Multi-Parametric Representation of Voxel-Based Quantitative Magnetic Resonance Imaging

The aim of the study was to explore the possibilities of multi-parametric representations of voxel-wise quantitative MRI data to objectively discriminate pathological cerebral tissue in patients with brain disorders. For this purpose, we recruited 19 patients with Multiple Sclerosis (MS) as benchmark samples and 19 age and gender matched healthy subjects as a reference group. The subjects were examined using quantitative Magnetic Resonance Imaging (MRI) measuring the tissue structure parameters: relaxation rates, R and R, and proton density. The resulting parameter images were normalized to a standard template. Tissue structure in MS patients was assessed by voxel-wise comparisons with the reference group and with correlation to a clinical measure, the Expanded Disability Status Scale (EDSS). The results were visualized by conventional geometric representations and also by multi-parametric representations. Data showed that MS patients had lower R and R, and higher proton density in periventricular white matter and in wide-spread areas encompassing central and sub-cortical white matter structures. MS-related tissue abnormality was highlighted in posterior white matter whereas EDSS correlation appeared especially in the frontal cortex. The multi-parameter representation highlighted disease-specific features. In conclusion, the proposed method has the potential to visualize both high-probability focal anomalies and diffuse tissue changes. Results from voxel-based statistical analysis, as exemplified in the present work, may guide radiologists where in the image to inspect for signs of disease. Future clinical studies must validate the usability of the method in clinical practice.     

Magnetic Resonance Assessment of Response to Therapy: Tumor Change Measurement,Truth Data and Error Sources

This article describes methods and issues that are specific to the assessment of change in tumor characteristics as measured using quantitative magnetic resonance (MR) techniques and how this relates to the establishment of quantitative MR imaging (MRI) biomarkers of patient response to therapy. The initial focus is on the various sources of bias and variance in the measurement of microvascular parameters and diffusion parameters as such parameters are being used relatively commonly as secondary or exploratory end points in current phase 1/2 clinical trails of conventional and targeted therapies. Several ongoing initiatives that seek to identify the magnitude of some of the sources of measurement variations are then discussed. Finally, resources being made available through the National Cancer Institute Reference Image Database to Evaluate Response (RIDER) project that might be of use in investigations of quantitative MRI biomarker change analysis are described. These resources include 1) data from phantom-based assessment of system response, including short-term (1 hour) and moderate-term (1 week) contrast response and relaxation time measurement, 2) data obtained from repeated dynamic contrast agent-enhanced MRI studies in intracranial tumors, and 3) data obtained from repeated diffusion MRI studies in both breast and brain. A concluding section briefly discusses issues that must be addressed to allow the transition of MR-based imaging biomarker measures from their current role as secondary/exploratory end points in clinical trials to primary/surrogate markers of response and, ultimately, in clinical application.     

Brain Characterization Using Normalized Quantitative Magnetic Resonance Imaging

Objectives

To present a method for generating reference maps of typical brain characteristics of groups of subjects using a novel combination of rapid quantitative Magnetic Resonance Imaging (qMRI) and brain normalization. The reference maps can be used to detect significant tissue differences in patients, both locally and globally.

Materials and Methods

A rapid qMRI method was used to obtain the longitudinal relaxation rate (R₁), the transverse relaxation rate (R₂) and the proton density (PD). These three tissue properties were measured in the brains of 32 healthy subjects and in one patient diagnosed with Multiple Sclerosis (MS). The maps were normalized to a standard brain template using a linear affine registration. The differences of the mean value ofR₁, R₂ and PD of 31 healthy subjects in comparison to the oldest healthy subject and in comparison to an MS patient were calculated. Larger anatomical structures were characterized using a standard atlas. The vector sum of the normalized differences was used to show significant tissue differences.

Results

The coefficient of variation of the reference maps was high at the edges of the brain and the ventricles, moderate in the cortical grey matter and low in white matter and the deep grey matter structures. The elderly subject mainly showed significantly lower R₁ and R₂ and higher PD values along all sulci. The MS patient showed significantly lower R₁ and R₂ and higher PD values at the edges of the ventricular system as well as throughout the periventricular white matter, at the internal and external capsules and at each of the MS lesions.

Conclusion

Brain normalization of rapid qMRI is a promising new method to generate reference maps of typical brain characteristics and to automatically detect deviating tissue properties in the brain.     

Monitoring Brain Tumor Vascular Heamodynamic following Anti-Angiogenic Therapy with Advanced Magnetic Resonance Imaging in Mice

Advanced MR imaging methods have an essential role in classification, grading, follow-up and therapeutic management in patients with brain tumors. With the introduction of new therapeutic options, the challenge for better tissue characterization and diagnosis increase, calling for new reliable non-invasive imaging methods. In the current study we evaluated the added value of a combined protocol of blood oxygen level dependent (BOLD) imaging during hyperoxic challenge (termed hemodynamic response imaging (HRI)) in an orthotopic mouse model for glioblastoma under anti-angiogenic treatment with B20-4.1.1, an anti-VEGF antibody. In glioblastoma tumors, the elevated HRI indicated progressive angiogenesis as further confirmed by histology. In the current glioblastoma model, B20-treatment caused delayed tumor progression with no significant changes in HRI yet with slightly reduced tumor vascularity as indicated by histology. Furthermore, fewer apoptotic cells and higher proliferation index were detected in the B20-treated tumors compared to control-treated tumors. In conclusion, HRI provides an easy, safe and contrast agent free method for the assessment of the brain hemodynamic function, an additionally important clinical information.     

Tumor Xenograft Response to Redox-Active Therapies Assessed by Magnetic Resonance Imaging Using a Thiol-Bearing DOTA Complex of Gadolinium

Gd-LC6-SH is a thiol-bearing DOTA complex of gadolinium designed to bind plasma albumin at the conserved Cys(34) site. The binding of Gd-LC6-SH shows sensitivity to the presence of competing thiols. We hypothesized that Gd-LC6-SH could provide magnetic resonance imaging (MRI) enhancement that is sensitive to tumor redox state and that the prolonged retention of albumin-bound Gd-LC6-SH in vivo can be exploited to identify a saturating dose above which the shortening of MRI longitudinal relaxation time (T(1)) of tissue is insensitive to the injected gadolinium dose. In the Mia-PaCa-2 pancreatic tumor xenograft model in SCID mice, both the small-molecule Gd-DTPA-BMA and the macromolecule Galbumin MRI contrast agents produced dose-dependent decreases in tumor T(1). By contrast, the decreases in tumor T(1) provided by Gd-LC6-SH at 0.05 and 0.1 mmol/kg were not significantly different at longer times after injection. SCID mice bearing Mia-PaCa-2 or NCI-N87 tumor xenografts were treated with either the glutathione synthesis inhibitor buthionine sulfoximine or the thiol-oxidizing anticancer drug Imexon, respectively. In both models, there was a significantly greater increase in tumor R(1) (=1/T(1)) 60 minutes after injection of Gd-LC6-SH in drug-treated animals relative to saline-treated controls. In addition, Mercury Orange staining for nonprotein sulfhydryls was significantly decreased by drug treatment relative to controls in both tumor models. In summary, these studies show that thiol-bearing complexes of gadolinium such as Gd-LC6-SH can serve as redox-sensitive MRI contrast agents for detecting differences in tumor redox status and can be used to evaluate the effects of redox-active drugs.     

Monitoring Early Response to Anti-Angiogenic Therapy: Diffusion-Weighted Magnetic Resonance Imaging and Volume Measurements in Colon Carcinoma Xenografts

Objectives

To evaluate the use of diffusion-weighted MRI (DW-MRI) and volume measurements for early monitoring of antiangiogenic therapy in an experimental tumor model.

Materials and Methods

23 athymic nude rats, bearing human colon carcinoma xenografts (HT-29) were examined before and after 6 days of treatment with regorafenib (n = 12) or placebo (n = 11) in a clinical 3-Tesla MRI. For DW-MRI, a single-shot EPI sequence with 9 b-values (10–800 s/mm²) was used. The apparent diffusion coefficient (ADC) was calculated voxelwise and its median value over a region of interest, covering the entire tumor, was defined as the tumor ADC. Tumor volume was determined using T2-weighted images. ADC and volume changes between first and second measurement were evaluated as classifiers by a receiver-operator-characteristic (ROC) analysis individually and combined using Fisher''s linear discriminant analysis (FLDA).

Results

All ADCs and volumes are stated as median±standard deviation. Tumor ADC increased significantly in the therapy group (0.76±0.09×10⁻³ mm²/s to 0.90±0.12×10⁻³ mm²/s; p<0.001), with significantly higher changes of tumor ADC than in the control group (0.10±0.11×10⁻³ mm²/s vs. 0.03±0.09×10⁻³ mm²/s; p = 0.027). Tumor volume increased significantly in both groups (therapy: 347.8±449.1 to 405.3±823.6 mm³; p = 0.034; control: 219.7±79.5 to 443.7±141.5 mm³; p<0.001), however, the therapy group showed significantly reduced tumor growth (33.30±47.30% vs. 96.43±31.66%; p<0.001). Area under the curve and accuracy of the ADC-based ROC analysis were 0.773 and 78.3%; and for the volume change 0.886 and 82.6%. The FLDA approach yielded an AUC of 0.985 and an accuracy of 95.7%.

Conclusions

Regorafenib therapy significantly increased tumor ADC after 6 days of treatment and also significantly reduced tumor growth. However, ROC analyses using each parameter individually revealed a lack of accuracy in discriminating between therapy and control group. The combination of both parameters using FLDA substantially improved diagnostic accuracy, thus highlighting the potential of multi-parameter MRI as an imaging biomarker for non-invasive early tumor therapy monitoring.     

磁共振成像对乳腺肿瘤的诊断价值

乳腺癌是危及女性健康的常见恶性肿瘤之一,病死率较高,且发病年龄呈年轻化趋势。目前临床对乳腺疾病的检查方法很多,既往检查主要包括钼靶、超声等,因价格便宜、操作方便,已成为常规的乳腺疾病检查方法,但两者的敏感性和特异性较低并有自身的局限性。CT软组织分辨率较高,但检查过程中的X线剂量较大,并且动态增强时间较长,故作为乳腺钼靶的补充检查手段。这些检查方法对乳腺疾病均有不同的诊断意义,在当前众多诊断乳腺疾病方法中,具有无辐射,较高软组织分辨力及可多方位多层面成像的乳腺磁共振(MRI)成像有其独到的优势,某些方面能弥补超声和钼靶检查的局限性,乳腺磁共振可提供病灶形态学和增强血流动力学表现,可用于常规检查方法不能确诊病灶的鉴别诊断。乳腺肿瘤MRI成像对临床诊断、鉴别诊断及手术方案的选择有着极其重要的作用。本文就乳腺MRI影像技术、MRI影像学表现及其临床应用予以综述,探讨MRI在乳腺肿瘤中的应用。     

Quantitative Imaging to Assess Tumor Response to Therapy: Common Themes of Measurement,Truth Data,and Error Sources

RATIONALE: Early detection of tumor response to therapy is a key goal. Finding measurement algorithms capable of early detection of tumor response could individualize therapy treatment as well as reduce the cost of bringing new drugs to market. On an individual basis, the urgency arises from the desire to prevent continued treatment of the patient with a high-cost and/or high-risk regimen with no demonstrated individual benefit and rapidly switch the patient to an alternative efficacious therapy for that patient. In the context of bringing new drugs to market, such algorithms could demonstrate efficacy in much smaller populations, which would allow phase 3 trials to achieve statistically significant decisions with fewer subjects in shorter trials. MATERIALS AND METHODS: This consensus-based article describes multiple, image modality-independent means to assess the relative performance of algorithms for measuring tumor change in response to therapy. In this setting, we describe specifically the example of measurement of tumor volume change from anatomic imaging as well as provide an overview of other promising generic analytic methods that can be used to assess change in heterogeneous tumors. To support assessment of the relative performance of algorithms for measuring small tumor change, data sources of truth are required. RESULTS: Very short interval clinical imaging examinations and phantom scans provide known truth for comparative evaluation of algorithms. CONCLUSIONS: For a given category of measurement methods, the algorithm that has the smallest measurement noise and least bias on average will perform best in early detection of true tumor change.     

基于fMRI观察正常人脑中枢对针刺得气感反应的初步研究

目的:运用功能性磁共振成像技术观察正常人脑中枢对针刺得气感的反应特点,探索针刺得气的物质基础。方法:按照纳入排除标准收集男、女健康志愿者各35例,随机分为2组,针刺组40人,假针刺组30人,分别以外关穴针刺与假针刺作为刺激因素。采用Block方法设计刺激程序,运用功能性磁共振成像技术收集脑中枢反应信号。扫描完毕随即使用针刺感觉量表评价受试对象的感觉,依据感觉量化结果将图像数据分为针刺得气感组与无感觉对照组,以P≤0.0001,uncorrected,K10为统计检验显著性标准,以对照无感觉组为基线,在Matlab平台上采用SPM2.0软件包对图像数据进行处理和分析。结果:(1)得气效应:针刺组29人、假针刺组1人以酸麻胀重等得气指征为主,VAS评分4.62±3.05;针刺组2人轻微刺痛感,假针刺组21人无感觉、5人轻微刺痛感。(2)脑中枢激活效应:针刺得气激活的脑功能区有双侧额上回(BA6)、额下回(BA47)、缘上回(BA40),左侧额中回(BA47)、中央前回(BA10)、颞中回(BA21),右侧额中回(BA10)、顶下小叶(BA40)、中央前回(BA6)、颞上回(BA10)、颞中回(BA39)、颞下回(BA20)。结论:针刺得气感能特异性的激活正常人脑功能区,针刺得气效应与脑中枢密切相关。     

兔大腿VX2移植瘤模型磁共振扩散成像研究

采用大腿肌肉注射法建立兔VX2肿瘤模型,于造模后第7天、14天及21天进行磁共振成像(MRI)平扫、增强及扩散加权成像(DWI)检查,观察不同时期MRI表现。并于造模后第21天对照大体标本测量结果比较DWI及T2WI图像肿瘤最大径,同时比较肿瘤实体部分与髂窝内转移淋巴结的表观弥散系数(ADC)值。结果显示,造模后第7天,12只模型兔MRI常规及DWI图像均可见成瘤;第14天,2例肿瘤内出现坏死灶;第21天,12例肿瘤内均出现坏死,DWI图像可发现局部淋巴结转移灶,DWI及T2WI图像肿瘤最大径与大体标本测量结果差别无统计学意义。髂窝内转移淋巴结的ADC值与原发肿瘤实体部分ADC值间差别无统计学意义。DWI可以监测兔大腿VX2肿瘤生长,有效区分肿瘤早期坏死成分,并判断相应引流区域淋巴结的性质。     

Establishing Intracranial Brain Tumor Xenografts With Subsequent Analysis of Tumor Growth and Response to Therapy using Bioluminescence Imaging

Transplantation models using human brain tumor cells have served an essential function in neuro-oncology research for many years. In the past, the most commonly used procedure for human tumor xenograft establishment consisted of the collection of cells from culture flasks, followed by the subcutaneous injection of the collected cells in immunocompromised mice. Whereas this approach still sees frequent use in many laboratories, there has been a significant shift in emphasis over the past decade towards orthotopic xenograft establishment, which, in the instance of brain tumors, requires tumor cell injection into appropriate neuroanatomical structures. Because intracranial xenograft establishment eliminates the ability to monitor tumor growth through direct measurement, such as by use of calipers, the shift in emphasis towards orthotopic brain tumor xenograft models has necessitated the utilization of non-invasive imaging for assessing tumor burden in host animals. Of the currently available imaging methods, bioluminescence monitoring is generally considered to offer the best combination of sensitivity, expediency, and cost. Here, we will demonstrate procedures for orthotopic brain tumor establishment, and for monitoring tumor growth and response to treatment when testing experimental therapies.     

Variations of Dynamic Contrast-Enhanced Magnetic Resonance Imaging in Evaluation of Breast Cancer Therapy Response: A Multicenter Data Analysis Challenge

Pharmacokinetic analysis of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) time-course data allows estimation of quantitative parameters such as K^trans (rate constant for plasma/interstitium contrast agent transfer), v_e (extravascular extracellular volume fraction), and v_p (plasma volume fraction). A plethora of factors in DCE-MRI data acquisition and analysis can affect accuracy and precision of these parameters and, consequently, the utility of quantitative DCE-MRI for assessing therapy response. In this multicenter data analysis challenge, DCE-MRI data acquired at one center from 10 patients with breast cancer before and after the first cycle of neoadjuvant chemotherapy were shared and processed with 12 software tools based on the Tofts model (TM), extended TM, and Shutter-Speed model. Inputs of tumor region of interest definition, pre-contrast T₁, and arterial input function were controlled to focus on the variations in parameter value and response prediction capability caused by differences in models and associated algorithms. Considerable parameter variations were observed with the within-subject coefficient of variation (wCV) values for K^trans and v_p being as high as 0.59 and 0.82, respectively. Parameter agreement improved when only algorithms based on the same model were compared, e.g., the K^trans intraclass correlation coefficient increased to as high as 0.84. Agreement in parameter percentage change was much better than that in absolute parameter value, e.g., the pairwise concordance correlation coefficient improved from 0.047 (for K^trans) to 0.92 (for K^trans percentage change) in comparing two TM algorithms. Nearly all algorithms provided good to excellent (univariate logistic regression c-statistic value ranging from 0.8 to 1.0) early prediction of therapy response using the metrics of mean tumor K^trans and k_ep (= K^trans/v_e, intravasation rate constant) after the first therapy cycle and the corresponding percentage changes. The results suggest that the interalgorithm parameter variations are largely systematic, which are not likely to significantly affect the utility of DCE-MRI for assessment of therapy response.     

动态增强磁共振监测VEGF反义核酸对兔颌面部VX2肿瘤放疗的增敏作用

目的:研究动态增强磁共振成像(dynamic contrast enhanced magnetic resonance imaging,DCE-MRI)监测VEGF反义核酸对兔颌面部VX2肿瘤放疗后的影响。方法:24只颌面部VX2荷瘤兔模型随机分4组:放疗组(A组):给予16Gy放疗;VEGF反义核酸治疗组(B组):肿瘤局部注入VEGF反义核酸150μg;VEGF反义核酸联合放疗组(C组):16Gy放疗后立即局部肿瘤内注射VEGF反义核酸150μg;对照组(D组):肿瘤内注射300μl5%葡萄糖水溶液。治疗后第3天、14天分别行DCE-MRI检查,计算MER(Maximal enhancement ratio,最大强化率)及SLE(Slope of enhancement,强化率斜率)值,14天处死动物行病理检查和VEGF免疫组化染色。结果:C组治疗后14天肿瘤体积明显缩小,与治疗前和治疗后三天及其它组比较差别具有统计学意义(P<0.01)。MER值降低和SLE值降低,与治疗前比较差别有统计学意义(P<0.05)。病理切片显示肿瘤细胞水肿、出血,坏死,血管壁增厚闭塞,VEGF免疫阳性表达下降,经IHS评分与A...     

磁共振成像设备发展趋势

本文主要叙述了磁共振设备的原理、构造、产品发展趋势。并对提高磁共振图像分辨的新技术,如Tim全景矩阵成像、自由浪潮技术、高清晰MRI技术和双梯度技术作了综述。     

Multimodality Multiparametric Imaging of Early Tumor Response to a Novel Antiangiogenic Therapy Based on Anticalins

Anticalins are a novel class of targeted protein therapeutics. The PEGylated Anticalin Angiocal (PRS-050-PEG40) is directed against VEGF-A. The purpose of our study was to compare the performance of diffusion weighted imaging (DWI), dynamic contrast enhanced magnetic resonance imaging (DCE)-MRI and positron emission tomography with the tracer [¹⁸F]fluorodeoxyglucose (FDG-PET) for monitoring early response to antiangiogenic therapy with PRS-050-PEG40. 31 mice were implanted subcutaneously with A673 rhabdomyosarcoma xenografts and underwent DWI, DCE-MRI and FDG-PET before and 2 days after i.p. injection of PRS-050-PEG40 (n = 13), Avastin (n = 6) or PBS (n = 12). Tumor size was measured manually with a caliper. Imaging results were correlated with histopathology. In the results, the tumor size was not significantly different in the treatment groups when compared to the control group on day 2 after therapy onset (P = 0.09). In contrast the imaging modalities DWI, DCE-MRI and FDG-PET showed significant differences between the therapeutic compared to the control group as early as 2 days after therapy onset (P<0.001). There was a strong correlation of the early changes in DWI, DCE-MRI and FDG-PET at day 2 after therapy onset and the change in tumor size at the end of therapy (r = −0.58, 0.71 and 0.67 respectively). The imaging results were confirmed by histopathology, showing early necrosis and necroptosis in the tumors. Thus multimodality multiparametric imaging was able to predict therapeutic success of PRS-050-PEG40 and Avastin as early as 2 days after onset of therapy and thus promising for monitoring early response of antiangiogenic therapy.     

Albumin-based Theranostic Nanosystem for Drug Controlled Release and Magnetic Resonance Imaging Guided Therapy

Chemotherapy is still a kind of important strategy for cancer treatment,but lacking effective delivery system limits the therapeutic outcome.Owing to the excell...     

磁共振波谱成像结合扩散加权成像在脑胶质瘤及脑转移瘤鉴别诊断中的意义

目的:评估磁共振波谱成像(Proton Magnetic Resonance Spectroscopy,1H-MRS)联合磁共振扩散加权成像(Diffusion Weighted Imaging,DWI)在鉴别脑胶质瘤及孤立的脑转移瘤中的作用。方法:应用3.0T磁共振扫描仪,对临床手术确诊及组织病理学诊断证实的49例脑肿瘤患者(35例多形性胶质母细胞瘤,14例脑转移瘤)进行常规磁共振成像、磁共振波谱成像及磁共振扩散加权成像,并并对获得的数据进一步测量瘤内及瘤周区的代谢比、N-乙酰天门冬氨酸(NAA)、胆碱(Cho)、肌酸(Cr)值以及表观弥散系数(ADC值),分析两肿瘤组之间不同参数的统计学差异。此外,我们研究了感兴趣区域(ROI)的大小对肿瘤区域的病变扩散性能潜在影响。结果:胶质母细胞瘤瘤周N-乙酰天门冬氨酸(NAA)、肌酸(Cr),胆碱(Cho)/Cr,Cho/NAA和r CBV显著高于颅内转移瘤(P0.05);ADC值在两肿瘤组之间无显著差异(P0.05)。结论:在瘤周区1H-MRS有助于鉴别胶质母细胞瘤与单发的脑转移瘤。在瘤内扩散性的定量特性依赖ROI大小的设置。     

Quantitative 3D Analysis of Plant Roots Growing in Soil Using Magnetic Resonance Imaging

Precise measurements of root system architecture traits are an important requirement for plant phenotyping. Most of the current methods for analyzing root growth require either artificial growing conditions (e.g. hydroponics), are severely restricted in the fraction of roots detectable (e.g. rhizotrons), or are destructive (e.g. soil coring). On the other hand, modalities such as magnetic resonance imaging (MRI) are noninvasive and allow high-quality three-dimensional imaging of roots in soil. Here, we present a plant root imaging and analysis pipeline using MRI together with an advanced image visualization and analysis software toolbox named NMRooting. Pots up to 117 mm in diameter and 800 mm in height can be measured with the 4.7 T MRI instrument used here. For 1.5 l pots (81 mm diameter, 300 mm high), a fully automated system was developed enabling measurement of up to 18 pots per day. The most important root traits that can be nondestructively monitored over time are root mass, length, diameter, tip number, and growth angles (in two-dimensional polar coordinates) and spatial distribution. Various validation measurements for these traits were performed, showing that roots down to a diameter range between 200 μm and 300 μm can be quantitatively measured. Root fresh weight correlates linearly with root mass determined by MRI. We demonstrate the capabilities of MRI and the dedicated imaging pipeline in experimental series performed on soil-grown maize (Zea mays) and barley (Hordeum vulgare) plants.The root system is of critical importance for the survival, development, and performance of higher plants, because it is the major organ for anchorage, acquisition of water and nutrients, and carbon storage. Therefore, there is a long-standing interest in the scientific community regarding the structure, function, and development of root systems. Rising concerns about the environmental impact and increasing cost of fertilizers have initiated breeding programs for more resource-efficient cultivars and the development of methods for phenotyping root systems. The opaque nature of soils generally demands destructive methods such as root excavation for subsequent optical assessment (Lynch, 2007; Trachsel et al., 2011). Although efficient for screening large numbers of plants for a limited set of clearly discernible traits, this approach does not allow detailed monitoring of root development over time. Other approaches, such as rhizotrons or mini-rhizotron tubes, where root growth is observed along transparent windows (Nagel et al., 2009), monitor only a fraction of the roots. Methods in which the whole root system is visible are typically based on artificial media such as paper pouches (Chen et al., 2011; Le Marié et al., 2014), three-dimensional (3D) gels (Iyer-Pascuzzi et al., 2010), and hydro- or aeroponics (Herdel et al., 2001). Results may thus not be directly transferable to plants grown in natural 3D soil environments (Gregory et al., 2003). For example, roots are known to grow faster and thinner when the penetration resistance is low (Bengough et al., 2011; Chimungu et al., 2015). Computed tomography (CT; both x-ray and neutron) has been proposed to overcome the mentioned difficulties with studying roots in natural soil. CT has been successfully used to obtain high-resolution images of roots (Moradi et al., 2009; Flavel et al., 2012; Mooney et al., 2012). High resolution is necessary for segmenting roots due to a poor contrast between roots and soil (Jassogne et al., 2009; Mairhofer et al., 2012; Mairhofer et al., 2013). A first direct comparison (to our knowledge) of magnetic resonance imaging (MRI) and x-ray CT for 3D root imaging has recently been published (Metzner et al., 2015), showing that the two modalities pose different opportunities and limitations for root imaging.MRI is based on the magnetic moment of atomic nuclei like ¹H (protons), which are highly abundant in living tissues, mainly in water molecules. The magnetic moment can be manipulated using strong magnetic and radio frequency fields that have no known impact on plant development to produce 3D datasets of samples. MRI offers several contrast parameters that can be manipulated for discriminating different structures such as roots from soil background (Rogers and Bottomley, 1987; Jahnke et al., 2009). The basic principles of MRI are described in detail in several textbooks (Callaghan, 1993; Haacke et al., 1999) or review articles (Köckenberger et al., 2004; Blümler et al., 2009; van As et al., 2009; Borisjuk et al., 2012). Research applications to plant roots range from phytopathology (Hillnhütter et al., 2012), across storage root internal structures (Metzner et al., 2014) and water uptake modeling (Stingaciu et al., 2013), to coregistration with positron emission tomography for investigating structure-function relations (Jahnke et al., 2009). Water mobility in roots and soil has also been shown to be detectable with MRI (MacFall and Johnson, 2012; Gruwel, 2014). In particular for imaging roots with MRI, these studies generally explored the applicability of MRI but largely lacked validation of the data against conventional techniques of root visualization after harvest. Our goal was to develop MRI protocols to image roots of plants growing in soil to obtain global root parameters such as root length, mass, or root diameters; gather root growth angles and number of root tips; get spatial information on the distribution of root system architecture (RSA) parameters such as root length densities; and, wherever possible, verify these parameters against harvest data.