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Slicer Training 1  Loading and Viewing Data Sonia Pujol, Ph.D. Randy Gollub, M.D., Ph.D.
Acknowledgments <ul><li>National Alliance for Medical Image Computing </li></ul><ul><li>NIH U54EB005149  </li></ul><ul><li...
Disclaimer <ul><li>It is the responsibility of the user of 3DSlicer </li></ul><ul><li>to comply with both the terms of the...
Welcome to 3D Slicer
Goal of the tutorial Guiding you step by step through the process of  Loading and Viewing  Data within Slicer
Material <ul><li>Slicer 2.6 </li></ul><ul><li>http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started </li><...
Goal of the tutorial Final result of the series of exercises
Overview <ul><li>Part 1: Slicer Interface </li></ul><ul><li>Part 2: Loading Data </li></ul><ul><li>Part 3: Interacting wit...
Slicer Interface Tk window Viewer Menu
Slicer Menu Select the  Volumes  Module
Panels and Tabs The Panel of the  Volumes  Module appears
Slicer Menu Panels Sliders Buttons Control Window
Main Menu Observe the different options of the Main Menu <ul><li>View </li></ul><ul><li>Selecting view mode </li></ul><ul>...
Viewer window <ul><li>Upper part is  </li></ul><ul><li>3D Viewer </li></ul><ul><li>Lower part is  2D Viewer </li></ul><ul>...
Slicer Modules The architecture of Slicer is modular  Select  Modules  in the SubMenu
Slicer Modules The list of  Slicer Modules categories  appears Settings IO Application Filtering  Segmentation Registratio...
Slicer Modules: tutorials Settings IO Application Filtering  Segmentation Registration Measurement Visualization Examples ...
Exercise 1: Slicer GUI <ul><li>Launch Slicer. </li></ul><ul><ul><li>Observe  Main  window and  Viewer  window. </li></ul><...
Overview <ul><li>Part 1: Slicer Interface </li></ul><ul><li>Part 2: Loading Data </li></ul><ul><li>Part 3: Interacting wit...
Loading Data <ul><li>Slicer can load </li></ul><ul><li>Volumes ………………….. </li></ul>
Loading Data <ul><li>Slicer can load </li></ul><ul><li>Volumes ………………….. </li></ul><ul><li>Models ……………………. </li></ul><ul>...
Loading Data <ul><li>Slicer can load </li></ul><ul><li>Volumes ………………….. </li></ul><ul><li>Models ……………………. </li></ul><ul>...
Loading Data Slicer Advantage Putting together Images and Surface
Data representation <ul><li>Volume  = collection of image files </li></ul><ul><li>Image file = header + raw data </li></ul...
Data representation <ul><li>Volume  = collection of image files </li></ul><ul><li>Image file = header + raw data </li></ul...
Loading DICOM Volumes Click on  Add Volume  in the Slicer Menu
Loading DICOM Volumes Left-click on the Menu Properties  and change  Basic to  DICOM The Panel  Props appears by default.
Loading DICOM Volumes Click on  Select DICOM Volume The DICOM panel appears
Loading DICOM Volumes Select the directory  dicom  in the Tutorial-with-dicom dataset
Loading DICOM Volumes The list of DICOM studies appears. Click  OK
Loading DICOM Volumes <ul><li>Name  :  The name that the  </li></ul><ul><li>volume will have within Slicer   </li></ul>Cha...
Loading DICOM Volumes <ul><li>The  DICOM Header </li></ul><ul><li>information  panel appears   </li></ul>Click  Apply
Loading DICOM Volumes <ul><li>Slicer loads the </li></ul><ul><li>DICOM volume of </li></ul><ul><li>the brain </li></ul>
Visualization Support <ul><li>Control Window : displays a zoomed view of the position of the mouse on the selected image <...
Visualization Support The value of the gray level of the pixel under the cursor appears in the corresponding slice
Viewing Volumes <ul><li>V  toggle button controls whether slice is visible in 3D Viewer </li></ul>Click on the three V but...
Viewing Volumes The Axial, Sagittal and Coronal Images appear in the Viewer
Manipulating the images Position the mouse  on the images inside the Viewer Left-click and move the mouse to the left <ul>...
Manipulating the images Position the mouse  on the images inside the Viewer Right-click and move the mouse down The viewer...
Manipulating the images Position the mouse  on the images inside the Viewer Right-click and move the mouse up The viewer m...
Viewing Volumes Select the  3D View The  View  Menu contains different options to visualize the data
Viewing Volumes 3D View focuses on 3D
Viewing Volumes Select  4x512 The  View  Menu contains different options to visualize the data
Viewing Volumes 4x512  view: larger image views to see details
Viewing Volumes Select  1x512 The  View  Menu contains different options to visualize the data
Viewing Volumes <ul><li>1x512:  </li></ul><ul><li>one  large TRANSVERSE </li></ul><ul><li>view and three small </li></ul><...
Viewing Volumes <ul><li>The  View  Menu contains </li></ul><ul><li>different options to visualize </li></ul><ul><li>the da...
Viewing Volumes 4x256  view: smaller equal-sized images Come back to Normal View
2D Viewer <ul><li>Three 2D windows (red, yellow, and green) </li></ul><ul><li>Slider selects which slice of volume to disp...
2D Viewer <ul><li>Bg  (Background): displays volume in background layer  </li></ul><ul><li>Fg  (Foreground): displays volu...
Volumes without Header <ul><li>Motivations: </li></ul><ul><li>The DICOM file format incorporates all the parameters that S...
Volumes without Header <ul><li>Motivations: </li></ul><ul><li>The DICOM file format incorporates all the parameters that S...
Volumes without Header 1.  Main    Data 2.  Add Volume 3.  Browse  to find the first image of the Volume  spgr  in the di...
<ul><ul><li>File Pattern : Pattern  </li></ul></ul><ul><ul><li>of file names, in C syntax.  Example: a file named  skin.00...
Volumes without Header <ul><ul><li>Pixel Size  in the x and y  </li></ul></ul><ul><ul><li>directions.  </li></ul></ul><ul>...
Volumes without Header <ul><ul><li>Num Scalars :  </li></ul></ul><ul><ul><li>Number of scalar components for each voxel. G...
Volumes without Header The  spgr  volume appears in the Viewer
Loading Data <ul><li>Slicer can load </li></ul><ul><li>Volumes ………………….. </li></ul><ul><li>Models ……………………. </li></ul><ul>...
Loading Models <ul><li>In the main Menu select the </li></ul><ul><li>module  Data  and Click on </li></ul><ul><li>Add Mode...
Loading Models <ul><li>The Props tab of the module </li></ul><ul><li>Models appears </li></ul>Select the model named  Vess...
Loading Models The model of the vessels appears in the Viewer.
Loading Data <ul><li>Slicer can load </li></ul><ul><li>Volumes ………………….. </li></ul><ul><li>Models ……………………. </li></ul><ul>...
Loading a Scene  <ul><li>Select  File      Open Scene   </li></ul><ul><li>in the Main Menu </li></ul><ul><li>Select the f...
Loading a Scene  The viewer displays the   tutorial  Scene
Loading a Scene  The elements of the Scene are listed in the Menu Window
Overview <ul><li>Part 1: Slicer Interface </li></ul><ul><li>Part 2: Loading Data </li></ul><ul><li>Part 3: Interacting wit...
Manipulating a Model <ul><li>The model appears in the  </li></ul><ul><li>3D Viewer . </li></ul><ul><li>Rotate the model: w...
Manipulating a Model Put the mouse on the 3D Slicer icon
Manipulating a Model The Control Window appears
Manipulating a Model Position the mouse on the R letter (Right) inside the window
Manipulating a Model The View Panel shows the model from the right side of the patient
Manipulating a Model Click on the Spin button
Manipulating a Model The model starts spinning inside the Viewer Panel.
Manipulating a Model Click on the Rock button
Manipulating a Model The model starts rocking inside the Viewer Panel.
Manipulating a Model Come back to initial orientation of the Viewer Panel by clicking on the A letter (Anterior) inside th...
Models representation <ul><li>A model is a 3D representation </li></ul><ul><li>of the anatomy. </li></ul>Type W (Wireframe...
Models representation <ul><li>The triangles of the  Model become visible in the Viewer.  </li></ul>Type S (Surface) to com...
Model Opacity <ul><li>Click on  Models  in the Main Menu  </li></ul><ul><li>Select the  Display  Tab  </li></ul><ul><li>Th...
Model Opacity Skin  model  Opacity = 0.5
Model Visibility <ul><li>Visibility  on and off by  </li></ul><ul><li>left clicking on the name of model in the list   </l...
Model Visibility Vessels  model  Visibility 0ff
Global Visibility <ul><li>Show All  to display all </li></ul><ul><li>models in the  3D Viewer. </li></ul>Click  Show None ...
Viewing 3D Models Show None:  the models have disappeared
2D Viewer <ul><li>Lb : displays label map  </li></ul><ul><li>Displays results of a segmentation </li></ul>Left click on Lb...
2D Viewer <ul><li>Lb : displays label map  </li></ul><ul><li>Displays results of a segmentation </li></ul>The segmented vo...
2D Viewer <ul><li>Lb : displays label map  </li></ul><ul><li>Displays results of a segmentation </li></ul>Left click on Lb...
2D Viewer <ul><li>Lb : displays label map  </li></ul><ul><li>Displays results of a segmentation </li></ul>The segmented vo...
2D Viewer Images in the label map layer appear as outlines around the structures that were segmented.
2D Viewer Left Click on  Fg  in the Axial View and select the Volume named  all  in the  Axial, Sagittal  and  Coronal  sl...
Image Fusion  <ul><li>Fade  slider: </li></ul><ul><li>fades between foreground  </li></ul><ul><li>and background . </li></...
2D Viewer The volume  all  is superimposed on the images
Clipping Models <ul><li>Clipping: cutting away sections of a model at one or more selected slices.  </li></ul><ul><li>The ...
Clipping Models <ul><li>1.  Click on  Show all  to make all the models visible  </li></ul><ul><li>2. Right-click the  Skin...
Clipping Models Click  +  or  -  to select which side of each slice to clip on. Set the sides to:  Red Slice + Yellow Slic...
Clipping Models Clipping Model Result
Conclusion <ul><li>Intuitive Interface for Loading and Visualizing Data </li></ul><ul><li>Slicer Outcome = fusion of Volum...
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Data Loading and Visualization-3735

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  • Transcript of "Data Loading and Visualization-3735"

    1. 1. Slicer Training 1 Loading and Viewing Data Sonia Pujol, Ph.D. Randy Gollub, M.D., Ph.D.
    2. 2. Acknowledgments <ul><li>National Alliance for Medical Image Computing </li></ul><ul><li>NIH U54EB005149 </li></ul><ul><li>Neuroimage Analysis Center </li></ul><ul><li>NIH P41RR013218 </li></ul>
    3. 3. Disclaimer <ul><li>It is the responsibility of the user of 3DSlicer </li></ul><ul><li>to comply with both the terms of the license </li></ul><ul><li>and with the applicable laws, regulations </li></ul><ul><li>and rules. </li></ul>
    4. 4. Welcome to 3D Slicer
    5. 5. Goal of the tutorial Guiding you step by step through the process of Loading and Viewing Data within Slicer
    6. 6. Material <ul><li>Slicer 2.6 </li></ul><ul><li>http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started </li></ul><ul><li>Sample Tutorial Data: tutorial-with-dicom.zip </li></ul><ul><li>http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 </li></ul>Questions Answers Exercises
    7. 7. Goal of the tutorial Final result of the series of exercises
    8. 8. Overview <ul><li>Part 1: Slicer Interface </li></ul><ul><li>Part 2: Loading Data </li></ul><ul><li>Part 3: Interacting with Data </li></ul>
    9. 9. Slicer Interface Tk window Viewer Menu
    10. 10. Slicer Menu Select the Volumes Module
    11. 11. Panels and Tabs The Panel of the Volumes Module appears
    12. 12. Slicer Menu Panels Sliders Buttons Control Window
    13. 13. Main Menu Observe the different options of the Main Menu <ul><li>View </li></ul><ul><li>Selecting view mode </li></ul><ul><li>Modules </li></ul><ul><li>Slicer Modules </li></ul><ul><li>File </li></ul><ul><ul><li>Opening files </li></ul></ul><ul><ul><li>Saving files </li></ul></ul><ul><ul><li>Closing files </li></ul></ul><ul><ul><li>Exit </li></ul></ul><ul><li>Help </li></ul><ul><li>Links to Slicer Modules information </li></ul>
    14. 14. Viewer window <ul><li>Upper part is </li></ul><ul><li>3D Viewer </li></ul><ul><li>Lower part is 2D Viewer </li></ul><ul><ul><li>3 separate views </li></ul></ul><ul><ul><li>Independent controls </li></ul></ul>Observe the Viewer Window
    15. 15. Slicer Modules The architecture of Slicer is modular Select Modules in the SubMenu
    16. 16. Slicer Modules The list of Slicer Modules categories appears Settings IO Application Filtering Segmentation Registration Measurement Visualization Examples Unfiled Alpha
    17. 17. Slicer Modules: tutorials Settings IO Application Filtering Segmentation Registration Measurement Visualization Examples Unfiled Alpha <ul><li>Editor …………….. SlicerTraining 2 </li></ul><ul><li>Level-Sets ……….. SlicerTraining 3 </li></ul><ul><li>fMRIEngine ………. SlicerTraining 5 </li></ul><ul><li>vtkFreeSurferReaders ... SlicerTraining 6 </li></ul><ul><li>DTMRI ……………. SlicerTraining 4 </li></ul>
    18. 18. Exercise 1: Slicer GUI <ul><li>Launch Slicer. </li></ul><ul><ul><li>Observe Main window and Viewer window. </li></ul></ul><ul><li>Click File , View , Help , and Modules </li></ul><ul><ul><li>Examine submenus </li></ul></ul><ul><li>Click Main Menu buttons: Data , Volumes , Models , Alignments , Editor , and ModelMaker </li></ul><ul><ul><li>Click tabs </li></ul></ul><ul><ul><li>Examine panels </li></ul></ul><ul><li>Click More </li></ul><ul><ul><li>Click modules: click tabs, examine panels </li></ul></ul>
    19. 19. Overview <ul><li>Part 1: Slicer Interface </li></ul><ul><li>Part 2: Loading Data </li></ul><ul><li>Part 3: Interacting with Data </li></ul>
    20. 20. Loading Data <ul><li>Slicer can load </li></ul><ul><li>Volumes ………………….. </li></ul>
    21. 21. Loading Data <ul><li>Slicer can load </li></ul><ul><li>Volumes ………………….. </li></ul><ul><li>Models ……………………. </li></ul><ul><li>A model is a 3D reconstruction of the anatomy </li></ul>
    22. 22. Loading Data <ul><li>Slicer can load </li></ul><ul><li>Volumes ………………….. </li></ul><ul><li>Models ……………………. </li></ul><ul><li>A model is a 3D reconstruction of the anatomy </li></ul><ul><li>Scenes ……………………. </li></ul><ul><li>Scene = Volume + Model </li></ul>
    23. 23. Loading Data Slicer Advantage Putting together Images and Surface
    24. 24. Data representation <ul><li>Volume = collection of image files </li></ul><ul><li>Image file = header + raw data </li></ul><ul><li>The header contains the parameters of the image. </li></ul>Header Raw Data Header Raw Data Header Raw Data Header Raw Data
    25. 25. Data representation <ul><li>Volume = collection of image files </li></ul><ul><li>Image file = header + raw data </li></ul><ul><li>The header contains the parameters of the image. </li></ul><ul><li>Representation of an image: </li></ul><ul><li>2D Array of pixels containing the intensity values </li></ul>Pixel (a,b) Intensity I (a,b) a b Header Raw Data Header Raw Data Header Raw Data Header Raw Data
    26. 26. Loading DICOM Volumes Click on Add Volume in the Slicer Menu
    27. 27. Loading DICOM Volumes Left-click on the Menu Properties and change Basic to DICOM The Panel Props appears by default.
    28. 28. Loading DICOM Volumes Click on Select DICOM Volume The DICOM panel appears
    29. 29. Loading DICOM Volumes Select the directory dicom in the Tutorial-with-dicom dataset
    30. 30. Loading DICOM Volumes The list of DICOM studies appears. Click OK
    31. 31. Loading DICOM Volumes <ul><li>Name : The name that the </li></ul><ul><li>volume will have within Slicer </li></ul>Change to something descriptive: Cortex and click on Header Slicer loads the dicom study
    32. 32. Loading DICOM Volumes <ul><li>The DICOM Header </li></ul><ul><li>information panel appears </li></ul>Click Apply
    33. 33. Loading DICOM Volumes <ul><li>Slicer loads the </li></ul><ul><li>DICOM volume of </li></ul><ul><li>the brain </li></ul>
    34. 34. Visualization Support <ul><li>Control Window : displays a zoomed view of the position of the mouse on the selected image </li></ul>Move the mouse inside an anatomical view
    35. 35. Visualization Support The value of the gray level of the pixel under the cursor appears in the corresponding slice
    36. 36. Viewing Volumes <ul><li>V toggle button controls whether slice is visible in 3D Viewer </li></ul>Click on the three V buttons to display the Axial, Sagittal and Coronal images inside the Viewer
    37. 37. Viewing Volumes The Axial, Sagittal and Coronal Images appear in the Viewer
    38. 38. Manipulating the images Position the mouse on the images inside the Viewer Left-click and move the mouse to the left <ul><li>Rotation </li></ul>The images move to the left
    39. 39. Manipulating the images Position the mouse on the images inside the Viewer Right-click and move the mouse down The viewer gets closer to the model <ul><li>Zoom </li></ul>
    40. 40. Manipulating the images Position the mouse on the images inside the Viewer Right-click and move the mouse up The viewer moves away from the model <ul><li>Zoom </li></ul>
    41. 41. Viewing Volumes Select the 3D View The View Menu contains different options to visualize the data
    42. 42. Viewing Volumes 3D View focuses on 3D
    43. 43. Viewing Volumes Select 4x512 The View Menu contains different options to visualize the data
    44. 44. Viewing Volumes 4x512 view: larger image views to see details
    45. 45. Viewing Volumes Select 1x512 The View Menu contains different options to visualize the data
    46. 46. Viewing Volumes <ul><li>1x512: </li></ul><ul><li>one large TRANSVERSE </li></ul><ul><li>view and three small </li></ul><ul><li>images </li></ul>1x512 COR: one large CORONAL view and three small images 1x512 SAG: one large SAGITTAL view and three small images
    47. 47. Viewing Volumes <ul><li>The View Menu contains </li></ul><ul><li>different options to visualize </li></ul><ul><li>the data </li></ul>Select 4x256
    48. 48. Viewing Volumes 4x256 view: smaller equal-sized images Come back to Normal View
    49. 49. 2D Viewer <ul><li>Three 2D windows (red, yellow, and green) </li></ul><ul><li>Slider selects which slice of volume to display </li></ul><ul><li>Field shows the slice number </li></ul>1 2 1 2 3 3
    50. 50. 2D Viewer <ul><li>Bg (Background): displays volume in background layer </li></ul><ul><li>Fg (Foreground): displays volume in foreground layer </li></ul><ul><li>Superimposed over the background layer </li></ul>4 5 4 5
    51. 51. Volumes without Header <ul><li>Motivations: </li></ul><ul><li>The DICOM file format incorporates all the parameters that Slicer requires to render the data </li></ul><ul><li>Other images files types may not </li></ul>
    52. 52. Volumes without Header <ul><li>Motivations: </li></ul><ul><li>The DICOM file format incorporates all the parameters that Slicer requires to render the data </li></ul><ul><li>Other images files types may not </li></ul>Slicer has a simple protocol for loading volumes without header
    53. 53. Volumes without Header 1. Main  Data 2. Add Volume 3. Browse to find the first image of the Volume spgr in the directory tutorial 4. Select first image I.001 of volume to load, and click Open 5. Click on Manual 6. Click on Apply
    54. 54. <ul><ul><li>File Pattern : Pattern </li></ul></ul><ul><ul><li>of file names, in C syntax. Example: a file named skin.001 has a pattern of %s.%03d. </li></ul></ul><ul><ul><li>Image Size : Number of </li></ul></ul><ul><ul><li>pixels of image in x and y </li></ul></ul><ul><ul><li>directions. </li></ul></ul>Volumes without Header 2 1 The Header section of the Props tab appears.
    55. 55. Volumes without Header <ul><ul><li>Pixel Size in the x and y </li></ul></ul><ul><ul><li>directions. </li></ul></ul><ul><ul><li>Slice Thickness z dimension </li></ul></ul><ul><ul><li>of the voxel. </li></ul></ul><ul><ul><li>Scan Order : </li></ul></ul><ul><ul><ul><li>LR = left to right </li></ul></ul></ul><ul><ul><ul><li>IS = inferior to superior </li></ul></ul></ul><ul><ul><ul><li>PA = posterior to anterior </li></ul></ul></ul><ul><ul><li>Scalar Type : </li></ul></ul><ul><ul><li>Data format of the pixel. </li></ul></ul><ul><ul><li>Generally, it is Short (16 bit integer). </li></ul></ul><ul><ul><li>Slice Tilt : </li></ul></ul><ul><ul><li>The tilt of the gantry during an MRI. </li></ul></ul>3 4 5 6 7 3 4 5 6 7
    56. 56. Volumes without Header <ul><ul><li>Num Scalars : </li></ul></ul><ul><ul><li>Number of scalar components for each voxel. Gray-scale data: 1. Color data: 3. </li></ul></ul><ul><ul><li>Little Endian : </li></ul></ul><ul><ul><li>In little-endian architectures, the rightmost bytes are most significant. In big-endian architectures (Slicer default), the leftmost bytes (those with a lower address) are most significant. </li></ul></ul><ul><ul><li>DTI data , Swap , No Swap : Placeholders for future. </li></ul></ul>8 9 10 Click Apply to load the volume. 8 9 10
    57. 57. Volumes without Header The spgr volume appears in the Viewer
    58. 58. Loading Data <ul><li>Slicer can load </li></ul><ul><li>Volumes ………………….. </li></ul><ul><li>Models ……………………. </li></ul><ul><li>A model is a 3D reconstruction of the anatomy </li></ul><ul><li>Scenes ……………………. </li></ul><ul><li>Scene = Volume + Model </li></ul>
    59. 59. Loading Models <ul><li>In the main Menu select the </li></ul><ul><li>module Data and Click on </li></ul><ul><li>Add Model. </li></ul>
    60. 60. Loading Models <ul><li>The Props tab of the module </li></ul><ul><li>Models appears </li></ul>Select the model named Vessels in the directory tutorial/models Click on Apply
    61. 61. Loading Models The model of the vessels appears in the Viewer.
    62. 62. Loading Data <ul><li>Slicer can load </li></ul><ul><li>Volumes ………………….. </li></ul><ul><li>Models ……………………. </li></ul><ul><li>A model is a 3D reconstruction of the anatomy </li></ul><ul><li>Scenes ……………………. </li></ul><ul><li>Scene = Volume + Model </li></ul>
    63. 63. Loading a Scene <ul><li>Select File  Open Scene </li></ul><ul><li>in the Main Menu </li></ul><ul><li>Select the file tutorial.xml in the directory Tutorial-with-dicom/tutorial. </li></ul>A Scene is represented as an Xml file.
    64. 64. Loading a Scene The viewer displays the tutorial Scene
    65. 65. Loading a Scene The elements of the Scene are listed in the Menu Window
    66. 66. Overview <ul><li>Part 1: Slicer Interface </li></ul><ul><li>Part 2: Loading Data </li></ul><ul><li>Part 3: Interacting with Data </li></ul>
    67. 67. Manipulating a Model <ul><li>The model appears in the </li></ul><ul><li>3D Viewer . </li></ul><ul><li>Rotate the model: with left mouse button </li></ul><ul><li>Zoom the model: with right mouse button </li></ul>
    68. 68. Manipulating a Model Put the mouse on the 3D Slicer icon
    69. 69. Manipulating a Model The Control Window appears
    70. 70. Manipulating a Model Position the mouse on the R letter (Right) inside the window
    71. 71. Manipulating a Model The View Panel shows the model from the right side of the patient
    72. 72. Manipulating a Model Click on the Spin button
    73. 73. Manipulating a Model The model starts spinning inside the Viewer Panel.
    74. 74. Manipulating a Model Click on the Rock button
    75. 75. Manipulating a Model The model starts rocking inside the Viewer Panel.
    76. 76. Manipulating a Model Come back to initial orientation of the Viewer Panel by clicking on the A letter (Anterior) inside the window.
    77. 77. Models representation <ul><li>A model is a 3D representation </li></ul><ul><li>of the anatomy. </li></ul>Type W (Wireframe) in the Main Window
    78. 78. Models representation <ul><li>The triangles of the Model become visible in the Viewer. </li></ul>Type S (Surface) to come back to Surface Mode rendering
    79. 79. Model Opacity <ul><li>Click on Models in the Main Menu </li></ul><ul><li>Select the Display Tab </li></ul><ul><li>The properties Panel of the model appears </li></ul><ul><li>3. Opacity </li></ul><ul><li>Set the opacity of the Skin model to 0.5 </li></ul>
    80. 80. Model Opacity Skin model Opacity = 0.5
    81. 81. Model Visibility <ul><li>Visibility on and off by </li></ul><ul><li>left clicking on the name of model in the list </li></ul>Left Click on the Vessels button in the list of models
    82. 82. Model Visibility Vessels model Visibility 0ff
    83. 83. Global Visibility <ul><li>Show All to display all </li></ul><ul><li>models in the 3D Viewer. </li></ul>Click Show None to display none of the models in the 3D Viewer
    84. 84. Viewing 3D Models Show None: the models have disappeared
    85. 85. 2D Viewer <ul><li>Lb : displays label map </li></ul><ul><li>Displays results of a segmentation </li></ul>Left click on Lb in the Axial View and select the Label Map named None
    86. 86. 2D Viewer <ul><li>Lb : displays label map </li></ul><ul><li>Displays results of a segmentation </li></ul>The segmented volume named all disappears from the 2D Viewer.
    87. 87. 2D Viewer <ul><li>Lb : displays label map </li></ul><ul><li>Displays results of a segmentation </li></ul>Left click on Lb in the Axial View and select the Label Map named all.
    88. 88. 2D Viewer <ul><li>Lb : displays label map </li></ul><ul><li>Displays results of a segmentation </li></ul>The segmented volume named all appears in the 2D Viewer.
    89. 89. 2D Viewer Images in the label map layer appear as outlines around the structures that were segmented.
    90. 90. 2D Viewer Left Click on Fg in the Axial View and select the Volume named all in the Axial, Sagittal and Coronal slices.
    91. 91. Image Fusion <ul><li>Fade slider: </li></ul><ul><li>fades between foreground </li></ul><ul><li>and background . </li></ul>Set the Fade slider to 0.5
    92. 92. 2D Viewer The volume all is superimposed on the images
    93. 93. Clipping Models <ul><li>Clipping: cutting away sections of a model at one or more selected slices. </li></ul><ul><li>The model is removed from one side of each selected slice, revealing the image of each selected slice and the rest of the visible model. </li></ul>Select the Models  Display tab
    94. 94. Clipping Models <ul><li>1. Click on Show all to make all the models visible </li></ul><ul><li>2. Right-click the Skin model in the list </li></ul><ul><ul><li>A drop-down menu appears. </li></ul></ul><ul><li>3. Check that the Clipping option is selected. </li></ul><ul><li>4. Set the opacity of the Skin model to 1.0 . </li></ul><ul><li>5. Select the Clip tab of the Models panel. </li></ul>
    95. 95. Clipping Models Click + or - to select which side of each slice to clip on. Set the sides to: Red Slice + Yellow Slice - Green Slice -
    96. 96. Clipping Models Clipping Model Result
    97. 97. Conclusion <ul><li>Intuitive Interface for Loading and Visualizing Data </li></ul><ul><li>Slicer Outcome = fusion of Volumes and Surface </li></ul><ul><li>Open-source tool for developing your own module </li></ul>
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