Philips 26PW8402137 User m Bedienungsanleitung

LCModel1& LCMgui User’sManualStephen ProvencherNovember 17, 20141LCModel Version 6.3-1K

10 CONTENTS11.13 Relaxation & Shift Priors . . . . . . . . . . . . . . . . . . . . . . . . . 14611.14 Detailed Output . . . . . . . . . . . . . .

100 CHAPTER 8. MAKING THE BASIS SETbe analyzed as “data” when BASCAL=T.NCALIB (integer) NCALIB > 0 sp ecifies that only NCALIB Basis Spectra f rom t

8.8. SUMMARY 101CHBCAL=’NAA2’NCALIB=1CHCALI(1)=’NAA’(You must also input NUNFIL, DELTAT & HZPPPM equal to those of the basisset.) Call the concent

Chapter 9Further Useful Options andInformationThis chapter specifies useful Control Parameters that you can input in the .CONTROLfile (or, with LCMgui,

9.2. MUSCLE SPECTRA 103landmarks (NAA, cholines and creatines) weaker than Lac & Glc (PLOT 13).SPTYPE = ’version5’ is for consistency with very ol

104 CHAPTER 9. FURTHER USEFUL OPTIONS AND INFORMATIONbaseline, keep PPMEND < 0. In future measurements, be sur e to increase the spectralbandwidth

9.2. MUSCLE SPECTRA 105Section 9.3.2.1 sp ecifies how to convert from resonance areas to (less convenient) concentra-tions.9.2.2.5 ReferencingYou only

106 CHAPTER 9. FURTHER USEFUL OPTIONS AND INFORMATIONCr : the Cr CH3signal around 3.03 ppm. However, some of the (orientation-depend ent) Tau signal m

9.3. LIPID SPECTRA (LIVER, BREAST, BONE, ETC.) 1079.3.1 InputLCMgui users can select any valid file name for the .BASIS file in Fig 6.4; it is notused.

108 CHAPTER 9. FURTHER USEFUL OPTIONS AND INFORMATION9.3.1.2 One spectrum: Single spectrum with no water suppressionThe Two-Spectra Method is u sually

9.3. LIPID SPECTRA (LIVER, BREAST, BONE, ETC.) 1099.3.2 OutputSee PLOT 11 in $HOME/.lcmodel/doc/figures.pdf.The main output is in the (top-right) Conc

Chapter 1Preface & O verviewThe LCMod el package is for the automatic quantitation of in vivo proton MR spec-tra [1]. LCMgui is a graphical user i

110 CHAPTER 9. FURTHER USEFUL OPTIONS AND INFORMATIONhave the heading /Water; this is only meaningful if you are using the On e-SpectrumMethod with no

9.4. MEGA-PRESS FOR GABA 1119.3.3.1 ReferencingThere is one prerequisite: water suppression must be balanced as follows: It mustbe strong enough so th

112 CHAPTER 9. FURTHER USEFUL OPTIONS AND INFORMATIONPPMEND = 1.95(LCMgui users use Fig 7.7 in Sec 7.3.4.)The above PPMEND cuts off dangerous artifacts

9.4. MEGA-PRESS FOR GABA 113Scaling in Sec 9.4.1.3 is needed if you want to estimate absolute concentrations.9.4.1.3 Water-ScalingFor this you need in

114 CHAPTER 9. FURTHER USEFUL OPTIONS AND INFORMATIONTable 9.1: Control Parameters for Filenames and Logical UnitsFilename Unit Default Alt. Extension

9.7. PRIOR PHASING INFORMATION 115and instead read Sec 6.3.3.) ECC requires that a second set of raw time-domain databe acquired with each set of in v

116 CHAPTER 9. FURTHER USEFUL OPTIONS AND INFORMATIONedge.SDDEGZ < 45. will cause LC Model to start looking for φ0at DEGZER.SDDEGZ ≥ 45. will not a

9.8. SPECIFYING THE BASIS SPECTRA FOR THE ANALYSIS 117in Sec 12.2.9.8 Specifying the Basis Spectra for the Analysis9.8.1 Omitting Basis Spect ra from

118 CHAPTER 9. FURTHER USEFUL OPTIONS AND INFORMATIONFor examp le,NKEEP=1CHKEEP(1)=’Lac’in the .CONTROL file would keep Lac in the current analysis, ev

9.9. ONE-PAGE OUTPUT 119The same goes even more so for GABA and Glu+Gln. The GABA signal is much weaker.So, you s hould not consider the sum GABA+Glu+

12 CHAPTER 1. PREFACE & OVERVIEWChapter 9 describes further useful Control Parameters.Chapter 10 need on ly be read if you want to estimate absolu

120 CHAPTER 9. FURTHER USEFUL OPTIONS AND INFORMATIONThe three elements of RGBBOL & RGBRAT spec ify the fractions of red, green & blue, respec

9.9. ONE-PAGE OUTPUT 121PAGEHT (real) the height of your page in cm. Default: PAGEHT = 27.9, i.e., 11 inches.PAGEWD (real) the width of your page in c

122 CHAPTER 9. FURTHER USEFUL OPTIONS AND INFORMATIONfor a slide or figure.Defaults: WDLINE = .06, .01, .005, .01, .04, .005RGBLIN (real(3,6)) RGBLIN(J

Chapter 10Absolute MetaboliteConcentrationsYou only need to read this chapter if you want to estimate absolute concentrations.Concentration ratios are

124 CHAPTER 10. ABSOLUTE METABOLITE CONCENTRATIONSWater-Scaling: The resonance area of the unsuppressed reference water signal (to-gether with the ass

10.1. CALIBRATION PHANTOMS 125in duration) [17]. For Siemens Vision data, LC Mgui sets TRAMP to the “raw” fileheader element G19.Acq3.Mr.TransmitterCal

126 CHAPTER 10. ABSOLUTE METABOLITE CONCENTRATIONS10.1.2 Scanner Calibration (inter-hardware)Even if your Basis Spectra were scaled as in Sec 10.1.1,

10.2. WATER-SCALING 12710.2 Water-Scaling10.2.1 MethodWith Water-Scaling, LCModel multiplies the data by fscaleto scale the data consistently with the

128 CHAPTER 10. ABSOLUTE METABOLITE CONCENTRATIONSWCONC (real) the NMR-visible water concentration (mM) in the voxel. This is55556βMRin [28], where ty

10.2. WATER-SCALING 12910.2.2.1 Bruker Da taLCMgui does n ot divide the Bruker data by the number of scans, NS, or by the totalgain, Gain. With Water-

1.4. ACKNOWLEDGMENTS 13File names and LCMod el input/output are written in the teletype style, as figures.pdf.Your home directory is specified by $HOME

Chapter 11Fine PointsThis chapter contains a collection of further topics and options. Scan the sectionheadings. Top ics that are of more restricted i

11.2. RELAXATION CORRECTIONS 131particularly of macromolecule and lipid signals. The (higher) coefficient of variationusing (the more realistic) LCModel

132 CHAPTER 11. FINE POINTSthe exponents contain only differences of relaxation times between the two metabo-lites.If you use Water-Scaling (Sec 10.2)

11.3. PRIOR REFERENCING INFORMATION 13311.3.2 Referencing to WaterIf your water suppression is not too extreme, it is convenient to use the huge water

134 CHAPTER 11. FINE POINTS11.3.4 Fixing the ShiftThe very first estimate of the starting shif t is from the cross-correlation function(CCF) described

11.4. MULTI-VOXEL DATA SETS 135To use the Lac doublet, input two PPMREF = 1.33 and the correspo nding twoHZREF = 3.6 & -3.6. However, lipid signal

136 CHAPTER 11. FINE POINTS11.4.3 Multi-Voxel FilenamesYou input a single TITLE a nd single output filenames, but there will be one for each voxel.Thes

11.4. MULTI-VOXEL DATA SETS 13711.4.4 Output for spreadsheetsAs specified in Sec 11.4.3, each voxel has its own set of files. Only the .CSV file c ombine

138 CHAPTER 11. FINE POINTS11.5 Basis Spectra in the Preliminary AnalysisThe Preliminary Analys is for initial referencing and phasing uses a reduced

11.7. SIMULATING BASIS SPECTRA 139NSIMUL (integer) is the number of Basis Spectra that you will simulate.Default: NSIMUL = 13.CHSIMU (character(60)*52

14 CHAPTER 1. PREFACE & OVERVIEWThe code generating the PostScript output files is based on advice and routines kindlyprovided by Christian Labadie

140 CHAPTER 11. FINE POINTS2 ppm. The respective AMP values in this region sum to 2.0, to estimate mMof CH2groups. The minor peaks at 2.8 & 3 ppm

11.8. CONCENTRATION RATIO PRIORS 141too many concentra tions to estimate without some type of stabilization. The ConcentrationRatio Priors below attem

142 CHAPTER 11. FINE POINTSCHRATO(10) = ’Glc/Big3 = 0.05 +- 0.075’CHRATO(11) = ’Scyllo/Big3 = 0.02 +- 0.02’CHRATO(12) = ’Tau/Big3 = 0.04 +- 0.06’CHRAT

11.9. COHERENT DATA AVERAGING 143In a restricted study, with more accurate expect from controls, you might be able to strengthensome constraints. Howe

144 CHAPTER 11. FINE POINTS11.9.2 Other Spectra with Identical Phases & Referencing ShiftUse Sec 11.9.1 for GE & Toshiba data. Use the Siemens

11.10. ANALYZING A (TIME) SERIES OF SPECTRA 145a (weighted) average over the series of .CORAW files (using your own script or program) toproduce an ave

146 CHAPTER 11. FINE POINTSFor better labeling of the wide ppm-axis (Sec 9.9.3.5), you might input:NSUBTK = 5XSTEP = 0.5This could be useful for Glc q

11.14. DETAILED OUTPUT 147EXT2 (“expectation of 1/T 2”) Control Parameters with this ending modify γ0ℓin [1,Eq (4)]. These Control Para meters specify

148 CHAPTER 11. FINE POINTSBasis-Spectra table in (d). Any shift that is more tha n 4σ(ǫℓ) in [1, Eq (4)], i.e., morethan 6 standard deviations in the

11.16. ANALYZING MAGNITUDE SPECTRA 149character, integer, logical & real, with alphabetical orde ring within each group.Most of these Control Para

Chapter 2One-Page OutputThe results of an LCModel analysis are summarized on the so-called One-Page Output(now usually two pages), contained in a Post

150 CHAPTER 11. FINE POINTSYEAR4D (logical) (“year with 4 digits”) The Sun, SGI & DE C versions now have a 4-digityear at the top o f the One-Page

Chapter 12Diagnostics and TroubleshootingHintsLCModel perform s extensive checks for abnormal conditions and has about 300 di-agnostic messages that g

152 CHAPTER 12. DIAGNOSTICS AND TROUBLESHOOTING HINTSruntime-messages, often showing exactly where the I/O error occurred.End-of-File during Read: The

12.2. STANDARD LCMODEL DIAGNOSTICS 153ERROR: an error condition has occur red, but corrective action has been taken; theresults could be affected.FATAL

154 CHAPTER 12. DIAGNOSTICS AND TROUBLESHOOTING HINTSanother singlet with WSMET, etc.2 One of the following was not input positive: N1HMET, ATTMET.3 T

12.2. STANDARD LCMODEL DIAGNOSTICS 15511 (FATAL) All channels or spectra to be averaged have been eliminated fromthe analysis.Hint: Check your input o

156 CHAPTER 12. DIAGNOSTICS AND TROUBLESHOOTING HINTS1 (ILLOGICAL) Meaning less argument in call to ERRMES.2 (FATAL) Stopping after MERMES = 2000 diag

12.2. STANDARD LCMODEL DIAGNOSTICS 157is wrong. Check for a wrong value of DEGPPM (default is 0.0.) or too smallan SDDEGP.With CSI data, do not input

158 CHAPTER 12. DIAGNOSTICS AND TROUBLESHOOTING HINTS2 (ILLOGICAL) Programming error.GETPHA (“Get phases”) Phas e the unsuppress e d water peak.1 (FAT

12.2. STANDARD LCMODEL DIAGNOSTICS 159CHMORE. If so, the Preliminary Analysis is then re peated with the CHLESS metabo-lites omitted. For the first thr

16 CHAPTER 2. ONE-PAGE OUTPUTThe ab breviations of the metabolites are in the 4th column. (Table 8.1 defines mostof these Metabolite Names.) The corres

160 CHAPTER 12. DIAGNOSTICS AND TROUBLESHOOTING HINTStable of Basis Spectra in the Detailed Output gives the Metabo lite Namecorres po nding to the Ba

12.2. STANDARD LCMODEL DIAGNOSTICS 161numerical problems, sdfw will be slightly increased.21 (warning) The element sdppm of a CHSIMU (Sec 11.7) is too

162 CHAPTER 12. DIAGNOSTICS AND TROUBLESHOOTING HINTSMYCONT reads the Control Parameters and does preliminary checks.1 (FATAL) An end-of-file was encou

12.2. STANDARD LCMODEL DIAGNOSTICS 16323 (FATAL) With SPTYPE=’lipid-8’, ’breast-8’ or ’liver-11’, the HiddenControl Parameter IPOWRG must b e 1 or 2.H

164 CHAPTER 12. DIAGNOSTICS AND TROUBLESHOOTING HINTS5 (ERROR) You have input a non-p ositive value for XSTEP. It will be set to 0.20.6 (FATAL) The pp

12.2. STANDARD LCMODEL DIAGNOSTICS 165characters.3 A Concentration Sum has more than 30 Metabolite Names.PHALIP Phases lipid spectra.1 The Hidden Cont

166 CHAPTER 12. DIAGNOSTICS AND TROUBLESHOOTING HINTSpected character instead of the end of the string was encountered.3nn metwt is missing or non-num

12.2. STANDARD LCMODEL DIAGNOSTICS 167Hints: Working Hard18 (info) αShas reached its maximum allowed value.Hints: Common with lipid spectra.SAVBES sav

168 CHAPTER 12. DIAGNOSTICS AND TROUBLESHOOTING HINTSfit to the data is perfect. Hints: As for FISHNI 1.9 (FATAL) The Hidden Control Parameter FRACTPOW

12.2. STANDARD LCMODEL DIAGNOSTICS 169incompletely suppressed water peak (or possibly a str ong lipid peak). A newCCF will be computed with NREFPK(2)

2.2. PLOT 172.1.3 Prior Ratio ProbabilitiesSection 11.8 s hows how prior probabilities (so-called “soft constraints”) are imposedon ratios of some poo

170 CHAPTER 12. DIAGNOSTICS AND TROUBLESHOOTING HINTS22 (FATAL) Your PPMST or PPMEND or one of the Control Parameters in INITIA1 is so unreas onable t

12.2. STANDARD LCMODEL DIAGNOSTICS 171Hints: Working Hard.8 (info) An extra iteration was required in determining the phases.Hints: Working Hard9 (inf

172 CHAPTER 12. DIAGNOSTICS AND TROUBLESHOOTING HINTS3 (FATAL) Er ror try ing to o pen FILRAW.Hints: Check fo r non-existent file or permissions.4 (FAT

Bibliography[1] S.W. ProvencherEstimation of metabolite concentrations from localized in vivo proton NMRspectra,Magn. Reson. Med. 30, 672–679 (1993).[

174 BIBLIOGRAPHY[9] M.A. McLean, F.G. Woermann, G.J. Barker, J.S. DuncanQuantitative analysis of short echo time1H–MRSI of cerebral gray and whitematt

BIBLIOGRAPHY 175[19] S.W. ProvencherLow-bias macroscopic analysis of polydispersityin Laser Light Scattering in Biochemistry, S.E. Harding, D.B. Satte

176 BIBLIOGRAPHY[29] P. Vermathen, C. Boesch, R. Kr eisMapping fiber orientation in human muscle by proton MR spectroscopic imag-ingMagn. Reson. Med. 4

Indexabsolute concentrations, 123LCMgui, 48absolute-value analyses, 149Absolute-Value Plot, 17ABSVAL, 149acquisition parameters, 20acquisition time, 3

178 INDEXConcentration Table, 15CONCSC, 94CONREL, 119constrained regularization, 140.CONTROL file, LCMgui, 60.CONTROL file, 37Control Parametersconventi

INDEX 179Gaps in ppm-axis, inserting, 145GE data, 24, 125, 143bandwidth at 3T, 74phase corrections, 74selecting frames, 74GE SAGE/LCModel interface, 5

18 CHAPTER 2. ONE-PAGE OUTPUTThe Absolute-Value Plot (of the test d ata) is illustrated in PLOT 5 in$HOME/.lcmodel/doc/figures.pdf, where the FATAL wa

180 INDEXNDROWS, 39NDSLIC, 39NEACH, 120NEXT2, 147NKEEP, 117NMALL, Namelist, 92NMEACH, Namelist, 94NMID, Namelist, 35NMKECC, Namelist, 86NMUSED, Nameli

INDEX 181RATIPM, 119.RAW file, LCMgui, 60.RAW file, 34rectangular subset, multi-voxel, 39referencing shift, 134correction, 146, 147sign convention, 98re

182 INDEXXTRASH, 95YBOTT, 121YEAR4D, 150YLABEL, 89YTOP, 121

Chapter 3Essentia l Gui deThis chapter briefly lists important guidelines and special cases. It refers you to otherchapters for details.Print out $HOME

LCModel, LCMgui and their documentation are copyrightedc 1992–2014 by StephenProvencher. All rights are reserved.The latest version of the complete L

20 CHAPTER 3. ESSENTIAL GUIDE• MEGA-PRESS: Input SPTYPE = ’mega-press-3’ for quantifying GABA[7] using MEGA-PRESS. To use this, you must read Sec 9.4.

3.4. ANALYSIS WINDOW 213.4 Analysis WindowTwo of the most im portant Control Parameters define the Analysis Wi ndow (thewindow of frequency-domain data

22 CHAPTER 3. ESSENTIAL GUIDE3.5 Criteria for Rejecting Analyses3.5.1 Non-Random ResidualsThe residuals are the data values minus the fit values. They

3.6. CAUSES & REMEDIES FOR FAILURES 233.6 Causes & Remedies for Failures3.6.1 ArtifactsIf the artifacts seem to be confined to an edge of the A

24 CHAPTER 3. ESSENTIAL GUIDE3.7 Vendor-Specific GuidelinesTo be certain, you can test the conversion of your data files w ith LCMgui and thereading of

3.7. VENDOR-SPECIFIC GUIDELINES 253.7.4 Marconi/Picker• LCMgui handles single-voxel spectroscopy fid “dump” files, obtained byclicking the “dump” button

26 CHAPTER 3. ESSENTIAL GUIDE• Export your data as .SDAT & .SPAR files.• Select the .SDAT file with LCMgui. In Fig 6.4 switch off “Doeddy-current cor

3.7. VENDOR-SPECIFIC GUIDELINES 273.7.9 Varian/Agilent• LCMgui handles single-channel fid files (CSI & single-voxel). It handlesmulti-channel singl

Chapter 4Install a ti on and Test RunsThe complete LCModel/LCMgui package can be downloaded from the WWW siteon Page 2. T he simp le instructions for

4.2. TEST RUNS USING LCMGUI 29Figure 4.1: Here you enter your command for displaying or pr inting PostScript files.gv or evince from your Linux distrib

Contents1 Preface & Overview 111.1 What You Must Read . . . . . . . . . . . . . . . . . . . . . . . . . . . 111.2 Normal Use of LCModel . . . . .

30 CHAPTER 4. INSTALLATION AND TEST RUNS4.2.3 No Printer or DisplayIf neither printing nor display is possible, then enter th e harmless commandtouchi

4.3. TEST RUNS WITHOUT LCMGUI 31• With Linux, simply entertouch $HOME/.lcmodel/licenseWith Sun , SGI or DEC/Compaq, install the license (Sec 7.2.5), b

32 CHAPTER 4. INSTALLATION AND TEST RUNSThe One-Page Output is then in the PostScript file$HOME/.lcmodel/test/output/test.psOn Linux systems, run-time

Chapter 5Running LCModel withoutLCMgui – Basic InputAlthough all users would benefit by becoming familiar with the Control Parametersin the chapter, LC

34 CHAPTER 5. RUNNING LCMODEL WITHOUT LCMGUI – BASIC INPUT.CONTROL for the file with the changes to the Control Parameters inp ut to LCModel,defined in

5.2. .RAW FILE 355.2.1 Namelist SEQPARThe Namelist SEQPAR is optional, but very useful. If it is included, its data will becompared with that in Namel

36 CHAPTER 5. RUNNING LCMODEL WITHOUT LCMGUI – BASIC INPUTID (character*20) a string that you can use to identify the data. It ap-pears in the so-call

5.3. .CONTROL FILE 375.2.3.1 CSI data setsThe time-domain data for one voxel must be immediately concatenated to the pre-ceding time data, with no bla

38 CHAPTER 5. RUNNING LCMODEL WITHOUT LCMGUI – BASIC INPUTTITLE, FILRAW, and FILPS. You should be able to write a simple Pre-FormattingProgram so that

5.3. .CONTROL FILE 39You specify the CSI data set dimensions of the .RAW file with the following ControlParameters:NDCOLS (integer) (“Number of data co

4 CONTENTS3.5.1 Non-Random Residuals . . . . . . . . . . . . . . . . . . . . . . 223.5.2 Wild Baseline . . . . . . . . . . . . . . . . . . . . . . . .

40 CHAPTER 5. RUNNING LCMODEL WITHOUT LCMGUI – BASIC INPUTThese two Control Parameters are the most important ones for salvaging problemspectra. They

5.3. .CONTROL FILE 415.3.5 First-Order Phase C orrectionThe first-order phase correction (φ1) is often small, and prior knowledge of this can beused to

42 CHAPTER 5. RUNNING LCMODEL WITHOUT LCMGUI – BASIC INPUT$HOME/.lcmodel/doc/figures.pdf) with the complete tables, if there isnot enough room on the

5.3. .CONTROL FILE 435.3.7.4 .COORD Coordinate FileIf you want to make your own plots, the .COORD file contains the coordinates of allcurves on the One

Chapter 6Elementary Guide to LCMguiThis chapter gives the basic steps for the Normal User in using LCMgui, with refer-ences to Chap 7 for details. Cha

6.2. SELECTING THE DATA TO BE ANALYZED 45Figure 6.1: The File Selector, shown here for GE LX files6.2.1 File Selector WindowWhen LCMgui is started, the

46 CHAPTER 6. ELEMENTARY GUIDE TO LCMGUIFigure 6.2: You selected a file of the wrong type in the File Selectorthe filter by clicking on the field (p*.7 P

6.3. CONTROL PARAMETERS WINDOW 47Figure 6.3: Note that GE Signa 5.x and LX (or higher) have distinct buttons.However, you should check the following i

48 CHAPTER 6. ELEMENTARY GUIDE TO LCMGUIFigure 6.4: The Control Parameters Windowfields). Instead you click on the green “Change BAS IS” button, and yo

6.3. CONTROL PARAMETERS WINDOW 49Concentration ratios are not affected by Water-Scaling and are less sensitive to relaxation and p artial-volume effects

CONTENTS 55 Running LCMode l without LCMgui – Basic Input 335.1 Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335.1.1

50 CHAPTER 6. ELEMENTARY GUIDE TO LCMGUIFigure 6.5: The instructions-part of the File S elector for the unsuppressed waterreference.clicking it) to th

6.5. WHERE IS THE OUTPUT? 51Overwrite archive files? LCMgui automatically archives the output in an ArchiveDirectory that is usually unique for each da

52 CHAPTER 6. ELEMENTARY GUIDE TO LCMGUIFigure 6.6: Here you decide how to save the settings from this session.Exit & Save : This is the normal ex

Chapter 7LCMgui Reference ManualThis chapter will allow you to fully exploit the fl exib ility of LC Mgui. It will also allowyou to optimally install &

54 CHAPTER 7. LCMGUI REFERENCE MANUALpurposes.The possibility of supplying your own s cr ipts in Steps (2), (3) & (5) makes LCMguivery flexible. At

7.2. INSTALLING LCMGUI 55• For the convenience of the other users, make all the initial installations(license, basis sets, etc), test runs and setting

56 CHAPTER 7. LCMGUI REFERENCE MANUALsuccessfully use LCMgui often simply by selecting the data file and clicking “RunLCModel”.The most important initi

7.2. INSTALLING LCMGUI 57Figure 7.1: The Ins tall License Window (with Sun, SGI or DEC/Compaq)• When you exit from LCMgui sessions after the first 3T s

58 CHAPTER 7. LCMGUI REFERENCE MANUALSDDEGZ: 999.0 (only for C SI)SDDEGZ: 3.0 (only for single-voxel data)SDDEGP: 1.0Start PPM: 4.0End PPM: 0.2Section

7.3. BASIC SETTINGS AND USAGE 59For the first run, you should follow Chap 6, including all the fine print. Particularly importantare your settings in th

6 CONTENTS6.6 Interactive P rocessing with LCMgui . . . . . . . . . . . . . . . . . . . 516.7 Getting out of LCMgui . . . . . . . . . . . . . . . . .

60 CHAPTER 7. LCMGUI REFERENCE MANUALFigure 7.2: The Control Parameters Window7.3.2 .BASIS fileYour .BASIS file s s hould go into the directo ry $HOME/.

7.3. BASIC SETTINGS AND USAGE 61Figure 7.3: You get this menu when you click the “Save File Ty pes” bu ttonin Fig 7.2.analyses) and the .PS file (with

62 CHAPTER 7. LCMGUI REFERENCE MANUALFigure 7.4: The window for permanently reconfiguring the structure of (Bruker)Archive Directories.7.3.3.3 Reconfigu

7.3. BASIC SETTINGS AND USAGE 63Note the following:• You can experiment, watching your progress in the field next to “Con-structed Save Directory”, and

64 CHAPTER 7. LCMGUI REFERENCE MANUALFigure 7.5: The window for permanently reconfiguring the structure of (Siemens)Archive Directories.Figure 7.6: You

7.3. BASIC SETTINGS AND USAGE 65Figure 7.7: You can v iew, edit, delete or add all Control Parameters here.You do this by clicking on th e “Advanced S

66 CHAPTER 7. LCMGUI REFERENCE MANUALFigure 7.8: You can save all the Control Parameters, including your modifications,for optional use as starting def

7.3. BASIC SETTINGS AND USAGE 67Figure 7.10: Here you select the Control-Defaults file to be used now and in thefuture.Defaults File used at the start

68 CHAPTER 7. LCMGUI REFERENCE MANUALFigure 7.11: At the end of a session, you can select a new User Profi le where all ofyour settings from the sessio

7.4. FURTHER USEFUL SETTINGS 69Figure 7.12: At the s tart of a session, you select the User Profile to be used.directory name. However, if it is identi

CONTENTS 78 Making the Basis Set 788.1 Compatibility Requirements . . . . . . . . . . . . . . . . . . . . . . . . 788.2 Model Metabolite Solutions . .

70 CHAPTER 7. LCMGUI REFERENCE MANUALFigure 7.13: Here you can set and execute your commands for printing and/or plot-ting previews of your data.If po

7.4. FURTHER USEFUL SETTINGS 71Figure 7.14: Here you can select the Execution Scrip t that will be started by LCMgui.7.4.2 Interactive ProcessingNorma

72 CHAPTER 7. LCMGUI REFERENCE MANUALprocessing analyses than you are in starting them, you may want to avoid overloadingit with many simultaneous job

7.4. FURTHER USEFUL SETTINGS 73Figure 7.15: Here you can view and/or change the Preprocessor th at will be used byLCMgui.Even after you make other/my-

74 CHAPTER 7. LCMGUI REFERENCE MANUAL• Click on “Ch an ge Pr eprocessor” to produce the window in Fig 7.15. (Ifthere is no Preprocessor script in the

7.5. FINE POINTS 75• In the main “Control Parameters” window, click on “Advanced Settings”to get the menu in Fig 7.6.• Click on “Change LCMgui Setting

76 CHAPTER 7. LCMGUI REFERENCE MANUALfrom “0” to “1”:ipreserveConfiguration 1Some of the critical defaults that are protected by the above setting are

7.5. FINE POINTS 777.5.1.6 ColorsThe five colors specified in gui-defaults all have (self-explanatory) indices beginningwith icolor. For example,icolorF

Chapter 8Making the Basis SetIt is only necessary to read this chapter if you must collect your own Basis Set of invitro model metabolite spectra. You

8.2. MODEL METABOLITE SOLUTIONS 798.2 Mod el Metabolite Solutions8.2.1 Choice of Model MetabolitesTable 8.1 shows most of the metabolites that have be

8 CONTENTS9 Further Useful Options and Information 1029.1 Special Types of Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . 1029.2 Muscle S

80 CHAPTER 8. MAKING THE BASIS SETmight want to replace Ins with a simulated Glyc (Sec 9.8.1), especially at long TE,where I ns is weak. In these path

8.2. MODEL METABOLITE SOLUTIONS 81Table 8.1: Concentrations and Allowed Names of Model MetabolitesAllowed Conc. Singlet # Vendor Order #Metabolite Nam

82 CHAPTER 8. MAKING THE BASIS SET8.2.3 PhantomUse a spherical phantom of plastic or glass with about 300 mL volume (smaller foranimal scanners). A si

8.3. ACQUIRING THE BASIS SPECTRA 83Room temperature is often adequate for acquiring the model spectra below 3T. Withhigh-resolution spectra (e.g., 9.4

84 CHAPTER 8. MAKING THE BASIS SETobvious conditions in the protocol. It is therefore best if all spectra are acquired inthe same time period.If you n

8.4. EDDY-CURRENT CORRECTION 858.4.1 ECC with LCMguiDuring one LCMgui session, you will probably do a series of ECCs, one for eachBasis Spectrum. The

86 CHAPTER 8. MAKING THE BASIS SETLCMgui session.(12) Click on “Next Analysis” to prepare an E CC of your next data file.For further ECCs during this L

8.5. PLOTTING .RAW FILES WITH PLOTRAW 878.5 Plotting .RAW Files with PlotRawThe program PlotRaw can plot the time-domain or frequency-domain data dire

88 CHAPTER 8. MAKING THE BASIS SETPLTIME (logical) .TRUE. to plot the real and imaginary parts of the time-domaindata (on one page). Default: PLTIME =

8.5. PLOTTING .RAW FILES WITH PLOTRAW 89quency domain, w here one Grid Point is 1/(2*NUNFIL*DELTAT) Hz. Th edefault value for SDPNTS is 1.0 in MakeBas

CONTENTS 910.2.2 Usage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12711 Fine Points 13011.1 E rror Estimates & Reproducibilit

90 CHAPTER 8. MAKING THE BASIS SET8 You must have SDPNTS ≤ 60.9 This would be my programming error.10 There is an error in your Namelist PLTRAW. See S

8.6. RUNNING MAKEBASIS 91therefore had to be suppressed (by setting AUTOSC = AUTOPH = F in makebasis.in).Thus the phase corrections and the TRAMP scal

92 CHAPTER 8. MAKING THE BASIS SETTRAMP is not important if you are using Au to-Scaling. A reasonable value is 1.0.If you do not u se Auto-Scaling, th

8.6. RUNNING MAKEBASIS 93FILBAS (character*255) the name of the .BASIS file to be output by MakeBasis.If you are going to use LCMgui, then follow the n

94 CHAPTER 8. MAKING THE BASIS SETPPMSCA (real) The chemical shift (accurate to within HWDSCA ppm) of your reference peak forscaling.Default: PPMSCA =

8.6. RUNNING MAKEBASIS 95PPMPK (real) (“ppm peak”) the chemical shift (in ppm) of the resonance thatwill be used for referen cing. Default: PPMPK = PP

96 CHAPTER 8. MAKING THE BASIS SETrange PPMOFF(1) > PPMOFF(2) is zero. So, you set this range where thereis only Baseline in the Basis Spectrum. It

8.6. RUNNING MAKEBASIS 973 You forgot to input DELTAT, NUNFIL, or HZPPPM in Namelist NMALL, or you input anon-positive value for one of them.4 When yo

98 CHAPTER 8. MAKING THE BASIS SET8.6.7 Output .BASIS FileAs in the test runs in Chap 4, this output file can be input directly without change to LCMod

8.7. CALIBRATING BASIS SPECTRA 99(Sec 11.3.3) might be needed in cases where the CHBCAL singlet must be greatly shiftedto the CHCALI singlet.When BASC