LCModel1 & LCMgui User’s Manual

1 LCModel1 & LCMgui user sManualStephen ProvencherMay 27, 20201 LCModel Version , LCMgui and their documentation are copyrightedc 1992 2020 by StephenProvencher. All rights are latest version of the complete LCModel/ LCMgui package and the documen-tation can be downloaded from the following site: also read the License Agreement for LCModel/ LCMgui ,which is sole task of LCModel is quantitation of proton MRS data, input in the standardLCModel format. To help users, most of the LCModel Manual nowcovers areas farbeyond this task. For example: Information on data acquisition, conversion and scaling for the numerousdata and hardware types is based on information kindly provided by may not be up to date, accurate or complete.

2 Consult the manufacturerof your hardware. Much additional information on possible applications is based on research,still in progress, and subject to error and LCModel Manual (LCModel & LCMgui user s Manual ) is available freeof charge, on the understanding that neither the author, nor LCMODELInc nor any contributors of information to the LCModel Manual shall beheld liable for possible errors or omissions in the LCModel Manual or theconsequences Preface & What You Must Read .. Normal Use of LCModel .. Conventions & Notation .. Figures .. Acknowledgments.

3 132 One-Page Concentration Table .. Upper Part .. Lower Part .. Prior Ratio Probabilities .. Plot .. Diagnostics .. Miscellaneous Output .. Input Changes .. 183 Essential Special Spectra .. Chemical Shift Imaging .. Acquisition Parameters .. Analysis Window .. Criteria for Rejecting Analyses .. Non-Random Residuals .. Wild Baseline .. Causes & Remedies for Failures .. Artifacts .. Referencing .. Phasing .. Smoothing .. Vendor-Specific Guidelines .. Bruker .. GE.

4 Hitachi .. Marconi/Picker .. Bruker, Philips, Siemens, Canon/Toshiba, Varian, Microsoft .. Philips .. Siemens .. Canon/Toshiba .. Varian/Agilent .. Other Vendors .. 274 Installation and Test PostScript Output .. Test Runs Using LCMgui .. Display on Your Screen .. PostScript Printer .. No Printer or Display .. Further Tests .. More Complete Test of LCMgui with a False License .. Starting Over .. Test Runs without LCMgui .. Benchmark Timings .. 32 CONTENTS55 Running LCModel without LCMgui Basic Conventions.

5 File extensions .. Control Parameter Conventions .. NamelistSEQPAR.. NamelistNMID.. Time-Domain Data .. Instrument and Acquisition .. Multi-Voxel Data Sets .. Analysis Window .. Eddy-Current Correction .. First-Order Phase Correction .. PostScript Output .. Archiving the Results .. Phantoms .. 436 Elementary Guide to Starting LCMgui .. Selecting the Data to be Analyzed .. File Selector Window .. Control Parameters Window .. Analyzing spectrum from: .. BASIS file: .. Do eddy-current correction.

6 Do water-scaling .. Only for Multi-Voxel data files: .. The Rest of the Control Parameters Window .. Reload Data .. Run LCModel .. Where is the Output? .. Interactive Processing with LCMgui .. Getting out of LCMgui .. 527 LCMgui Reference LCMgui Structure .. Limitations .. Installing LCMgui .. Multi- user Installations .. Starting LCMgui .. First Test Runs .. Install Model Spectra .. Install License .. Installing Updates & Upgrades .. Basic Settings and Usage .. Vendor-Specific Guidelines.

7 Archiving the LCModel Results .. View/Edit Control Parameters .. Saving Your Control Parameters .. Changing your Default Control Parameters .. user Profiles .. Further Useful Settings .. Previewing Data .. Interactive Processing .. Execution Scripts .. Processing Non-Standard Data Files .. Optional Preprocessor .. Changing the License & the Print Command .. Fine Points .. File .. Cleaning up the File System .. 77 CONTENTS78 Making the Basis Compatibility Requirements .. Model Metabolite Solutions.

8 Choice of Model Metabolites .. Reference Markers .. Phantom .. Solutions .. Acquiring the Basis Spectra .. Quality .. Consistency .. Acquisition Time and Bandwidth .. Repetition Time .. Eddy-Current Correction .. ECC with LCMgui .. ECC without LCMgui .. with PlotRaw .. Test Run of PlotRaw .. PlotRaw Diagnostics .. Running MakeBasis .. Auto-Scaling .. Judging the Basis Spectra .. MEGA-PRESS .. MakeBasis Diagnostics .. Calibrating Basis Spectra .. Calibrating GPC/PCh & NAA/NAAG.

9 Adding New Basis Spectra .. Summary .. 1018 CONTENTS9 Further Useful Options and Special Types of Spectra .. Muscle Spectra .. Standard Input .. Additional Input .. Output .. Lipid Spectra (Liver, Breast, Bone, etc.) .. Input .. Output .. Estimating only choline .. MEGA-PRESS for GABA .. Input .. Output .. Internal Logical Units .. Eddy-Current Correction .. Prior Phasing Information .. Estimating AppropriateSDDEGZ, SDDEGP, DEGZER & DEGPPM. Specifying the Basis Spectra for the Analysis .. Omitting Basis Spectra from the Analysis.

10 Keeping Basis Spectra in the Analysis .. One-Page Output .. Concentration Table .. Diagnostics Table .. Plot .. Miscellaneous Output Table .. 12210 Absolute Metabolite Calibration Phantoms .. Data Scaling (intra-hardware) .. Scanner Calibration (inter-hardware) .. Water-Scaling .. Method .. Usage .. 12811 Fine Error Estimates & Reproducibility .. Averaging Concentrations over a Series of Analyses .. Relaxation Corrections .. Prior Referencing Information .. Off-Resonance Spectra .. Referencing to Water .. Inputting a Starting Shift.