UMMPerfusion: an open source software tool towards quantitative MRI perfusion analysis in clinical routine

Simultaneous 18F-FDG PET/MRI Radiomics and Machine Learning Analysis of the Primary Breast Tumor for the Preoperative Prediction of Axillary Lymph Node Status in Breast Cancer

In this prospective study, 117 female patients (mean age = 53 years) with 127 histologically proven breast cancer lesions (lymph node (LN) positive = 85, LN negative = 42) underwent simultaneous 18F-FDG PET/MRI of the breast. Quantitative parameters were calculated from dynamic contrast-enhanced (DCE) imaging (tumor Mean Transit Time, Volume Distribution, Plasma Flow), diffusion-weighted imaging (DWI) (tumor ADCmean), and PET (tumor SUVmax, mean and minimum, SUVmean of ipsilateral breast parenchyma). Manual whole-lesion segmentation was also performed on DCE, T2-weighted, DWI, and PET images, and radiomic features were extracted. The dataset was divided into a training (70%) and a test set (30%). Multi-step feature selection was performed, and a support vector machine classifier was trained and tested for predicting axillary LN status. 13 radiomic features from DCE, DWI, T2-weighted, and PET images were selected for model building. The classifier obtained an accuracy of 79.8 (AUC = 0.798) in the training set and 78.6% (AUC = 0.839), with sensitivity and specificity of 67.9% and 100%, respectively, in the test set. A machine learning-based radiomics model comprising 18F-FDG PET/MRI radiomic features extracted from the primary breast cancer lesions allows high accuracy in non-invasive identification of axillary LN metastasis.

Long-term evaluation of uterine fibroid embolisation using MRI perfusion parameters and patient questionnaires: preliminary results

BACKGROUND

Uterine fibroid embolisation (UFE) is an established treatment method for symptomatic uterine myomas. This study evaluates the efficacy of UFE using objective magnetic resonance imaging (MRI) data for size and perfusion analysis as well as patient questionnaires assessing fibroid-related symptoms.

METHOD

Patients underwent MR-Angiography before UFE and 4 days, 6 and 12 months after the procedure. The images were evaluated using dedicated software. Patient questionnaires were completed before UFE and at 12 months follow-up, focussing on the embolization procedure and symptoms associated with uterine fibroids. Statistical analysis of the questionnaires was performed using paired sample t-test and Wilcoxon signed rank test, while Kruskal-Wallis test and Friedman test were applied for MRI-analysis.

RESULTS

Eleven women were included. There was a significant reduction in fibroid-related symptoms. The volume reduction after 12 months was significant in both, uterus and myomas, after an initial increase in uterine volume at the first post-interventional MRI. The perfusion analysis showed that blood flow to the fibroids could be significantly reduced up to 12 months after UFE while uterine tissue was not affected.

CONCLUSION

This study shows that uterine fibroid embolisation induces a significant long-term decrease in myoma size and perfusion while healthy uterine tissue remains unaffected. Fibroid-related symptoms are reduced for the sake of improved quality of life.

A Simultaneous Multiparametric 18F-FDG PET/MRI Radiomics Model for the Diagnosis of Triple Negative Breast Cancer

Simple Summary

In this study, we aimed to build a machine-learning predictive model for the identification of triple negative breast cancer, the most aggressive subtype, using quantitative parameters and radiomics features extracted from tumor lesions on hybrid PET/MRI. The good performance of the model supports the hypothesis that hybrid PET/MRI can provide quantitative data able to non-invasively detect tumor biological characteristics using artificial intelligence software and further encourages the conduction of additional studies for this purpose.

Abstract

Purpose: To investigate whether a machine learning (ML)-based radiomics model applied to ¹⁸F-FDG PET/MRI is effective in molecular subtyping of breast cancer (BC) and specifically in discriminating triple negative (TN) from other molecular subtypes of BC. Methods: Eighty-six patients with 98 BC lesions (Luminal A = 10, Luminal B = 51, HER2+ = 12, TN = 25) were included and underwent simultaneous ¹⁸F-FDG PET/MRI of the breast. A 3D segmentation of BC lesion was performed on T2w, DCE, DWI and PET images. Quantitative diffusion and metabolic parameters were calculated and radiomics features extracted. Data were selected using the LASSO regression and used by a fine gaussian support vector machine (SVM) classifier with a 5-fold cross validation for identification of TNBC lesions. Results: Eight radiomics models were built based on different combinations of quantitative parameters and/or radiomic features. The best performance (AUROC 0.887, accuracy 82.8%, sensitivity 79.7%, specificity 86%, PPV 85.3%, NPV 80.8%) was found for the model combining first order, neighborhood gray level dependence matrix and size zone matrix-based radiomics features extracted from ADC and PET images. Conclusion: A ML-based radiomics model applied to ¹⁸F-FDG PET/MRI is able to non-invasively discriminate TNBC lesions from other BC molecular subtypes with high accuracy. In a future perspective, a “virtual biopsy” might be performed with radiomics signatures.

MR lung perfusion measurements in adolescents after congenital diaphragmatic hernia: correlation with spirometric lung function tests

OBJECTIVES

To evaluate whether lung perfusion continues to be reduced in 10-year-old children after congenital diaphragmatic hernia (CDH) and whether lung perfusion values correlate with spirometric lung function measurements.

METHODS

Fifty-four patients after CDH repair received dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI)-based lung perfusion measurements at the age of 10 years (10.2 ± 1.0 years). Additionally, a control group of 10 children has been examined according to the same protocol. Lung spirometry was additionally available in 43 patients of the CDH group. A comparison of ipsilateral and contralateral parameters was performed.

RESULTS

Pulmonary blood flow (PBF) was reduced on the ipsilateral side in CDH patients (60.4 ± 23.8 vs. 93.3 ± 16.09 mL/100 mL/min; p < 0.0001). In comparison to the control group, especially the ratio of ipsilateral to contralateral, PBF was reduced in CDH patients (0.669 ± 0.152 vs. 0.975 ± 0.091; p < 0.0001). There is a positive correlation between ipsilateral pulmonary blood flow, and spirometric forced 1-s volume (r = 0.45; p = 0.0024).

CONCLUSIONS

Pulmonary blood flow impairment persists during childhood and correlates with spirometric measurements. Without the need for ionizing radiation, MRI measurements seem promising as follow-up parameters after CDH.

KEY POINTS

• Ten-year-old children after congenital diaphragmatic hernia continue to show reduced perfusion of ipsilateral lung. • Lung perfusion values correlate with lung function tests after congenital diaphragmatic hernia.

The number of glomeruli and pyruvate metabolism is not strongly coupled in the healthy rat kidney

PURPOSE

The number of glomeruli is different in men and women, as they also present different prevalence and progression of chronic kidney disease. A recent study has demonstrated a potential difference in renal metabolism between sexes, and a potential explanation could be the differences in glomeruli number. This study investigates the potential correlation between glomerular number and pyruvate metabolism in healthy kidneys.

METHODS

This study is an experimental study with rats (N = 12). We used cationized-ferritin MRI to visualize and count glomeruli and hyperpolarized [1-¹³ C]pyruvate to map the metabolism. Dynamic contrast-enhanced MRI was used to analyze kidney hemodynamics using gadolinium tracer.

RESULTS

Data showed no or subtle correlation between the number of glomeruli and the pyruvate metabolism. Minor differences were observed in the number of glomeruli (female = 24,509 vs. male = 26 350; p = .16), renal plasma flow (female = 606.6 vs. male= 455.7 ml/min/100 g; p = .18), and volume of distribution (female = 87.44 vs. male = 76.61 ml/100 ml; p = .54) between sexes. Mean transit time was significantly prolonged in males compared with females (female = 8.868 s vs. male = 10.63 s; p = .04).

CONCLUSION

No strong statistically significant correlation between the number of glomeruli and the pyruvate metabolism was found in healthy rat kidneys.

AI-enhanced simultaneous multiparametric 18F-FDG PET/MRI for accurate breast cancer diagnosis

Purpose

To assess whether a radiomics and machine learning (ML) model combining quantitative parameters and radiomics features extracted from simultaneous multiparametric ¹⁸F-FDG PET/MRI can discriminate between benign and malignant breast lesions.

Methods

A population of 102 patients with 120 breast lesions (101 malignant and 19 benign) detected on ultrasound and/or mammography was prospectively enrolled. All patients underwent hybrid ¹⁸F-FDG PET/MRI for diagnostic purposes. Quantitative parameters were extracted from DCE (MTT, VD, PF), DW (mean ADC of breast lesions and contralateral breast parenchyma), PET (SUVmax, SUVmean, and SUVminimum of breast lesions, as well as SUVmean of the contralateral breast parenchyma), and T2-weighted images. Radiomics features were extracted from DCE, T2-weighted, ADC, and PET images. Different diagnostic models were developed using a fine Gaussian support vector machine algorithm which explored different combinations of quantitative parameters and radiomics features to obtain the highest accuracy in discriminating between benign and malignant breast lesions using fivefold cross-validation. The performance of the best radiomics and ML model was compared with that of expert reader review using McNemar’s test.

Results

Eight radiomics models were developed. The integrated model combining MTT and ADC with radiomics features extracted from PET and ADC images obtained the highest accuracy for breast cancer diagnosis (AUC 0.983), although its accuracy was not significantly higher than that of expert reader review (AUC 0.868) (p = 0.508).

Conclusion

A radiomics and ML model combining quantitative parameters and radiomics features extracted from simultaneous multiparametric ¹⁸F-FDG PET/MRI images can accurately discriminate between benign and malignant breast lesions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00259-021-05492-z.

Intraindividual Comparison of Compressed Sensing-Accelerated Cartesian and Radial Arterial Phase Imaging of the Liver in an Experimental Tumor Model

OBJECTIVES

The aim of this study was to intraindividually compare the performance of 2 compressed sensing (CS)-accelerated magnetic resonance imaging (MRI) sequences, 1 featuring Cartesian (compressed sensing volumetric interpolated breath-hold examination [CS-VIBE]) and the other radial (golden-angle radial sparse parallel [GRASP]) k-space sampling in continuous dynamic imaging during hepatic vascular phases, using extracellular and hepatocyte-specific contrast agents.

MATERIALS AND METHODS

Seven New Zealand white rabbits, with induced VX2 liver tumors (median number of lesions, 2 ± 0.83; range, 1-3), received 2 continuously acquired T1-weighted prototype CS-accelerated MRI sequences (CS-VIBE and GRASP) with high spatial (0.8 × 0.8 × 1.5 mm) and temporal resolution (3.5 seconds) in randomized order on 2 separate days using a 1.5-T scanner. In all animals, imaging was performed using first gadobutrol at a dose of 0.1 mmol/kg and, then 45 minutes later, gadoxetic acid at a dose of 0.025 mmol/kg.The following qualitative parameters were assessed using 3- and 5-point Likert scales (3 and 5 being the highest scores respectively): image quality (IQ), arterial and venous vessel delineation, tumor enhancement, motion artifacts, and sequence-specific artifacts. Furthermore, the following quantitative parameters were obtained: relative peak signal enhancement, time to peak, mean transit time, and plasma flow ratios. Paired sampled t tests and Wilcoxon signed rank tests were used for intraindividual comparison. Image analysis was performed by 2 radiologists.

RESULTS

Six of 7 animals underwent the full imaging protocol and obtained data were analyzed statistically. Overall IQ was rated moderate to excellent, not differing significantly between the 2 sequences.Gadobutrol-enhanced CS-VIBE examinations revealed the highest mean Likert scale values in terms of vessel delineation and tumor enhancement (arterial 4.4 [4-5], venous 4.3 [3-5], and tumor 2.9 [2-3]). Significantly, more sequence-specific artifacts were seen in GRASP examinations (P = 0.008-0.031). However, these artifacts did not impair IQ. Excellent Likert scale ratings were found for motion artifacts in both sequences. In both sequences, a maximum of 4 hepatic arterial dominant phases were obtained. Regarding the relative peak signal enhancement, CS-VIBE and GRASP showed similar results. The relative peak signal enhancement values did not differ significantly between the 2 sequences in the aorta, the hepatic artery, or the inferior vena cava (P = 0.063-0.536). However, significantly higher values were noted for CS-VIBE in gadoxetic acid-enhanced examinations in the portal vein (P = 0.031) and regarding the tumor enhancement (P = 0.005). Time to peak and mean transit time or plasma flow ratios did not differ significantly between the sequences.

CONCLUSIONS

Both CS-VIBE and GRASP provide excellent results in dynamic liver MRI using extracellular and hepatocyte-specific contrast agents, in terms of IQ, peak signal intensity, and presence of artifacts.

Sex Differences in Kidney Function and Metabolism Assessed Using Hyperpolarized [1-13C]Pyruvate Interleaved Spectroscopy and Nonspecific Imaging

Metabolic sex differences have recently been shown to be particularly important in tailoring treatment strategies. Sex has a major effect on fat turnover rates and plasma lipid delivery in the body. Differences in kidney structure and transporters between male and female animals have been found. Here we investigated sex-specific renal pyruvate metabolic flux and whole-kidney functional status in age-matched healthy Wistar rats. Blood oxygenation level–dependent and dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) were used to assess functional status. Hyperpolarized [1-¹³C]pyruvate was used to assess the metabolic differences between male and female rats. Female rats had a 41% ± 3% and 41% ± 5% lower absolute body and kidney weight, respectively, than age-matched male rats. No difference was seen between age-matched male and female rats in the kidney-to-body weight ratio. A 56% ± 11% lower lactate production per mL/100 mL/min was found in female rats than in age-matched male rats measured by hyperpolarized magnetic resonance and DCE MRI. Female rats had a 33% ± 11% higher glomerular filtration rate than age-matched male rats measured by DCE MRI. A similar renal oxygen tension (T2*) was found between age-matched male and female rats as shown by blood oxygenation level–dependent MRI. The results were largely independent of the pyruvate volume and the difference in body weight. This study shows an existing metabolic difference between kidneys in age-matched male and female rats, which indicates that sex differences need to be considered when performing animal experiments.

Analysis Protocol for Dynamic Contrast Enhanced (DCE) MRI of Renal Perfusion and Filtration

Here we present an analysis protocol for dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data of the kidneys. It covers comprehensive steps to facilitate signal to contrast agent concentration mapping via T1 mapping and the calculation of renal perfusion and filtration parametric maps using model-free approaches, model free analysis using deconvolution, the Toft's model and a Bayesian approach.This chapter is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers. This analysis protocol chapter is complemented by two separate chapters describing the basic concept and experimental procedure.

The hemodynamic and metabolic effects of spironolactone treatment in acute kidney injury assessed by hyperpolarized MRI

Renal ischemia-reperfusion injury (IRI) is one of the most common types of acute kidney injury. Spironolactone has shown promising kidney protective effects in renal IRI in rats. We investigated the hemodynamic and metabolic effects of spironolactone (100 mg/kg) administered immediately after 40 min unilateral kidney ischemia in rats. Hyperpolarized MRI using co-polarized [1-¹³ C]pyruvate and [¹³ C,¹⁵ N₂ ]urea as well as ¹ H dynamic contrast-enhanced (DCE) MRI was performed 24 h after induction of ischemia. We found a significant decrease in renal blood flow (RBF) in the ischemic kidney compared with the contralateral one measured using DCE and [¹³ C,¹⁵ N₂ ]urea. The RBF measured using [1-¹³ C]pyruvate and [¹³ C,¹⁵ N₂ ]urea was significantly altered by spironolactone. The RBFs in the ischemic kidney compared with the contralateral kidney were decreased similarly as measured using both [¹³ C,¹⁵ N₂ ]urea and [1-¹³ C]pyruvate in the spironolactone-treated group. Spironolactone treatment increased the perfusion-corrected pyruvate metabolism by 54% in both the ischemic and contralateral kidney. Furthermore, we showed a correlation between vascular permeability using a histological Evans blue analysis and the ratio of the volumes of distribution (VoDs), ie VoD-[¹³ C,¹⁵ N₂ ]urea/VoD-[1-¹³ C]pyruvate. This suggests that [¹³ C,¹⁵ N₂ ]urea/[1-¹³ C]pyruvate VoD ratio may be a novel indicator of renal vascular permeability associated with renal damage in rodents.

Graft assessment of the ex vivo perfused porcine kidney using hyperpolarized [1-13 C]pyruvate

PURPOSE

Normothermic perfusion is an emerging strategy for donor organ preservation and therapy, incited by the high worldwide demand for organs for transplantation. Hyperpolarized MRI and MRS using [1-¹³ C]pyruvate and other ¹³ C-labeled molecules pose a novel way to acquire highly detailed information about metabolism and function in a noninvasive manner. This study investigates the use of this methodology as a means to study and monitor the state of ex vivo perfused porcine kidneys, in the context of kidney graft preservation research.

METHODS

Kidneys from four 40-kg Danish domestic pigs were perfused ex vivo with whole blood under normothermic conditions, using an MR-compatible perfusion system. Kidneys were investigated using ¹ H MRI as well as hyperpolarized [1-¹³ C]pyruvate MRI and MRS. Using the acquired anatomical, functional and metabolic data, the state of the ex vivo perfused porcine kidney could be quantified.

RESULTS

Four kidneys were successfully perfused for 120 minutes and verified using a DCE perfusion experiment. Renal metabolism was examined using hyperpolarized [1-¹³ C]pyruvate MRI and MRS, and displayed an apparent reduction in pyruvate turnover compared with the usual case in vivo. Perfusion and blood gas parameters were in the normal ex vivo range.

CONCLUSION

This study demonstrates the ability to monitor ex vivo graft metabolism and function in a large animal model, resembling human renal physiology. The ability of hyperpolarized MRI and MRS to directly compare the metabolic state of an organ in vivo and ex vivo, in combination with the simple MR implementation of normothermic perfusion, renders this methodology a powerful future tool for graft preservation research.

Hyperpolarized [1,4-13C]fumarate imaging detects microvascular complications and hypoxia mediated cell death in diabetic nephropathy

Today, there is a general lack of prognostic biomarkers for development of renal disease and in particular diabetic nephropathy. Increased glycolytic activity, lactate accumulation and altered mitochondrial oxygen utilization are hallmarks of diabetic kidney disease. Fumarate hydratase activity has been linked to mitochondrial dysfunction as well as activation of the hypoxia inducible factor, induction of apoptosis and necrosis. Here, we investigate fumarate hydratase activity in biofluids in combination with the molecular imaging probe, hyperpolarized [1,4-¹³C₂]fumarate, to identify the early changes associated with hemodynamics and cell death in a streptozotocin rat model of type 1 diabetes. We found a significantly altered hemodynamic signature of [1,4-¹³C₂]fumarate in the diabetic kidneys as well as an systemic increased metabolic conversion of fumarate-to-malate, indicative of increased cell death associated with progression of diabetes, while little to no renal specific conversion was observed. This suggest apoptosis as the main cause of cell death in the diabetic kidney. This is likely resulting from an increased reactive oxygen species production following uncoupling of the electron transport chain at complex II. The mechanism coupling the enzyme leakage and apoptotic phenotype is hypoxia inducible factor independent and seemingly functions as a protective mechanism in the kidney cells.

Dual assessment of kidney perfusion and pH by exploiting a dynamic CEST-MRI approach in an acute kidney ischemia-reperfusion injury murine model

Several factors can lead to acute kidney injury, but damage following ischemia and reperfusion injuries is the main risk factor and usually develops into chronic disease. MRI has often been proposed as a method with which to assess renal function. It does so by measuring the renal perfusion of an injected Gd-based contrast agent. The use of pH-responsive agents as part of the CEST (chemical exchange saturation transfer)-MRI technique has recently shown that pH homeostasis is also an important indicator of kidney functionality. However, there is still a need for methods that can provide more than one type of information following the injection of a single contrast agent for the characterization of renal function. Herein we propose, for the first time, dynamic CEST acquisition following iopamidol injection to quantify renal function by assessing both perfusion and pH homeostasis. The aim of this study is to assess renal functionality in a murine unilateral ischemia-reperfusion injury model at two time points (3 and 7 days) after acute kidney injury. The renal-perfusion estimates measured with iopamidol were compared with those obtained with a gadolinium-based agent, via a dynamic contrast enhanced (DCE)-MRI approach, to validate the proposed method. Compared with the contralateral kidneys, the clamped ones showed a significant decrease in renal perfusion, as measured using the DCE-MRI approach, which is consistent with reduced filtration capability. Dynamic CEST-MRI findings provided similar results, indicating that the clamped kidneys displayed significantly reduced renal filtration that persisted up to 7 days after the damage. In addition, CEST-MRI pH imaging showed that the clamped kidneys displayed significantly increased pH values, reflecting the disturbance to pH homeostasis. Our results demonstrate that a single CEST-MRI contrast agent can provide multiple types of information related to renal function and can discern healthy kidneys from pathological ones by combining perfusion measurements with renal pH mapping.

Noninvasive Monitoring of the Response of Human Lungs to Low-Dose Lipopolysaccharide Inhalation Challenge Using MRI: A Feasibility Study

BACKGROUND

Development of antiinflammatory drugs for lung diseases demands novel methods for noninvasive assessment of inflammatory processes in the lung.

PURPOSE

To investigate the feasibility of hyperpolarized ¹²⁹ Xe MRI, ¹ H T₁ time mapping, and dynamic contrast-enhanced (DCE) perfusion MRI for monitoring the response of human lungs to low-dose inhaled lipopolysaccharide (LPS) challenge compared to inflammatory cell counts from induced-sputum analysis.

STUDY TYPE

Prospective feasibility study.

POPULATION

Ten healthy volunteers underwent MRI before and 6 hours after inhaled LPS challenge with subsequent induced-sputum collection.

FIELD STRENGTH/SEQUENCES

1.5T/hyperpolarized ¹²⁹ Xe MRI: Interleaved multiecho imaging of dissolved and gas phase, ventilation imaging, dissolved-phase spectroscopy, and chemical shift saturation recovery spectroscopy. ¹ H MRI: Inversion recovery fast low-angle shot imaging for T₁ mapping, time-resolved angiography with stochastic trajectories for DCE MRI.

ASSESSMENT

Dissolved-phase ratios of ¹²⁹ Xe in red blood cells (RBC), tissue/plasma (TP) and gas phase (GP), ventilation defect percentage, septal wall thickness, surface-to-volume ratio, capillary transit time, lineshape parameters in dissolved-phase spectroscopy, ¹ H T₁ time, blood volume, flow, and mean transit time were determined and compared to cell counts.

STATISTICAL TESTS

Wilcoxon signed-rank test, Pearson correlation.

RESULTS

The percentage of neutrophils in sputum was markedly increased after LPS inhalation compared to baseline, P = 0.002. The group median RBC-TP ratio was significantly reduced from 0.40 to 0.31, P = 0.004, and ¹ H T₁ was significantly elevated from 1157.6 msec to 1187.8 msec after LPS challenge, P = 0.027. DCE MRI exhibited no significant changes in blood volume, P = 0.64, flow, P = 0.17, and mean transit time, P = 0.11.

DATA CONCLUSION

Hyperpolarized ¹²⁹ Xe dissolved-phase MRI and ¹ H T₁ mapping may provide biomarkers for noninvasive assessment of the response of human lungs to LPS inhalation. By its specificity to the alveolar region, hyperpolarized ¹²⁹ Xe MRI together with ¹ H T₁ mapping adds value to sputum analysis.

LEVEL OF EVIDENCE

1 Technical Efficacy Stage: 2 J. Magn. Reson. Imaging 2020;51:1669-1676.

Open Electronics for Medical Devices: State-of-Art and Unique Advantages

A wide range of medical devices have significant electronic components. Compared to open-source medical software, open (and open-source) electronic hardware has been less published in peer-reviewed literature. In this review, we explore the developments, significance, and advantages of using open platform electronic hardware for medical devices. Open hardware electronics platforms offer not just shorter development times, reduced costs, and customization; they also offer a key potential advantage which current commercial medical devices lack—seamless data sharing for machine learning and artificial intelligence. We explore how various electronic platforms such as microcontrollers, single board computers, field programmable gate arrays, development boards, and integrated circuits have been used by researchers to design medical devices. Researchers interested in designing low cost, customizable, and innovative medical devices can find references to various easily available electronic components as well as design methodologies to integrate those components for a successful design.

Impact of the Number of Iterations in Compressed Sensing Reconstruction on Ultrafast Dynamic Contrast-enhanced Breast MR Imaging

PURPOSE

To assess the impact of the number of iterations of compressed sensing (CS) reconstruction on the kinetic parameters and image quality in dynamic contrast-enhanced (DCE)-MRI of the breast, with prospectively undersampled CS-accelerated scans.

MATERIALS AND METHODS

Breast examinations including ultrafast DCE-MRI using CS were conducted for 21 patients. Images were reconstructed with different numbers of iterations. The peak enhancement ratio of the aorta and wash-in slope, initial area under the curve, and Ktrans of the breast lesions were measured. The root mean square error and structural similarity between the images using 50 iterations and images with a lower number of iterations were evaluated as criterion for quantitative image evaluation.

RESULTS

Using an insufficient number of iterations, the contrast-enhanced effect was highly underestimated. In all semi-quantitative parameters, the number of iterations that stabilized the parameters in malignant lesions was higher than that in benign lesions. At least 15 iterations were needed for semi-quantitative parameters. For Ktrans, there were no significant differences between 10 and 50 iterations in both malignant and benign lesions.

CONCLUSION

The kinetic parameters using ultrafast DCE-MRI with CS are affected by the number of iterations, especially in malignant lesions. However, if the images are reconstructed with an adequate number of iterations, ultrafast DCE-MRI with CS can be a powerful technique having high temporal and spatial resolution.

A modified two-compartment model for measurement of renal function using dynamic contrast-enhanced computed tomography

Objectives

To validate and adapt a modified two-compartment model, originally developed for magnetic resonance imaging, for measuring human single-kidney glomerular filtration rate (GFR) and perfusion using dynamic contrast-enhanced computed tomography (DCE-CT).

Methods

This prospective study was approved by the institutional review board, and written informed consent was obtained from all patients. Thirty-eight patients with essential hypertension (EH, n = 13) or atherosclerotic renal artery stenosis (ARAS, n = 25) underwent renal DCE-CT for GFR and perfusion measurement using a modified two-compartment model. Iothalamate clearance was used to measure reference total GFR, which was apportioned into single-kidney GFR by renal blood flow. Renal perfusion was also calculated using a conventional deconvolution algorithm. Validation of GFR and perfusion and inter-observer reproducibility, were conducted by using the Pearson correlation and Bland-Altman analysis.

Results

Both the two-compartment model and iothalamate clearance detected in ARAS patients lower GFR in the stenotic compared to the contralateral and EH kidneys. GFRs measured by DCE-CT and iothalamate clearance showed a close match (r = 0.94, P<0.001, and mean difference 2.5±12.2mL/min). Inter-observer bias and variation in model-derived GFR (r = 0.97, P<0.001; mean difference, 0.3±7.7mL/min) were minimal. Renal perfusion by deconvolution agreed well with that by the compartment model when the blood transit delay from abdominal aorta to kidney was negligible.

Conclusion

The proposed two-compartment model faithfully depicts contrast dynamics using DCE-CT and may provide a reliable tool for measuring human single-kidney GFR and perfusion.

Deep semantic lung segmentation for tracking potential pulmonary perfusion biomarkers in chronic obstructive pulmonary disease (COPD): The multi-ethnic study of atherosclerosis COPD study

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is associated with high morbidity and mortality. Identification of imaging biomarkers for phenotyping is necessary for future treatment and therapy monitoring. However, translation of visual analytic pipelines into clinics or their use in large-scale studies is significantly slowed by time-consuming postprocessing steps.

PURPOSE

To implement an automated tool chain for regional quantification of pulmonary microvascular blood flow in order to reduce analysis time and user variability.

STUDY TYPE

Prospective.

POPULATION

In all, 90 MRI scans of 63 patients, of which 31 had a COPD with a mean Global Initiative for Chronic Obstructive Lung Disease status of 1.9 ± 0.64 (μ ± σ).

FIELD STRENGTH/SEQUENCE

1.5T dynamic gadolinium-enhanced MRI measurement using 4D dynamic contrast material-enhanced (DCE) time-resolved angiography acquired in a single breath-hold in inspiration. [Correction added on August 20, 2019, after first online publication: The field strength in the preceding sentence was corrected.] ASSESSMENT: We built a 3D convolutional neural network for semantic segmentation using 29 manually segmented perfusion maps. All five lobes of the lung are denoted, including the middle lobe. Evaluation was performed on 61 independent cases from two sites of the Multi-Ethnic Study of Arteriosclerosis (MESA)-COPD study. We publish our implementation of a model-free deconvolution filter according to Sourbron et al for 4D DCE MRI scans as open source.

STATISTICAL TEST

Cross-validation 29/61 (# training / # testing), intraclass correlation coefficient (ICC), Spearman ρ, Pearson r, Sørensen-Dice coefficient, and overlap.

RESULTS

Segmentations and derived clinical parameters were processed in ~90 seconds per case on a Xeon E5-2637v4 workstation with Tesla P40 GPUs. Clinical parameters and predicted segmentations exhibit high concordance with the ground truth regarding median perfusion for all lobes with an ICC of 0.99 and a Sørensen-Dice coefficient of 93.4 ± 2.8 (μ ± σ).

DATA CONCLUSION

We present a robust end-to-end pipeline that allows for the extraction of perfusion-based biomarkers for all lung lobes in 4D DCE MRI scans by combining model-free deconvolution with deep learning.

LEVEL OF EVIDENCE

3 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2020;51:571-579.

MITK-ModelFit: A generic open-source framework for model fits and their exploration in medical imaging - design, implementation and application on the example of DCE-MRI

Background

Many medical imaging techniques utilize fitting approaches for quantitative parameter estimation and analysis. Common examples are pharmacokinetic modeling in dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI)/computed tomography (CT), apparent diffusion coefficient calculations and intravoxel incoherent motion modeling in diffusion-weighted MRI and Z-spectra analysis in chemical exchange saturation transfer MRI. Most available software tools are limited to a special purpose and do not allow for own developments and extensions. Furthermore, they are mostly designed as stand-alone solutions using external frameworks and thus cannot be easily incorporated natively in the analysis workflow.

Results

We present a framework for medical image fitting tasks that is included in the Medical Imaging Interaction Toolkit MITK, following a rigorous open-source, well-integrated and operating system independent policy. Software engineering-wise, the local models, the fitting infrastructure and the results representation are abstracted and thus can be easily adapted to any model fitting task on image data, independent of image modality or model. Several ready-to-use libraries for model fitting and use-cases, including fit evaluation and visualization, were implemented. Their embedding into MITK allows for easy data loading, pre- and post-processing and thus a natural inclusion of model fitting into an overarching workflow. As an example, we present a comprehensive set of plug-ins for the analysis of DCE MRI data, which we validated on existing and novel digital phantoms, yielding competitive deviations between fit and ground truth.

Conclusions

Providing a very flexible environment, our software mainly addresses developers of medical imaging software that includes model fitting algorithms and tools. Additionally, the framework is of high interest to users in the domain of perfusion MRI, as it offers feature-rich, freely available, validated tools to perform pharmacokinetic analysis on DCE MRI data, with both interactive and automatized batch processing workflows.

Glucagon infusion alters the hyperpolarized 13 C-urea renal hemodynamic signature

Renal urea handling is central to the urine concentrating mechanism, and as such the ability to image urea transport in the kidney is an important potential imaging biomarker for renal functional assessment. Glucagon levels associated with changes in dietary protein intake have been shown to influence renal urea handling; however, the exact mechanism has still to be fully understood. Here we investigate renal function and osmolite distribution using [¹³ C,¹⁵ N] urea dynamics and ²³ Na distribution before and 60 min after glucagon infusion in six female rats. Glucagon infusion increased the renal [¹³ C,¹⁵ N] urea mean transit time by 14%, while no change was seen in the sodium distribution, glomerular filtration rate or oxygen consumption. This change is related to the well-known effect of increased urea excretion associated with glucagon infusion, independent of renal functional effects. This study demonstrates for the first time that hyperpolarized ¹³ C-urea enables monitoring of renal urinary excretion effects in vivo.

Altered Regional Cerebral Blood Flow Associated with Mood and Sleep in Shift Workers: Cerebral Perfusion Magnetic Resonance Imaging Study

BACKGROUND AND PURPOSE

Shift work disrupts the body's circadian rhythms and increases the risk of health problems. Despite evidence of neuropsychological disturbances in shift workers (SW), the brain functional status as measured by brain perfusion in chronic shift work has not been evaluated previously. We investigated the regional cerebral blood flow (rCBF) in SW using perfusion MRI (pMRI) and evaluated the relationships between altered rCBF and sleep, mood, psychometric measures, and quality of life.

METHODS

Fifteen rotational SW and 15 day workers (DW) were enrolled. The participants were all female nurses working at a university-affiliated hospital. During 2 weeks of actigraphy they underwent pMRI scanning and psychometric testing on the last day immediately after working. Demographic characteristics, insomnia, daytime sleepiness, and mood were compared between the groups.

RESULTS

The participants were aged 35.3±2.9 years (mean±SD) and had been performing their current work for more than 2 years. The demographic characteristics did not differ between SW and DW, but the levels of insomnia, anxiety, depression, and hyperactivity-restlessness in psychometric measures were higher in SW than in DW. Cerebral perfusion in SW was significantly decreased in the cuneus, fusiform/parahippocampal gyri, and cerebellum of the right hemisphere, while it was increased in the inferior occipital gyrus of the left hemisphere. Perfusion changes in SW were significantly correlated with depression and insomnia severity. The onset and duration irregularity of sleep among SW were related to insomnia, mood, hyperactivity/ restlessness, and quality of life.

CONCLUSIONS

SW experience considerably more insomnia and mood disturbances than do DW, and this is significantly related to perfusion changes in multiple brain areas.

Quantitative Perfusion Analysis of the Rectum Using Golden-Angle Radial Sparse Parallel Magnetic Resonance Imaging: Initial Experience and Comparison to Time-Resolved Angiography With Interleaved Stochastic Trajectories

OBJECTIVES

Purpose of this study was to compare the quality of perfusion maps obtained from prototypical free-breathing magnetic resonance imaging (MRI) with continuous golden-angle radial sampling and iterative reconstruction (GRASP) to conventional acquisition using time-resolved angiography with interleaved stochastic trajectories (TWIST) in patients with rectal cancer.

MATERIAL AND METHODS

Forty cases were included for retrospective analysis. Twenty of the patients received routine multiparametric MRI at 3 T for rectal cancer staging, including perfusion measurement with GRASP or TWIST (10 patients for each technique, including 5 prechemoradiation and 5 postchemoradiation). Twenty patients without history of rectal disease served as control group (10 GRASP, 10 TWIST). GRASP images were reconstructed at temporal resolution of 3.45 seconds (21 spokes/frame). A voxel-by-voxel deconvolution approach was used to determine rectal plasma flow (mL/100 mL per minute). Regions of interest were placed at 3 levels within the tumor and normal rectum (lower, middle, and upper part). The quality of morphologic images, perfusion maps, and arterial input function were scored by 2 blinded radiologists. Independent t tests were applied.

RESULTS

Three patients of the TWIST control group had to be excluded due to technical failure of the sequence. Significantly higher scores for the perfusion maps and arterial input functions (total cohort) were obtained using GRASP (P < 0.05). Artifacts in the perfusion maps were rated significantly lower than for TWIST (P < 0.05). In the healthy rectum cohort, the average plasma flow of normal rectal wall was 31.78 ± 7.39 mL/100 mL per minute with GRASP, compared with 77.62 ± 34.08 mL/100 mL per minute with TWIST, indicating much lower variance for GRASP. Plasma flow values obtained with both methods enabled distinguishing between normal rectal wall and rectal cancer, both before and after chemoradiation. Morphologic image quality was generally higher with GRASP (P < 0.01).

CONCLUSIONS

GRASP perfusion imaging can distinguish between normal rectum and rectal cancers with higher image quality and less variance than TWIST. Additional morphologic assessment with high spatial resolution from the GRASP acquisition may increase the accuracy and diagnostic confidence of the examination.

Detection of Local Recurrence with 3-Tesla MRI After Radical Prostatectomy: A Useful Method for Radiation Treatment Planning?

BACKGROUND/AIM

Salvage radiotherapy improves biochemical control in patients with recurrence of prostate cancer after prostatectomy. Radiotherapy target volumes of the prostatic fossa are based on empirical data and differ between different guidelines. Localization of recurrence with multiparametric magnetic resonance imaging (MRI) might be a feasible approach to localize recurrent lesions.

PATIENTS AND METHODS

Twenty-one patients with biochemical recurrence after radical prostatectomy were included (median prostate-specific antigen (PSA) =0.17 ng/ml). Multi-parametric MRI was performed using a 3-T MR system.

RESULTS

Lesions were detected in seven patients with a median PSA of 0.86 ng/ml (minimum= 0.31 ng/ml). Patients without detectable recurrence had a median PSA of 0.12 ng/ml. All patients with detectable lesions responded to radiotherapy. Eleven out of 14 patients without detectable recurrence also responded. Plasma flow in suspicious lesions was correlated with PSA level.

CONCLUSION

Detection of recurrence at the prostatic fossa with our approach was possible in a minority of patients with a low PSA level. Clinical relevance of plasma flow in suspicious lesions should be further investigated.

The impact of injector-based contrast agent administration in time-resolved MRA

OBJECTIVES

Time-resolved contrast-enhanced MR angiography (4D-MRA), which allows the simultaneous visualization of the vasculature and blood-flow dynamics, is widely used in clinical routine. In this study, the impact of two different contrast agent injection methods on 4D-MRA was examined in a controlled, standardized setting in an animal model.

METHODS

Six anesthetized Goettingen minipigs underwent two identical 4D-MRA examinations at 1.5 T in a single session. The contrast agent (0.1 mmol/kg body weight gadobutrol, followed by 20 ml saline) was injected using either manual injection or an automated injection system. A quantitative comparison of vascular signal enhancement and quantitative renal perfusion analyses were performed.

RESULTS

Analysis of signal enhancement revealed higher peak enhancements and shorter time to peak intervals for the automated injection. Significantly different bolus shapes were found: automated injection resulted in a compact first-pass bolus shape clearly separated from the recirculation while manual injection resulted in a disrupted first-pass bolus with two peaks. In the quantitative perfusion analyses, statistically significant differences in plasma flow values were found between the injection methods.

CONCLUSIONS

The results of both qualitative and quantitative 4D-MRA depend on the contrast agent injection method, with automated injection providing more defined bolus shapes and more standardized examination protocols.

KEY POINTS

• Automated and manual contrast agent injection result in different bolus shapes in 4D-MRA. • Manual injection results in an undefined and interrupted bolus with two peaks. • Automated injection provides more defined bolus shapes. • Automated injection can lead to more standardized examination protocols.

Hyperpolarized [1-13C]-acetate Renal Metabolic Clearance Rate Mapping

¹¹C-acetate is a positron emission tomography (PET) tracer of oxidative metabolism, whereas hyperpolarized ¹³C-acetate can be used in magnetic resonance imaging (MRI) for investigating specific metabolic processes. The aims of this study were to examine if the kinetic formalism of ¹¹C-acetate PET in the kidneys is comparable to that of ¹³C-acetate MRI, and to compare the dynamic metabolic information of hyperpolarized ¹³C-acetate MRI with that obtained with ¹¹C-acetate PET. Rats were examined with dynamic hyperpolarized ¹³C-acetate MRI or ¹¹C-acetate PET before and after intravenous injection of furosemide, a loop diuretic known to alter both the hemodynamics and oxygen consumption in the kidney. The metabolic clearance rates (MCR) were estimated and compared between the two modalities experimentally in vivo and in simulations. There was a clear dependency on the mean transit time and MCR for both ¹³C-acetate and ¹¹C-acetate following furosemide administration, while no dependencies on the apparent renal perfusion were observed. This study demonstrated that hyperpolarized ¹³C-acetate MRI is feasible for measurements of the intrarenal energetic demand via the MCR, and that the quantitative measures are correlated with those measured by ¹¹C-acetate PET, even though the temporal window is more than 30 times longer with ¹¹C-acetate.

"One-Stop Shop": Free-Breathing Dynamic Contrast-Enhanced Magnetic Resonance Imaging of the Kidney Using Iterative Reconstruction and Continuous Golden-Angle Radial Sampling

AIMS AND OBJECTIVES

The purpose of the present study was to evaluate a recently introduced technique for free-breathing dynamic contrast-enhanced renal magnetic resonance imaging (MRI) applying a combination of radial k-space sampling, parallel imaging, and compressed sensing. The technique allows retrospective reconstruction of 2 motion-suppressed sets of images from the same acquisition: one with lower temporal resolution but improved image quality for subjective image analysis, and one with high temporal resolution for quantitative perfusion analysis.

MATERIALS AND METHODS

In this study, 25 patients underwent a kidney examination, including a prototypical fat-suppressed, golden-angle radial stack-of-stars T1-weighted 3-dimensional spoiled gradient-echo examination (GRASP) performed after contrast agent administration during free breathing. Images were reconstructed at temporal resolutions of 55 spokes per frame (6.2 seconds) and 13 spokes per frame (1.5 seconds). The GRASP images were evaluated by 2 blinded radiologists. First, the reconstructions with low temporal resolution underwent subjective image analysis: the radiologists assessed the best arterial phase and the best renal phase and rated image quality score for each patient on a 5-point Likert-type scale.In addition, the diagnostic confidence was rated according to a 3-point Likert-type scale. Similarly, respiratory motion artifacts and streak artifacts were rated according to a 3-point Likert-type scale.Then, the reconstructions with high temporal resolution were analyzed with a voxel-by-voxel deconvolution approach to determine the renal plasma flow, and the results were compared with values reported in previous literature.

RESULTS

Reader 1 and reader 2 rated the overall image quality score for the best arterial phase and the best renal phase with a median image quality score of 4 (good image quality) for both phases, respectively. A high diagnostic confidence (median score of 3) was observed. There were no respiratory motion artifacts in any of the patients. Streak artifacts were present in all of the patients, but did not compromise diagnostic image quality.The estimated renal plasma flow was slightly higher (295 ± 78 mL/100 mL per minute) than reported in previous MRI-based studies, but also closer to the physiologically expected value.

CONCLUSIONS

Dynamic, motion-suppressed contrast-enhanced renal MRI can be performed in high diagnostic quality during free breathing using a combination of golden-angle radial sampling, parallel imaging, and compressed sensing. Both morphologic and quantitative functional information can be acquired within a single acquisition.

Comparison of perfusion models for quantitative T1 weighted DCE-MRI of rectal cancer

In this work, the two compartment exchange model and two compartment uptake model were applied to obtain quantitative perfusion parameters in rectum carcinoma and the results were compared to those obtained by the deconvolution algorithm. Eighteen patients with newly diagnosed rectal carcinoma underwent 3 T MRI of the pelvis including a T₁ weighted dynamic contrastenhanced (DCE) protocol before treatment. Mean values for Plasma Flow (PF), Plasma Volume (PV) and Mean Transit Time (MTT) were obtained for all three approaches and visualized in parameter cards. For the two compartment models, Akaike Information Criterion (AIC) and [Formula: see text] were calculated. Perfusion parameters determined with the compartment models show results in accordance with previous studies focusing on rectal cancer DCE-CT (PF_2CX = 68 ± 44 ml/100 ml/min, PF_2CU = 55 ± 36 ml/100 ml/min) with similar fit quality (AIC:169 ± 81/179 ± 77, [Formula: see text]:10 ± 12/9 ± 10). Values for PF are overestimated whereas PV and MTT are underestimated compared to results of the deconvolution algorithm. Significant differences were found among all models for perfusion parameters as well as between the AIC and [Formula: see text] values. Quantitative perfusion parameters are dependent on the chosen tracer kinetic model. According to the obtained parameters, all approaches seem capable of providing quantitative perfusion values in DCE-MRI of rectal cancer.

Can Hyperpolarized 13C-Urea be Used to Assess Glomerular Filtration Rate? A Retrospective Study

This study investigated a simple method for calculating the single-kidney glomerular filtration rate (GFR) using dynamic hyperpolarized ¹³C-urea magnetic resonance (MR) renography. A retrospective data analysis was applied to renal hyperpolarized ¹³C-urea MR data acquired from control rats, prediabetic nephropathy rats, and rats in which 1 kidney was subjected to ischemia-reperfusion. Renal blood flow was determined by the model-free bolus differentiation method, GFR was determined using the Baumann–Rudin model method. Reference single-kidney and total GFRs were measured by plasma creatinine content and compared to ¹H dynamic contrast-enhanced estimated GFR and fluorescein isothiocyanate-inulin clearance GFR estimation. In healthy and prediabetic nephropathy rats, single-kidney hyperpolarized ¹³C-urea GFR was estimated to be 2.5 ± 0.7 mL/min in good agreement with both gold-standard inulin clearance GFR (2.7 ± 1.2 ml/min) and ¹H dynamic contrast-enhanced estimated GFR (1.8 ± 0.8 mL/min), as well as plasma creatinine measurements and literature findings. Following ischemia-reperfusion, hyperpolarized ¹³C-urea revealed a significant reduction in single-kidney GFR of 57% compared with the contralateral kidney. Hyperpolarized ¹³C MR could be a promising tool for accurate determination of GFR. The model-free renal blood flow and arterial input function-insensitive GFR estimations are simple to implement and warrant further translational adaptation.

Comprehensive Multi-Dimensional MRI for the Simultaneous Assessment of Cardiopulmonary Anatomy and Physiology

Diagnostic testing often assesses the cardiovascular or respiratory systems in isolation, ignoring the major pathophysiologic interactions between the systems in many diseases. When both systems are assessed currently, multiple modalities are utilized in costly fashion with burdensome logistics and decreased accessibility. Thus, we have developed a new acquisition and reconstruction paradigm using the flexibility of MRI to enable a comprehensive exam from a single 5-15 min scan. We constructed a compressive-sensing approach to pseudo-randomly acquire highly subsampled, multi-dimensionally-encoded and time-stamped data from which we reconstruct volumetric cardiac and respiratory motion phases, contrast-agent dynamics, and blood flow velocity fields. The proposed method, named XD flow, is demonstrated for (a) evaluating congenital heart disease, where the impact of bulk motion is reduced in a non-sedated neonatal patient and (b) where the observation of the impact of respiration on flow is necessary for diagnostics; (c) cardiopulmonary imaging, where cardiovascular flow, function, and anatomy information is needed along with pulmonary perfusion quantification; and in (d) renal function imaging, where blood velocities and glomerular filtration rates are simultaneously measured, which highlights the generality of the technique. XD flow has the ability to improve quantification and to provide additional data for patient diagnosis for comprehensive evaluations.

Color-coded visualization of magnetic resonance imaging multiparametric maps

Multiparametric magnetic resonance imaging (mpMRI) data are emergingly used in the clinic e.g. for the diagnosis of prostate cancer. In contrast to conventional MR imaging data, multiparametric data typically include functional measurements such as diffusion and perfusion imaging sequences. Conventionally, these measurements are visualized with a one-dimensional color scale, allowing only for one-dimensional information to be encoded. Yet, human perception places visual information in a three-dimensional color space. In theory, each dimension of this space can be utilized to encode visual information. We addressed this issue and developed a new method for tri-variate color-coded visualization of mpMRI data sets. We showed the usefulness of our method in a preclinical and in a clinical setting: In imaging data of a rat model of acute kidney injury, the method yielded characteristic visual patterns. In a clinical data set of N = 13 prostate cancer mpMRI data, we assessed diagnostic performance in a blinded study with N = 5 observers. Compared to conventional radiological evaluation, color-coded visualization was comparable in terms of positive and negative predictive values. Thus, we showed that human observers can successfully make use of the novel method. This method can be broadly applied to visualize different types of multivariate MRI data.

[Quantitative perfusion imaging in magnetic resonance imaging]

CLINICAL/METHODICAL ISSUE

Magnetic resonance imaging (MRI) is recognized for its superior tissue contrast while being non-invasive and free of ionizing radiation. Due to the development of new scanner hardware and fast imaging techniques during the last decades, access to tissue and organ functions became possible. One of these functional imaging techniques is perfusion imaging with which tissue perfusion and capillary permeability can be determined from dynamic imaging data.

STANDARD RADIOLOGICAL METHODS

Perfusion imaging by MRI can be performed by two approaches, arterial spin labeling (ASL) and dynamic contrast-enhanced (DCE) MRI. While the first method uses magnetically labelled water protons in arterial blood as an endogenous tracer, the latter involves the injection of a contrast agent, usually gadolinium (Gd), as a tracer for calculating hemodynamic parameters.

PERFORMANCE

Studies have demonstrated the potential of perfusion MRI for diagnostics and also for therapy monitoring.

ACHIEVEMENTS

The utilization and application of perfusion MRI are still restricted to specialized centers, such as university hospitals. A broad application of the technique has not yet been implemented.

PRACTICAL RECOMMENDATIONS

The MRI perfusion technique is a valuable tool that might come broadly available after implementation of standards on European and international levels. Such efforts are being promoted by the respective professional bodies.

Practical aspects of prostate MRI: hardware and software considerations, protocols, and patient preparation

The use of multiparametric MRI scans for the evaluation of men with prostate cancer has increased dramatically and is likely to continue expanding as new developments come to practice. However, it has not yet gained the same level of acceptance of other imaging tests. Partly, this is because of the use of suboptimal protocols, lack of standardization, and inadequate patient preparation. In this manuscript, we describe several practical aspects of prostate MRI that may facilitate the implementation of new prostate imaging programs or the expansion of existing ones.

An open source software for analysis of dynamic contrast enhanced magnetic resonance images: UMMPerfusion revisited

Background

Perfusion imaging has become an important image based tool to derive the physiological information in various applications, like tumor diagnostics and therapy, stroke, (cardio-) vascular diseases, or functional assessment of organs. However, even after 20 years of intense research in this field, perfusion imaging still remains a research tool without a broad clinical usage. One problem is the lack of standardization in technical aspects which have to be considered for successful quantitative evaluation; the second problem is a lack of tools that allow a direct integration into the diagnostic workflow in radiology.

Results

Five compartment models, namely, a one compartment model (1CP), a two compartment exchange (2CXM), a two compartment uptake model (2CUM), a two compartment filtration model (2FM) and eventually the extended Toft’s model (ETM) were implemented as plugin for the DICOM workstation OsiriX. Moreover, the plugin has a clean graphical user interface and provides means for quality management during the perfusion data analysis. Based on reference test data, the implementation was validated against a reference implementation. No differences were found in the calculated parameters.

Conclusion

We developed open source software to analyse DCE-MRI perfusion data. The software is designed as plugin for the DICOM Workstation OsiriX. It features a clean GUI and provides a simple workflow for data analysis while it could also be seen as a toolbox providing an implementation of several recent compartment models to be applied in research tasks. Integration into the infrastructure of a radiology department is given via OsiriX. Results can be saved automatically and reports generated automatically during data analysis ensure certain quality control.

Dynamic contrast-enhanced MRI: Study of inter-software accuracy and reproducibility using simulated and clinical data

PURPOSE

To test the reproducibility and accuracy of pharmacokinetic parameter measurements on five analysis software packages (SPs) for dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), using simulated and clinical data.

MATERIALS AND METHODS

This retrospective study was Institutional Review Board-approved. Simulated tissues consisted of pixel clusters of calculated dynamic signal changes for combinations of Tofts model pharmacokinetic parameters (volume transfer constant [K(trans) ], extravascular extracellular volume fraction [ve ]), longitudinal relaxation time (T1 ). The clinical group comprised 27 patients treated for rectal cancer, with 36 3T DCE-MR scans performed between November 2012 and February 2014, including dual-flip-angle T1 mapping and a dynamic postcontrast T1 -weighted, 3D spoiled gradient-echo sequence. The clinical and simulated images were postprocessed with five SPs to measure K(trans) , ve , and the initial area under the gadolinium curve (iAUGC). Modified Bland-Altman analysis was conducted, intraclass correlation coefficients (ICCs) and within-subject coefficients of variation were calculated.

RESULTS

Thirty-one examinations from 23 patients were of sufficient technical quality and postprocessed. Measurement errors were observed on the simulated data for all the pharmacokinetic parameters and SPs, with a bias ranging from -0.19 min(-1) to 0.09 min(-1) for K(trans) , -0.15 to 0.01 for ve , and -0.65 to 1.66 mmol.L(-1) .min for iAUGC. The ICC between SPs revealed moderate agreement for the simulated data (K(trans) : 0.50; ve : 0.67; iAUGC: 0.77) and very poor agreement for the clinical data (K(trans) : 0.10; ve : 0.16; iAUGC: 0.21).

CONCLUSION

Significant errors were found in the calculated DCE-MRI pharmacokinetic parameters for the perfusion analysis SPs, resulting in poor inter-software reproducibility. J. Magn. Reson. Imaging 2016;43:1288-1300.

ROCKETSHIP: a flexible and modular software tool for the planning, processing and analysis of dynamic MRI studies

BACKGROUND

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a promising technique to characterize pathology and evaluate treatment response. However, analysis of DCE-MRI data is complex and benefits from concurrent analysis of multiple kinetic models and parameters. Few software tools are currently available that specifically focuses on DCE-MRI analysis with multiple kinetic models. Here, we developed ROCKETSHIP, an open-source, flexible and modular software for DCE-MRI analysis. ROCKETSHIP incorporates analyses with multiple kinetic models, including data-driven nested model analysis.

RESULTS

ROCKETSHIP was implemented using the MATLAB programming language. Robustness of the software to provide reliable fits using multiple kinetic models is demonstrated using simulated data. Simulations also demonstrate the utility of the data-driven nested model analysis. Applicability of ROCKETSHIP for both preclinical and clinical studies is shown using DCE-MRI studies of the human brain and a murine tumor model.

CONCLUSION

A DCE-MRI software suite was implemented and tested using simulations. Its applicability to both preclinical and clinical datasets is shown. ROCKETSHIP was designed to be easily accessible for the beginner, but flexible enough for changes or additions to be made by the advanced user as well. The availability of a flexible analysis tool will aid future studies using DCE-MRI. A public release of ROCKETSHIP is available at https://github.com/petmri/ROCKETSHIP .

Dynamic contrast-enhanced magnetic resonance imaging assessment of kidney function and renal masses: single slice versus whole organ/tumor

OBJECTIVES

The aim of this study was to compare single-slice and 3-dimensional (3D) analysis for magnetic resonance renography (plasma flow [FP], plasma volume [VP], and glomerular filtration rate [GFR]) and for dynamic contrast-enhanced magnetic resonance imaging (MRI) of renal tumors (FP, VP, permeability-surface area product), respectively.

MATERIAL AND METHODS

We prospectively included 22 patients (43 kidneys with 22 suspicious renal lesions) and performed preoperative and postoperative imaging before and after partial nephrectomy, respectively. Of the 22 renal lesions, 15 turned out to be renal cell carcinoma and were included in the tumor analysis, altogether leading to 86 renal and 15 tumor MRI scans, respectively. Dynamic contrast-enhanced MRI was performed with a time-resolved angiography with stochastic trajectories sequence (spatial resolution, 2.6 × 2.6 × 2.6 mm3; temporal resolution, 2.5 seconds) at 3 T (Magnetom Verio; Siemens Healthcare Sector) after injection of 0.05 mmol/kg body weight Gadobutrol (Bayer Healthcare Pharmaceuticals). Analysis was performed using regions of interest encompassing a single central slice and the whole kidney/tumor, respectively. A 2-compartment model yielding FP, VP, GFR, or tumor permeability-surface area product was used for kinetic modelling. Modelling was performed based on relative contrast enhancement to account for coil-related inhomogeneity. Significance in difference, agreement, and goodness of fit of the data to the curve was assessed with paired t tests, Bland-Altman plots, and χ2 test, respectively.

RESULTS

Bland-Altman analysis revealed a good agreement between both types of measurement for kidneys and tumors, respectively. Results between single-slice and whole-kidney regions of interest showed significant differences for Fp (single slice, 256.1 ± 104.1 mL/100 mL/min; whole kidney, 217.2 ± 92.5 mL/100 mL/min; P < 0.01). Regarding VP and GFR, no significant differences were observed. The χ2 test showed a significantly better goodness of fit of the data to the curve for whole kidneys (0.30% ± 0.18%) than for single slices (0.43% ± 0.26%) (P < 0.01). In contrast to renal assessment, tumor analysis showed no significant differences regarding functional parameters and χ test, respectively.

CONCLUSION

In dynamic contrast-enhanced MRI of the kidney, both 3D whole-organ/tumor and single-slice analyses provide roughly comparable values in functional analysis. However, 3D assessment is considerably more precise and should be preferred if available.

Feasibility study of high-resolution DCE-MRI for glomerular filtration rate (GFR) measurement in a routine clinical modal

Dynamic contrast enhanced (DCE) MR renography has been identified as an interesting tool to determine single-kidney GFR. However, a fundamental issue for the applicability of MR-based estimate of single-kidney GFR is selecting a balance between spatial and temporal resolution of DCE-MRI data. The purpose is to assess the feasibility of GFR estimate from high-resolution (HR) dynamic contrast-enhanced (DCE) MRI in a routine clinical modal. Standard MR renography (2.4s/phase, total 4min; 4-ml Gd) and five-phase, HR-based imaging protocol (0, 30, 70, 120, and 240s; 0.05mmol/kg Gd) were prospectively performed in twelve volunteers who were scheduled for routine renal MRI. Data were plotted with Patlak, two-compartment modified Tofts model (2CTM), and two-compartment filtration model (2CFM) for GFR estimate. During all the measurements, only the signal intensities in the aorta and whole kidney parenchyma were considered. Standard 2CFM and 2CTM produced lower residuals over the fitted interval than HR-based measures (p<0.05); and HR-bases 2CFM and 2CTM did not reflect significant correlation to standard values. Standard Patlak plots with 0-240s data points produced significantly lower GFR and higher residuals than that plots with 0-120s data points (p<0.05). HR-based Patlak plots with 0, 30, 70, and 120s data points significantly correlated with reference values (Pearson ρ=0.97, p<0.01), and produced a 33.2% underestimation of reference value, which was better than that plots with 0, 30, 70, 120, and 240s data points (ρ=0.92, p<0.01; 58.6% underestimation of reference value). It concludes that it is feasible to estimate GFR with HR-based DCE-MRI and appreciate kinetic model. Patlak plots from 0, 30, 70, and 120s data points is better than plots from 0, 30, 70, 120, and 240s data points.

DCEMRI.jl: a fast, validated, open source toolkit for dynamic contrast enhanced MRI analysis

We present a fast, validated, open-source toolkit for processing dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data. We validate it against the Quantitative Imaging Biomarkers Alliance (QIBA) Standard and Extended Tofts-Kety phantoms and find near perfect recovery in the absence of noise, with an estimated 10-20× speedup in run time compared to existing tools. To explain the observed trends in the fitting errors, we present an argument about the conditioning of the Jacobian in the limit of small and large parameter values. We also demonstrate its use on an in vivo data set to measure performance on a realistic application. For a 192 × 192 breast image, we achieved run times of <1 s. Finally, we analyze run times scaling with problem size and find that the run time per voxel scales as O(N (1.9)), where N is the number of time points in the tissue concentration curve. DCEMRI.jl was much faster than any other analysis package tested and produced comparable accuracy, even in the presence of noise.

Development and validation of an open source quantification tool for DSC-MRI studies

MOTIVATION

This work presents the development of an open source tool for the quantification of dynamic susceptibility-weighted contrast-enhanced (DSC) perfusion studies. The development of this tool is motivated by the lack of open source tools implemented on open platforms to allow external developers to implement their own quantification methods easily and without the need of paying for a development license.

MATERIALS AND METHODS

This quantification tool was developed as a plugin for the ImageJ image analysis platform using the Java programming language. A modular approach was used in the implementation of the components, in such a way that the addition of new methods can be done without breaking any of the existing functionalities. For the validation process, images from seven patients with brain tumors were acquired and quantified with the presented tool and with a widely used clinical software package. The resulting perfusion parameters were then compared.

RESULTS

Perfusion parameters and the corresponding parametric images were obtained. When no gamma-fitting is used, an excellent agreement with the tool used as a gold-standard was obtained (R(2)>0.8 and values are within 95% CI limits in Bland-Altman plots).

CONCLUSION

An open source tool that performs quantification of perfusion studies using magnetic resonance imaging has been developed and validated using a clinical software package. It works as an ImageJ plugin and the source code has been published with an open source license.

High temporal versus high spatial resolution in MR quantitative pulmonary perfusion imaging of two-year old children after congenital diaphragmatic hernia repair

OBJECTIVES

Congenital diaphragmatic hernia (CDH) leads to lung hypoplasia. Using dynamic contrast-enhanced (DCE) MR imaging, lung perfusion can be quantified. As MR perfusion values depend on temporal resolution, we compared two protocols to investigate whether ipsilateral lung perfusion is impaired after CDH, whether there are protocol-dependent differences, and which protocol is preferred.

METHODS

DCE-MRI was performed in 36 2-year old children after CDH on a 3 T MRI system; protocol A (n = 18) based on a high spatial (3.0 s; voxel: 1.25 mm(3)) and protocol B (n = 18) on a high temporal resolution (1.5 s; voxel: 2 mm(3)). Pulmonary blood flow (PBF), pulmonary blood volume (PBV), mean transit time (MTT), and peak-contrast-to-noise-ratio (PCNR) were quantified.

RESULTS

PBF was reduced ipsilaterally, with ipsilateral PBF of 45 ± 26 ml/100 ml/min to contralateral PBF of 63 ± 28 ml/100 ml/min (p = 0.0016) for protocol A; and for protocol B, side differences were equivalent (ipsilateral PBF = 62 ± 24 vs. contralateral PBF = 85 ± 30 ml/100 ml/min; p = 0.0034). PCNR was higher for protocol B (30 ± 18 vs. 20 ± 9; p = 0.0294). Protocol B showed higher values of PBF in comparison to protocol A (p always <0.05).

CONCLUSIONS

Ipsilateral lung perfusion is reduced in 2-year old children following CDH repair. Higher temporal resolution and increased voxel size show a gain in PCNR and lead to higher perfusion values. Protocol B is therefore preferred.

KEY POINTS

• Quantitative lung perfusion parameters depend on temporal and spatial resolution. • Reduction of lung perfusion in CDH can be measured with different MR protocols. • Temporal resolution of 1.5 s with spatial resolution of 2 mm (3) is suitable.

Incremental learning with SVM for multimodal classification of prostatic adenocarcinoma

Robust detection of prostatic cancer is a challenge due to the multitude of variants and their representation in MR images. We propose a pattern recognition system with an incremental learning ensemble algorithm using support vector machines (SVM) tackling this problem employing multimodal MR images and a texture-based information strategy. The proposed system integrates anatomic, texture, and functional features. The data set was preprocessed using B-Spline interpolation, bias field correction and intensity standardization. First- and second-order angular independent statistical approaches and rotation invariant local phase quantization (RI-LPQ) were utilized to quantify texture information. An incremental learning ensemble SVM was implemented to suit working conditions in medical applications and to improve effectiveness and robustness of the system. The probability estimation of cancer structures was calculated using SVM and the corresponding optimization was carried out with a heuristic method together with a 3-fold cross-validation methodology. We achieved an average sensitivity of 0.844 ± 0.068 and a specificity of 0.780 ± 0.038, which yielded superior or similar performance to current state of the art using a total database of only 41 slices from twelve patients with histological confirmed information, including cancerous, unhealthy non-cancerous and healthy prostate tissue. Our results show the feasibility of an ensemble SVM being able to learn additional information from new data while preserving previously acquired knowledge and preventing unlearning. The use of texture descriptors provides more salient discriminative patterns than the functional information used. Furthermore, the system improves selection of information, efficiency and robustness of the classification. The generated probability map enables radiologists to have a lower variability in diagnosis, decrease false negative rates and reduce the time to recognize and delineate structures in the prostate.

Multi-parametric MRI of rectal cancer - do quantitative functional MR measurements correlate with radiologic and pathologic tumor stages?

PURPOSE

The purpose of this study is two-fold. First, to evaluate, whether functional rectal MRI techniques can be analyzed in a reproducible manner by different readers and second, to assess whether different clinical and pathologic T and N stages can be differentiated by functional MRI measurements.

MATERIALS AND METHODS

54 patients (38 men, 16 female; mean age 63.2 ± 12.2 years) with pathologically proven rectal cancer were included in this retrospective IRB-approved study. All patients were referred for a multi-parametric MRI protocol on a 3 Tesla MR-system, consisting of a high-resolution, axial T2 TSE sequence, DWI and perfusion imaging (plasma flow -s PFTumor) prior to any treatment. Two experienced radiologists evaluated the MRI measurements, blinded to clinical data and outcome. Inter-reader correlation and the association of functional MRI parameters with c- and p-staging were analyzed.

RESULTS

The inter-reader correlation for lymph node (ρ 0.76-0.94; p<0.0002) and primary tumor (ρ 0.78-0.92; p<0.0001) apparent diffusion coefficient and plasma flow (PF) values was good to very good. PFTumor values decreased with cT stage with significant differences identified between cT2 and cT3 tumors (229 versus 107.6 ml/100ml/min; p=0.05). ADCTumor values did not differ significantly. No substantial discrepancies in lymph node ADCLn values or short axis diameter were found among cN1-3 stages, whereas PFLn values were distinct between cN1 versus cN2 stages (p=0.03). In the patients without neoadjuvant RCT no statistically significant differences in the assessed functional parameters on the basis of pathologic stage were found.

CONCLUSION

This study illustrates that ADC as well as MR perfusion values can be analyzed with good interobserver agreement in patients with rectal cancer. Moreover, MR perfusion parameters may allow accurate differentiation of tumor stages. Both findings suggest that functional MRI parameters may help to discriminate T and N stages for clinical decision making.

Functional imaging of acute kidney injury at 3 Tesla: investigating multiple parameters using DCE-MRI and a two-compartment filtration model

OBJECT

To investigate how MR-based parameters reflect functional changes in kidneys with acute kidney injury (AKI) using dynamic contrast enhanced MRI and a two-compartment renal filtration model.

MATERIALS AND METHODS

MRI data of eight male Lewis rats were analyzed retrospectively. Five animals were subjected to AKI, three native rats served as control. All animals underwent perfusion imaging by dynamic contrast-enhanced MRI. Renal blood volume, glomerular filtration rate (GFR) as well as plasma and tubular mean transit times were estimated from regions-of-interest drawn in the renal cortex. Differences between healthy kidneys and kidneys subjected to AKI were analyzed using a paired t-test.

RESULTS

Significant differences between ischemic and healthy kidneys could only be detected for the glomerular filtration rate. For all other calculated parameters, differences were present, however not significant. In rats with AKI, average single kidney GFR was 0.66 ± 0.37 ml/min for contralateral and 0.26 ± 0.12 ml/ min for diseased kidneys (P = 0.0254). For the healthy control group, the average GFR was 0.39 ± 0.06 ml/min and 0.41 ± 0.11 ml/min, respectively. Differences between diseased kidneys of AKI rats and ipsilateral kidneys of the healthy control group were significant (P = 0.0381).

CONCLUSION

Significant differences of functional parameters reflecting damage of the renal tissue of kidneys with AKI compared to the contralateral, healthy kidneys could only be detected by GFR. GFR might be a useful parameter that allows for a spatially resolved detection of abnormal changes of renal tissue by AKI.

Renal perfusion in acute kidney injury with DCE-MRI: deconvolution analysis versus two-compartment filtration model

PURPOSE

To investigate the results of different pharmacokinetic models of a quantitative analysis of renal blood flow (RBF) in acute kidney injury using deconvolution analysis and a two-compartment renal filtration model.

MATERIALS AND METHODS

MRI data of ten male Lewis rats were analyzed retrospectively. Six animals were subjected to unilateral acute kidney injury and underwent perfusion imaging by dynamic contrast-enhanced MRI (DCE-MRI). Renal blood flow was estimated from regions-of-interest depicting the cortex in the DCE-MRI perfusion maps. The perfusion models were compared by a paired t-test and Bland-Altman plots.

RESULTS

No significant difference was found between the two compartment model and the deconvolution analysis (P=0.2807). Differences between healthy and diseased kidney in the AKI model were significant for both methods (P<0.05). A Bland-Altman plot showed no systematic errors, and values were equally distributed around the mean difference between the methods lying within the range of 1.96 standard deviations.

CONCLUSION

Both quantification strategies could detect the kidneys that were impaired by AKI. When just aiming at RBF as a marker, a deconvolution analysis can provide similar values as the 2CFM. If functional parameters beyond RBF like glomerular filtration rate are needed, the 2CFM should be employed.

Simultaneous measurement of kidney function by dynamic contrast enhanced MRI and FITC-sinistrin clearance in rats at 3 tesla: initial results

Glomerular filtration rate (GFR) is an essential parameter of kidney function which can be measured by dynamic contrast enhanced magnetic resonance imaging (MRI-GFR) and transcutaneous approaches based on fluorescent tracer molecules (optical-GFR). In an initial study comparing both techniques in separate measurements on the same animal, the correlation of the obtained GFR was poor. The goal of this study was to investigate if a simultaneous measurement was feasible and if thereby, the discrepancies in MRI-GFR and optical-GFR could be reduced. For the experiments healthy and unilateral nephrectomised (UNX) Sprague Dawley (SD) rats were used. The miniaturized fluorescent sensor was fixed on the depilated back of an anesthetized rat. A bolus of 5 mg/100 g b.w. of FITC-sinistrin was intravenously injected. For dynamic contrast enhanced perfusion imaging (DCE-MRI) a 3D time-resolved angiography with stochastic trajectories (TWIST) sequence was used. By means of a one compartment model the excretion half-life (t1/2) of FITC-sinistrin was calculated and converted into GFR. GFR from DCE-MRI was calculated by fitting pixel-wise a two compartment renal filtration model. Mean cortical GFR and GFR by FITC-sinistrin were compared by Bland-Altman plots and pair-wise t-test. Results show that a simultaneous GFR measurement using both techniques is feasible. Mean optical-GFR was 4.34 ± 2.22 ml/min (healthy SD rats) and 2.34 ± 0.90 ml/min (UNX rats) whereas MRI-GFR was 2.10 ± 0.64 ml/min (SD rats) and 1.17 ± 0.38 ml/min (UNX rats). Differences between healthy and UNX rats were significant (p<0.05) and almost equal percentage difference (46.1% and 44.3%) in mean GFR were assessed with both techniques. Overall mean optical-GFR values were approximately twice as high compared to MRI-GFR values. However, compared to a previous study, our results showed a higher agreement. In conclusion, the possibility to use the transcutaneous method in MRI may have a huge impact in improving and validating MRI methods for GFR assessment in animal models.