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Imaging Software and Applications Alan Rath, Ph.D. Senior Scientist Varian NMR and MRI Systems.

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Presentation on theme: "Imaging Software and Applications Alan Rath, Ph.D. Senior Scientist Varian NMR and MRI Systems."— Presentation transcript:

1 Imaging Software and Applications Alan Rath, Ph.D. Senior Scientist Varian NMR and MRI Systems

2 VnmrJ Interface Locator Study Queue Graphics area Parameter panels Review Queue

3 VnmrJ

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

5 Setting up Viewports Edit  Viewports

6 3 Viewports displayed

7 1 Viewport displayed

8 Display Manager – Locator

9 Display Manager – Layout

10 Display Manager – Movie

11 Display Manager – ROI

12 Display Manager - ROI

13 Display Manager – Image

14 Annotations editor

15 Review Queue

16 Autosaving Data File  Save data setup

17 Experiment Protocol Selector

18 Multi-level Protocol Library

19 Study Queue & Experiment Selector

20 Experiment Selector

21 Exp Selector: Menus

22 Exp Selector: 1 st level menu

23 Exp Selector: 2 nd level menu

24 Protocol Management

25 Bob’s your uncle!

26 Applications Directories

27 Sharing Applications

28 Customizing the Toolbar Edit  Toolbar

29 Customizing the Toolbar Drag to Toolbar

30 Customizing the Toolbar Label and Command

31 3D Slice Extraction

32 3D Tools

33 3D Viewer

34 3D: Rotate viewing angle

35 3D: Rotate slice angle

36 3D: Advanced Preferences

37 3D: “Box off”

38 3D: Interactive 2D slice view

39 3D: Color and transparency prefs

40 3D: Interactive 2D orthogonal view

41 3D: Slice Extraction

42 3D: Interactive 3-Axis Survey

43 3D: Interactive Volumetric & 3-Axis

44 3D: Oblique Viewing

45 3D: Oblique Slice Extraction

46 3D: Angiography

47 3D: 3-Axis MIP

48 3D: Interactive Volumetric MIP

49 Prescan Start folder  Prescan tab

50 Prescan Setup Prescan  Modify Setup  Prescan Setup

51 Prescan: Setup Modify or Add new RF Coil

52 Prescan: Add a new coil entry New Entry  enter a name, change attributes, Save

53 GEMS “Scan” Most commonly changed parameters

54 2D Plan Interactive planning control

55 GEMS “Advanced” More advanced parameters

56 GEMS “Options” Detailed parameters for each available sequence option

57 GEMS “RF Pulses” Advanced  Show RF & Grad  RF Pulses

58 GEMS “Gradients” Advanced  Show RF & Grad  Gradients

59 FSEMS “Scan”

60 Parameter template editor

61 Menus /vnmr/imaging/templates/vnmrj/interface MainMenu-----.xml

62 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)

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

64 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

65 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

66 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

67 Exec Parameters Utilities  Configure EXEC parameters

68 Protocols /vnmr/imaging/templates/vnmrj/protocols Edit  Create Protocols Edit  Composite Protocol

69 Display Options: Modify fonts & colors Utilities  Display Options

70 Pulse Sequence Developments Alan Rath Senior Scientist Varian NMR Systems

71 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

72 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, 0 th & 1 st moments, etc.

73 Shaped Gradient Programming Declare shape structures SLICE_SELECT_GRADIENTslice; REFOCUS_GRADIENTrefocus; 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;

74 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);

75 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

76 Instant Parameter Checking Select mininum TE

77 Instant Parameter Checking TE updated by pulse sequence

78 Instant Parameter Checking Turn on Flow Compensation

79 Instant Parameter Checking

80 /* 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); }

81 VnmrJ Software Extensive Library of Push-Button Applications

82 More MRI Data on the Web


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