Vespa – Priorset User Manual and Reference - VeSPA
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1. On the Menu Bar View this menu affects the plots in the currently active Priorset tab ZeroLine Show toggle zero line off on ZeroLine Top Middle Bottom display the zero line in the top 10 region middle or bottom 10 region of the canvas as it is drawn on the screen Xaxis Show display the x axis or not Xaxis PPM Hz x axis value in PPM or Hz Data Type select Real Imaginary or Magnitude spectral data to display Plot Views Final All Three select whether only the final simulated spectrum is displayed or the final spectrum the metabolite signals and baseline signals are each displayed in their own plot Output Experiment Text displays the selected Experiment object in text format in a separate text editor similarly to what can be displayed in the Vespa Simulation application gt Output View gt lt various gt writes the entire plot to file as either PNG SVG EPS or PDF format 2 3 Mouse Events in Plots Most processing sub tabs have plots in their right hand panels These plots may contain one or more axes which may change dynamically Typically the Priorset plot will show either one spectrum which is the sum of metabolite signals baseline signals noise or three plots which display the summed spectrum the metabolite spectrum and the baseline spectrum respectively You can control a number of functions by using your mouse interactively within the plot area of most sub tabs Vespa P2. 0 036154 Use the Priorset Open Priorset menu to open saved priorsets into tabs or the Priorset New Priorset from Experiment menu to create a new priorset Shown below is a screen shot of a Vespa Priorset session showing data from a PRESS 144ms simulation The functionality of all sub tabs will be described further in the following sections Loopi 1 Loop2 2 Metabolite Signals Metabolites Area Scale T2 Ta Decay Factor sec VINAAG truncated 0 13422 Ss _ s0 30000 V aspartate 0 51200 0 30000 V choline truncated 0 64000 0 30000 7 creatine 0 64000 0 30000 V gaba 0 26214 0 30000 J glutamate 0 80000 0 30000 V glutamine 0 20972 0 30000 V lactate 0 32768 0 30000 7 myo inositol 1 56250 0 30000 Z n acetylaspartate 1 00000 0 30000 V scyllo nositol 0 16777 0 30000 7 taurine 0 40960 0 30000 3 0 pas 2 0 Frequency ppm msasa Hen 1275515 Value O 0010985267314 Area 0 00 RMS 0000000 4 501 Hz 1275 515 Value 0 00109989267314 Area 0 00 RMS 0 000000 2 The Priorset Main Window This is a view of the main Vespa Priorset user interface window It is the first window that appears when you run the program It contains the priorset notebook a menu bar and status bar The priorset notebook can be populated with one or more priorset tabs each
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4. be prompted to select a director filename for the output Use the Priorset Export Spectrum and Priorset Export Monte Carlo menu items to select if you want to output just the single spectrum shown on the plot or if you want Priorset to create an output file with multiple spectra consisting of copies of the pure metabolite baseline signals with different noise signals Use the Voxels in Dataset spin control on the Spectral Settings sub tab to indicate how many voxels to create in the Monte Carlo output file Note in a Monte Carlo output file the data will be stored as a two dimension data set with Spectral points and Voxels in Dataset spin control values as the dimensions Both single spectrum and Monte Carlo priorsets can be output to VIFF Vespa Interchange File Format Raw Data format In both cases the data output is time domain k space data The VIFF Raw Data format is importable into Vespa Analysis and has the added benefit of being able to store a full provenance of the creation of the simulated data in its XML hierarchy Similarly both single spectrum and Monte Carlo priorsets can be saved to the VASF VA San Francisco file format This is a simple double file text header and binary data format The rsd option will save data single or Monte Carlo to file as time domain data For the single spectrum you can also select the VASF sid option which will save the frequency domain data to file rather than the time domain data
5. in the plots on each sub tab of the active priorset tab including display a zero line turn x axis on off or choose units select the data type real imag magn displayed and various output options for all plot windows and experiment in text format Help User Manual Launches the user manual from vespa docs into a PDF file reader Help Priorset Vespa Online Help Online wiki for the Priorset application and Vespa project Help About Giving credit where credit is due 2 1 The Priorset Notebook The priorset notebook offers a lot of flexibility Multiple tabs can be opened up inside the window They can be moved around arranged and docked as the user desires by left click and dragging the desired tab to a new location inside the notebook boundaries In this manner the tabs can be positioned side by side top to bottom or stacked They can also be arranged in any mixture of these positions There is only the one Notebook in the Priorset application but it can display multiple simulated MRS data sets by loading them into Priorset tabs 2 2 Priorset Tabs The priorset notebook can be populated with one or more priorset tabs each of which contains the spectral settings metabolite signals and baseline signals of one priorset Tabs for priorsets are arranged along the top of the notebook and can be grabbed left click and drag and moved to different locations inside the notebook as you like Tabs can be closed using the X box on the
6. non standard data access closed source multiple language software that complicates algorithm extension and comparison lack of integration between programs for sharing prior information and incomplete or missing documentation and educational content Introduction to Vespa Priorset Vespa Priorset is application written in the Python programming language that allows users to create simulated MR data sets Vespa Priorset allows users to 1 Select from existing Vespa Simulation Experiment in the Vespa database 2 Specify a single set of Experiment loop parameters if more than one on which to base the priorset s metabolite basis functions 3 Specify the spectral resolution as the bandwidth and number of points in the FIDs 4 Scale individual metabolite areas 5 Create a Voigt lineshape envelope that has a specific T T2 value for each metabolite and a global T T2 value for the entire priorset 6 Add unlimited Gaussian spectral peaks with independent area ppm linewidth and phase to create simulated metabolite baseline signals 7 SNR can be set using an independent reference line not included in spectrum to maintain RMS noise levels even as metabolite line shape changes 8 Output to Vespa Analysis compatible data format or a simple text binary header data format 9 Output a single simulated spectrum or an array of spectra containing the same signal model but different noise for use in Monte Carlo evaluations What
7. of which contains input settings and simulated data from one priorset As described above a priorset is a comprised of spectral settings metabolite signals and baseline signals each of which has its own sub tab in the respective priorset tab Sub tabs are organized along the bottom edge while priorset tabs are organized along the top edge The priorset Notebook is loaded From the Priorset menu bar you can 1 open a priorset that has previously been processed by Priorset and then saved into the Priorset VIFF XML format or 2 create a a W Wla new priorset In either Aa awe case a tab will appear for each priorset that is opened or imported m Se S aa i i PO TOE i initially populated with a welcome text window but no priorsets are A P Li Priorset n Saas Priorset View Help Welcome Info x Welcome to Priorset The View menu items set the plotting options for whichever sub tab is Ss oe active The Help menu s a a a i provides links to useful icine resources Currently there are no priorsets loaded You can use the Priorset menu to browse for a Vespa Simulation experiment from which to create a priorset The status bar provides information about where i the cursor is located within the various plots in the interface throughout the program During plot zooms or region selections it also provides useful information about the curso
8. Priorset View Help Priorseti X Source Example Spin Echo Scale 1 0000 Loop1 1 Loop2 1 Loop3 1 Metabolite Spectral Settings l Set metabolite spectral resolution and basis PPM range Tb sec 0 095 Line Width Hz 6 500 Phase 0 deg 0 00 BO shift Hz 0 00 Left Shift pts 0 Applied only on the plot not on output Phase 1 deg 0 00 Phase 1Pivot ppm 4 70 Priorset Noise Settings fw Display noise in plot Noise Ref Peak Area spins 3 000 Effective SNR Noise Ref Peak Ta sec 0 300 Effective Linewidth 2 500 Noise Ref Peak Tb sec 0 300 Noise RMS Multiplier 0 1000 10 00 Monte Carlo Dataset Settings Number of voxels in priorset eg 10 or 1000 4 45 4 0 3 5 3 0 2 5 2 0 15 Metabolite Signals Baseline Signals Frequency ppm Hz 496 752 Value 0 0195175083235 Theoretical Details The formula below describes how the simulated data signals are created in the time domain as a sum of metabolite M t baseline B t and noise N t functions and subsequently transformed into the spectral domain using the FFT for display in the Priorset plot panel The metabolite signal starts with a set of basis functions generated from the a priori Simulation Experiment information The set of all a priori resonance lines for each metabolite are indexed over n from 1 to Nm These sinusoids are created at the digital spectral resolu
9. S 0 000000 I SH PPM 4 783 4 2 Metabolite Signals Parameters The metabolites included in the spectrum can be selected in two ways First as shown in the previous section a metabolite inclusion range in PPM can be set using the spectral resolution dialog Depending on the spectral lines in each metabolite the metabolite list is repopulated with metabolites that have lines within this range Second the user can explicitly select a metabolite for inclusion by clicking on the check box at the start of a line in the metabolite list Metabolite areas and an intrinsic T decay value can be set in each line for each metabolite The plot to the right displays the spectrum you are designing The top plot shows the summed metabolite baseline noise signals The middle plot shows the summed metabolite signals black overlaid on the individual metabolite signals blue The bottom plot shows the summed baseline signals black overlaid on the individual baseline signals blue You can zoom in out of this plot the same as described in Section 2 3 You will likely need to zoom in to clearly see the lines you are creating 15 5 Baseline Signals Sub tab 5 1 General Each priorset tab has three sub tabs called Spectral Settings Metabolite Signals and Baseline Signals The Baseline Signals tab is shown below Priorset View Help Priorset2 X Source PRESS Ideal TE 30 and 144 Scale 0 3522 Loop
10. Vespa Priorset User Manual and Reference Version 0 8 1 Release date July 17 2014 Developed by Brian J Soher Ph D Philip Semanchuk Duke University Medical Center Department of Radiology Durham NC Karl Young Ph D David Todd Ph D University of California San Francisco Department of Radiology San Francisco CA Developed with support from NIH grant EB008387 01A1 Table of Contents Overview of the Vespa Package cccccccccceceeeeeeeceeeeeeeeeeeeeeeeeeeess 3 Introduction to VeSpa PriOrSet cccscscscscsessseeessececesensnecanaeees 4 Using Priorset A User Manual cccscecececeeceeesensneeeneneenees 6 1 Overview How to launch Vespa Priorset ccceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee 6 2 The Priorset Main Window ccccceeeeeeeeeeeeeeceeeeeeeeeeeeeeeaaeeeeeeeeeeeeeeneeeaaees 8 2 1 The Priorset Notebook ss vieccchscissacdeccssapectanenscasnedteieteaceiaduatbaladaoeevendastnenteneetembansatee 9 PE AAL TADS A E E T ead taa tae 9 2 3 M use Events in PIOUS ierse e diguas tian Saaai eaa Caa a Epai 10 3 Spectral Settings SUD lab casa ca Ane ae aes 12 e SINS E EE Gane eves Sekt das ets cata A Secs ecb nna E aaa aes ene 12 3 2 Metabolite Spectral Settings S CtION cece eeeeeeeeeeeeeeeeeeeeeaeeeeeeetaeeeenenaas 13 3 3 Dataset Noise Settings SeCtiON ccccceeeeeseceeeeeeeteeeeeeeeaeeeeeeeaeeeseeseeeeeteneaaees 14 4 Metabolite S
11. e default reference line is a singlet peak with 3 spins aka CH3 group The user sets the Reference Peak Ta and Tb values to achieve the desired Effective Linewidth value and then scales to the desired SNR level using the Noise RMS Multiplier spin control Finally the user can select to turn the noise in the spectrum on off using the Display noise in the spectrum check box This is a convenience function only 14 4 Metabolite Signals Sub tab 4 1 General Each priorset tab has three sub tabs called Spectral Settings Metabolite Signals and Baseline Signals The Spectral Settings tab is shown below LJ Prior priorset_PRESS_Ideal_TE_30and144xml Eram Priorset View Help Priorset2 X Source PRESS Ideal TE 30 and 144 Scale 0 3522 E Loop1 1 Loop2 2 Loop3 1 Metabolite Signals Metabolites Area Scale T2 Ta Decay ctor sec NAAG truncated 0 13422 0 30000 V aspartate 0 51200 0 30000 V choline truncated 0 64000 0 30000 V creatine 0 64000 0 30000 V gaba 0 26214 0 30000 J glutamate 0 80000 0 30000 V glutamine 0 16777 0 30000 lactate 0 16777 l 9 30000 myo inositol 1 00000 0 30000 V n acetylaspartate 1 00000 0 30000 I Z scyloinositol 0 16777 l 0 30000 7 taurine 0 32768 l 9 30000 Select All l Select None 4 a 3 2 Baseline Signals Frequency ppm Spectral Settings Hz 1239 407 Value 0 000644413411787 Area 0 01 RM
12. i 1 Loop2 2 Loop3 1 Macromolecules Peaks PPM Area Factor Linewidth Hz 2 346 0 50000 20 000 v 2 890 S 0 50000 20 000 7i 2 142 3 50000 60 000 A 1 638 1 00000 35 000 1 357 1 00000 35 000 7 0 900 S 1 00000 S 45 000 7 3 810 5 80000 120 000 Select All Select None Delete Selected Add Line m Spectral Settings Metabolite Signals iB Is Frequency ppm PPM 4 039 Hz 1334 636 Value 0 00892581478743 Area 0 01 RMS 0 000000 szan Rio 5 2 Baseline Signals Controls You can add delete as many lines to the Baseline signals list as you like using the Add Line Delete Selected Select All and Select None Only the lines that have a check in the box will be included in the baseline signal For each line you can specify the PPM value for the peak center the area of the peak and the Gaussian line width The plot to the right displays the spectrum you are designing The top plot shows the summed metabolite baseline noise signals The middle plot shows the summed metabolite signals black overlaid on the individual metabolite signals blue The bottom plot shows the summed baseline signals black overlaid on the individual baseline signals blue You can zoom in out of this plot the same as described in Section 2 3 You will likely need to zoom in to clearly see the lines you are creating 16 6 Results Output 6 1 Plot results to image file f
13. ignals Sub tab 0 eeeeccceeeeeeeeeeeeeeeeceeeeeeeeeeeeesaeeeeeeeeeeeeeneees 15 Biel Generalne e Olas eases seta Ri a eed axe ee 15 4 2 Metabolite Signals Parameters ccccccccceeesseeceeeeeeeeeeeeeeaaeeeeeesaaaeeeessnaaeeeeneaas 15 5 Baseline Signals Sub tab cei ich ee eee ie Oe Oe ae Oe he 16 Sati Generale ar A r a ce a ater er Cree eer nee 16 5 2 Baseline Signals Controls ccccccccceeeeeeeeeeeeeeeeeeeeeeeceeeeeeenaeeeseseeeeeeeteneeeeeeeennees 16 sy Res lts O tp t insanin a a Gees a a E ee 17 6 1 Plot results to image file formats scc cssccdosicebhveaslncedtecetdnctigaathdeneacenaihledialectaetaweenees 17 8 2 Plot results to vector graphics formats 2 cccccceeeeseeeeeceeeeeeeeeeeeeeeeeeeeeeeeeneeees 17 6 3 Simulated Data Output to File ssssssssnnnesseenneeeenenssrtrrssttrntrettnnnssrrrnnnrtnnnnrsrennsnee 17 Overview of the Vespa Package The Vespa package enhances and extends three previously developed magnetic resonance spectroscopy MRS software tools by migrating them into an integrated open source open development platform Vespa stands for Versatile Priorset Pulses and Priorset The original tools that have been migrated into this package include e GAVA Gamma software for spectral simulation e MatPulse software for RF pulse design e IDL_Vespa a package for spectral data processing and analysis The new Vespa project addresses current software limitations including
14. ine the area under the peak values that are displayed in the status bar While performing a right click and drag to create a cursor span the status bar will also display the start end location of the span and the delta Hz and delta PPM size of the span The roller bar can be used to increment decrement the Y axis scale value A maximum value for the Y axis scale is determined the first time a priorset is loaded and displayed That max value is the value displayed in the scale widget top right in the priorset and used when you zoom all the way out As you roll the ball up down or you click on the SpinCtrl widget next to the scale field the scale value changes and the plot is updated Note It may be necessary to actually 10 click in the plot window to move the focus of the scroll wheel into the plot before the scroll wheel events will be applied to the Scale value Roller balls can typically be used also as a middle button but pushing down on it without rolling it up or down Priorset plots do not make use of events from this middle button Click and release the left mouse button in place and the plot will zoom out to its max setting Click and release the right mouse button in place and the cursor span will be turned off 11 3 Spectral Settings Sub tab 3 1 General Each priorset tab has three sub tabs called Spectral Settings Metabolite Signals and Baseline Signals The Spectral Settings tab is shown below mo E E
15. is a Priorset A Priorset consists of a simulated MR spectroscopy MRS data set that has be created using prior information from a Vespa Simulation Experiment The combination of prior information data set has been shortened to priorset in this manual A priorset can only contain metabolites from a single set of loop parameters from the Experiment On output the priorset contains header information about all signals processing and noise that were performed to create the data What is the Priorset Notebook This is the main window of the Priorset application It contains One or more tabs each of which contains the data and processing for an entire priorset Multiple priorsets can be created loaded as tabs in the Priorset notebook Priorsets are created in three steps organized as three sub tabs in each Priorset tab These sub tabs are Spectral Settings Metabolite Signals and Baseline Signals Upon output a full provenance for sub tab parameters is created as part of the Priorset XML output data format A variety of graphical and text based methods are available for saving results as well The following chapters run through the operation of the Vespa Priorset program both in general and widget by widget In this manual command line instructions will appear in a fixed width font on individual lines for example Vespa Priorset 1s Specific file and directory names will appear in a fixed width font wi
16. nd Metabolite Inclusion x Spectral Resolution Spectral Data Points 2048 Spectral Sweep Width Hz 2500 0 Resonance Frequency MHz 128 000 Metabolite Indusion Range Start ppm 3 292 End ppm 12 700 cancel _ on which you can set the Frequency Spectral Points Spectral Width and metabolite inclusion range in PPM using spin control widget Note changes to any of these widgets will result in a recalculation of all basis functions from the selected Experiment but not until you hit the OK button Depending on the number of steps in all Experiment parameter loops this recalculation can take an appreciable amount of time However it does speed up display of different basis sets when the Loop indices change 13 The Phase 0 and BO shift widget spin controls set these global values for the simulated data The Tb spin control is used to set effects of simulated T2 line broadening An estimate of the resulting Line Width in Hz is displayed in the field below This estimate is based on an assumed T T2 value of 0 3 seconds because each metabolite can have its own T2 value thus we use this value as a reasonable average 3 3 Dataset Noise Settings Section The Dataset Noise Settings section contains parameters that affect the amount of noise that is added to each simulated spectrum The data in the plot on the right will update interactively as you change parameters Note the noise displayed is updated eve
17. ormats The plots displayed in all sub tabs which contain View panels can all be saved to file in PNG portable network graphic PDF portable document file or EPS encapsulated postscript formats to save the results as an image The Vespa Priorset View menu lists commands that only apply to the active Priorset tab and selected processing sub tab Select the View Output option and further select either Plot to PNG Plot to PDF or Plot to EPS item The user will be prompted to pick an output filename to which will be appended the appropriate suffix 8 2 Plot results to vector graphics formats The plots displayed in all sub tabs which contain View panels can all be saved to file in SVG scalable vector graphics or EPS encapsulated postscript formats to save the results as a vector graphics file that can be decomposed into various parts This is particularly desirable when creating graphics in PowerPoint or other drawing programs At the time of writing this only the EPS files were readable into PowerPoint The Vespa Priorset View menu lists commands that only apply to the active Priorset tab and selected processing sub tab Select the View Output option and further select either Plot to SVG or Plot to EPS item The user will be prompted to pick an output filename to which will be appended the appropriate suffix 6 3 Simulated Data Output to File The simulated data can be output to file in a number of formats In all cases you will
18. r start and end points and the distance between Finally it also reports short messages that reflect current processing while events are running On the Menu Bar Priorset Open Hz 89 207 Value 0 00100281877038 Area 30 46 RMS 0 036154 Opens an existing VIFF priorset XML file into a new priorset tab in the priorset Notebook The state of the priorset as it was saved including all sub tab settings and simulated data are restored as the priorset is opened into its tab Priorset New Priorset Save Priorset Save As Priorset Close Priorset Export Spectrum lt various gt Allows the user to create a new priorset in a new Tab Saves the state of the priorset as it currently exists including all sub tab settings and data into a VIFF Vespa Interchange File Format XML file Same as Save but allows the user to change the file name into which the priorset is saved Closes the active tab Writes the simulated data from the priorset out to various formats For formats that allow it provenance for the simulated data is included Otherwise Provenance is saved to a separate text file in the same directory Priorset Export Monte Carlo lt various gt Similar to Export Spectrum but an array of spectral data with the same signal model but different added noise is saved out to various formats Priorset Exit Closes the application window View lt various gt Changes plot options
19. riorset is best used with a two button mouse that has a scroll wheel but can also work fine with a two button mouse as most mouse driven features for the scroll wheel also have a corresponding widget that can be clicked on or typed in to cause the same effect The following describes the typical actions that can be effected using the mouse in a plot window Any variations from this will be noted in the following sub tab sections The mouse can be used to set the X axis and cursor values in sub tab plots When there are three plots the same X axis or cursors are set on all three The left mouse button sets the X axis zoom range Click and hold the left mouse button in the window and a vertical cursor will appear Drag the mouse either left or right and a second vertical cursor will appear PPM value changes will be reflected in the status bar Release the mouse and the plot will be redisplayed for the axis span selected This zoom span will display its range in a pale yellow that disappears when the left mouse is released Click in place with the left button and the plot will zoom out to its max x and y axis settings In a similar fashion two vertical cursors can be set inside the plot window Click and drag then release to set the two cursors anywhere in the window This cursor xpan will display as a light gray span Click in place with the right mouse button and the xursor span will be turned off The cursor values are used to determ
20. ry time a parameter is changed thus low SNR plots will change appreciably each time a parameter changes Background on SNR calculation Arrays of random noise are created using the numpy random randn method which creates random floats sampled from a univariate normal Gaussian distribution of mean O and variance 1 Two numpy ndarrays of the proper length are combined to create a complex set of random noise samples The normalized noise is scaled to create a particular SNR setting based on the traditional peak height divided by RMS noise value method In Priorset the RMS noise is taken directly from the randn method but the peak height is measured from a user defined reference peak that is set up on the Spectral Settings sub tab The reference peak is not plotted as part of the final spectrum Its definition is used to create a temporary peak at high spectral resolution whose peak height for a given line and sweep width can be measured This is the peak height used to calculate the SNR value displayed in the Effective SNR field The reason we use the reference method is that it allows us to keep the same noise scaling factor as metabolite line width changes Thus we can create priorsets that have the same noise level and the same metabolite areas but at different peak line widths It also allows users to use a simple definition of SNR in spectra that do not have simple singlet lines against which to set an SNR value Th
21. tab or with a middle click on the tab itself When a tab is closed the priorset is removed from memory but can be restored to its current state at a future time assuming it was saved to Priorset VIFF format Each priorset tab has three sub tabs that represent the spectral settings metabolite signals and baseline signals in the data Each processing sub tab is described in more detail in the following section Priorsets are only saved to file when specifically requested by the user On selecting Priorset Save the current state of the priorset ie all settings and results in all tabs is saved into a file in the Vespa Interchange File Format or VIFF This file can be updated when desired by the user by again hitting Save or a new filename can be used to save different states in different files by using Priorset Save As When a VIFF file is opened in Priorset all tabs and results are restored to the state they were in upon save Each processing sub tab displays name of the Simulation Experiment that provides the basis functions for the metabolites the indices of the specific Experiment set of loop parameters that is being used and the y scale of the plot in the sub tab The View menu on the main menu bar can be used to modify the display of the plots in the active sub tab The state of plot options in each sub tab is maintained in each sub tab as the user switches between them The following lists the functions on the View menu item
22. thin the main text Online Resources The Vespa project and each of its applications have Trac Wiki sites with extensive information about how to use and develop new functionality for each application These can be accessed through the main portal site at http scion duhs duke edu vespa Using Priorset A User Manual This section assumes Vespa Priorset has been downloaded and installed See the Vespa Installation guide on the Vespa main project wiki for details on how to install the software and package dependencies http scion duhs duke edu vespa In the following screenshots are based on running Priorset on the Windows OS but aside from starting the program the basic commands are the same on all platforms 1 Overview How to launch Vespa Priorset Double click on the Priorset icon that the installer created on your Desktop Shown below is the Vespa Priorset main window as it appears on first opening No actual Priorset windows are open only the Welcome banner is displayed i Priorset Priorset View Help Welcome Info x elas Welcome to Priorset EEE ala billed adal add Se ae ol ae eee ae ee 5 a 3 2 1 5 a 3 2 1 Frequency ppm Frequency ppm Currently there are no priorsets loaded You can use the Priorset menu to browse for a Vespa Simulation experiment from which to create a priorset Hz 89 207 Value 0 00100281877038 Area 30 46 RMS
23. tion set by the user Only the metabolites selected by the user are included Metabolite basis functions are modified by the user specified area Am and T2 decay Ta and global frequency shift wo phase 0 o and T2 decay 7 terms If the Left Shift parameter is not zero then after the time domain FID has been calculated it is truncated by N integer points as set by the spectral resolution widget before being Fourier transformed The value N is taken from the Left Shift widget setting 12 s w FFT M t B t N N t numpy random randn dims 0 Bas 2 B t gt Ape illontwottpole rs b 1 a priori relative area frequency and phase of all resonances for each metabolite 2 M t gt gt AA enilwotomeron eole rm l rs mini y o o if ff metabolite area global global metabolite concentration of frequency zero order specific T each metabolite shift phase decay global T decay 3 2 Metabolite Spectral Settings Section The Metabolite Spectral Settings section contains controls that affect the spectral resolution SNR and global spectral parameters for the simulated data The data in the plot on the right will update interactively as you change parameters Spectral resolution and the PPM range of metabolite basis peaks is set by using the Set metabolite spectral resolution and basis PPM range button This button will launch a dialog shown below BE Spectral Resolution a
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