Open-radiomics: A Collection of Standardized Datasets and a Technical Protocol for Reproducible Radiomics Machine Learning Pipelines

Purpose: As an important branch of machine learning pipelines in medical imaging, radiomics faces two major challenges namely reproducibility and accessibility. In this work, we introduce open-radiomics, a set of radiomics datasets along with a comprehensive radiomics pipeline based on our proposed technical protocol to investigate the effects of radiomics feature extraction on the reproducibility of the results. Materials and Methods: Experiments are conducted on BraTS 2020 open-source Magnetic Resonance Imaging (MRI) dataset that includes 369 adult patients with brain tumors (76 low-grade glioma (LGG), and 293 high-grade glioma (HGG)). Using PyRadiomics library for LGG vs. HGG classification, 288 radiomics datasets are formed; the combinations of 4 MRI sequences, 3 binWidths, 6 image normalization methods, and 4 tumor subregions. Random Forest classifiers were used, and for each radiomics dataset the training-validation-test (60%/20%/20%) experiment with different data splits and model random states was repeated 100 times (28,800 test results) and Area Under Receiver Operating Characteristic Curve (AUC) was calculated. Results: Unlike binWidth and image normalization, tumor subregion and imaging sequence significantly affected performance of the models. T1 contrast-enhanced sequence and the union of necrotic and the non-enhancing tumor core subregions resulted in the highest AUCs (average test AUC 0.951, 95% confidence interval of (0.949, 0.952)). Although 28 settings and data splits yielded test AUC of 1, they were irreproducible. Conclusion: Our experiments demonstrate the sources of variability in radiomics pipelines (e.g., tumor subregion) can have a significant impact on the results, which may lead to superficial perfect performances that are irreproducible

Bayesian pharmacokinetic modeling of dynamic contrast-enhanced magnetic resonance imaging: validation and application

Tracer-kinetic analysis of dynamic contrast-enhanced magnetic resonance imaging data is commonly performed with the well-known Tofts model and nonlinear least squares (NLLS) regression. This approach yields point estimates of model parameters, uncertainty of these estimates can be assessed e.g. by an additional bootstrapping analysis. Here, we present a Bayesian probabilistic modeling approach for tracer-kinetic analysis with a Tofts model, which yields posterior probability distributions of perfusion parameters and therefore promises a robust and information-enriched alternative based on a framework of probability distributions. In this manuscript, we use the quantitative imaging biomarkers alliance (QIBA) Tofts phantom to evaluate the Bayesian tofts model (BTM) against a bootstrapped NLLS approach. Furthermore, we demonstrate how Bayesian posterior probability distributions can be employed to assess treatment response in a breast cancer DCE-MRI dataset using Cohen's d. Accuracy and precision of the BTM posterior distributions were validated and found to be in good agreement with the NLLS approaches, and assessment of therapy response with respect to uncertainty in parameter estimates was found to be excellent. In conclusion, the Bayesian modeling approach provides an elegant means to determine uncertainty via posterior distributions within a single step and provides honest information about changes in parameter estimates

MRI evidence for altered venous drainage and intracranial compliance in mild traumatic brain injury.

To compare venous drainage patterns and associated intracranial hydrodynamics between subjects who experienced mild traumatic brain injury (mTBI) and age- and gender-matched controls. Thirty adult subjects (15 with mTBI and 15 age- and gender-matched controls) were investigated using a 3T MR scanner. Time since trauma was 0.5 to 29 years (mean 11.4 years). A 2D-time-of-flight MR-venography of the upper neck was performed to visualize the cervical venous vasculature. Cerebral venous drainage through primary and secondary channels, and intracranial compliance index and pressure were derived using cine-phase contrast imaging of the cerebral arterial inflow, venous outflow, and the craniospinal CSF flow. The intracranial compliance index is the defined as the ratio of maximal intracranial volume and pressure changes during the cardiac cycle. MR estimated ICP was then obtained through the inverse relationship between compliance and ICP. Compared to the controls, subjects with mTBI demonstrated a significantly smaller percentage of venous outflow through internal jugular veins (60.9±21% vs. controls: 76.8±10%; p = 0.01) compensated by an increased drainage through secondary veins (12.3±10.9% vs. 5.5±3.3%; p<0.03). Mean intracranial compliance index was significantly lower in the mTBI cohort (5.8±1.4 vs. controls 8.4±1.9; p<0.0007). Consequently, MR estimate of intracranial pressure was significantly higher in the mTBI cohort (12.5±2.9 mmHg vs. 8.8±2.0 mmHg; p<0.0007). mTBI is associated with increased venous drainage through secondary pathways. This reflects higher outflow impedance, which may explain the finding of reduced intracranial compliance. These results suggest that hemodynamic and hydrodynamic changes following mTBI persist even in the absence of clinical symptoms and abnormal findings in conventional MR imaging

Feasibility and morbidity of combined hyperthermia and radiochemotherapy in recurrent rectal cancer - Preliminary results

Background: The local recurrence rate of colorectal cancer has been significantly reduced due to the use of combined radiochemotherapy. Despite this improvement regarding locally advanced tumour recurrences, the treatment strategy for pre-treated patients remains difficult and unresolved. Patients and Methods: We analysed treatment and follow-up data of 14 patients with local recurrence of rectal cancer who were treated with radiation therapy (RT), chemotherapy (CT) and regional hyperthermia (RHT) from November 1997 to December 2001. Nine of these patients had received irradiation and CT (=pre-treated patients) in the past. For this group, 30.6-39.6 Gy RT, 5-fluorouracil (5-FU) as a continuous infusion over 5 days per week (350 mg/m(2)/24 h) combined with RHT twice a week was given. The 5 remaining patients (=not pre-treated) received conformal irradiation of 45 Gy with a boost between 9 and 14.4 Gy, combined with continuous infusion of 5-FU on days 1-4, and 29-33 (500 mg/m(2)/24 h), and RHT twice a week. Response to therapy was evaluated by means of computed tomography (CT) or magnetic resonance imaging (MRI) and by clinical follow-up. Results: Among 13 evaluated cases, the overall objective response rate was 54% (5 complete responses, 2 partial responses). At mean follow-up of 13.9 months (range 5-32 months) 7 patients were alive. Conclusion: The therapeutic regimen appears to be active in the treatment of local recurrences of rectal cancer. Larger-scaled studies are needed to evaluate the potency of hyperthermia in this therapeutic strategy

Intravenous Delayed Gadolinium-Enhanced MR Imaging of the Endolymphatic Space: A Methodological Comparative Study

In-vivo non-invasive verification of endolymphatic hydrops (ELH) by means of intravenous delayed gadolinium (Gd) enhanced magnetic resonance imaging of the inner ear (iMRI) is rapidly developing into a standard clinical tool to investigate peripheral vestibulo-cochlear syndromes. In this context, methodological comparative studies providing standardization and comparability between labs seem even more important, but so far very few are available. One hundred eight participants [75 patients with Meniere's disease (MD; 55.2 ± 14.9 years) and 33 vestibular healthy controls (HC; 46.4 ± 15.6 years)] were examined. The aim was to understand (i) how variations in acquisition protocols influence endolymphatic space (ELS) MR-signals; (ii) how ELS quantification methods correlate to each other or clinical data; and finally, (iii) how ELS extent influences MR-signals. Diagnostics included neuro-otological assessment, video-oculography during caloric stimulation, head-impulse test, audiometry, and iMRI. Data analysis provided semi-quantitative (SQ) visual grading and automatic algorithmic quantitative segmentation of ELS area [2D, mm2] and volume [3D, mm3] using deep learning-based segmentation and volumetric local thresholding. Within the range of 0.1–0.2 mmol/kg Gd dosage and a 4 h ± 30 min time delay, SQ grading and 2D- or 3D-quantifications were independent of signal intensity (SI) and signal-to-noise ratio (SNR; FWE corrected, p < 0.05). The ELS quantification methods used were highly reproducible across raters or thresholds and correlated strongly (0.3–0.8). However, 3D-quantifications showed the least variability. Asymmetry indices and normalized ELH proved the most useful for predicting quantitative clinical data. ELH size influenced SI (cochlear basal turn p < 0.001), but not SNR. SI could not predict the presence of ELH. In conclusion, (1) Gd dosage of 0.1–0.2 mmol/kg after 4 h ± 30 min time delay suffices for ELS quantification. (2) A consensus is needed on a clinical SQ grading classification including a standardized level of evaluation reconstructed to anatomical fixpoints. (3) 3D-quantification methods of the ELS are best suited for correlations with clinical variables and should include both ears and ELS values reported relative or normalized to size. (4) The presence of ELH increases signal intensity in the basal cochlear turn weakly, but cannot predict the presence of ELH

Use of diffusion-weighted MRI to modify radiosurgery planning in brain metastases may reduce local recurrence

Stereotactic radiosurgery (SRS) is an effective and well tolerated treatment for selected brain metastases; however, local recurrence still occurs. We investigated the use of diffusion weighted MRI (DWI) as an adjunct for SRS treatment planning in brain metastases. Seventeen consecutive patients undergoing complete surgical resection of a solitary brain metastasis underwent image analysis retrospectively. SRS treatment plans were generated based on standard 3D post-contrast T1-weighted sequences at 1.5T and then separately using apparent diffusion coefficient (ADC) maps in a blinded fashion. Control scans immediately post operation confirmed complete tumour resection. Treatment plans were compared to one another and with volume of local recurrence at progression quantitatively and qualitatively by calculating the conformity index (CI), the overlapping volume as a proportion of the total combined volume, where 1 = identical plans and 0 = no conformation whatsoever. Gross tumour volumes (GTVs) using ADC and post-contrast T1-weighted sequences were quantitatively the same (related samples Wilcoxon signed rank test = −0.45, p = 0.653) but showed differing conformations (CI 0.53, p < 0.001). The diffusion treatment volume (DTV) obtained by combining the two target volumes was significantly greater than the treatment volume based on post contrast T1-weighted MRI alone, both quantitatively (median 13.65 vs. 9.52 cm(3), related samples Wilcoxon signed rank test p < 0.001) and qualitatively (CI 0.74, p = 0.001). This DTV covered a greater volume of subsequent tumour recurrence than the standard plan (median 3.53 cm(3) vs. 3.84 cm(3), p = 0.002). ADC maps may be a useful tool in addition to the standard post-contrast T1-weighted sequence used for SRS planning

Investigation of potential adverse central nervous system effects after long term oral administration of gadolinium in mice

Objectives: To examine potential gadolinium (Gd) accumulation in the brain of healthy mice after long-term oral administration of Gd-containing food pellets and to investigate whether Gd leads to adverse central nervous system (CNS) effects, specifically focussing on locomotor impairment in Gd exposed compared to control animals. Materials and methods: The local Animal Experimental Ethics Committee approved all procedures and applications. Fifteen female C57Bl/6 mice were orally exposed to a daily intake of 0.57 mmol Gd chloride/kg body weight over a period of 90 weeks from the age of 4 weeks on. Gd-free, but otherwise equivalent experimental diets were given to the control group (N = 13). The animals were monitored daily by animal caretakers regarding any visible signs of distress and evaluated clinically every four weeks for the first 60 weeks and afterwards every two weeks for a better temporal resolution of potential long-term effects regarding impairment of motor performance and loss of body weight. The individual Gd content was measured using mass spectrometry in a sub-cohort of N = 6 mice. Results The absolute brain Gd levels of the Gd-exposed mice were significantly increased compared to control mice (0.033 +/- 0.009 vs. 0.006 +/- 0.002 nmol Gd/g brain tissue). Long-term oral Gd exposure over almost the entire life-span did not lead to adverse CNS effects including locomotor changes (rotarod performance, p = 0.1467) in healthy mice throughout the study period. Gd-exposed mice showed less increased body weight compared to control mice during the study period (p = 0.0423). Histopathological alterations, such as hepatocellular vacuolization due to fatty change in the liver and a loss of nucleated cells in the red pulp of the spleen, were found in peripheral organs of both groups. Conclusions: Low levels of intracerebral Gd caused by chronic oral exposure over almost the entire life span of mice did not lead to alterations in locomotor abilities in healthy mice throughout the normal aging process