User Manual
Contents
1. sss 5 4 W width at half height reegt 5 4 Z zero order phase parameter 5 16 August 11 2003 7 5 Index 7 6 August 11 20032. Ge SH E ett 5 8 5 9 Lorentzian IIYe sasacircitntineruicettntceipron 5 13 low order z shim 1 1 1 2 5 8 5 12 O optimization M GETI Of nonoina dL sue 1 2 3 2 maeltB etica eti ul leo 4 of all Shi nica cune dace reet 5 9 mim 4 1 44 5 16 of non spinning shim EE 5 9 MAGICA ssania OIMSEDATMEISE roseis 5 12 5 13 6 22 shimit all 6 4 BEE 6 4 Pp MAGICA E Soe dis partly saturated sample 5 11 magnet MUTI UNB so aisha gei ute a e Te A ai apeduE 1 1 3 3 specific parameter cccecceccsssesssessseessseessseeesees 5 10 permanent installation 4 Pu pM ts bn cdi js noni NEP 5 1 5 2 5 6 mana c shimmuing E re NE 5 16 6 1 sii EARE EE aia positional information sss 3 3 maximum number of DPR lg kns 5 12 pre acquisition delay NU 5 H irri D P 5 6 5 7 public EE 1 1 MENU SYStEM E 5 7 5 10 5 14 MEHUD me M 4 1 August 11 2003 7 3 Index R Eeer 4 5 parameters 5 2 5 4 5 5 5 6 5 7 5 17 a Rede M ME E E AM 5 557 510 relaxation time sss 5 11 6 1 ional E mensis 5 11 5 12 Report Hg sostienen ient 5 16 software resonance frequency distribution 3 3 DNS EE 6 1 response sure 3 2 3 3 locking EE 6 2 room temperature shim 2 2 6 3 Specification of shim name 5 9 root privileges 4 3 spectral resolution eeeeeeeeeeeeccecsseseeeeeeeesessesneee 6 3 rp Phase tere 5 16 spectrometer Softwar
3. User Manual Automated Shimming Software VNMR Client Version 0 8 U S Patents 5 218 299 And 5 572 125 Copyright ShimIt Software Copyright C 2000 by ScienceSoft LLC All Rights Reserved It is illegal to copy modify or otherwise distribute this software without the prior specific written consent of the ScienceSoft LLC Dr Reinhard Dunkel ScienceSoft LLC 9934 Pinehurst Dr Sandy UT 84092 http www ScienceSoft net dunkel ScienceSoft net phone 801 816 0163 FAX 209 755 7800 SCIENCESOFT LLC AND ITS SUPPLIERS DISCLAIM ANY AND ALL WARRANTIES WITH REGARD TO THE SOFTWARE AND DOCUMENTATION WHETHER EXPRESSED OR IMPLIED AND INCLUDING ANY WARRANTIES OF MERCHANTABILITY OR FITNESS FOR PARTICULAR PURPOSE IN NO EVENT SHALL SCIENCESOFT LLC OR ANY OF ITS SUPPLIERS BE LIABLE FOR ANY DAMAGES WHETHER GENERAL SPECIAL INDIRECT OR CONSEQUENTIAL DAMAGES RESULTING FROM LOSS OF USE DATA OR PROFITS WHETHER IN ANY ACTION UNDER CONTRACT NEGLIGENCE OR OTHER TORTIOUS ACTION ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE Trademarks and Acknowledgments Sun is a registered trademark and SunOS SOLARIS Network File System and NFS are trademarks of Sun Microsystems Inc UNIX is a registered trademark licensed exclusively by X Open Company Ltd VXR is a registered trademark and VNMR is a trademark of Varian Associates Inc Other brand or product names are the trademarks or registered t
4. Error Mo Program Sbimit rins Integral rp Phase Mo Width Start Mo 44 6368 44 6363 Error Mo 7 Best Mo This Mo Starting Poin 7 0 Integral rp Phase Mo Width Start Mo 03 5634 55 0634 2 15 1849 2 53591 55 5634 3 98916E408 Effect Shim z 3 4 01660E 06 14 6658 9 10537 55 6634 Program Sbimit Report FIR Best Ho This Mo Report FID Integral yp Phase Mn Width Start Mo Best Wo This Mo Error Mo 2 Integral rp Phase Mo Width Start Mo Effect Shim zd 3 94882E 96 15 1373 8 52591 55 5634 53 7600 2 t 53 7600 Error Mo Gest Shims So F 26 3 98059E 406 15 0993 53591 55 5634 41 2291 41 2291 17 282795 August 11 2003 Optimization Of All Shims Program Report FID OR D ntegral Sbimit Best Sbims So 28 4 02203E 406 rp Phase 13 9467 Mn Width 8 535091 Start Mo 55 0634 Best Mo this Mo 36 8119 36 9119 Error Plo 16 732 Program Sbimit est Shims So Far Integral yp Phase Mn Width Start Mo Best Mo This Mo Error Mo 8 53591 55 5634 33 0731 33 0731 22 9012 Report FID 4 lntegral rp Phase Mn Width Start Mo Best Mo This Mo Error Ho Best Shims 33 3 99831E406 11 3209 8 53591 55 5634 33 8532 33 8532 27 0147 Program Shimit Report F
5. Fin Integral rp Phase Mo Width Start Mo Best Ho This Mo Error Mo 19 0045 Sbimit Best Sbimsi i 1 557344 10 6875 1 19094 9 906440 7 05151 7 05151 5 22374 August 11 2003 6 11 Automated Shimming Example Program Sbimit it Program Sbimit Report Best Shis So Far Report Final shims FID 25 rins 36 Integral 1 098250b407 A Integral 1 56471E 07 rp Phase 12 3571 rp Phase 12 1440 Mo Width 0 939769 Mo Width 1 04817 Start Mo 9 96440 Start Mo 9 964640 Best Ho 6 92465 Best Ho 6 906655 This Mo 6 924565 i This Mo 6 90663 Error Mo 4 9223 Error Mo 2 4220 6 3 Optimization Of Non Spinning Shims VV ck C Ck CC Ck Sk Ck Sk Ck Ck Ck Ck kk Sk Ck Ck Ck Ck kk kk ck kk kk kk ck kk Sk Ck kk kk ck kk Sk ck kk ck kk Sk kk ko Sk kk Ck ko kkkkk km x Ts MAGICAL macro shimit non z ZP x KW deg Optimize non spinning shims using non spinning sample using Sch W auto shimming software ShimIt ZP x Kal We C Reinhard Dunkel Nov 29 1994 x x VV C C Ck Ck Ck Ck Ck Ck Ck Ck kk kk Ck Ck Ck kk kk kk Sk kk kk Sk kk kk Sk kk ck Ck Ck ko kk Sk ck Sk kk kk Sk kk ko Sk kk kk ko kk ko kk spin 0 No sample spinning spin Stop spinning now alock u No Varian locking lockpower 0 No power for lock channel lockgain 0 Don t detect lock signal in n No checking of lock or spin shimit init Create ShimIt variables 6 12
6. These changes can be automatically performed from macros which use Shimlt as their basic shimming engine see CHAPTER 6 Automated Shimming Example The values listed at the left side of the spectrum are Shimlt s analysis results of this spectrum The Report line lists remarks from ShimIt about the currently displayed spectrum such as the Best Shims So Far message displayed above The FID line shows the number of the current FID acquired for this shimming run The displayed number is counted from minus the number of requested steady state cycles sscycles variable over zero for the starting spectrum to the number of acquired FIDs for the shim optimization The determined area of the displayed spectral region is listed in the Integral line A decrease of the listed integral during a ShimIt run is normally due to progressive sample satu ration If the selected spectral area initially did not contain the complete signal intensity the integral might slightly increase as the magnet homogeneity improves ShimIt always normal izes the absolute value integral of the analyzed spectral area before determining the line moment and hence is fairly insensitive to modest integral changes Every acquired FID is phase corrected by adjusting the Varian zero order phase parameter rp The rp Phase line shows the currently used phase parameter The shape of an NMR line is determined by the T relaxation time of the observed nucleus and the inhomogeneity of
7. 2 1513X August 11 2003 6 21 Automated Shimming Example Final comparison Initial Spectrum Final Spectrum In the final spectrum the first spinning sidebands 35 Hz cannot even be seen The visible low frequency second spinning sideband stems from the NCC Z SPEC probe and is not a shim ming problem The center resonance is not quite Lorentzian in shape yet Further ShimIt low order z shimming using a low order parameter value would obtain the desired lineshape However given the current implementation of ShimIt manual or automated lock level shim ming would likely be faster for this final stage 6 22 August 11 2003 Index CHAPTER 7 Symbols TUM ae osi UE DAI ave RUN IRRUR 4 3 Numerics 90 degree pulse width 5 11 A absolute valne mode sse ertt 3 3 acquisition in Progress 5 6 additional main menu 5 1 5 2 5 7 alpha window ssss 5 7 5 17 asynchronous communication 5 13 ue qu ICON ME TET 6 2 automated shimming 1 1 5 8 5 9 5 10 6 1 automatic processing sss 5 6 B baseline distortion 5 13 Best Molme 5 16 Binary Compatibility Package 4 5 bringing up a magnet 2 1 button Abort Acq sse 5 6 EE E 5 8 DS ee 5 9 Convergence 5 12 EA M 5 4 Help iecit ee AE 5 2 Non Spinning see 5 9 Order etes 5 13 Return sse 5 7 5 10 5 14 ET 5 5 5 10 S
8. August 11 2003 Optimization Of Non Spinning Shims shims task sscycles shimstep order converge timeout radial shims shimit init shim 1 sp sp WwW iWord REPEAT current_shim iWord tr shims UNTIL current_shim iWord 8 subs max fid cr s Srflrf rfp rfl sp s cr rfp oldtof tof oldtof sw 2 rfp rfl rfl Soldtof IF sw sfrq 15 THI rfl p 80 Gr eet Lee p cr rfp Soldsw sw rfl ENDIF at 75 at sw 2 wp np nt 1 rm userdir ShimIt non z mv userdir ShimIt userdir ShimIt non z shimit z fine menu shimit shimit start wshimit SEL 5 Soldsw 2 sw 2 trunc sh range 8 1 0 order wp 100 2 SiWord 1 SiWord 1 current shim rtl rtp Optimize spinning shims Initialize ShimIt Set ShimIt to auto shimming No sample saturation expected z shims partly optimized Increase weight of signal height Termination by max fid Time out after 5 minutes idle Display 40 Hz around signal Count number of selected shims Coarse shim adjustment Cursor to middle of display Assign 0 Hz to cursor position Center display area in spectrum Fix spectral referencing Limit spectral width to 15 ppm Fix spectral referencing Display 75 points 1 Hz pt No time for signal averaging Delete old ShimIt directory
9. Fix spectral referencing Display 75 points 35 Hz pt No time for signal averaging Delete old ShimIt directory On termination Save output Show main ShimIt menu Start ShimIt August 11 2003 6 19 Automated Shimming Example Integral rp Phase Mo Width Start Mo m i Error Mo j Best Ho This Mo Integral rp Phase Mo Width i 8 9 i Start Ho i Best Ho This Mo Error Mo 846166 07 23504 503641 09258 09258 09258 Program Report FIQ Sbimit Integral rp Phase Mo Width Start Mo Best Mo This Mo Error Mo Program Report rins Sbimit Best amp Integral rp Phase Mo Width Start Mo Best Mo This Mo Error Mo z en 0 936288 8 5220X 6 20 August 11 2003 Further Optimization Of Spinning z Shims Program Sbimit Report por est Shims So Far rins P Integral 1 667755 Integral rp Phase rp Phase Mo Width 0 445416 Mo Width Start Mo 1 090258 Start Mo Best Ho 0 911920 Best Mo This Mo 0 911920 This Mo Error Mo 13 970 Error Mo Program Sbimit Report z i FIR 29 Integral 1 5 46 Integral 1 592275 rp Phase 5 054 E rp Phase 2 907907 Mo Width 9 2 i Mo Width 0 594676 Start Mo 1 09258 Start Mo 1 99258 Best Mo 0 904121 i Best Mo 9 900991 This Mo 9 904121 1 This Mo 0 900991 Error Mo 2 9613 i Error Mo
10. N ratio of the spectrum is sufficient The SS Cycles button allows one to set the sscycles vari able interactively ShimIt performs the specified number of sscycles steady state cycles of acquiring and analyzing an FID to reach the steady state sample saturation before starting the auto shimming process ShimIt will normally recover from a partial sample saturation occurring during the auto shim ming However specifying a few steady state cycles to be performed before the analysis of a partially saturating signal can improve the speed of the shimming process Frequently sscyles 3 is sufficient to approximate the final level of sample saturation The default value of sscycles is zero Shim Step Button ShimIt does not perform a sensitivity analysis of the individual shims specified for optimiza tion Using this button the shimstep variable can be set interactively This variable speci fies the initial shim change for ShimIt to be used for the auto shimming process During the shimming the step size of each shim is automatically adjusted as needed The default value of shimstep is 256 The value for shimstep should be chosen so that each shim adjusted by the specified value causes a visible change in the shape of the displayed line After Shimlt is started the program shows the starting spectrum and a spectrum for each selected shim with the requested initial shim change applied If the effect of the shim change is either too small or too l
11. goal of shimming is to obtain a constant magnetic field Sup pose the shim coil currents are changed and the following hypothetical mag netic field plot is obtained August 11 2003 3 1 How Shimlt Works Magnetic 4 Field Strength Magnet Z Direction The homogeneity obviously worsened but a lock level indicator would show an improvement because the magnetic field strength is constant over a wider z range than before causing the height of the lock signal to improve At the same time the lineshape of the signal wors ened but this is of no relevance to the lock level height Choosing the lock level as homogeneity criterion turns shimming into a highly nonlinear opti mization problem resulting in a response surface which has numerous local minima likely to trap any human or automated uphill optimization approach It is crucial however to notice that the complexity of the response surface is a function of the chosen optimization criterion and does not allow any con clusions about the intrinsic complexity of the shimming problem Magnetic Field Strength Prem Magnet Z Direction ShimIt approaches this problem as fol lows Suppose we calculate the average magnetic field strength and determine the absolute value area between the observed and average field strength as shown in the figure In contrast to the lock level this area is a true representa tion of the remaining field in
12. ing in this regard The ShimIt analysis parameters can now be set from the ShimIt menus and the shimming pro cess can be started using menu buttons as discussed in previous chapters However the com plete shimming of the room temperature shims from scratch involves several steps with increasing spectral resolution and some steps should be performed with a spinning sample and others without sample spinning This general process can be done conveniently using macros instead of the menu buttons In this chapter the parameters for the auto shimming are set from a series of MAGICAL macros Besides convenience there is no difference between issuing the commands manually vs issuing them from macros August 11 2003 6 3 Automated Shimming Example The series of macros is started using the shimit all command The shimit all macro optimizes all shims using a non spinning sample as described in SECTION 6 1 Optimiza tion Of All Shims On completion ofthe shimit all macro the shimit z macro starts and optimizes the z shims using sample spinning as described in SECTION 6 2 Optimiza tion Of Spinning z Shims After shimit z the shimit non z macro starts and opti mizes the non spinning shims as described in SECTION 6 3 Optimization Of Non Spinning Shims Finally macro shimit z fine starts and further improves the z shims as described in SECTION 6 4 Further Optimization Of Spinning z Shims Each section shows the macro used and the spectr
13. nal bases while smaller order values lead to higher signals with generally smaller width at half height values The default value of order is one corresponding to the minimization of the first absolute value central moment The order parameter should be kept between 1 and 0 1 There seems to be no advantage of choosing an order parameter value above one The second central moment of an absorption mode Lorentzian line order 2 is already infinite for an infinite spectral width causing instabilities of the shimming algorithm Setting the order parameter to a negative value causes Shimlt to destroy rather than improve the magnet homogeneity It should be noted that only for order values of one and higher has it been proven that moment minimization always leads to the best magnet homogeneity So order 1 should always be used until a good homogeneity has been found If so desired the value of the order parameter can then be decreased but kept above zero to cause ShimIt to more strongly weight the height of the displayed resonance for the optimization Timeout Button The VNMR client software of ShimIt was written solely based on the user documentation of the Varian spectrometer system Besides an avoidable runtime overhead this also resulted in an asynchronous communication of ShimIt with both the spectrometer and the VNMR soft ware Using the Timeout button the timeout variable can be set interactively If the spec trometer has not suc
14. of field gradients In the absence of field gradients fields would have to be mapped mechanically using specially designed probes In either case shimming through field determination is both expensive and of limited accuracy Most shim coil sets are build to produce fields which resemble spherical harmonics The shape of a magnetic field produced by a shim coil should hence be known and the effect of different shim fields should be independent In practice however every coil produces higher order effects and due to design compromises and winding imperfections lower order effects as well So the design of the shim set might be used as a guiding principle during the shim ming process but the final shim result should not depend on any assumed functional form of the shim coils 2 2 August 11 2003 CHAPTER 3 How Sh mlt Wor Ks Shimming is the optimization of shim coil currents to maximize the magnet homogeneity in a volume of interest The crucial question for this multi parameter optimization which makes the difference between a black art and a reliable shimming method is how the current mag net homogeneity is determined Magnetic ii Field Strength Magnet Z Directior The most widely used criterion for magnet homogeneity is the lock level which can be thought of as the height of the deuterium lock signal The graphic shows a hypothetical magnetic field plot along the z direction of the magnet The
15. the current magnetic field The Mn Width line shows Shimlt s estimate of what the width of the displayed line would be without magnetic field inhomogeneities The following three lines in the graphic window show the lineshape moment at start of Shimlt Start Mo line the best moment found so far Best Mo line and the moment of the cur rently displayed spectral area This Mo line Notice that Shimlt uses an iterative shimming approach and the moment of the currently displayed spectrum might in fact be worse than the best moment or even the starting moment The Error Mo line provides an estimate of the 8 Shimlt does not modify the user set frequency dependent first order phase parameter 1p 5 16 August 11 2003 Displayed Shimming Results percent uncertainty in the best moment determined so far The error value is given after ShimlIt has probed the sensitivity of the shims to be optimized and the value is then updated after each acquired FID The listed error will decrease during shimming and hence is used in conjunction with the converge parameter as a termination criterion The nonlinear nature of the optimization algorithm and instabilities in both the instrumental response and the spectral analysis can cause the listed error value to fluctuate somewhat The bottom window alpha window in the above figure lists the current ShimIt parameters and the values of the shims to be optimized for the displayed spectrum For an explan
16. to be optimized during the auto mated shimming For the optimization of the z shims the sample should in general be spinning and the displayed spectral area should not contain the spinning sidebands Should a clear sep 3 The z0 shim is used to compensate for magnetic field drifts a process called locking This shim should not change the signal lineshape and hence is irrelevant for shimming 4 Ifa fine shim is specified in the list the corresponding coarse shim is automatically adjusted if the corresponding z toz c variable is set to a value greater than zero 5 As magnets using new shim sets become available this check mechanism will have to be extended or disabled 5 8 August 11 2003 Shims Submenu aration of center resonance and spinning sidebands not be possible use the A11 button instead To decrease the height of spinning sidebands stop the sample spinning and use the Non Spinning button instead Non Spinning Button This button selects all non spinning shims also called non axial shims in the current shim set to be optimized during the automated shimming For a spinning sample the non spinning shims influence the height of the spinning sidebands For the optimization of non spinning shims the sample spinning has to be stopped so that the moment of the center line is influ enced by the off axis homogeneity Some magnets show a strong interaction between spin ning and non spinning shims Hence the spinning
17. E407 8 06422 1165768 9 75002 7 96602 7 96602 14 393X ing 3e Far Best Sbims 32 i 15389107 9 641260 1 63741 9 75002 7 89335 Error Mo 12 911X August 11 2003 6 15 Automated Shimming Example Program Sbimit Best Shims 35 i Integral 1 16485t40P rp Phase 8 83164 Mn Width 3 14671 Start Mo 9 275002 Best Mo 7 80037 This Mo 7 80037 Error Mo 12 977 integral rp Phase Mo Width Start Mo Best Ho This Mo Error Mo 4 690635 Far Program Sbimit Report Fin Integral rp Phase Mo Width Start Mo Best Ho This Mo Error Mo Report FIQ Integral rp Phase Mo Width Start Mo 7 66234 7 086234 Best Mo This Mo Error Mo Gest Shins s 42 1 16026E 07 1 88295 9 795002 3 8903 6 16 August 11 2003 Optimization Of Non Spinning Shims Program Sbimit Program Sbimit Best Shims i Report Best Shims So Far 49 i FIR 52 i Integral 1 16539t407 i Integral 1 18787b407 rp Phase 8 60060 j rp Phase 8 7638068 Mn Width 1 79600 7 Me Width 1 87136 Start Mo 9 75002 7 Start Ho 9 75002 Best Ho 7 686171 i Best Ho 7 600195 This Mo 7 66171 This Mo 7 60195 Error Mo 3 1559 i Error Mo 2 9784 Program Sbimit Best Shims Zo Far Report Best Shims 5 E FIR
18. Finished Save amp start z fine shimming Show main ShimIt menu Start ShimIt August 11 2003 6 13 Automated Shimming Example FIO SS Integral 1 159226 07 rp Phase 8 80283 Mo Width 1 57569 Start Mo 9 75002 Best Mo 9 75002 This Mo 75002 Error Mo Program Zitt Effect Shih m S A kl D 3k li Noes Integral i 151026407 rp Phase 8 97291 Mo Width 1 57957 Start Mo 9 75002 Best Mo 8 99949 This Mo 8 99949 Error Mo Report rins Integral rp Phase Mo Width Start Mo Best Mo This Mo Error Mo Program Report FIR Integral rp Phase Mo Width Start Mo 8 56134 8 565134 Best Mo This Mo Error Mo Sbimit 20 Effect Shin yz 1 165958 07 Best Shims 1 16304E407 2 20795 1 64475 9 75002 9 9152 6 14 August 11 2003 Optimization Of Non Spinning Shims Report FIO 4 Integral rp Phase Mo Width Start Mo Best Ho This Mo Error Mo Far Program Sbimit Integral rp Phase Mo Width Start Mo Best Mo This Mo Error Mo 12 3764 Program Zielt Report Fin Integral rp Phase Mo Width Start Mo Best Mo This Mo trroc Mo 2 t Integral rp Phase Mo Width Start Mo 7 89335 Best Ho This Mo Best Shi 26 1 15847
19. ID Integral rp Phase Mn Width Start Mo Best Ho This Mo Error Mo Best Shims S 49 i 4 02153Eb406 19 2360 9 37430 55 5634 31 9032 31 5532 20 308 August 1 1 2003 Automated Shimming Example Program Report FID integral vp Phase Mn bBidth Start Mo Best Mo This Mo Error Mo Sbimit Best Sbim 72 4 02713E 98 17 8418 8 53591 55 5634 31 2889 31 2889 11 812 Program Shimit i Report FID integral vp Phase Mn Width Start Mo Best Mo This Mo Error Mo Best Shims Soitar b 4 04013r406 15 3895 53591 55 5634 29 1813 29 1913 15 297 Program Report FID amp Integral vp Phase Bo Width Start Mo Best Mo This Mo Error Mo Report FID amp Integral vp Phase Mn Width Start Mo Best Mo Thies Mo Error Ho Sbimit Best Sbi 74 4 04526E4 12 6897 853594 55 5634 29 7094 29 7094 12 2494 Program Shimit Final shims 97 3 99894E 9 99960 3 53591 55 5634 27 5509 27 5509 8 3996 August 11 2003 Optimization Of Spinning z Shims 6 2 Optimization Of Spinning z Shims VV Ck C Ck Ck Ck Ck Ck Ck Ck Ck kk kk Ck Ck Ck kk Ck kk Sk kk kk kk Sk Sk ck Sk Ck kk kk Sk kk Sk ck Sk Ck ck kk Sk Sk kk Sk ko Sk Ck Sk ko kk ko kk We We We We We We W
20. Integral 1 1856897 Integral rp Phase 8 12758 rp Phase Mo Width 1 62658 i Mo Width Start Mo 3 75002 Start Mo Best Mo 7 56693 i Best Mo This Mo 7 56683 i This Mo 7 Error Mo 3 2481 ioi Error Mo 1 43004 August 11 2003 6 17 Automated Shimming Example Program Sbimit Program Sbimi Best Shims S Report 67 i FIQ Integral 1 165626 07 Integral 1 161006407 rp Phase 7 91963 i rp Phase Mo Width 1 61554 i i Mo Width Start Mo 9 275002 i Start Mo 9 75992 Best Ho 7 90149 i Best Mo 7 49293 This Mo 7 50149 H This Mo 7 49293 Error Mo 1 94184 Error Mo 1 3302 6 4 Further Optimization Of Spinning z Shims VV c Ck C C Ck Ck kk Ck Ck Ck kkkkkk Ck Sk Ck Ck kk kk ck ck ck ck kk kk kk Sk Ck ko ck kk Sk kk Sk kk kk kk Sk kk ko Sk kk Ck ko ko kk ko Ok x x x MAGICAL macro shimit z fine XH x X x Final optimization of spinning shims using spinning sample with Sch x auto shimming software ShimIt Kl x X We C Reinhard Dunkel Nov 29 1994 x x x VV c C C CC kk Ck Ck Ck Ck Ck kk kk ck Ck Ck kk kk Sk kk Ck Ck Sk kk kk Sk Ck ko ck kk ck kk Sk kk kk ck kk ke kk Sk ko Sk kk ko kk ko kk spin 35 Spin sample at 35 Hz spin Regulate spinning now alock u No Varian locking lockpower 0 No power for lock channel lockgain 0 Don t detect lock signal in n No checking of lock or sp
21. a representing the successive improvements in magnet homogeneity Notice that an auto shimming run can also be started from the other macros if the magnet homogeneity is already sufficiently high While the shimming macros are assumed to be gen erally applicable it is quite instructive to at least once shim a magnet using ShimIt without additional macros The macros themselves don t try to provide much of a user interface and should at this point be regarded as a demonstration of what ShimIt can do and how to integrate Shimlt in other software systems 6 1 Optimization Of All Shims VV ck ck ck Ck Ck kk kk kk KK kk kk ck KK ko kk ck kk kk ck KKK KKK kk ko ck ck KK ck ko ck ko ko ck ko ck kk ck kk ck ko Sk sk ck ck ck Sk ck kk KM x W Hose MAGICAL macro shimit all SCH x KA os Optimize all shims using non spinning sample with auto shimming wt d software ShimIt an Wk kx W C Reinhard Dunkel Nov 29 1994 27 Wk km Nkkkxk xx x xk xkxkxkxkxkxkxkxkxkxkxkxkxkxkxkxkxkxkxkxkxkxkxkxkxkxkxkxkxkxkxkkxkxkkxk xkxkxkxkxkxkxkxkxkxkxkxkxkxkxkkkkxkxkxkxk kxkxkxkkxk xkxx x spin 0 No sample spinning spin Stop spinning now alock u No Varian locking lockpower 0 No power for lock channel lockgain 0 Don t detect lock signal in n No checking of lock or spin 6 4 August 11 2003 Optimization Of All Shims shimit init shims axial shims radial_ shims shimit init task shim ssc
22. adjustments such as between sample changes the lock level optimization currently has a speed advantage over Shimlt The second class of competing auto shimming methods involves the determination of the actual three dimensional field strength through imaging or special Nuclear Magnetic Resonance NMR mapping probes The problem of such techniques is that they require the use of special probes and have sensitivity problems limiting their applications to proton nor mally water samples ShimIt has none of these limitations In fact knowledge of the three dimensional field strength is not needed for shimming and in the time needed to acquire and reconstruct a single image ShimIt can acquire and analyze several Free Induction Decays FIDs Hence after integration of ShimIt into a spectrometer system the software could favorably compete even in cases where imaging techniques are applicable Another strength of Shimlt is that the method is independent of the spectrometer and magnet used In practice however ShimlIt has to cooperate with spectrometer software and know at least what shims are available on the magnet used To reflect this complexity Shimlt is cur rently implemented as a server process incorporating the general shimming method and addi tional client software incorporating the spectrometer and magnet specific information The strength of the current server client implementation of Shimlt is the flexibility to adjust the software to diffe
23. arge the shim ming process can be stopped with the Stop button in the main ShimIt menu the best shim settings found so far can be recalled with the Show Best button in the main Shimlt August 11 2003 5 11 Using The VNMR Shimlt Client Software menu the shimstep variable can be adjusted using this Shim Step button and the auto shimming process can be restarted 7 FIDs Button Using this button the max id variable can be set interactively For an unattended shimming run this variable is useful to limit the time spend by Shimlt for auto shimming ShimIt works in logical iteration steps and each step can result in the acquisition of several FIDs So when the specified maximum number of FIDs are acquired Shimlt finishes the current logical itera tion step and then terminates Hence the acquired number of FIDs can slightly exceed the number of FIDs specified by the max id variable The default value of max iter is 100 and the recommended value for fast shimming is eight times the number of selected shims to be optimized Convergence Button ShimIt optimizes the moment of the displayed line This Convergence button allows one to interactively specify the converge variable This variable causes termination of the auto shimming process when the smallest determined moment is estimated to lie within con verge percent of its optimal value Notice that the stability of an NMR instrument and the finite S N ratio of the spect
24. ation of the displayed parameters see SECTION 4 2 Magnet Specific Customization SECTION 5 1 ShimIt Main Menu and SECTION 5 3 Setup Submenu Created Files ShimIt generates several files during a shimming run and stores them in directory SHOME vnmrsys ShimIt When Shimlt is started all files from a previous shimming run are deleted The first file generated is called start and contains all ShimIt and VNMR parameters relevant to the shimming run In the file ShimIt log written next are stored during a shimming run the spectrometer commands issued and the shimming results obtained Finally each FID acquired which constitutes an improvement in magnet homogeneity over all previous FIDs is stored in a directory called Best fid in SHOME vnmrsys ShimIt Directory Best01 fid contains the starting FID and the Best id directory with the highest number contains the best FID acquired so far August 11 2003 S 17 Using The VNMR Shimlt Client Software S 18 August 11 2003 CHAPTER 6 Automated Shimming Example The biggest challenge for manual and automated shimming alike is to shim a magnet starting without knowing initial shim values Using a 300 MHz Varian UNITY spectrometer with an NCC Z Spec probe this shimming example demonstrates how ShimIt can shim such a magnet in less than an hour starting from all shim values set to zero The examples were run using a Sun SPARC II computer The speed of ShimIt is compute limited an
25. ation thereof In principle the list can contain all shims recognized by VNMR except for the z0 shim and the coarse shims The macro parse shims also verifies that the specified shims are contained in the selected shim set The default value of shims are all z shims in the selected shim set Using these menu functions provides several advantages over setting the shims variable directly from the command line From the VNMR shimset variable the available shims are already known and can be specified in groups e g all z shims and all non spinning shims The menu also allows one to conveniently add and remove shims from the current selection Finally all user input is parsed directly and so input errors are discovered immediately When setting the shims variable from the command line possible errors are only detected at the start of Shimlt z1 z3 Button This button selects the z1 z2 and z3 shims to be optimized during the automated shimming The low order z shims are related to quite visible lineshape distortions and tend to be adjusted after every sample change Notice that the moment optimization used by Shimlt is very sensi tive to high order z shims allowing Shimlt to be quite effective in their optimization So the All z button should be used if high order shims might be able to correct some of the observed distortions of the spinning lineshape All z Button This button selects all z axial shims in the current shim set
26. cessfully acquired a spectrum requested by ShimIt within timeout seconds or ShimIt has not analyzed an FID within this time frame the auto shimming is aborted The default value of timeout is 300 seconds August 11 2003 S 13 Using The VNMR Shimlt Client Software Return Button The Return button causes the menu system to return to the main ShimIt menu 5 4 Displayed Shimming Results During a shimming run Shimlt displays all variable settings acquired spectra and obtained analysis results For further speed improvement future versions of Shimlt will likely provide an option to reduce the amount of displayed information While the ShimIt homogeneity opti mization is in progress the VNMR display typically shows the following components S 14 August 11 2003 Displayed Shimming Results My Width tart Ro S delta cr S 152 9 converge n order 105 timeout 300 wshimit MAGNET PARAMETERS sh range 2047 30 2 46 5 August 11 2003 S 15 Using The VNMR Shimlt Client Software The status line of the Menu window shows messages like Experiment started The graphic window is used to display the area of the current spectrum used for auto shimming Both phasing and current position of the analyzed spectral region are updated for every acquired FID ShimIt does however not adjust the width of the displayed spectral area or the number of points in the analysis range
27. cking system is active For the UNITY 300 spectrometer used for this example the spectrum of the proton lineshape sample with all shims set to zero and no locking or sample spinning looks as follows Even though the shimming will only be based on the center resonance the acquired spectral width should be chosen wider For speed reasons ShimlIt performs locking not by adjusting z0 but by shifting the analysis window over the acquired spectrum to compensate for constant offsets in impure shims On the other hand the acquired spectral width should only be chosen as large as necessary During a ShimIt run a large number of FIDs are acquired and a large 2 Shimlt can indeed also shift the field by adjusting z0 A currently disabled feature of Shimlt is to function as a software lock for data acquisitions where the normal deuterium hardware lock is not applicable 6 2 August 11 2003 spectral width has to be digitized by a large number of points which slows down the Fast Fou rier Transform FFT of the FIDs The next step in preparation of the autoshimming is to reduce the displayed spectral region to be analyzed for the auto shimming The goal here is to include the signal and its tails but hardly any baseline For this example the chosen area is Admittedly the chosen spectral range does not completely include the signal tails as assumed for the mathematical derivation of the method However ShimIt was found to be very forgiv
28. d faster workstations obtain a significant speed up Experienced spectroscopists typically need at least a day to shim a magnet from scratch Currently the phasing module of ShimIt assumes that the signal in both the real and imaginary part of the displayed spectrum arises from the resonance to be optimized So the shimming should be based on an isolated line in the spectrum Another requirement for fast shimming is a short relaxation time of the observed resonance to avoid an excessive sample saturation For the following example a plain water sample is used Shimlt contains a software lock which shifts the position of the analysis region in the acquired spectrum to compensate for resonance frequency shifts between FIDs Therefore the Vari 1 Some research samples might not have a sufficiently isolated signal for use by the current version of Shimlt Future Shimlt versions will address this issue August 11 2003 6 1 Automated Shimming Example autolock should be set to off Even for samples which in contrast to the water sample used contain a lock substance the Varian autolock mechanisms should normally be turned off at least during coarse shimming The danger of using Varian s autolock is that when the lock signal is lost during the auto shimming the lock mechanism wildly changes the field to search for the lock signal even if an acquisition is in progress ShimIt performs the software locking whether or not the spectrometer lo
29. e We MAGICAL macro shimit z C Reinhard Dunkel x x x Optimize spinning shims using spinning sample with auto shimming software ShimIt x x Nov 29 1994 EM x Nkkkxk xkxkxkxkxkxkxkxkxkxkxkxkxkxkxkxkxkkxkxkxkkxkxkxkxkxkxkkxkxkxkkxkxkxkxkkkxkxkxkxkkxkxkxkxkkxkxkxkxkxkkxkxkkkkxkxkxkkkxkxkxx x spin 50 spin alock lockpower lockgain in shimit init shims shimit init task sscycles shimstep order converge timeout sp D max fid cr Srflrfp rfp rfl sp cr rfp Soldtof Tut axial shims shim 1 sp substr shims UNTIL current shim SiWord 8 er rtlrfp Sp Or TTP trunc sh_range 4 1 0 order wp spin 1 5 2 Ww spin 1 5 iWord REP current shim SiWord 1 SiWord 1 current shim rfl rfp Spin sample at 50 Hz Regulate spinning now No Varian locking No power for lock channel Don t detect lock signal No checking of lock or spin Create ShimIt variables Optimize spinning shims Initialize ShimIt Set ShimIt to auto shimming No sample saturation expected z shims partly optimized Minimize first central moment Termination by max fid Time out after 5 minutes idle Exclude spinning sidebands Narrow displayed spectral area Count number of selected shims bb mn Y Y Coarse shim adjustment Cursor to middle of display Assign 0 Hz to cursor pos
30. e 1 1 1 2 runtime overhead ene EET S spherical harmonies iccsccscacacitisnceardeinnows 2 2 spinning sample IT 5 8 5 9 saturation 5 11 5 16 6 1 EE 5 9 6 3 spinning sssssetees 5 9 6 2 6 4 sideband s 5 8 5 9 6 22 Mee 7 l Start Mo line 5 16 second central moment 5 13 sane linen e dE 5 7 5 16 selected shims suem m abren 5 12 steady state REESEN 1 2 Kuere 5 11 5 16 server client implementation PEERS 1 2 FID 5 7 aiiis super conducting Magnet occ 2 2 CO cheats 2 1 2 2 3 1 3 3 COM EN 2 2 T ETT EATE AE 2 2 5 8 5 9 5 13 T2 relaxation time sss 5 16 Shimlt M FC NNNM 1 2 temporarily installation ss 4 1 GE 5 4 termination criterion 5 17 installation 4 4 i main mem 5 2 5 7 This Mo line 5 16 e e E WE E 5 6 5 7 7 4 August 11 2003 trademark PRED E 0 2 SOLARIS iecit itte reet ar decns 0 2 UNIX EE 0 2 Ka II 0 2 U unattended shimming 5 12 UNITY spectrometer deed 6 1 V variable CODVErge voc ecseessseesssesssssssssscsssecsssesssseessssessuessssessseses 5 12 MAX fidesi aneha aeiaai 5 12 PATH a eam tdi a 4 2 4 4 EEN 5 8 ehumeten nenne 5 11 EE 5 11 5 16 timeout 5 13 Ka IT 1 1 1 2 4 1 alpha window ssseettetentt nes 5 7 client software 5 13 command line sss 5 10 menu system ssssseeeees 4 5 5 1 ehimget ttt tentenenca 4 5 8 status line
31. elp maclibpath tmp maclib menulibpath tmp menulib Known ShimlIt Incompatibilities In order to make the ShimIt submenus accessible from the VNMR menu system a ShimIt button has to be placed in one of the existing menus The Shimlt software con tains a modified VNMR 4 3 main2 menu which allows one to start the ShimIt menu system For VNMR sites using an already modified main2 menu both main2 files will have to be merged manually For reasons of speed all ShimIt computations are done in a binary program called for Sun SPARC computers shimit SunOS and for timing purposes the binary program usleep SunOS is used These executables were build on a Sun SPARC running SunOS 4 1 In order to run the executables under Solaris 2 3 SunOS 5 3 the Binary Compatibility Package which is part of the Solaris 2 3 environment has to be installed 42 Magnet Specific Customization One of the major strengths of Shimlt is that the software can shim magnets even when no rea sonable starting values for the shims are know To do so requires the knowledge of the range in which shim values can be adjusted which coarse shims are available and what the sensitiv ity ratio of present coarse to fine shims is ShimIt uses the following global VNMR variables to provide information about the magnet used August 11 2003 4 5 VNMR Shimlt Installation sh range Maximum range of shim values zltozic Sensitivity ratio zl fi
32. him t nnan 4 5 Shims ienien na 5 5 5 7 August 11 2003 Index Show amp Pts esee 5 4 E Show Best 5 7 5 11 SS Cycles sssssssnnrioicleciscluctracsatatsondnersondas SA1 ror A 5 16 Stop ee 5 6 5 11 eror value 5 17 Tmeout tres 5 13 F C ee Fast Fourier Transform EFT 6 3 eka Maiti mre ue REUS 5 16 client software E 1 2 field coarse shim 4 1 4 5 4 6 4 7 5 8 ERR 33 command line sss 5 5 5 8 TA IIS PADO DONOR 2 2 DE rar EEN 42 plot EE 3 1 3 2 3 3 convergence criterion gg eege Tur COVER 12 first absolute value central moment 3 3 5 13 Shimlt ees 0 2 Free Induction Decay FID 1 2 current shim selection 00 0 0 cece 5 9 G D graphic wmdow 5 16 data EOS EE 5 4 decomposition model 3 3 H default value of j as 4 1 CODVETge isssssssseeettetrteetnette teens 5 12 Di 4 Gre EE ER high order z shim s 5 8 OLEE eu EE See 5 8 sh meten EEN 5 11 I rt nae sj Maging MRD E E E 33 EI STEE 6 2 Oe 5 8 installing new probe 2 1 7 2 August 11 2003 ae deli HEEN 4 1 5 1 6 3 interactive input request 5 9 SB Mn Width lime vomere baniniecusis 5 16 L N linear set of equations oce pho Mp 3 3 NMRanalyst lineshape moment 34 5 74 5 16 automated nD spectral analysis 1 1 e 6 2 non axial shim en Ss lock level vn ji idoeiggsg HEED T minea eae 6 22 sample idee
33. homoge neity But such field plots are not easy to obtain Fortunately such areas can be determined from the observed line shape Consider a sample along the magnet z axis Each spin in the sample resonates corresponding to the experienced magnetic field strength August 11 2003 Hence the field plot can be trans Magnetic FieldStrength lated into a distribution of reso nance frequencies as shown for a coarse grid of positions inside the magnet This operation does not preserve the positional information of a field plot and hence is not reversible But the distortion area in the one dimensional examples above as well as the three dimen sional distortion integrals in real magnets are always proportional to the first absolute value central moment of the resonance frequency distribution obtained from the resulting NMR line Resonance Frequency Distribution Magnet Z Direction The remaining problem is to determine this resonance frequency distribution from an observed NMR line Unfortunately dispersion mode signals as well as all phase insensitive methods of displaying NMR data e g absolute value mode cause lineshapes whose first absolute value central moment is infinite rendering them unusable for shimming based on lineshape moments ShimIt determines the resonance frequency distribution from the analysis of the spectral signal using a decomposition model See U S Patent 5 218 299 for details The mag
34. ic of the moment criterion is that its associated response surface can be proven to be describable by a linear set of equations Since a linear set of equations cannot have local minima ShimIt s inhomogeneity minimization cannot get trapped with a set of shim values far from the best possible homogeneity Instrumental instabilities determine how close Shimlt can approach this best possible homogeneity in a reasonable amount of time Notice that the moment criterion makes no assumptions about the number of shims to be adjusted whether or not a shim coil works or what the actual shape of a shim s produced magnetic field is Hence Shimlt itself does not depend on such factors either August 11 2003 3 3 How Shimlt Works 3 4 August 11 2003 CHAPTER A VNMR Sh mlt Installation The VNMR 4 3 Shimlt software consists of macros menus and help files These files need to be placed in directories recognized by VNMR as described in SECTION 4 1 Installing Mac ros Menus and Help Files ShimIt was written to work with all seven shim sets recognized by VNMR 4 3 Unfortunately for some magnets Varian chose to generate the current for one magnet coil from two parameters a coarse shim and a fine shim Based on the setting of the VNMR shimset variable ShimIt knows which coarse shims are available But the sensitivity ratio between coarse and fine shim varies between spectrometers and Varian failed to make these ratios accessible through
35. imIt menu Help button displays the following short description of the use of Shimlt 5 2 August 11 2003 Shimlt Main Menu Show Pts Button The Shimlt software adjusts the magnet homogeneity based on the shape of an isolated NMR signal So before optimizing shim values the user needs to display an isolated signal with a small amount of baseline on the screen for the ShimIt optimization August 11 2003 5 3 Using The VNMR Shimlt Client Software Manual lineshape shimming tends to focus on making the upper part of the line Lorentzian in shape A main focus might be to minimize the width at half height of the line ShimIt focuses on optimizing the base of the signal which eventually leads to a minimization of the width of the signal as well Selecting a reasonably good range around the signal for the ShimIt optimi zation is demonstrated in CHAPTER 6 Automated Shimming Example A major concern for the use of Shimlt is the number of points in the displayed spectral area which Shimlt has to analyze for each acquired FID This Show Pts button causes the current number of complex spectral points in the displayed spectral area to be shown in the VNMR status line So the spectral area shown contains 42 complex valued spectral points The time Shimlt spends on analyzing each FID is normally small compared to the overhead of the Varian soft ware for acquiring a spectrum However an excessive number of poin
36. in shimit init Create ShimIt variables 6 18 August 11 2003 Further Optimization Of Spinning z Shims shims axial shims shimit init task shim sscycles 0 shimstep trunc sh range 8 order 0 5 converge 1 0 order timeout 300 sp sp wp spin 2 wp spin 0 8 SiWord 1 REPEAT current shim SiWord iWord 1 substr shims S iWord 1 current shim UNTIL current shim max fid iWord 10 cr sp wp 2 Srflrfp rfl rfp rfp 0 rfl cer rflrfp sp sp cr rfp cr rfp Soldtof tof tof Soldtof sw 2 rfp rfl rfl rfl Soldtof tof IF sw sfrq 10 THEN Soldsw sw sfrq 10 rfl Soldsw 2 sw 2 sw rfl ENDIF at 75 at sw 2 wp np nt 1 rm userdirt ShimIt_z fine mv userdir ShimIt userdir ShimIt z fine wshimit menu shimit shimit start wshimit Optimize spinning shims Initialize ShimIt Set ShimIt to auto shimming No sample saturation expected z shims pre optimized Increase weight of signal height Termination by max fid Time out after 5 minutes idle Exclude spinning sidebands Narrow displayed spectral area Count number of selected shims bb Coarse shim adjustment Cursor to middle of display Assign 0 Hz to cursor position Center display area in spectrum Fix spectral referencing Limit spectral width to 10 ppm
37. ition Center display area in spectrum August 11 2003 6 9 Automated Shimming Example tof Soldtof sw 2 rfp rfl rfl rfl Soldtof tof Fix spectral referencing IF sw gt sfrq 15 THEN Limit spectral width to 15 ppm Soldsw sw sw sfrq 15 rfl rfl Soldsw 2 sw 2 Fix spectral referencing ENDIF at 100 at sw 2 wp np Display 100 points 75 Hz pt nt 1 No time for signal averaging rm userdir ShimIt z Delete old ShimIt directory wshimit mv userdir ShimIt N userdir ShimIt z N IT shimit non zi Finished Save amp start non z shimming menu shimit Show main ShimIt menu shimit start Start ShimIt FIO o Integral 1 790958E407 Integral rp Phase 14 9228 rp Phase Mo Width 1 19094 Mo Width Start Mo 9 96440 Start Ho 9 Best Mo 9 96440 Best Mo 9 58170 This Mo 9 964409 This Mo 9 558170 Error Mo 7 f Error Mo 6 10 August 11 2003 Optimization Of Spinning z Shims Program Sbimit Integral rp Phase Me Width Start Mo Best Mo This Mo Error Mo Program Effect Shim z3 3 1 64578E407 12 6925 1 19094 9 96440 9 13216 z CEA Sbimit Integral rp Phase Me Width Start Mo Best Mo This Mo Error Mo 19 0045 Report FIR Integral rp Phase Mo Width Start Mo Best Ho This Mo Error Mo Program Report
38. lt is now ready for the first public release of the software Running Shimlt is similar to manual shimming based upon the shape of a displayed NMR sig nal Shimlt runs inside the spectrometer software here VNMR so all commands and dis plays of the spectrometer software remain user accessible For the interactive shimming on a displayed lineshape a spectroscopist acquires a spectrum changes the shim values and repeats this cycle until a satisfactory homogeneity is obtained In contrast ShimIt only needs to be told which shim values to optimize and then loops through changing these shim values and acquiring new spectra without the need for further user interaction The difference between manual and ShimlIt optimization of the lineshape is that Shimlt evaluates the line shape in a way which has been mathematically proven to lead to the optimal homogeneity without the risk of getting trapped with sub optimal shim values There are two competing approaches for automated shimming Automated lock level optimi zation is based on special lock hardware and is quite fast and effective for touching up low 1 U S Patent No 5 218 299 and 5 572 125 August 11 2003 1 1 Introduction order z shims However like the manual lineshape optimization the lock level optimization is plagued by local optima in the optimization criterion So ShimIt should be used for every major homogeneity adjustment However for minor low order z shim
39. nal main menu main2 containing a button to show the main ShimIt menu The VNMR menu system consists of two rows of buttons The top row is accessible at all times and is referred to as the permanent menu The second row can be customized and is used to display the three ShimIt menus After the start of VNMR or after clicking on the Main Menu button in the permanent menu the following menus are displayed 1 The ShimIt menu files are called shimit shims and params Unfortunately the menu name setup was already in use in VNMR 4 3 August 11 2003 5 1 Using The VNMR Shimlt Client Software Click on the More button to start the modified additional main menu containing the but ton to start the ShimIt main menu 5 1 Shimlt Main Menu The ShimIt main menu can be reached from the modified additional main menu discussed above by clicking on the ShimIt button All functions of Shimlt are available from this menu To aid in the editing of ShimIt parame ters the Shims and Setup submenus are provided and are accessible from this menu see SEC TION 5 2 Shims Submenu and SECTION 5 3 Setup Submenu for details To display a short description of the function of a ShimIt menu click on the Help button in the perma nent menu while the menu of interest is displayed Help Button The Help button in the permanent menu explains the function of the menu buttons This main Sh
40. ne shims is determined by the shimming hard ware the spectrometer vendor Varian should be able to provide missing values This table 1 To have Shimlt recognize a so far unknown shim set or to customize an already defined shim set the macro shimit init and the menu file shims have to be customized accordingly 2 Shimlt can be configured to ignore a coarse shim by setting the corresponding z toz c variable to 1 or to only use the coarse shims by setting the variable to 1 4 6 August 11 2003 Magnet Specific Customization is contained in macro shimit init and to activate the appropriate definitions remove the double quotes from the appropriate lines An experimental procedure to estimate these sensitivity ratios is to change a coarse shim by a given number of steps and to determine how many steps of the fine shim are needed to com pensate The corresponding z toz c shim should be set to the absolute value of the number of determined fine shim steps divided by the number of coarse shim steps Once these variable values have been determined they should be entered in macro shimit init so each user will get the determined sensitivity ratios by default August 11 2003 4 7 VNMR Shimlt Installation 4 8 August 11 2003 CHAPTER 5 Using The VNMR Shimlt Client Software The ShimIt version for VNMR consists of menus macros and help files The user interface consists of three ShimIt menus and a modified additio
41. ne to coarse shim z2toz2c Sensitivity ratio z2 fine to coarse shim z3toz3c Sensitivity ratio z3 fine to coarse shim z4toz4c Sensitivity ratio z4 fine to coarse shim VNMR 4 3 recognizes seven shim sets and for each of the recognized shim sets defines the maximum allowable shim range sh range and which coarse shims are available for each So Shimlt sets these variables automatically when the main ShimIt menu is displayed for the first time For VNMR s shim sets 3 4 6 and 7 which have no coarse shims the Shimlt soft ware installation is completed Both shim sets 1 and 2 have a z1c and z2c shim and shim set 5 has all four coarse shims z1c z2c z3c z4c Varian failed to specify the sensitivity of fine to coarse shim values So Shimlt sets the z toz c variables of unavailable coarse shims to minus one and to a default value of 20 for available coarse shims The value twenty means that the corresponding coarse shim is assumed to have twenty times the effect of the corresponding fine shim Unfortunately the default value is not sufficiently accurate for most spectrometers The fol lowing table of sensitivity ratios was determined from the Schematics Package of the corre sponding spectrometers Spectrometer shimset zltozlc z2toz2c Unity 300 1 30 2 46 5 VXR 500 2 24 95 19 55 Additional spectrometers will be added to the table as the corresponding values become avail able Since the sensitivity ratio of coarse and fi
42. net The magnet specific parameters are set during the installation of ShimIt as described in SECTION 4 2 Magnet Specific Customization The shims to be adjusted can be chosen from the Shims submenu described in SECTION 5 2 Shims Submenu The final group of parameters determines how the auto shimming is performed and these parameters can be set from this submenu Note that all ShimIt parameters can also be set from the VNMR command line 6 The menu file for the Setup submenu is called params since the name setup is used by VNMR 4 3 for other purposes 7 Strictly speaking splitting a magnet shim into a coarse and fine dial is a function of both the software and the DACs used to generate the shimming currents and is not really a function of the magnet S 10 August 11 2003 Setup Submenu SS Cycles Button ShimlIt acquires FIDs in rapid succession during shimming If the relaxation time of the reso nance selected for shimming is longer than the repetition time of Shimlt the sample progres sively saturates during the shimming run A time consuming method to avoid this problem is to increase the pre acquisition delay d1 and thereby to slow down the data acquisition A faster approach is to decrease the amount of sample saturation and to auto shim on the partly saturated sample The amount of sample saturation during the shimming run can be decreased by lowering the 90 degree pulse width provided the signal to noise S
43. on In cases where a good starting set of shims is not avail able such as when bringing up a magnet or installing a new probe the magnet shimming can take hours or even days to complete Shimming is often regarded as a black art requiring a good knowledge of the particular magnet and extensive experience with magnet shimming in general The field distortions of an NMR magnet over the sample volume should be no greater than a fraction of the natural linewidth of the slowest relaxing nucleus to be observed For a 750 MHz magnet and a 0 1 Hertz proton resonance linewidth this calls for a field accuracy of bet ter than 1 7 500 000 000 Raw magnetic fields are typically several orders of magnitude less homogeneous Hence shim coils of different shape are placed inside the raw magnet to pro duce additional magnetic fields to compensate for remaining inhomogeneities State of the art 1 Chmurny GN Hoult D I The Ancient and Honourable Art of Shimming Concepts in Magnetic Resonance 1990 2 131 149 August 11 2003 2 1 The Need For Magnet Shimming NMR super conducting magnets have typically between 10 and 40 room temperature shim coils The best shim setting could be determined analytically if the shape of the raw magnetic field the shape of all shim fields and the field distortions caused by probe and sample were known In NMR imaging MRI the shape of the magnetic field can be approximately determined through the use
44. p In s tmp maclib SHOME vnmrsys maclib In s tmp menulib SHOME vnmrsys menulib oe oe oo If links for these files are not desired the installation becomes more tedious To increase the efficiency of the ShimlIt software the macros shimit SunOS and usleep SunOS are actually binary programs The Shimlt software is configured to search for these executables in the directories in the user s PATH variable in SHOME bin SHOME vnmrsys maclib vnmr bin and vnmr maclib For UNIX to find the binary program in a non standard directory either extend the PATH vari able with oe PATH tmp SPATH export PATH Borne and Korn shell set path tmp Spath C shell or copy move or link both files to a recognized directory here the user s bin directory oe ln s tmp maclib shimit SunOS HOME bin ln s tmp maclib usleep SunOS HOME bin oe or modify the maclib shimit start and maclib shimit client macros to include the chosen directory in the PATH variable before calling shimit SunOS and usleep SunOS 4 4 August 11 2003 Magnet Specific Customization Finally VNMR has to be told where to search for the new menus macros and help files So inside VNMR issue the following commands ignore VNMR create warnings about already existing variables create helppath string global create maclibpath string global create menulibpath string global helppath tmp h
45. rademarks of their respective holders CHAPTER 0 Table of Contents CHAPTER 1 Introduction esses hehehe enne 1 1 CHAPTER 2 The Need For Magnet Shimming 2 1 CHAPTER 3 How ShimlIt Works eee ettet ene ena honte 3 1 CHAPTER 4 VNMR Shimlt Installation eese 4 1 41 Installing Macros Menus and Help Files is eie eteiaestent bec ene pub Re a Lapae duns 1 42 Magnet Specific CUSIDIDIEBDIGE secari bip ERU Ea eranan EEI O E O CHAPTER 5 Using The VNMR Shimlt Client Software 5 1 5 1 pit NOU IIR o oerte or ber xS Dr tkt PH SEX ERE Mot et PH SEU td PE MR MESA 2 S2 cin 3 0 co AU enr 7 So Soup URDU diri ei ER EFRUR FERE FUE FREE mit eRe eae 10 August 11 2003 3 Contents CHAPTER 6 CHAPTER 7 a4 Diplaycd Shining Results iui e bares ei hb bn bM acus baa Ae bros 14 Automated Shimming Evomnple sss 6 1 6l Optimization OF ACERO 4 6 2 Optimization Of Spinning 2 SIMS cscs vacate ecescasskdavassivsivalassaoasiaeas rnani ieia 9 63 Optimization Of Non Spinning Shims aisssiatssis hannsin ieuna atashe aani oia se anii 12 64 Further Optimization Of Spmning Z Shims mtra 18 LU TE 7 1 August 11 2003 Shimlt User Manual CHAPTER 1 Intr oduction The Shimlt auto shimming system was written in 1990 as a side product of the NMRanalyst software With further improvements in user interface and documentation as well as patent protection Shim
46. rent spectrometer systems and to experiment with different user interfaces Since shimming is such a fundamental problem in NMR each spectrometer system should be delivered with a reliable auto shimming system Due to the cost of spectrometer time ShimIt should be ultimately integrated into each spectrometer system to achieve maximum shimming speed Currently the only ShimIt client available is for Varian VNMR 4 3 or newer systems Development of client software for other spectrometer systems is planned for future releases of ShimlIt The VNMR client recognizes all seven shim sets understood by VNMR 4 3 Despite extensive testing the ShimlIt client software probably still has deficiencies Please report all problems and suggestions for improvement to me at the contact information given earlier Please note that this software is protected by copyright and the underlying shimming method is patented 2 With minor hardware changes it would be possible to acquired complete FIDs through the lock channel These FIDs could then be used for the Shimlt optimization of the magnet homogeneity 1 2 August 11 2003 CHAPTER 2 The Need For Magnet Shimming Magnet shimming remains one of the few areas of NMR where automated procedures have failed to replace the tedious manual optimization of experimental conditions Even experi enced spectroscopists spend a significant amount of spectrometer time on touching up shims before each data acquisiti
47. rum limit the accuracy of determined moments The default value of converge is 1 A value for the order parameter of less than one decreases the fluctuation of the determined moment and the converge value should be decreased accordingly Setting this variable to much less than the default value can significantly delay the convergence of ShimIt without further improve ments in the magnet homogeneity Order Button Lock level shimming concentrates on maximizing the height of the lock signal As a result the lock level is quite effective for touching up the low order z shims Unfortunately in all other cases lock level optimization tends to run astray and to result in less than optimal lock level maxima Shimlt on the other hand optimizes the absolute value normally first central 5 12 August 11 2003 Setup Submenu moment of an observed line This reliably minimizes the width of the base of a signal and minimizes remaining baseline distortions Given an imperfect shim set the maximum height and the best narrow base of a signal can frequently not be obtained simultaneously Many spectroscopists favor an improved signal height at the expense of a deterioration of the baseline and width of the signal base The Order button allows one to interactively set the order parameter This parameter determines the order of the absolute value lineshape moment which Shimlt optimizes Large order values favor flatter baselines and narrower sig
48. shims might need to be readjusted after the optimization of the non spinning shims All Button This button selects all shims in the current shim set to be optimized during the automated shimming Selecting the optimization of all shims is only necessary when the magnet homo geneity is too bad for the sample spinning to baseline separate the spinning sidebands from the center resonance Otherwise optimizing the non spinning shims first followed by the optimi zation of the spinning shims will in general yield a better spinning lineshape Add Button This button starts an interactive input request for the specification of shim names to be added to the current shim selection Duplicate shim names are deleted from the resulting list Remove Button This button starts an interactive input request for the specification of shim names to be deleted from the current shim selection August 11 2003 5 9 Using The VNMR Shimlt Client Software Specify Button This button starts an interactive input request for the specification of a new list of shim names to be optimized during the automated shimming Return Button This Return button causes the menu system to return to the main ShimIt menu 5 3 Setup Submenu SL Index The Setup button in the main ShimlIt menu starts the Setup submenu shown above There are three groups of parameters which influence the way ShimIt performs the auto shim ming of a mag
49. software or even to document them Hence these sensitivity ratios might need to be determined and specified during the ShimlIt software installation as described in SECTION 4 2 Magnet Specific Customization 41 Installing Macros Menus and Help Files The ShimIt macros should be placed in a VNMR recognized mac1ib directory the menus in amenulib directory and the help files in a help directory To install ShimIt temporarily or for only one user the maclib menulib and help directories in SHOME vnmrsys should be used For the permanent installation for all users the maclib menulib and August 11 2003 4 1 VNMR Shimlt Installation help directories in vnmr should be used The last possibility is to place the software any where in the filesystem and to set the UNIX PATH variable and various VNMR parameters accordingly The Shimlt software is distributed as a compressed tar file named shimit tar 2Z The file contains the following directories and files help ShimIt Manual ps main2 params shimit shims maclib parse shims remove shims shimit SunOS shimit_all shimit client shimit display shimit finish shimit init shimit non z shrmrt Start shimit z shimit z fine usleep SunOS menulib main2 params shimit shims First load the file shimit tar Z from the distribution medium Consult your system administrator in case of problems To simplify the following discussion it is assumed that 4 2 Augus
50. t 11 2003 Installing Macros Menus and Help Files shimit tar Z is loaded in the directory tmp Now install the software in one of the fol lowing three ways System Wide Installation To install the ShimIt software system wide obtain root privileges using symbolizes the user prompt su and specify the password Then change the current directory to vnmr symbolizes the root prompt by typing cd vnmr and uncompress zcat and untar tar xvf the shimit tar Z file in the current direc tory by entering zcat tmp shimit tar Z tar xvf This command installs all files in their intended places Single User Installation To install the ShimIt software only for the current user issue the following commands oe cd SHOME vnmrsys zcat tmp shimit tar Z tar xvf Installation In Unsupported Directory To install the ShimIt software in an unsupported directory here assumed to be tmp issue the following UNIX commands August 11 2003 4 3 VNMR Shimlt Installation oo cd tmp zcat tmp shimit tar Z tar xvf oo Notice that in contrast to the previous examples three new directories are created help maclib menulib The fastest approach to using an unsupported directory for the Shimlt installation is to link all files in the created directories to the corresponding VNMR directories which completes the installation of Shimlt files In s tmp help SHOME vnmrsys hel
51. trum and the Show Best button is displayed Whenever Shimlt is stopped manually or stops due to a time out this Show Best button should be used to retrieve the best acquired FID and its shim values If ShimIt terminates normally either by converging or by reaching the maximum number of iterations the best spectrum is retrieved automatically at the end of the shimming run Return Button The Return button in the main ShimIt menu causes the menu system to return to the additional main menu menu file main2 5 2 Shims Submenu inning 4 811 5 6dd 6 The Shims button in the ShimIt main menu starts the Shims submenu shown above The purpose of this submenu is to aid in the selection of shim variables to be adjusted by Shimlt On start of this submenu the ShimIt parameters are displayed in the VNMR alpha window using the dg command The current selection of shim values is displayed both in the alpha window as well as in the status line as shown in the figure above As the selection of shims is changed using these menu functions both the dg display in the alpha window as well as the status line are updated accordingly August 11 2003 5 7 Using The VNMR Shimlt Client Software The current selection of shims is stored in the shims variable as a list of shim names sepa rated by blanks To specify a list of shim values the shim names can be separated by a blank comma semicolon colon or any non empty combin
52. ts in the selected spec tral area can lead to a noticeable slow down of ShimlIt So this number should be kept as small as possible On slow workstations the number should be around 50 and faster workstations can normally handle 100 points without causing significant delays To decrease the number of points in the spectral area decrease the acquisition time re acquire the spectrum and use the Show Pts button to check the current number of complex points again dgQ Button Several parameters are provided to customize Shimlt s behavior All ShimIt parameters can be displayed in a data group dg using this dg button The button action is equivalent to issuing dg dg shimit from the command line 2 Currently VNMR and Shimlt read the acquired FIDs and FFT the data separately This inefficiency causes most of the Shimlt response time for analyzing an FID 5 4 August 11 2003 Shimlt Main Menu All displayed parameter values can be changed from the command line The SELECTED SHIMS group is described in SECTION 5 2 Shims Submenu The Shims menu started by the Shims button allows one to change the selection of shims to be optimized The SHIMIT PARAMETERS are described in SECTION 5 3 Setup Submenu These parame ters can be interactively changed from the Setup menu started by the Setup button Finally the MAGNET PARAMETERS group values should be set during the software installa tion and should not require further c
53. ustomization See SECTION 4 2 Magnet Specific Cus tomization for details Shims Button The Shims button starts the Shims submenu of ShimIt This submenu provides a conve nient way to specify the shims to be optimized during the shimming process See the discus sion of this submenu in SECTION 5 2 Shims Submenu for details Setup Button The Setup button starts the Setup submenu of ShimIt This submenu provides a conve nient way to interactively specify the ShimIt parameters controlling the iterative shimming process See the discussion of this submenu in SECTION 5 3 Setup Submenu for details August 11 2003 5 5 Using The VNMR Shimlt Client Software Start Stop Button This button can be used to start the shimming process once an isolated NMR signal is dis played and the ShimIt parameters are set as desired On start of ShimIt the button label toggles from Start to Stop The Stop button can then be used to terminate the running ShimIt program The Stop button only terminates the ShimlIt run but does not terminate an acquisition in progress To terminate an acquisition click on the Abort Acq button in the permanent menu The Stop button changes back to Start whenever Shimlt termi nates due to a user request the set maximum number of iterations is reached the convergence criterion is satisfied or the response from spectrometer or Shimlt exceeds the set time out period VNMR provides se
54. veral means of automatic processing which slow down or even interfere with ShimIt To make ShimIt easy to use the automatically called MAGICAL macro shimit start switches all automatic VNMR features off before beginning an auto shim ming run Should this behavior be undesirable comment out the corresponding lines in this macro No automatic VNMR processing load n Don t load shim values from experiment yet wshim n No automatic shimming besides ShimIt alock n Leave lock in its current state spin n Leave spin rate at currently used value gain y No automatic adjustment of receiver gain hdwshim n No hardware zl shimming in ni No interlock don t adjust lock level or spin rate wexp K No action yet when experiment completes werr No action for acquisition error wbs 5t No action after bs transients wnt II No action after nt transients Delay acquisition until new shim values stabilize UI UI IF pad dl 1 THEN d1 1 pad ENDIF 5 6 August 11 2003 Shims Submenu Show Best Button ShimIt improves the magnet homogeneity iteratively As a result several FIDs might be acquired with a homogeneity worse than previous FIDs On start of ShimIt the Show Best button is only displayed if a Best spectrum from a previous Shimlt run is still avail able After the requested steady state FIDs are completed Shimlt saves the starting spec
55. ycles 0 shimstep trunc sh range 2 order 1 converge 1 0 order timeout 300 SiWord 1 REPEAT Scurrent_shim SiWord iWord 1 substr shims S iWord 1 current shim UNTIL current shim SiWord 8 wp 2 rfl rfp max fid cr sp Srflrfp rfp 0 rfl cr rflrfp sp sp cr rfp cr rfp Soldtof tof tof Soldtof sw 2 rfp rfl rfl rfl Soldtof tof IF sw gt sfrq 20 THEN Soldsw sw sfrq 20 rfl Soldsw 2 sw 2 sw rfl ENDIF at 75 at sw 2 wp np nt 1 rm userdir ShimIt all wshimit mv userdir ShimIt N userdir ShimIt all N shimit zi menu shimit shimit start Create ShimIt variables Optimize all available shims Initialize ShimIt Set ShimIt to auto shimming No sample saturation expected Shims completely unknown Minimize first central moment ww Termination by max fid Time out after 5 minutes idle Count number of selected shims Coarse shim adjustment Cursor to middle of display Assign 0 Hz to cursor position Center display area in spectrum Fix spectral referencing Limit spectral width to 20 ppm Fix spectral referencing Use 75 points for display No time for signal averaging Delete old ShimIt directory Finished Save amp start z shimming Show main ShimIt menu Start ShimIt August 11 2003 6 5 Automated Shimming Example Best Mo This Mo
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