Preclinical MRI of the Kidney: Methods and Protocols

Description

This Open Access volume provides readers with an open access protocol collection and wide-ranging recommendations for preclinical renal MRI used in translational research. The chapters in this book are interdisciplinary in nature and bridge the gaps between physics, physiology, and medicine. They are designed to enhance training in renal MRI sciences and improve the reproducibility of renal imaging research. Chapters provide guidance for exploring, using and developing small animal renal MRI in your laboratory as a unique tool for advanced in vivo phenotyping, diagnostic imaging, and research into potential new therapies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Preclinical MRI of the Kidney: Methods and Protocols is a valuable resource and will be of importance to anyone interested in the preclinical aspect of renal and cardiorenal diseases in the fields of physiology, nephrology, radiology, and cardiology. This publication is based upon work from COST Action PARENCHIMA, supported by European Cooperation in Science and Technology (COST). COST (www.cost.eu) is a funding agency for research and innovation networks. COST Actions help connect research initiatives across Europe and enable scientists to grow their ideas by sharing them with their peers. This boosts their research, career and innovation. PARENCHIMA (renalmri.org) is a community-driven Action in the COST program of the European Union, which unites more than 200 experts in renal MRI from 30 countries with the aim to improve the reproducibility and standardization of renal MRI biomarkers. Preface Preclinical MRI for Renal Health Contents Contributors Part I: Introduction Chapter 1: Recommendations for Preclinical Renal MRI: A Comprehensive Open-Access Protocol Collection to Improve Training, Rep... 1 Who Is Pulling the Brakes in Renal MRI? 1.1 Renal MRI in Clinical Practice-Fantasy, Dream, or Reality? 1.2 Renal MRI, Where Are You? 1.3 Function, Function, Function 1.4 Research Activity in Renal MRI 1.5 The Usual Suspects 2 How Can Training and Standardization Be Improved? 2.1 A Roadmap for Improved Training and Standardization of Renal MRI 2.2 Driving on the Road to more Efficient Renal MRI Research: Are We There Yet? 3 The Springer Protocols Book on Preclinical Renal MRI 3.1 Concept and Special Features of the Book 3.1.1 Provide all the Necessary Information for each Method 3.1.2 Generalize Protocols by Peer Review 3.1.3 Avoid Magic Numbers 3.1.4 Describe the Pragmatic Way for Data Analyses 3.1.5 Prevent Tunnel Vision-A Successful Study Needs More Than an MRI Protocol 3.1.6 Embrace Competition-There Are Other Great Techniques Besides MRI 3.1.7 Make Access to This Information Free of Charge 3.2 Content of the Book 3.2.1 Part I-Introduction 3.2.2 Part II-Animal Models, Preparation, Monitoring, and Physiological Interventions 3.2.3 Part III-Basic Concepts of Measurement Techniques 3.2.4 Part IV-Experimental Protocols 3.2.5 Part V-Protocols for Advanced Analyses 3.3 Mission and Vision 4 Notes References Part II: Animal Models, Preparation, Monitoring, and Physiological Interventions Chapter 2: Animal Models of Renal Pathophysiology and Disease 1 Introduction 2 Ethical Issues 3 General Guidelines for Choosing an Animal Model 3.1 Rat or Mouse? 3.2 Which Strain? 3.3 Sex 3.4 Other Species 4 Models of AKI 4.1 Ischemia-Reperfusion Injury 4.2 Renal Transplantation 4.3 Sepsis-Induced AKI 4.4 Toxin-Induced AKI 4.4.1 Cisplatin 4.4.2 Contrast-Induced AKI (CIAKI) 4.4.3 Aristolochic Acid and Folic Acid 4.4.4 Glycerol 5 Models of CKD 5.1 Unilateral Ureteral Obstruction (UUO) 5.2 5/6 Nephrectomy 5.3 Models of DKD 5.4 Models of Polycystic Kidney Disease 5.5 Models of Hypertension 5.5.1 Spontaneously Hypertensive Rats (SHR) 5.5.2 Deoxycorticosterone Acetate (DOCA)-Salt Hypertension 5.6 Podocyte Injury Models 6 Humanized Mouse Models References Chapter 3: Preparation and Monitoring of Small Animals in Renal MRI 1 Introduction 2 Hydration 3 Anesthesia 3.1 Injectable Anesthetics 3.2 Inhalable Anesthetics 4 Physiological Monitoring 4.1 Body Temperature 4.2 Respiration 4.3 Cardiovascular System 5 Recovery 5.1 Analgesia 5.2 Antibiotics References Chapter 4: Reversible (Patho)Physiologically Relevant Test Interventions: Rationale and Examples 1 Introduction 2 Specifics of Renal Hemodynamics and Oxygenation 3 Dedicated Reversible Test Interventions 3.1 Short Periods of Occlusion of the Renal Artery or Renal Vein 3.2 Servocontrolled Changes in Renal Arterial Pressure 3.3 Short Periods of Changes in the Inspiratory Gas Mixture 3.4 Administration of Drugs and Endogenous Vasoactive Substances References Chapter 5: Preparation of Ex Vivo Rodent Phantoms for Developing, Testing, and Training MR Imaging of the Kidney and Other Org... 1 Introduction 2 Materials 2.1 Animals 2.2 Perfusion and Dissection 2.3 Latex Covering 3 Methods 3.1 Perfusion and Fixation 3.2 Disarticulation 3.3 Coating with Gauze and Latex 4 Example Images 4.1 Rat 4.2 Mouse 5 Notes References Part III: Basic Concepts of Measurement Techniques Chapter 6: Quantitative Assessment of Renal Perfusion and Oxygenation by Invasive Probes: Basic Concepts 1 Introduction 2 Heterogeneity of Intrarenal Perfusion and Oxygenation-Causes and Degree of Variability 3 Methods: Methodologic Principles, Advantages, and Disadvantages 3.1 Transonic Flow Probes 3.2 Laser-Doppler Optodes 3.3 Clark-Type Electrodes 3.4 Fluorescence-Quenching Optodes 3.5 Monitoring of Arterial Blood Pressure 3.6 Pimonidazole Adduct Immunohistochemistry 3.7 Examples of Methods That Are Not Generally Available 3.7.1 Bladder pO2 3.7.2 Near Infrared Spectroscopy 3.7.3 Intravital Microscopy References Chapter 7: Ultrasound and Photoacoustic Imaging of the Kidney: Basic Concepts and Protocols 1 Introduction 2 Measurement Concepts of Ultrasound and Photoacoustics 3 Overview of Applications 3.1 Evaluating Kidney Size and Anatomy 3.2 Visualization of Blood Flow 3.3 Perfusion Imaging 3.4 Molecular Information 3.5 Interventional Procedures 4 Protocols 4.1 Standard Renal Exam 4.2 Perfusion Studies 4.3 Photoacoustic Exam to Monitor Oxygen Saturation 4.4 Image Guided Needle Injections 4.5 Analysis References Chapter 8: Hardware Considerations for Preclinical Magnetic Resonance of the Kidney 1 Introduction 2 Static Magnetic Field Strength (B0) 2.1 SNR Comparison for Magnetic Field Strength 2.2 Magnetic Field Strengths Used in Recently Published Studies 3 Gradient Systems 4 Radio Frequency (RF) Coils 4.1 Commercially Available RF Coils Suitable for Kidney MRI in Rats 4.2 Commercially Available RF Coils Suitable for Kidney MRI in Mice 5 Multinuclear Imaging 6 Physiological Monitoring 7 Practical Points to Consider When Planning a Study 7.1 MRI System 7.1.1 Clinical or Preclinical? 7.1.2 Should I Consider Moving to a High Magnetic Field Strength? 7.1.3 Higher Magnetic Fields Are All Rainbows and Unicorns, and Should Always Be Used, Right? 7.1.4 OK, But ... Which B0 Is Everyone Else Using? 7.1.5 What About the Gradient System? 7.2 RF Coil Setup 7.2.1 Which Kind of RF Coil Should I Use to Get the Most Juice from My Clinical MR Scanner? 7.2.2 Which RF Coil Setups Are the Most Suitable for Renal Applications in My Preclinical MR Scanner? 7.3 X-Nuclei 7.3.1 What If I Want to Perform X-Nuclei MRI/MRS? 7.4 Animal Handling and Physiological Monitoring 7.4.1 How Should I Position the Rodent in the Animal Bed Prior to the Experiment? 7.4.2 What Is the Essential Physiological Monitoring that Should Be Performed During Small-Animal Renal MR Experiments? 7.4.3 What Other Physiological Parameters Can I Measure, and Which Equipment Should I Use? 7.5 Image Acquisition 7.5.1 Should I Perform B0 Shimming in Every MR Study? 7.5.2 Should I Always Do Triggering of the Signal? What Are my Options? 8 Notes References Chapter 9: MRI Mapping of Renal T1: Basic Concept 1 Introduction 2 Measurement Concept 2.1 Basic Concept of T1 Mapping 2.2 Overview of T1 Mapping Techniques 2.2.1 The Saturation Recovery or VTR Method 2.2.2 The VFA Method 2.2.3 The Look-Locker Modified IR Method 2.2.4 The PD Method 2.2.5 MR Fingerprinting 3 Overview of Applications on Preclinical and Clinical MR Instruments References Chapter 10: MRI Mapping of the Blood Oxygenation Sensitive Parameter T2* in the Kidney: Basic Concept 1 Introduction 2 Measurement Concept 2.1 Basic Concept of BOLD Contrast 2.2 BOLD MRI Acquisition Methods and Strategies for Kidney Oxygenation Measurement in Rodents 2.3 Limitations of BOLD MRI for Absolute pO2 Measurement 2.3.1 R2′ Measurement 2.4 Considerations Regarding Animal Preparation 3 Overview of Preclinical Applications 3.1 Application to Disease Models References Chapter 11: Renal Diffusion-Weighted Imaging (DWI) for Apparent Diffusion Coefficient (ADC), Intravoxel Incoherent Motion (IVI... 1 Introduction 2 Diffusion Weighted Imaging Concepts 2.1 Fundamental Concept 2.2 Water Motion and Relation to Microstructure 3 Diffusion Modeling 3.1 Monoexponential Apparent Diffusion Coefficient (ADC) 3.2 Intravoxel Incoherent Motion (IVIM) 3.3 Diffusion Tensor Imaging (DTI) 4 Diffusion Imaging in the Kidney 5 Diffusion Acquisition Considerations 6 Notes References Chapter 12: Dynamic Contrast Enhancement (DCE) MRI-Derived Renal Perfusion and Filtration: Basic Concepts 1 Introduction 2 Measurement Concept 2.1 Basic Concept of DCE 2.2 Gadolinium-Based Contrast Agents 2.3 Conversion of Signal into Contrast Agent Concentration 2.4 Imaging Readout 2.4.1 Gradient-Echo 2.4.2 Echo-Planar Imaging 2.4.3 Keyhole Imaging 2.5 T1 Mapping 2.5.1 Saturation Recovery 2.5.2 Inversion Recovery 2.5.3 Variable Flip Angle (VFA) 2.6 Renal Handling of Contrast Agents 2.7 Analysis Methods 2.7.1 Semiquantitative Analysis 2.7.2 Quantitative-Pharmacokinetic Models 2.7.3 Model Selection 2.7.4 Bayesian Probability Theory 2.8 Practical Considerations 3 Overview of Applications 3.1 DCE-MRI Validation Studies in Animal Models 3.2 DCE-MRI for Assessing Kidney Damages in Animal Models References Chapter 13: Noninvasive Renal Perfusion Measurement Using Arterial Spin Labeling (ASL) MRI: Basic Concept 1 Introduction 2 Measurement Concept 2.1 Basic Concept of ASL-MRI 2.2 Labeling Methods and Strategies for Kidney perfusion Measurement in Rodents 2.2.1 Pulsed ASL (PASL) 2.2.2 Continuous ASL (CASL) and Pseudo-Continuous ASL (pCASL) 2.3 Imaging Readout 3 Overview of Applications 3.1 ASL for Measuring Kidney Perfusion in Animal Models References Chapter 14: Renal pH Imaging Using Chemical Exchange Saturation Transfer (CEST) MRI: Basic Concept 1 Introduction 2 Measurement Concept 2.1 Basic Concept of Chemical Exchange Saturation Transfer (CEST) Imaging 2.2 CEST Contrast Agents for Imaging Kidneys and Mapping pH 2.2.1 Diamagnetic CEST Agents 2.2.2 Paramagnetic CEST Agents 2.3 Imaging Readout 2.3.1 Rapid Imaging with Refocused Echoes (RARE) 2.3.2 Fast Imaging with Steady-State Precession (FISP) 2.3.3 Spin-Echo Echo Planar Imaging (EPI) 3 Overview of Applications 3.1 Endogenous CEST Methods for Assessing Renal Diseases 3.2 CEST pH Imaging for Assessing Renal Diseases 3.3 GlucoCEST Imaging for Assessing Renal Diseases References Chapter 15: Sodium (23Na) MRI of the Kidney: Basic Concept 1 Introduction 2 Measurement Concept 2.1 Basic Concept of Sodium Imaging 2.2 Sodium Imaging Methods 2.2.1 Sodium MRI Hardware 2.2.2 Total Sodium Imaging 2.2.3 Triple Quantum Filtering (TQF) 2.2.4 Inversion Recovery 2.2.5 T2* Mapping 2.3 Imaging Readout 2.3.1 3D Cartesian Imaging 2.3.2 Ultrashort Echo Time (UTE) Imaging 2.4 Reconstruction 2.5 Sodium Phantoms 2.6 Segmentation 3 Overview of Applications 3.1 Total sodium Imaging for Assessing Alterations in the Corticomedullary sodium Gradient 3.2 Potential Future Applications of sodium Imaging 3.3 Acute Kidney Disease 3.4 Chronic Kidney Disease 4 Notes References Chapter 16: Hyperpolarized Carbon (13C) MRI of the Kidneys: Basic Concept 1 Introduction 2 Measurement Concept 2.1 Basic Concept of HP 13C MRI 2.2 Renal Functional and Metabolic Investigations Using HP 13C MRI 2.2.1 [13C]Urea 2.2.2 [1-13C]Pyruvate 2.2.3 [1,4-13C2]Fumarate 2.2.4 [1-13C]Dehydroascorbate 2.2.5 [13C]Acetoacetate 3 Overview of Applications 3.1 Kidney Cancer 3.2 Diabetic Nephropathy 3.3 Ischemic Kidney Injury 4 Notes References Chapter 17: Functional Imaging Using Fluorine (19F) MR Methods: Basic Concepts 1 Introduction 2 Overview of Applications 2.1 19F MRI to Study Environmental Changes in the Kidney In Vivo 2.1.1 Renal Tissue Oxygenation 2.1.2 Acid-Base Homeostasis in the Kidney and pH Sensors 2.2 19F MRI to Study Renal Inflammation In Vivo 3 Basic Concepts of 19F MRI 3.1 19F imaging Probes 3.1.1 19F Probes for Cellular Uptake 3.1.2 19F Probes with Increased Signal Sensitivity 3.2 MR Data Acquisition 3.2.1 Pulse Sequence Optimization 3.3 Hardware Considerations 3.3.1 Cryogenic Cooling 3.3.2 Magnetic Field Strengths References Chapter 18: MR Elastography of the Abdomen: Basic Concepts 1 Introduction 2 Measurement Concept 2.1 Basic Concept of Stiffness Measured Using MRE 2.2 Generating Propagating Shear Waves 2.3 Pulse Sequence for MRE Motion Encoding 3 Applications of MRE to the Abdomen 3.1 MRE for Evaluation of Liver Fibrosis 3.2 MRE for Evaluation of Liver Tumors 3.3 MRE of the Spleen for Evaluation of Portal Hypertension 3.4 MRE of the Kidney 3.5 MRE of the Pancreas 3.6 Other MRE Body Applications 4 Influence of Perfusion on Abdominal Organs 4.1 Post-prandial Influence on Liver Stiffness 4.2 Influence of Hydration on Renal Stiffness 4.3 Stenotic Kidney MRE 5 Preclinical MRE 5.1 Considerations Regarding Animal Preparation 6 Conclusion References Part IV: Experimental Protocols Chapter 19: Monitoring Renal Hemodynamics and Oxygenation by Invasive Probes: Experimental Protocol 1 Introduction 2 Materials 2.1 Animals 2.2 Surgical Preparation 2.3 Magnetic Resonance Imaging (for MR-PHYSIOL) 2.4 Test Interventions 3 Methods 3.1 Surgical Preparation 3.2 Setting Up Animal for MR-PHYSIOL Examination 3.3 Experimental Procedures 3.4 End of Experiment 3.5 Data Analysis 4 Notes References Chapter 20: Essential Practical Steps for MRI of the Kidney in Experimental Research 1 Introduction 2 Materials 2.1 Animals 2.2 Lab Equipment 2.3 MRI Hardware 2.4 MRI Techniques 3 Methods 3.1 MR Protocol Setup 3.1.1 Multislice Tripilot Scan (R01_TriPilotmulti) 3.1.2 Axial Multislice Pilot Scan 3.1.3 Coronal Pilot Scan 3.1.4 Abdominal Time-of-Flight (TOF) Angiography 3.1.5 Kidney TOF-Angiography 3.2 Animal Preparation 3.3 Pilot Scans and Slice Positioning Coronal to tthe Kidney 3.3.1 Slice Planning: From Pilot Scan to the Coronal-to-the-Kidney Image 3.3.2 Transferring the Coronal-to-the-Kidney Geometry to Other Scans 3.3.3 Reducing Aortic Flow Artifacts (Optional) 3.3.4 Multislice and Covering Both Kidneys (Optional) 3.4 Localized Shimming 3.4.1 Planning the Shim Volume (Bruker ParaVision) 3.4.2 Shimming (Bruker ParaVision) 3.4.3 Shimming on a Clinical MR System (Siemens Syngo) 3.5 Fast and Simple Test of Renal Blood Flow (Optional) 3.5.1 Measurement Concept 3.5.2 Protocol 4 Notes Chapter 21: Assessment of Renal Volume with MRI: Experimental Protocol 1 Introduction 2 Materials 2.1 Animals 2.2 Lab Equipment 2.3 MRI Hardware 2.4 MRI Protocols 2.5 Image Analysis Tools 3 Methods 3.1 MR Protocol Setup 3.1.1 Multislice Multiecho Sequence for T2 Imaging 3.2 In Vivo MR Imaging 3.2.1 Scanner Adjustments and Anatomical Imaging 3.2.2 Morphometric MR Imaging 4 Notes References Chapter 22: Experimental Protocols for MRI Mapping of Renal T1 1 Introduction 1.1 Motivation for Measuring T1 in Animal Kidneys 1.2 Study Design Concepts 1.3 Data Quality 2 General Considerations 2.1 Magnetic Field Strengths 2.2 Physiologic Motion 3 Imaging Techniques 3.1 RARE-VTR 3.1.1 Protocol Description 3.1.2 Repetition Times 3.2 Recovery Techniques: Look-Locker and Derivatives 3.2.1 Protocol Description 3.2.2 Types of Readouts, and Corresponding Specific Points of Attention 3.2.3 Duration of Imaging Readouts 3.2.4 Number of Imaging Readouts 3.2.5 Repetition Time 3.2.6 Inversion Pulses 3.3 Variable Flip Angle Techniques 4 Methods 4.1 MR Protocol Setup 4.1.1 2D RARE VTR in Bruker ParaVision 6 4.1.2 Inversion Recovery Sequence in Bruker ParaVision 6 4.1.3 Modified Look-Locker Inversion Recovery (MOLLI) Sequence for Rats on a Siemens Clinical Scanner 4.2 Calibrated Phantom Acquisitions 4.3 Animal Experiments (Dedicated Small Animal MR Systems) References Chapter 23: Experimental Protocol for MRI Mapping of the Blood Oxygenation-Sensitive Parameters T2* and T2 in the Kidney 1 Introduction 2 Materials 2.1 Animals 2.2 Lab Equipment 2.3 MRI Hardware 2.4 MRI Techniques 3 Methods 3.1 MR Protocol Setup 3.1.1 Multi-gradient-Echo Sequence for T2*-Mapping 3.1.2 Multi-spin-Echo Sequence for T2-Mapping (Optional) 3.1.3 Field Map (Optional) 3.2 In Vivo Blood Oxygenation Sensitive Imaging 3.2.1 Animal Preparation 3.2.2 Scanner Adjustments and Anatomical Imaging 3.2.3 Baseline Condition 3.2.4 Hypoxia/Hyperoxia for Benchmarking (optional) 3.2.5 Noise Scan 4 Notes Reference Chapter 24: Renal MRI Diffusion: Experimental Protocol 1 Introduction 2 Materials 2.1 Animals 2.2 Lab Equipment and Chemicals 2.3 MRI Hardware 2.4 MRI Techniques 3 Methods 3.1 MR Protocol Setup 3.1.1 DW-EPI for ADC 3.1.2 DW-EPI for IVIM 3.2 In Vivo DWI 3.2.1 Animal Preparation 3.2.2 Scanner Adjustments and Anatomical Imaging 3.2.3 Baseline Condition 4 Notes References Chapter 25: Dynamic Contrast Enhanced (DCE) MRI-Derived Renal Perfusion and Filtration: Experimental Protocol 1 Introduction 2 Materials 2.1 Animals 2.2 Lab Equipment and Chemicals 2.3 MRI Hardware 2.4 MRI Techniques 3 Methods 3.1 MR Protocol Setup 3.1.1 Variable Repetition Time (VTR) Acquisition for T1 Mapping 3.1.2 Variable Flip Angle (VFA) Acquisition for T1 Mapping 3.1.3 Fast Low Angle Shot (FLASH) T1-Weighted Sequence for DCE-MRI Experiments 3.2 Preparations of the Contrast Agent Injection and of the Catheter 3.3 Preparations of the Mouse 3.4 In Vivo T1 Mapping 3.4.1 DCE-MRI Experiment 4 Notes References Chapter 26: Renal Blood Flow Using Arterial Spin Labeling (ASL) MRI: Experimental Protocol and Principles 1 Introduction 2 Materials 2.1 Animals 2.2 Lab Equipment 2.3 MRI Hardware 2.4 MRI Sequences 3 Methods 3.1 Animal Preparations and Initial Setups for Imaging 3.2 Renal Perfusion Imaging 3.2.1 Baseline Condition (Healthy Animal) 3.2.2 Hypoxia/Hyperoxia/Hypercapnia for Benchmarking (Optional) 3.2.3 Perfusion Map 4 Notes References Chapter 27: Renal pH Mapping Using Chemical Exchange Saturation Transfer (CEST) MRI: Experimental Protocol 1 Introduction 2 Materials 2.1 Animals 2.2 Lab Equipment and Chemicals 2.3 MRI Hardware 2.4 MRI Sequences 3 Methods 3.1 MR Protocol Setup 3.1.1 Rapid Acquisition with Refocused Echoes Sequence for External B0 Mapping Using WASSR 3.1.2 Full Z-Spectrum Acquisition for CEST-pH Mapping 3.1.3 Rapid Acquisition with Refocused Echoes Sequence for CEST pH and Perfusion Measurements 3.2 Setting of the pH Calibration Curve 3.3 Preparations of the Contrast Agent Injection and of the Catheter 3.4 Preparation of the Mouse 3.5 B0 Mapping 3.5.1 External B0 Mapping 3.5.2 Internal B0 Mapping 3.6 CEST Acquisition for pH Mapping 3.6.1 pH Mapping with Conventional Ratiometric Method (Full Z-Spectrum) 3.6.2 pH Mapping with Power Ratiometric Method (Full Z-Spectrum) 3.6.3 pH and Perfusion Mapping with Two Offset Sampling 4 Notes References Chapter 28: Sodium (23Na) MRI of the Kidney: Experimental Protocol 1 Introduction 2 Materials 2.1 Calibration Phantom Preparation: Rodent 2.1.1 Lab Equipment and Components 2.1.2 Process to Make 4% Agarose Phantoms (Example 60 and 150 mmol/L Phantoms) 2.2 Animals 2.3 Lab Equipment 2.4 MRI Hardware 3 Methods 3.1 MR Protocol Setup 3.1.1 Total Sodium Imaging (BRUKER) 3.1.2 Total Sodium Imaging (General Electric) 3.1.3 Mapping (BRUKER) 3.1.4 Total Sodium Imaging Agilent) 3.1.5 Calibration Scans 3.2 In Vivo Sodium Imaging 3.2.1 Preparations 3.2.2 Baseline Condition 3.2.3 Imaging Furosemide Action 3.2.4 Mapping 4 Notes References Chapter 29: Hyperpolarized Carbon (13C) MRI of the Kidney: Experimental Protocol 1 Introduction 2 Materials 2.1 Animals 2.2 Lab Equipment 2.3 MRI Hardware 3 Methods 3.1 MRI Protocol Setup 3.1.1 Prescan 3.1.2 2D/3D Slice Selective Chemical Shift Imaging (CSI) 3.1.3 2D/3D Echo-Planar Spectroscopic Imaging (EPSI) 3.1.4 Multi-echo Gradient-Echo Sequence for IDEAL Mapping 3.1.5 Spectral-Spatial Imaging 3.1.6 Perfusion Imaging 3.2 In Vivo 13C MR 3.2.1 Preparations 3.2.2 Hyperpolarized 13C Metabolic and Functional Imaging 3.3 Emerging Sequences 4 Notes References Chapter 30: Fluorine (19F) MRI for Assessing Inflammatory Cells in the Kidney: Experimental Protocol 1 Introduction 2 Materials 2.1 Animals 2.1.1 Lab Equipment 2.2 MRI Hardware 2.3 MRI Techniques 3 Methods 3.1 MR Protocol Setup 3.1.1 19F MR Imaging 3.2 19F Nanoparticle Preparation, Characterization, and Application 3.3 Preparation Prior to 19F/1H MRI Scans 3.4 19F/1H MRI of the Kidney 3.4.1 In Vivo 19F/1H MRI Using a Room Temperature Mouse Body Volume 19F/1H RF Resonator 3.4.2 High Spatial Resolution 19F MRI of Ex Vivo Kidney Using a 19F CryoProbe 4 Notes References Chapter 31: Fluorine (19F) MRI to Measure Renal Oxygen Tension and Blood Volume: Experimental Protocol 1 Introduction 2 Materials 2.1 Animals 2.2 Lab Equipment 2.3 MRI Hardware 2.4 MRI Techniques 3 Methods 3.1 PFC Nanoparticle Formulation 3.2 PFC NP Injection and Imaging 3.3 Coil Sensitivity Profiling for Quantification of 19F Signal Intensity 3.4 Calibration of 19F R1 vs. pO2 Curve In Vitro 3.5 Quantification of 19F Based pO2 Measurement In Vivo 4 Notes References Chapter 32: MR Elastography of the Abdomen: Experimental Protocols 1 Introduction 1.1 Magnetic Resonance Elastography 1.2 Modulus of Elasticity 1.3 Need for Preclinical MRE 1.4 Quest for Renal MRE 2 Materials 2.1 Animals 2.2 Lab Equipment 2.3 MRI Hardware 2.3.1 Generating Propagating Shear Waves in the Abdomen: Hardware 2.3.2 Pulse Sequence for MRE Motion Encoding: Software 2.4 Image Postprocessing: Generating Elastograms for Stiffness Estimation 2.5 Periodic Quality Assurance (QA) 3 Methods 3.1 Animal Setup on the Scanner 3.2 Scanner Adjustments and Anatomical Imaging 3.3 MRE Imaging 3.4 Image Review to Ensure Technical Success 3.5 Color Display of Images 3.6 Drawing Regions of Interest to Measure Stiffness 3.7 Image Interpretation 3.8 Role of Preclinical MRE 3.9 Application to Renal Disease Models References Part V: Protocols for Advanced Analyses Chapter 33: Subsegmentation of the Kidney in Experimental MR Images Using Morphology-Based Regions-of-Interest or Multiple-Lay... 1 Introduction 2 Materials 2.1 Software Requirements 2.1.1 Essential Tools 2.1.2 Toolboxes 2.1.3 Software 2.2 Source Data: Format Requirements 2.2.1 Imaging Planes 2.2.2 Input Requirements 3 Methods 3.1 Segmentation of Morphology-Based Renal Regions-of-Interest (SOMBRERO) 3.1.1 Settings 3.1.2 Loading Images 3.1.3 Definition of Bounding Box 3.1.4 Diagonal Boundary Selection 3.1.5 Generation of Mask for Imaging Series 3.1.6 Saving Mask 3.1.7 Loading Mask 3.2 Multilayer Concentric Objects (MLCO) Segmentation 3.2.1 Load an Image or a List of Images in a Matlab Array 3.2.2 Defining the Number of Layers 3.2.3 Segmenting the Area of Your Choice in the Image 3.2.4 Build the List of Masks That Realizes the Concentric Object Technique 3.2.5 Basic Script for Applying the Concentric Object Technique 3.2.6 Exclusion of Regions 4 Notes References Chapter 34: Denoising for Improved Parametric MRI of the Kidney: Protocol for Nonlocal Means Filtering 1 Introduction 2 Materials 2.1 Software Requirements 2.2 Data Requirements 3 Methods 3.1 Data Import 3.1.1 DICOM Data 3.1.2 Bruker Data 3.2 Correct Data Scaling 3.3 Noise Level Estimation 3.4 Application of the NLM Filter 3.4.1 Filtering of Individual Echoes with 2D-NLM 3.4.2 Filtering Using stackNLM 3.4.3 Filtering Using MATLAB´s Imnlmfilt 3.5 Bias Correction 4 Notes References Chapter 35: Analysis Protocols for MRI Mapping of Renal T1 1 Introduction 2 Materials 2.1 Software Requirements 2.2 Source Data: Format Requirements and Quality Check 2.2.1 Input Requirements 2.2.2 Physiologic Motion Check 2.2.3 Acquisition Geometry Check 2.2.4 Acquisition Parameters Consistency Check (Multiple Scans Case Only) 2.2.5 Receiver Gain Consistency Check (Multiple Scans Case Only) 2.2.6 Data Intensity Scaling Consistency Check (Multiple Scans Case Only) 3 Methods 3.1 Data Exclusion 3.2 Data Coregistration 3.3 Model Fitting 3.3.1 Fitting Data for Saturation Recovery Experiments 3.3.2 Fitting Data for Inversion Recovery Experiments 3.3.3 Fitting Data for Variable Flip Angle Experiments 3.4 Visual Display 3.5 Quantification 3.6 Results Validation 3.6.1 Evaluation of Analysis Errors and Variability Using Synthetic Data 3.6.2 Comparison with Reference Values from the Literature 4 Notes References Chapter 36: Analysis Protocols for MRI Mapping of the Blood Oxygenation-Sensitive Parameters T2* and T2 in the Kidney 1 Introduction 2 Materials 2.1 Software Requirements 2.1.1 Essential Tools 2.1.2 Optional Tools 2.2 Source Data: Format Requirements and Quality Check 2.2.1 Input Requirements 2.2.2 Open/Import Images 2.2.3 Motion Artifacts Check 2.2.4 Susceptibility Artifacts Check on T2*-Weighted Images 2.2.5 Signal-to-Noise Ratio Check 3 Methods 3.1 Data Exclusion and Model Fitting (Siemens Syngo) 3.2 Model Fitting (General Electric T2(*) Map Ready View) 3.3 Model Fitting (Philips) 3.4 Data Preparation and Model Fitting (Custom Program) 3.4.1 Data Import and Exclusion of First TE (Only for T2) 3.4.2 Rician Noise Bias Correction 3.4.3 Fitting Model 3.4.4 Starting Values 3.4.5 Fitting Algorithm 3.4.6 Visual Display 3.5 Quantification 3.6 Methods for Result Validation 3.6.1 Evaluation of Analysis Errors and Variability Using Synthetic Data 3.6.2 Comparison with Reference Values from the Literature 4 Notes References Chapter 37: Analysis of Renal Diffusion-Weighted Imaging (DWI) Using Apparent Diffusion Coefficient (ADC) and Intravoxel Incoh... 1 Introduction 2 Materials 2.1 Data Format and Quality 2.2 Software Requirements 2.3 Fitting Algorithms, Limits, and Initialization 3 Methods 3.1 Generalized Steps for Diffusion-Weighted Image Processing 3.2 Diffusion Weighted Imaging: Apparent Diffusion Coefficient (ADC) 3.2.1 Preparation of Image Data for Fitting 3.2.2 Least Squares Fitting for Apparent Diffusion Coefficient ADC 3.2.3 Extraction of Parameter Results 3.2.4 Linear Regression and Matrix Inversion for ADC 3.2.5 Computed Diffusion Images 3.3 Intravoxel Incoherent Motion (IVIM) 3.3.1 Preparation of Image Data for Fitting 3.3.2 Segmented Fitting for Diffusion Coefficient D 3.3.3 Segmented Fitting for Pseudodiffusion Fraction f 3.3.4 Fitting for Pseudodiffusion Coefficient D* 3.3.5 Least-Squares Fitting for Full IVIM Model 3.3.6 Spatial Information and Bayesian Fitting Algorithms 4 Methods for Results Validation 4.1 Validation of Fitting Algorithm 4.2 Visualization of Fitted Curves 4.3 Residuals and Systematic Bias 4.4 Information Criteria and Model Selection 4.5 Covariance and Repeatability 4.6 Final Analysis Quality Check 5 Notes References Chapter 38: Analysis Protocol for Dynamic Contrast Enhanced (DCE) MRI of Renal Perfusion and Filtration 1 Introduction 2 Materials 2.1 Software Requirements 2.2 Source Data: Format Requirements and Quality Check 2.2.1 Input Requirements 2.2.2 Prequality Check 3 Methods 3.1 Segmentation 3.2 T1 Mapping 3.2.1 VTR Analysis 3.2.2 VFA Analysis 3.3 Model Selection and Quantification 3.4 Deconvolution Approach 3.5 Toft´s Model 3.6 Bayesian Model Selection 3.6.1 Analyzing Regions of Interest Data Using the Enter ASCII Model Package 3.6.2 Model Selection and Analysis of Region of Interest Data Using the Enter ASCII Model Selection Package 3.7 Voxel-Wise Image Analysis 3.7.1 Analyzing Image Data Using the Analyze Image Pixels Package 3.7.2 Model Selection and Analysis of Image Data Using the Image Model Selection Package 3.8 Results Validation 3.8.1 Evaluation of Analysis Errors and Variability Using Synthetic Data 3.8.2 Comparison with Reference Values from the Literature 4 Notes References Chapter 39: Quantitative Analysis of Renal Perfusion by Arterial Spin Labeling 1 Introduction 2 Materials 2.1 Software Requirements 2.2 Source Data: Format Requirements 2.2.1 Input Requirements 2.2.2 Intensity Scaling of Multiple Delay ASL Data 2.2.3 Format Conversion 3 Methods 3.1 Quality Control/Data Exclusion 3.2 Motion Correction 3.3 Quantification of M0 and T1 3.3.1 Model Equations 3.3.2 Starting Values 3.3.3 Fitting Algorithm 3.3.4 Visual Display 3.4 Quantification of Perfusion 3.4.1 Model Equation for FAIR-ASL 3.4.2 Pairwise Subtraction 3.4.3 Starting Values 3.4.4 Fitting Algorithm 3.4.5 Visual Display 3.5 Regional Analysis 3.6 Results Validation 3.6.1 Comparison with Tissue Values Under Hypercapnia or Hyperoxia 3.6.2 Comparison with Reference Values from the Literature 4 Notes References Chapter 40: Analysis Protocol for the Quantification of Renal pH Using Chemical Exchange Saturation Transfer (CEST) MRI 1 Introduction 2 Materials 2.1 Software Requirements 2.1.1 Essential Tools 2.1.2 Optional Tools 2.2 Source Data: Format Requirements and Data Preprocessing 2.2.1 Input Requirements 2.2.2 Background Removal 3 Methods 3.1 Motion Correction 3.2 Z-Spectra Analysis 3.2.1 Multi Pool Lorentzian Fitting 3.2.2 Image Down-Sampling Expedited Adaptive Least-Squares (IDEAL) Fitting Algorithm 3.2.3 Smoothing Splines Interpolation 3.3 CEST Quantification 3.3.1 CEST Ration Calculation by Asymmetry Analysis 3.3.2 CEST Ratio Calculation from Lorentzian Fitting 3.3.3 Chemical Shift-Based Ratiometric CEST Analysis 3.3.4 RF Power-based Ratiometric CEST Analysis 3.3.5 The Generalized RF Power- and Chemical Shift-Hybrid Ratiometric CEST Analysis 3.4 Set-Up of pH Calibration Curve 3.5 In Vivo Application for pH Mapping 3.5.1 pH Mapping by Lorentzian Fitting or IDEAL Approach 3.5.2 pH Mapping by Using the Smoothing Splines Approach 3.6 Representation 3.7 Quantitative Analysis 3.8 Results Validation 3.8.1 Evaluation of Analysis Errors 3.8.2 Comparison with Reference Values from the Literature 4 Notes References Chapter 41: Analysis Protocol for Renal Sodium (23Na) MR Imaging 1 Introduction 2 Materials 2.1 Software Requirements 2.2 Source Data: Format Requirements and Quality Check 2.2.1 Input Requirements 2.2.2 Data Exclusion 2.2.3 SNR Check for T2* Mapping 2.2.4 Dual Flip Angle B1 Mapping for Sodium Concentration Mapping 3 Methods 3.1 Sodium Concentration Mapping 3.1.1 Algorithm for Sodium Concentration Mapping 3.1.2 Example Matlab Code 3.1.3 Biexponential T2* Mapping 3.1.4 Algorithm for T2* Mapping 3.1.5 Example Matlab Fitting Code 3.2 Visual Display 3.3 Quantification 3.4 Results Validation 3.4.1 Comparison with Tissue Values from Biopsy 3.4.2 Comparison with Reference Values from the Literature 4 Notes References Chapter 42: Analysis Methods for Hyperpolarized Carbon (13C) MRI of the Kidney 1 Introduction 2 Materials 2.1 Software Analysis Tools 3 Methods 3.1 Quantitative Perfusion Imaging 3.2 Relaxation Mapping 3.3 Glomerular Filtration Rate Estimation 3.4 Metabolic Rate Constant Estimation 3.5 Results Validation References Chapter 43: Data Preparation Protocol for Low Signal-to-Noise Ratio Fluorine-19 MRI 1 Introduction 2 Materials 2.1 Software Requirements 3 Methods 3.1 Data Import and Scaling 3.1.1 DICOM Data 3.1.2 Bruker Data 3.2 Correct Data Scaling 3.3 Noise Level Estimation 3.3.1 Estimation Based on a Background Region 3.3.2 Estimation Based on a Noise Scan 3.4 Bias Correction 3.5 Background Subtraction 3.6 Proton/Fluorine-19 Overlays 4 Notes References Index