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User Guide: Imaging User Guide: Imaging Horizontal and Micro NMR Imaging With VNMR 6.1C Software Pub. No. 01-999163-00, Rev. A0201 User Guide: Imaging Horizontal and Micro NMR Imaging With VNMR 6.1C Software Pub. No. 01-999163-00, Rev. A0201 User Guide: Imaging Horizontal and Micro NMR Imaging With VNMR 6.1C Software Pub. No. 01-999163-00, Rev. A0201 Revision history: A0800 – Initial release for VNMR 6.1C. A0201 – Removed obsolete dslice macro per C. Hofstetter and M. Hedehus. Applicability of manual: Imaging modules on Varian NMR superconducting spectrometer systems with VnmrIMAGE version 4.4 software installed. Technical contributors: Simon Chu, Matt Howitt, Chris Price, Alan Rath, Subramaniam Sukumar, Evan Williams Technical writers: Michael Carlisle, Dan Steele Technical editor: Dan Steele Copyright 2000–2001 by Varian, Inc. 3120 Hansen Way, Palo Alto, California 94304 http://www.varianinc.com All rights reserved. Printed in the United States. The information in this document has been carefully checked and is believed to be entirely reliable. However, no responsibility is assumed for inaccuracies. Statements in this document are not intended to create any warranty, expressed or implied. Specifications and performance characteristics of the software described in this manual may be changed at any time without notice. Varian reserves the right to make changes in any products herein to improve reliability, function, or design. Varian does not assume any liability arising out of the application or use of any product or circuit described herein; neither does it convey any license under its patent rights nor the rights of others. Inclusion in this document does not imply that any particular feature is standard on the instrument. UNITYINOVA, MERCURY-VX, MERCURY, Gemini, GEMINI 2000, UNITYplus, UNITY, VXR, XL, VNMR, VnmrS, VnmrX, VnmrI, VnmrV, VnmrSGI, MAGICAL II, AutoLock, AutoShim, AutoPhase, limNET, ASM, and SMS are registered trademarks or trademarks of Varian, Inc. Sun, Solaris, CDE, Suninstall, Ultra, SPARC, SPARCstation, SunCD, and NFS are registered trademarks or trademarks of Sun Microsystems, Inc. and SPARC International. Oxford is a registered trademark of Oxford Instruments LTD. Ethernet is a registered trademark of Xerox Corporation. VxWORKS and VxWORKS POWERED are registered trademarks of WindRiver Inc. Other product names in this document are registered trademarks or trademarks of their respective holders. Overview of Contents SAFETY PRECAUTIONS ................................................................................. 11 Introduction ..................................................................................................... 15 Chapter 1. First Steps: Making an Image ..................................................... 17 Chapter 2. Imaging Experiments .................................................................. 25 Chapter 3. Imaging Pulse Sequences .......................................................... 41 Chapter 4. Image Browser ............................................................................. 65 Chapter 5. Image Browser Math Processing ............................................. 111 Chapter 6. CSI Data Processing .................................................................. 129 Chapter 7. High-Performance Auxiliary and Microimaging Gradients .... 175 Chapter 8. Digital Eddy Current Compensation ........................................ 197 Chapter 9. Physiological Gating Module .................................................... 205 Chapter 10. 2D and 3D Backprojection ...................................................... 223 Chapter 11. Interactive Image Planning ..................................................... 251 Appendix A. Commands, Macros, and Parameters .................................... 253 Index ............................................................................................................... 345 01-999163-00 A0201 VNMR 6.1C User Guide: Imaging 3 4 VNMR 6.1C User Guide: Imaging 01-999163-00 A0201 Table of Contents SAFETY PRECAUTIONS ................................................................................. 11 Introduction ..................................................................................................... 15 Chapter 1. First Steps: Making an Image ..................................................... 17 1.1 Making an Initial Scout Image .................................................................................... 17 1.2 Using the Scout Image to Plan a New Target Image ................................................... 22 Chapter 2. Imaging Experiments .................................................................. 25 2.1 Basic Imaging Principles ............................................................................................ 25 2.2 Time Domain to Spatial Domain Conversion ............................................................. 26 2.3 Slice Selection ............................................................................................................. 29 2.4 Frequency Encoding ................................................................................................... 32 2.5 Phase Encoding ........................................................................................................... 34 2.6 Image Resolution ........................................................................................................ 35 2.7 Spatial Frame of Reference ......................................................................................... 37 2.8 Image Reconstruction ................................................................................................. 38 2.9 Important Imaging Parameters .................................................................................... 38 Chapter 3. Imaging Pulse Sequences .......................................................... 41 3.1 Initial Setup ................................................................................................................. 41 3.2 Conditions for Use ...................................................................................................... 42 3.3 GEMS Multislice Imaging .......................................................................................... 44 3.4 Obtaining a GEMS Image ........................................................................................... 49 3.5 Echo Planar Imaging and Phase Correction Map Files .............................................. 51 3.6 Commands, Macros, and Parameters .......................................................................... 62 Chapter 4. Image Browser ............................................................................. 65 4.1 Overview ..................................................................................................................... 65 4.2 Getting Started ............................................................................................................ 68 4.3 Graphics Tools ............................................................................................................ 80 4.4 Data Processing ........................................................................................................... 90 4.5 Macros .........................................................................................................................98 4.6 Files and Other Items ................................................................................................ 104 Chapter 5. Image Browser Math Processing ............................................. 111 5.1 Opening Image Browser Math .................................................................................. 111 5.2 Image Browser Math Expressions ............................................................................ 112 5.3 Image Browser Math Functions ................................................................................ 113 5.4 The Fit Program ........................................................................................................ 120 5.5 Problems with Image Browser Math ........................................................................ 127 Chapter 6. CSI Data Processing .................................................................. 129 6.1 Overview of CSI ....................................................................................................... 129 01-999163-00 A0201 VNMR 6.1C User Guide: Imaging 5 Table of Contents 6.2 Getting Started .......................................................................................................... 133 6.3 Tools .......................................................................................................................... 147 6.4 Processing Functions ................................................................................................ 156 6.5 Files and Other Items ................................................................................................ 167 Chapter 7. High-Performance Auxiliary and Microimaging Gradients .... 175 7.1 HPAG-183 Hardware ................................................................................................ 175 7.2 Experimental Setup ................................................................................................... 183 7.3 Performance Specifications ....................................................................................... 189 7.4 Microimaging Hardware ..........................................................................................
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