evaluated via area under the ROC curve.

Results

The boosted DT classifier yielded the highest cross-validated AUC (= 0.744) for detecting PCa in the discovery cohort. However, in independent validation, the boosted QDA classifier was identified as the most accurate and robust for voxel-wise detection of PCa extent (AUCs of 0.735, 0.683, 0.768 across the 3 sites). The next most accurate and robust classifier was the single QDA classifier, which also enjoyed the advantage of significantly lower computation times compared to any of the other methods.

Conclusions

Our results therefore suggest that simpler classifiers (such as QDA and its ensemble variants) may be more robust, accurate, and efficient for prostate cancer CAD problems, especially in the context of multi-site validation.

Robust, atlas-free, automatic segmentation of brain MRI in health and disease

Background

Brain- and lesion-volumes derived from magnetic resonance images (MRI) serve as important imaging markers of disease progression in neurodegenerative diseases and aging. While manual segmentation of these volumes is both tedious and impractical in large cohorts of subjects, automated segmentation methods often fail in accurate segmentation of brains with severe atrophy or high lesion loads. The purpose of this study was to develop an atlas-free brain Classification using DErivative-based Features (C-DEF), which utilizes all scans that may be acquired during the course of a routine MRI study at any center.

Methods

Proton-density, T₂-weighted, T₁-weighted, brain-free water, 3D FLAIR, 3D T₂-weighted, and 3D T₂*-weighted images, collected routinely on patients with neuroinflammatory diseases at the NIH, were used to optimize the C-DEF algorithm on healthy volunteers and HIV + subjects (cohort 1). First, manually marked lesions and eroded FreeSurfer brain segmentation masks (compiled into gray and white matter, globus pallidus, CSF labels) were used in training. Next, the optimized C-DEF was applied on a separate cohort of HIV + subjects (cohort two), and the results were compared with that of FreeSurfer and Lesion-TOADS. Finally, C-DEF segmentation was evaluated on subjects clinically diagnosed with various other neurological diseases (cohort three).

Results

C-DEF algorithm was optimized using leave-one-out cross validation on five healthy subjects (age 36 ± 11 years), and five subjects infected with HIV (age 57 ± 2.6 years) in cohort one. The optimized C-DEF algorithm outperformed FreeSurfer and Lesion-TOADS segmentation in 49 other subjects infected with HIV (cohort two, age 54 ± 6 years) in qualitative and quantitative comparisons. Although trained only on HIV brains, sensitivity to detect lesions using C-DEF increased by 45% in HTLV-I-associated myelopathy/tropical spastic paraparesis (n = 5; age 58 ± 7 years), 33% in multiple sclerosis (n = 5; 42 ± 9 years old), and 4% in subjects with polymorphism of the cytotoxic T-lymphocyte-associated protein 4 gene (n = 5; age 24 ± 12 years) compared to Lesion-TOADS.

Conclusion

C-DEF outperformed other segmentation algorithms in the various neurological diseases explored herein, especially in lesion segmentation. While the results reported are from routine images acquired at the NIH, the algorithm can be easily trained and optimized for any set of contrasts and protocols for wider application. We are currently exploring various technical aspects of optimal implementation of CDEF in a clinical setting and evaluating a larger cohort of patients with other neurological diseases. Improving the accuracy of brain segmentation methodology will help better understand the relationship of imaging abnormalities to clinical and neuropsychological markers in disease.

The Applications of Radiomics in Precision Diagnosis and Treatment of Oncology: Opportunities and Challenges

Medical imaging can assess the tumor and its environment in their entirety, which makes it suitable for monitoring the temporal and spatial characteristics of the tumor. Progress in computational methods, especially in artificial intelligence for medical image process and analysis, has converted these images into quantitative and minable data associated with clinical events in oncology management. This concept was first described as radiomics in 2012. Since then, computer scientists, radiologists, and oncologists have gravitated towards this new tool and exploited advanced methodologies to mine the information behind medical images. On the basis of a great quantity of radiographic images and novel computational technologies, researchers developed and validated radiomic models that may improve the accuracy of diagnoses and therapy response assessments. Here, we review the recent methodological developments in radiomics, including data acquisition, tumor segmentation, feature extraction, and modelling, as well as the rapidly developing deep learning technology. Moreover, we outline the main applications of radiomics in diagnosis, treatment planning and evaluations in the field of oncology with the aim of developing quantitative and personalized medicine. Finally, we discuss the challenges in the field of radiomics and the scope and clinical applicability of these methods.

MRI of pancreatic ductal adenocarcinoma: texture analysis of T2-weighted images for predicting long-term outcome

PURPOSE

To assess the association between T2-weighted imaging (T2WI) texture-analysis parameters and the pathological aggressiveness or long-term outcomes in pancreatic ductal adenocarcinoma (PDAC) patients.

METHODS

A total of 66 patients (mean age 65.3 ± 9.0 years) who underwent preoperative MRI followed by pancreatectomy for PDAC between 2013 and 2015 were included in this study. A radiologist performed a texture analysis twice on one axial image using commercial software. Differences in the tex parameters, according to pathological factors, were analyzed using a Student's t test or an ANOVA with Tukey's test. Univariate and multivariate Cox proportional hazards regression analyses were used to evaluate the association between tex parameters and recurrence-free survival (RFS) or overall survival (OS).

RESULTS

The mean follow-up time was 18.5 months, and there were 58 recurrences and 39 deaths. The mean of the positive pixel (MPP)-related factors was significantly lower in poorly differentiated tumors than in well-differentiated tumors as well as in cases with perineural invasion. The univariate Cox proportional hazards analysis showed a significant association between the tex parameters and RFS or OS. However, only tumor size was statistically significant after the multivariate analysis. Only tumor size and entropy with medium texture were significantly associated with OS after the multivariate analysis.

CONCLUSIONS

Tumor size was a significant predictive factor for RFS and OS in PDAC patients. Although entropy with medium texture analysis was significantly associated with OS, there were also limitations in the texture analysis; thus, further study is necessary.

Quantitative magnetic resonance imaging and radiogenomic biomarkers for glioma characterisation: a systematic review

OBJECTIVE:

The diversity of tumour characteristics among glioma patients, even within same tumour grade, is a big challenge for disease outcome prediction. A possible approach for improved radiological imaging could come from combining information obtained at the molecular level. This review assembles recent evidence highlighting the value of using radiogenomic biomarkers to infer the underlying biology of gliomas and its correlation with imaging features.

METHODS:

A literature search was done for articles published between 2002 and 2017 on Medline electronic databases. Of 249 titles identified, 38 fulfilled the inclusion criteria, with 14 articles related to quantifiable imaging parameters (heterogeneity, vascularity, diffusion, cell density, infiltrations, perfusion, and metabolite changes) and 24 articles relevant to molecular biomarkers linked to imaging.

RESULTS:

Genes found to correlate with various imaging phenotypes were EGFR, MGMT, IDH1, VEGF, PDGF, TP53, and Ki-67. EGFR is the most studied gene related to imaging characteristics in the studies reviewed (41.7%), followed by MGMT (20.8%) and IDH1 (16.7%). A summary of the relationship amongst glioma morphology, gene expressions, imaging characteristics, prognosis and therapeutic response are presented.

CONCLUSION:

The use of radiogenomics can provide insights to understanding tumour biology and the underlying molecular pathways. Certain MRI characteristics that show strong correlations with EGFR, MGMT and IDH1 could be used as imaging biomarkers. Knowing the pathways involved in tumour progression and their associated imaging patterns may assist in diagnosis, prognosis and treatment management, while facilitating personalised medicine.

ADVANCES IN KNOWLEDGE:

Radiogenomics can offer clinicians better insight into diagnosis, prognosis, and prediction of therapeutic responses of glioma.

Texture Analysis to Detect Cerebral Degeneration in Amyotrophic Lateral Sclerosis

BACKGROUND

Evidence of cerebral degeneration is not apparent on routine brain MRI in amyotrophic lateral sclerosis (ALS). Texture analysis can detect change in images based on the statistical properties of voxel intensities. Our objective was to test the utility of texture analysis in detecting cerebral degeneration in ALS. A secondary objective was to determine whether the performance of texture analysis is dependent on image resolution.

METHODS

High-resolution (0.5×0.5 mm2 in-plane) coronal T2-weighted MRI of the brain were acquired from 12 patients with ALS and 19 healthy controls on a 4.7 Tesla MRI system. Image data sets at lower resolutions were created by down-sampling to 1×1, 2×2, 3×3, and 4×4 mm2. Texture features were extracted from a slice encompassing the corticospinal tract at the different resolutions and tested for their discriminatory power and correlations with clinical measures. Subjects were also classified by visual assessment by expert reviewers.

RESULTS

Texture features were different between ALS patients and healthy controls at 1×1, 2×2, and 3×3 mm2 resolutions. Texture features correlated with measures of upper motor neuron function and disability. Optimal classification performance was achieved when best-performing texture features were combined with visual assessment at 2×2 mm2 resolution (0.851 area under the curve, 83% sensitivity, 79% specificity).

CONCLUSIONS

Texture analysis can detect subtle abnormalities in MRI of ALS patients. The clinical yield of the method is dependent on image resolution. Texture analysis holds promise as a potential source of neuroimaging biomarkers in ALS.

Classification of suspicious lesions on prostate multiparametric MRI using machine learning

We present a radiomics-based approach developed for the SPIE-AAPM-NCI PROSTATEx challenge. The task was to classify clinically significant prostate cancer in multiparametric (mp) MRI. Data consisted of a "training dataset" (330 suspected lesions from 204 patients) and a "test dataset" (208 lesions/140 patients). All studies included T2-weighted (T2-W), proton density-weighted, dynamic contrast enhanced, and diffusion-weighted imaging. Analysis of the images was performed using the MIM imaging platform (MIM Software, Cleveland, Ohio). Prostate and peripheral zone contours were manually outlined on the T2-W images. A workflow for rigid fusion of the aforementioned images to T2-W was created in MIM. The suspicious lesion was outlined using the high b-value image. Intensity and texture features were extracted on four imaging modalities and characterized using nine histogram descriptors: 10%, 25%, 50%, 75%, 90%, mean, standard deviation, kurtosis, and skewness (216 features). Three classification methods were used: classification and regression trees (CART), random forests, and adaptive least absolute shrinkage and selection operator (LASSO). In the held out by the organizers test dataset, the areas under the curve (AUCs) were: 0.82 (random forests), 0.76 (CART), and 0.76 (adaptive LASSO). AUC of 0.82 was the fourth-highest score of 71 entries (32 teams) and the highest for feature-based methods.

Quantitative Radiomics: Impact of Pulse Sequence Parameter Selection on MRI-Based Textural Features of the Brain

Objectives

Radiomic features extracted from diverse MRI modalities have been investigated regarding their predictive and/or prognostic value in a variety of cancers. With the aid of a 3D realistic digital MRI phantom of the brain, the aim of this study was to examine the impact of pulse sequence parameter selection on MRI-based textural parameters of the brain.

Methods

MR images of the employed digital phantom were realized with SimuBloch, a simulation package made for fast generation of image sequences based on the Bloch equations. Pulse sequences being investigated consisted of spin echo (SE), gradient echo (GRE), spoiled gradient echo (SP-GRE), inversion recovery spin echo (IR-SE), and inversion recovery gradient echo (IR-GRE). Twenty-nine radiomic textural features related, respectively, to gray-level intensity histograms (GLIH), cooccurrence matrices (GLCOM), zone size matrices (GLZSM), and neighborhood difference matrices (GLNDM) were evaluated for the obtained MR realizations, and differences were identified.

Results

It was found that radiomic features vary considerably among images generated by the five different T1-weighted pulse sequences, and the deviations from those measured on the T1 map vary among features, from a few percent to over 100%. Radiomic features extracted from T1-weighted spin-echo images with TR varying from 360 ms to 620 ms and TE = 3.4 ms showed coefficients of variation (CV) up to 45%, while up to 70%, for T2-weighted spin-echo images with TE varying over the range 60-120 ms and TR = 6400 ms.

Conclusion

Variability of radiologic textural appearance on MR realizations with respect to the choice of pulse sequence and imaging parameters is feature-dependent and can be substantial. It calls for caution in employing MRI-derived radiomic features especially when pooling imaging data from multiple institutions with intention of correlating with clinical endpoints.

Magnetic resonance imaging (MRI)-based radiomics for prostate cancer radiotherapy

In radiotherapy (RT) of prostate cancer, dose escalation has been shown to reduce biochemical failure. Dose escalation only to determinate prostate tumor habitats has the potential to improve tumor control with less toxicity than when the entire prostate is dose escalated. Other issues in the treatment of the RT patient include the choice of the RT technique (hypo- or standard fractionation) and the use and length of concurrent/adjuvant androgen deprivation therapy (ADT). Up to 50% of high-risk men demonstrate biochemical failure suggesting that additional strategies for defining and treating patients based on improved risk stratification are required. The use of multiparametric MRI (mpMRI) is rapidly gaining momentum in the management of prostate cancer because of its improved diagnostic potential and its ability to combine functional and anatomical information. Currently, the Prostate Imaging, Reporting and Diagnosis System (PIRADS) is the standard of care for region of interest (ROI) identification and risk classification. However, PIRADS was not designed for 3D tumor volume delineation; there is a large degree of subjectivity and PIRADS does not accurately and reproducibly elucidate inter- and intra-lesional spatial heterogeneity. "Radiomics", as it refers to the extraction and analysis of large number of advanced quantitative radiological features from medical images using high throughput methods, is perfectly suited as an engine to effectively sift through the multiple series of prostate mpMRI sequences and quantify regions of interest. The radiomic efforts can be summarized in two main areas: (I) detection/segmentation of the suspicious lesion; and (II) assessment of the aggressiveness of prostate cancer. As related to RT, the goal of the latter is in particular to identify patients at high risk for metastatic disease; and the aim of the former is to identify and segment cancerous lesions and thus provide targets for radiation boost. The article is structured as follows: first, we describe the radiomic approach; and second, we discuss the radiomic pipeline as tailored for RT of prostate cancer. In this process we summarize the current efforts and progress in integrating mpMRI radiomics into the radiotherapeutic management of prostate cancer with emphasis placed on its role in treatment target definition, treatment plan strategizing, and prognostic assessment. The described concepts, methods and tools are not currently applicable to the radiation oncology practice outside of the research setting. More data are required in the form of clinical trials to assess the robustness of radiomics-based predictive models, and to maximize the efficacy of these models.

Evaluation of radiomic texture feature error due to MRI acquisition and reconstruction: A simulation study utilizing ground truth

The purpose of this study was to examine the dependence of image texture features on MR acquisition parameters and reconstruction using a digital MR imaging phantom. MR signal was simulated in a parallel imaging radiofrequency coil setting as well as a single element volume coil setting, with varying levels of acquisition noise, three acceleration factors, and four image reconstruction algorithms. Twenty-six texture features were measured on the simulated images, ground truth images, and clinical brain images. Subtle algorithm-dependent errors were observed on reconstructed phantom images, even in the absence of added noise. Sources of image error include Gibbs ringing at image edge gradients (tissue interfaces) and well-known artifacts due to high acceleration; two of the iterative reconstruction algorithms studied were able to mitigate these image errors. The difference of the texture features from ground truth, and their variance over reconstruction algorithm and parallel imaging acceleration factor, were compared to the clinical "effect size", i.e., the feature difference between high- and low-grade tumors on T1- and T2-weighted brain MR images of twenty glioma patients. The measured feature error (difference from ground truth) was small for some features, but substantial for others. The feature variance due to reconstruction algorithm and acceleration factor were generally smaller than the clinical effect size. Certain texture features may be preserved by MR imaging, but adequate precautions need to be taken regarding their validity and reliability. We present a general simulation framework for assessing the robustness and accuracy of radiomic textural features under various MR acquisition/reconstruction scenarios.

Texture analysis of diffusion weighted imaging for the evaluation of glioma heterogeneity based on different regions of interest

The present study aimed to explore the role of texture analysis with apparent diffusion coefficient (ADC) maps based on different regions of interest (ROI) in determining glioma grade. Thirty patients with glioma underwent diffusion-weighted imaging (DWI). ADC values were determined from the following three ROIs: i) whole tumor; ii) solid portion; and iii) peritumoral edema. Texture features were compared between high-grade gliomas (HGGs) and low-grade gliomas (LGGs) using the non-parametric Wilcoxon rank-sum test or the unpaired Student's t-test. Receiver operating characteristic (ROC) curves were constructed to determine the optimum threshold for inhomogeneity values in discrimination of HGGs from LGGs. With a spearman rank correlation model, the aforementioned ADC inhomogeneity values were correlated with the Ki-67 labeling index. With whole tumor ROI, inhomogeneity values proved to be significantly different between HGGs and LGGs (P<0.001). With solid portion ROI, inhomogeneity and median values showed significant difference between HGGs and LGGs (P=0.001 and P=0.043, respectively). With peritumoral edema ROI, entropy and edema volume demonstrated positive results (P=0.016, P<0.001). The whole tumor inhomogeneity parameter performed with better diagnostic accuracy (P=0.048) than selecting the solid portion ROI. The association between inhomogeneity and Ki-67 labeling index was significantly positive in whole tumor and solid portion ROI (R=0.628, P<0.001 and R=0.470, P=0.009). Texture analysis of DWI based on different ROI can provide various significant parameters to evaluate tumor heterogeneity, which were correlated with tumor grade. Particularly, the inhomogeneity value derived from whole tumor ROI provided high diagnostic value and predicting the status of tumor proliferation.

Experimental Texture Analysis in Glioblastoma: A Methodological Study

OBJECTIVES

Analysis of a single slice of a tumor to extract biomarkers for texture analysis may result in loss of information. We investigated correlation of fractional volumes to entire tumor volumes and introduced expanded regions of interest (ROIs) outside the visual tumor borders in glioblastoma.

MATERIALS AND METHODS

Retrospective slice-by-slice volumetric texture analysis on 46 brain magnetic resonance imaging subjects with histologically confirmed glioblastoma was performed. Fractional volumes were analyzed for correlation to total volume. Expanded ROIs were analyzed for significant differences to conservative ROIs.

RESULTS

As fractional tumor volumes increased, correlation with total volume values for mean, SD, mean of positive pixels, skewness, and kurtosis increased. Expanding ROI by 2 mm resulted in significant differences in all textural values.

CONCLUSIONS

Fractional volumes may provide an optimal trade-off for texture analysis in the clinical setting. All texture parameters proved significantly different with minimal expansion of the ROI, underlining the susceptibility of texture analysis to generating misrepresentative tumor information.

Magnetic Resonance Image Texture Analysis of the Periaqueductal Gray Matter in Episodic Migraine Patients without T2-Visible Lesions

Objective

The periaqueductal gray matter (PAG), a small midbrain structure, presents dysfunction in migraine. However, the precise neurological mechanism is still not well understood. Herein, the aim of this study was to investigate the texture characteristics of altered PAG in episodic migraine (EM) patients based on high resolution brain structural magnetic resonance (MR) images.

Materials and Methods

The brain structural MR images were obtained from 18 normal controls (NC), 18 EM patients and 16 chronic migraine (CM) patients using a 3T MR system. A PAG template was created using the International Consortium Brain Mapping 152 gray matter model, and the individual PAG segment was developed by applying the deformation field from the structural image segment to the PAG template. A grey level co-occurrence matrix was used to calculate the texture parameters including the angular second moment (ASM), contrast, correlation, inverse difference moment (IDM) and entropy.

Results

There was a significant difference for ASM, IDM and entropy in the EM group (998.629 ± 0.162 × 10⁻³, 999.311 ± 0.073 × 10⁻³, 916.354 ± 0.947 × 10⁻⁵) compared to that found in the NC group (998.760 ± 0.110 × 10⁻³, 999.358 ± 0.037 × 10⁻³ and 841.198 ± 0.575 × 10⁻⁵) (p < 0.05). The entropy was significantly lower among the patients with CM (864.116 ± 0.571 × 10⁻⁵) than that found among patients with EM (p < 0.05). The area under the receiver operating characteristic curve was 0.776 and 0.750 for ASM and entropy in the distinction of the EM from NC groups, respectively. ASM was negatively related to disease duration (DD) and the Migraine Disability Assessment Scale (MIDAS) scores in the EM group, and entropy was positively related to DD and MIDAS in the EM group (p < 0.05).

Conclusion

The present study identified altered MR image texture characteristics of the PAG in EM. The identified texture characteristics could be considered as imaging biomarkers for EM.

Characterisation of heterogeneity and spatial autocorrelation in phase separating mixtures using Moran's I

In complex colloidal systems, particle-poor regions can develop within particle-rich phases during sedimentation or creaming. These particle-poor regions are overlooked by 1D profiles, which are typically used to assess particle distributions in a sample. Alternative methods to visualise and quantify these regions are required to better understand phase separation, which is the focus of this paper. Magnetic resonance imaging has been used to monitor the development of compositional heterogeneity in a vesicle-polymer mixture undergoing creaming. T₂ relaxation time maps were used to identify the distribution of vesicles, with vesicle-poor regions exhibiting higher T₂ relaxation times than regions richer in vesicles. Phase separated structures displayed a range of different morphologies and a variety of image analysis methods, including first-order statistics, Fourier transformation, grey level co-occurrence matrices and Moran's I spatial autocorrelation, were used to characterise these structures, and quantify their heterogeneity. Of the image analysis techniques used, Moran's I was found to be the most effective at quantifying the degree and morphology of phase separation, providing a robust, quantitative measure by which comparisons can be made between a diverse range of systems undergoing phase separation. The sensitivity of Moran's I can be enhanced by the choice of weight matrices used.

Texture-based classification of different single liver lesion based on SPAIR T2W MRI images

Background

To assess the feasibility of texture analysis (TA) based on spectral attenuated inversion-recovery T2 weighted magnetic resonance imaging (SPAIR T2W-MRI) for the classification of hepatic hemangioma (HH), hepatic metastases (HM) and hepatocellular carcinoma (HCC).

Methods

The SPAIR T2W-MRI data of 162 patients with HH (n=55), HM (n=67) and HCC (n=40) were retrospectively analyzed. We used two independent cohorts for training (n = 112 patients) and validation (n = 50 patients). The TA was performed and textual parameters derived from the gray level co-occurrence matrix (GLCM), gray level gradient co-occurrence matrix (GLGCM), gray-level run-length matrix (GLRLM), Gabor wavelet transform (GWTF), intensity-size-zone matrix (ISZM), and histogram features were calculated. The capacity of each parameter to classify three types of single liver lesions was assessed using the Kruskal-Wallis test. Specificity and sensitivity for each of the studied parameters were derived using ROC curves. Four supervised classification algorithms were trained with the most influential textural features in the classification of tumor types. The test datasets validated the reliability of the models.

Results

The texture analyses showed that the HH versus HM, HM versus HCC, and HH versus HCC could be differentiated by 9, 16 and 10 feature parameters, respectively. The model’s misclassification rates were 11.7, 9.6 and 9.7% respectively. No texture feature was able to adequately distinguish among the three types of single liver lesions at the same time. The BP-ANN model had better predictive ability.

Conclusion

Texture features of SPAIR T2W-MRI can classify the three types of single liver lesions (HH, HM and HCC) and may serve as an adjunct tool for accurate diagnosis of these diseases.

Electronic supplementary material

The online version of this article (doi:10.1186/s12880-017-0212-x) contains supplementary material, which is available to authorized users.

Lack of robustness of textural measures obtained from 3D brain tumor MRIs impose a need for standardization

Purpose

Textural measures have been widely explored as imaging biomarkers in cancer. However, their robustness under dynamic range and spatial resolution changes in brain 3D magnetic resonance images (MRI) has not been assessed. The aim of this work was to study potential variations of textural measures due to changes in MRI protocols.

Materials and methods

Twenty patients harboring glioblastoma with pretreatment 3D T1-weighted MRIs were included in the study. Four different spatial resolution combinations and three dynamic ranges were studied for each patient. Sixteen three-dimensional textural heterogeneity measures were computed for each patient and configuration including co-occurrence matrices (CM) features and run-length matrices (RLM) features. The coefficient of variation was used to assess the robustness of the measures in two series of experiments corresponding to (i) changing the dynamic range and (ii) changing the matrix size.

Results

No textural measures were robust under dynamic range changes. Entropy was the only textural feature robust under spatial resolution changes (coefficient of variation under 10% in all cases).

Conclusion

Textural measures of three-dimensional brain tumor images are not robust neither under dynamic range nor under matrix size changes. Standards should be harmonized to use textural features as imaging biomarkers in radiomic-based studies. The implications of this work go beyond the specific tumor type studied here and pose the need for standardization in textural feature calculation of oncological images.

Texture features of periaqueductal gray in the patients with medication-overuse headache

BACKGROUND

Periaqueductal gray (PAG) is the descending pain modulatory center, and PAG dysfunction had been recognized in migraine. Here we propose to investigate altered PAG texture features (quantitative approach for extracting texture descriptors for images) in the patients with medication-overuse headache (MOH) based on high resolution brain structural image to understand the MOH pathogenesis.

METHODS

The brain structural images were obtained from 32 normal controls (NC) and 44 MOH patients on 3.0 T MR system. PAG template was created based on the ICBM152 gray matter template, and the individual PAG segment was performed by applying the deformation field to the PAG template after structural image segment. Grey-level co-occurrence matrix (GLCM) was performed to measure the texture parameters including angular second moment (ASM), Contrast, Correlation, inverse difference moment (IDM) and Entropy.

RESULTS

Contrast was increased in MOH patients (9.28 ± 3.11) compared with that in NC (7.94 ± 0.65) (P < 0.05), and other texture features showed no significant difference between MOH and NC (P > 0.05). The area under the ROC curve was 0.697 for Contrast in the distinction of MOH from NC, and the cut-off value of Contrast was 8.11 with sensitivity 70.5% and specificity 62.5%. The contrast was negatively with the sleep scores (r = -0.434, P = 0.003).

CONCLUSION

Texture Contrast could be used to identify the altered MR imaging characteristics in MOH in understanding the MOH pathogenesis, and it could also be considered as imaging biomarker in for MOH diagnosis.

Computer-aided grading of gliomas based on local and global MRI features

BACKGROUND AND OBJECTIVES

A computer-aided diagnosis (CAD) system based on quantitative magnetic resonance imaging (MRI) features was developed to evaluate the malignancy of diffuse gliomas, which are central nervous system tumors.

METHODS

The acquired image database for the CAD performance evaluation was composed of 34 glioblastomas and 73 diffuse lower-grade gliomas. In each case, tissues enclosed in a delineated tumor area were analyzed according to their gray-scale intensities on MRI scans. Four histogram moment features describing the global gray-scale distributions of gliomas tissues and 14 textural features were used to interpret local correlations between adjacent pixel values. With a logistic regression model, the individual feature set and a combination of both feature sets were used to establish the malignancy prediction model.

RESULTS

Performances of the CAD system using global, local, and the combination of both image feature sets achieved accuracies of 76%, 83%, and 88%, respectively. Compared to global features, the combined features had significantly better accuracy (p = 0.0213). With respect to the pathology results, the CAD classification obtained substantial agreement κ = 0.698, p < 0.001.

CONCLUSIONS

Numerous proposed image features were significant in distinguishing glioblastomas from lower-grade gliomas. Combining them further into a malignancy prediction model would be promising in providing diagnostic suggestions for clinical use.

Impact of TIEG1 on the structural properties of fast- and slow-twitch skeletal muscle

INTRODUCTION

Transforming growth factor-beta (TGF-β)-inducible early gene-1 (TIEG1) is a transcription factor that is highly expressed in skeletal muscle. The purpose of this study was to characterize the structural properties of both fast-twitch (EDL) and slow-twitch (soleus) muscles in the hindlimb of TIEG1-deficient (TIEG1^-/- ) mice.

METHODS

Ten slow and 10 fast muscles were analyzed from TIEG1^-/- and wild-type (WT) mice using MRI texture (MRI-TA) and histological analyses.

RESULTS

MRI-TA could discriminate between WT slow and fast muscles. Deletion of the TIEG1 gene led to changes in the texture profile within both muscle types. Specifically, muscle isolated from TIEG1^-/- mice displayed hypertrophy, hyperplasia, and a modification of fiber area distribution.

CONCLUSIONS

We demonstrated that TIEG1 plays an important role in the structural properties of skeletal muscle. This study further implicates important roles for TIEG1 in the development of skeletal muscle and suggests that defects in TIEG1 expression and/or function may be associated with muscle disease. Muscle Nerve 55: 410-416, 2017.

Adaptive Dimensionality Reduction with Semi-Supervision (AdDReSS): Classifying Multi-Attribute Biomedical Data

Medical diagnostics is often a multi-attribute problem, necessitating sophisticated tools for analyzing high-dimensional biomedical data. Mining this data often results in two crucial bottlenecks: 1) high dimensionality of features used to represent rich biological data and 2) small amounts of labelled training data due to the expense of consulting highly specific medical expertise necessary to assess each study. Currently, no approach that we are aware of has attempted to use active learning in the context of dimensionality reduction approaches for improving the construction of low dimensional representations. We present our novel methodology, AdDReSS (Adaptive Dimensionality Reduction with Semi-Supervision), to demonstrate that fewer labeled instances identified via AL in embedding space are needed for creating a more discriminative embedding representation compared to randomly selected instances. We tested our methodology on a wide variety of domains ranging from prostate gene expression, ovarian proteomic spectra, brain magnetic resonance imaging, and breast histopathology. Across these various high dimensional biomedical datasets with 100+ observations each and all parameters considered, the median classification accuracy across all experiments showed AdDReSS (88.7%) to outperform SSAGE, a SSDR method using random sampling (85.5%), and Graph Embedding (81.5%). Furthermore, we found that embeddings generated via AdDReSS achieved a mean 35.95% improvement in Raghavan efficiency, a measure of learning rate, over SSAGE. Our results demonstrate the value of AdDReSS to provide low dimensional representations of high dimensional biomedical data while achieving higher classification rates with fewer labelled examples as compared to without active learning.