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VnmrJ Interface

Review Queue. VnmrJ Interface. Locator Study Queue. Graphics area Parameter panels. Viewports. Use the three Viewports to Plan subsequent scans Check on status of Current scan Review previous scans. Display Manager. Display Manager – Locator. Display Manager – Layout.

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VnmrJ Interface

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  1. Review Queue VnmrJ Interface • Locator • Study Queue Graphics area Parameter panels

  2. Viewports • Use the three Viewports to • Plan subsequent scans • Check on status of Current scan • Review previous scans

  3. Display Manager

  4. Display Manager – Locator

  5. Display Manager – Layout

  6. Display Manager – Movie

  7. Display Manager – ROI

  8. Display Manager - ROI

  9. Display Manager – Image

  10. Annotations editor

  11. Review Queue

  12. Pulse Sequences – gems

  13. Pulse Sequences – mems

  14. Enhanced Prescan • New functionalities • Frequency • fat frequency • Power • fine power optimization • Shim • Fastmap or 3D gradient shimming • User-defined List of Prescan • Data saved with study for review

  15. Menus • /vnmr/imaging/templates/vnmrj/interface • MainMenu-----.xml

  16. Menus • File • Open, save files • Save data setup • Edit • Protocols, Exec Parameters, Parameter Pages • Customize Tool Bar, Display Options, Annotations • Edit Parameter pages • Setup Viewports • Acquisition • Parameter arryays • Display Pulse Sequence (dps) • Tools • Locator • Update, Import files • System Settings (config)

  17. Tool Bar • vnmrsys/templates/vnmrj/interface/DefaultToolBar.xml • Edit  Customize Tool Bar

  18. Action Bar: Top of parameter window • /vnmr/imaging/templates/layout/default • sample_action.xml • acq_action.xml • Prescan • Prepare to scan • Start scan: acquire(‘start’) • Stop • proc_action.xml • Process • Stop

  19. Viewports • Edit  Viewports

  20. Autosaving Data • File  Save data setup

  21. Layout: parameter and vertical panels • /vnmr/imaging/templates/layout • vnmrsys/templates/layout • Default • Panels common to all sequences • Sequence specific templates • E.g., gems, mems, etc. • toolPanels: vertical panels • Controlled through “layout” parameter • E.g., layout=‘gems’ • Edit parameter panels • Edit menu  “Parameter Pages

  22. Exec Parameters • Contol of experiment setup and execution • execprep: check and setup parameters before scan • execpprescan: control of gain prescan • execprocess: processing at exp complete • execsetup: (liquids use) • Example: • execprep = im2D(‘prep’) • execpprescan = im2D(‘prescan’) • execprocess = im2D(‘proc) • No more go_ macros

  23. Exec Parameters • Utilities  Configure EXEC parameters

  24. Protocols • /vnmr/imaging/templates/vnmrj/protocols • Edit  Create Protocols • Edit  Composite Protocol

  25. Display Options: Modify fonts & colors • Utilities  Display Options

  26. Pulse Sequence Developments Alan Rath Senior Scientist Varian NMR Systems

  27. Shaped Gradient Library • Collection of new PSG functions • Create gradient shapes for common gradient events • Simple declaration and initialization • Waveform controlled ramps • More precise gradient events • More accurate rotations • Slew rate selection and checking in sequence

  28. Shaped Gradient Library • Creation of common gradient shapes • Trapezoid, Butterfly, Triangle, Flow-comp • Selectable ramps: linear, sine, sine-squared • Built-in physics calculations • Calculation of moments, timing, amplitudes, etc. • Pass information from one gradient event to another • E.g., balance slice refocusing gradient • Results available in sequence • Every gradient is described by a comprehensive structure • Ramp times, integrals, amplitudes, 0th & 1st moments, etc.

  29. Shaped Gradient Programming • Declare shape structures • SLICE_SELECT_GRADIENT slice; • REFOCUS_GRADIENT refocus; • Initialize entries in structures • init_slice_select(&slice); • init_refocus(&refocus); • Assign some specific values for slice selection • slice.rf_duration = p1; • slice.rf_fraction = 0.5; • slice.thickness = thk;

  30. Shaped Gradient Programming • Compute slice shape, update parameter values • calc_slice(&slice) • gss = slice.amplitude • putCmd(“gss=%f”, gss); • Compute refocus shape, update parameter values • refocus.moment_0 = slice.moment_0; • calc_refocus(&refocus); • gssr = refocus.amplitude; • putCmd("gssr=%f",gssr);

  31. Instant Parameter Checking • New features of VnmrJ and pulse sequences • go(‘check’) • Runs pulse sequence code without starting experiment • All sequence calculations performed (not DPS) • Normal warning and error messages are printed • putCmd • Pulse sequence function sends any command string to VnmrJ • Update computed parameter values • Updated values saved with data

  32. Instant Parameter Checking • Select mininum TE

  33. Instant Parameter Checking • TE updated by pulse sequence

  34. Instant Parameter Checking • Turn on Flow Compensation

  35. Instant Parameter Checking

  36. Instant Parameter Checking • /* Check minimum TE */ • if (minte[0] == 'y'){ • te = temin; • putCmd("setvalue('te',%f,'current')\n",te); • } • /* Check crusher ampltiudes */ • if ((ir[0] == 'y‘ || sat[0]=='y') && gcrush>gt3){ • /* crush at max allowable gradient strength */ • gcrush = gt3; • warn_message("gcrush reduced to %.2f g/cm • \n",gcrush); • putCmd("gcrush=%f",gcrush); • }

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