EBS User`s Manual
Contents
1. 34 26048 Screw Widget 4 zn a si a nn Rn DR TES 34 2 6 49 Fixation Plate 36 2 6 SODbJeCts ua a cr Sexe eH er debe es 37 2 6 6 Selection Properties dos mas Bee u he a 38 Main Ment 2 5 ts ho EEE Sele Er EIC EIS dS 38 2 Eller te By gba bd ae et et 38 DD SENE ee ee LP 39 2 4 9 NEW snm Sa BR R Bei VES REIS S v EUR 39 274 Help zone Seq xag EVE S 40 Objects 4 u rn uel geste e edes ex ede ee veo Mp 40 Opt ons DIaloB reas pi APRI ore Ry ae ai es Ee RR obere ir 41 Additional Features de OE Eee ES ee weed rex 41 2 10 1 Display Calibration s vus 58 RU ne me Eg 41 2102 Grd Eines ccs Huby actos woe Ae er NODE Ins Re 41 Ekliptik EBS CONTENTS iii 2 10 3 Anaglyph steteo en EAR RE BR 42 2 10 4 CollisionDetection 42 2 10 5 3D Connexiornimouse e RUBUS E TRUM 42 3 Tasks 43 3 1 Segmentation s 5 cu snos PS EEG E ERAS aue E ERG 43 31 11 Importing Examination en 43 3 1 2 Filtering Dataset rar ar det Hv mese dE 44 3 1 3 Region Of Interest ROD e RR RE 8 2 8 RR S SERE 44 3 1 4 Segmentation looo pope Per ER RUE S S 44 3 15 Further PFoCessmg lt 5 USES ERA RUE Hu dee tee 44 252 SReQUCCOILD 2 5 4 usi2. 2 6 4 7 Lookup Table Edit Tool wh a Shortcut L Lookup table defines a mapping between a scalar value and display color EBS uses lookup table to transform dataset values for display of slice to map values calculated in intensity projection view or to define color and opacity for for volume rendering Window center and width define extent of lookup table Colors inside the window can be defined using gradient points All colors outside the window assume either low color in case the value is below lower limit of the window or high color in case value is above upper limit of the window Window center can be quickly changed by dragging mouse horizontally in display region Window width is changed by draging mouse vertically in display region Window center and extents are also denoted in gradient bar as vertical lines They can be dragged by mouse Ekliptik EBS 18 User Interface Inside window gradient points can be added by clicking anywhere in the empty area or removed by dragging gradient point gradient bar The color for specific gradient point can be defined by clicking on the color bar bellow the gradient bar Vertical position of gradient point denotes opacity This is currently only used in Volume render 2 6 1 8 Slice Tool e Shortcut Z Click and or drag mouse in a view to change the slice position In slice and 3D view mouse click or drag will display slice at the position pointed by mouse This tool can be also
3. v bone 6 doe v bone 7 v bone 8 HO v bone 9 HO bone 10 v Figure 2 23 Objects list Objects box contains list of all labels fixation plates and screws in the document Each object is represented by one row in the list and contains following information Visibility Object is visible when check box is checked Name Color Color can be changed by clicking on the color button Surface status for labels or object icon for fixation plates and screws 3Surface status shows the status of surface object in relation to the voxel data of a label There are 4 status icons Ekliptik EBS 2 9 Options Dialog 41 Mesh is build and it reflects current state of the label Label does not contain enough voxels to build mesh from it Mesh is not build or contains old state of the label Build is required Build process can be started by clicking on the icon D Mesh is being built Mesh is already build building collision detection mesh 2 9 Options Dialog Use options dialog to set application preferences 2 10 Additional Features 2 10 1 Display Calibration Operating system does not provide accurate information on display device physical size To get 1 1 scaling to work correctly display has to be calibrated Calibration is done in options Edit Options Display Calibration by entering pixel vertical and horizontal size In case this information is not available physical display device width or resolution
4. This gives in beter perception of depth relation Ekliptik EBS 8 User Interface among the parts of objects In case size is important especially for comparison among different parts of structures orthographic projection should be used Focal length is enabled only when using perspective projection It is the property of camera which defines angular extent of the observable scene 2 5 1 4 Multiplanar Reconstruction View Multiplanar Reconstruction view displays either a single slice from dataset planar reconstruction of dataset in arbitrary orientation or curvelinear reconstruction of dataset using user defined path The mode can be selected in Slice Section property In all of the cases images are shown in an isometric 2D view Figure 2 6 Multiplanar Reconstruction View 2 5 1 2 Intensity Projection View Ekliptik EBS 2 5 View Area 9 Intensity Projection view displays a projection of dataset voxels inside ROI onto a view plane For each pixel in display image ray is traced in view direction from the eye Based on selected transfer function the value for output pixel is calculated from voxels intersected by each ray as MIP Maximum Intensity Projection shows the maximum voxel intensity on ray path MinIP Minimum Intensity Projection shows the minimum voxel intensity on ray path Integrate shows the sum of voxel intensities on ray path The result obtained is 2D XRay image Figure 2 7 Intensity Projec
5. can be specified to calculate the pixels size 2 10 2 Grid Lines EBS can overlay grid lines to help define spatial relations among the objects The grid lines are enabled in the main menu View Grid Lines or in the options dialog Edit Options Display Grid Lines The options panel enables to select grid lines to be Non Metric distance between the lines in grid is defined in pixels Non metric grid is drawn in blue color Metric distance between the lines is defied in milimeters Metric grid is drawn in green color Metric grid can be used to measure physical size of the objects It works only in views with an orhographic projection Non Metric grid can be overlayed on any kind of view To be sure that grid is always metric select Metric Gridlines and uncheck Allow display of nonmetric gridlines in perspective views Ekliptik EBS 42 User Interface 2 10 3 Anaglyph Stereo EBS supports 3D stereoscopic display by using anaglyph stereo glasses Red cyan colored glasses with red filter over left eye are required Figure 2 24 Anaglyph stereo glasses Stereo view be enabled in the options dialog Edit Options View Stereo or trough the View Stereo menu The stereo effect depends on eye separation It is advisable that you manually change the eye separation untill image is comfortable to view The eye separation can be changed using F5 and F6 shortcut keys or by using the Stereo options panel Turning on stereo
6. temporarily activated by clicking on the middle mouse button 2 6 1 9 Delete Command Delete selected objects 2 6 2 Segmentation Toolbox 2 6 2 4 Segmentation Wizard Wizard opens a new tool panel and guides a user trough steps of segmentation process as described in Segmentation task 2 6 2 2 Filter amp Filter the dataset with low pass filter Dialog box offering filters is shown There are 3 distinct smoothing filters available Recursive Gaussian this filter is using ITK RecursiveGaussianImageFilter filter to process the dataset Gradient Anisotropic Diffusion this filter is using ITK GradientAnisotropicDiffusionImageFilter to process the dataset Ekliptik EBS 2 6 Toolbar 19 Curvature Anisotropic Diffusion this filter is using ITK CurvatureAnisotropicDiffusionImageFilter to process the dataset 2 6 2 3 Segmentation Tool wa Segmentation tool creates initial label from the dataset based on voxel values The tool sets a threshold value for the threshold filter The threshold edge is drawn on the slice Segmentation will be executed with a click on Apply button in the tool panel Based on selected options some of the following filters might be executed on the label as a post processing step Opening ITK BinaryMorphologicalOpeningImageFilter Voting Erode ITK VotingBinaryHoleFillingImageFilter where background value is set to label and fore ground value is set to empty space effectivelly reversing
7. triangle icon in bottom right hand corner Only one tool can be active at any time When tool is active it might display additional tool properties panel inside the toolbox 2 4 Widget Widget is a visual element that is displayed inside view and can be manipulated by clicking or dragging on one of its handles As a general rule when both tool is active and widget is present widget has a priority When mouse is clicked on the widget handle widget will accept the action Some tools like Lookup Table Editor Tool display additional widgets Global options can be set using Options Dialog Additional EBS features are described in appendix 2 5 View Area View area contains panes with views onto the document Based on selected layout there is one or up to four panes displayed at the same time View layout can be modified by selecting desired item from the View Layout menu While in one of the panes spacebar toggles between single pane layout and multiple pane layout Figure 2 1 Single Pane Layout Ekliptik EBS 2 5 View Area Figure 2 2 Four Panes Split Bottom Figure 2 3 Four Panes Ekliptik EBS 6 User Interface Figure 2 4 Three Panes Split Right Ekliptik EBS 2 5 View Area 7 2 5 1 View Types Views display contents of a document Different view types are available each focusing on different aspect of the data View type of selected pane can be modified by clicking on view type icon in the t
8. 5 Separate Q 3 Move spatially un connected volumes in selected label into separate labels 2 6 3 6 Split Tool 3 Split label into multiple labels based seed points Based on dataset labels grow from seed points The seed points can be defined in dataset or 3D view When seed point is clicked in 3D view it may move away from clicked point This is to assure the optimal placement Verify that seed point is still inside object to be separated Split Tool uses ROI For further instructions see an example Ekliptik EBS 2 6 Toolbar 21 2 6 3 7 Cut Tool Cut label by drawing a cutting plane One or more cutting planes can be defined by clicking on the 3D view Object separated will lay in one of the partitions of the cutting planes For further instructions see an example 2 6 3 8 Split Tool Illustration This is a step by step example of Split Tool usage on a case of splitting pelvis into separate bone fragments Split Tool can be used to split label based on Dataset It works by specifying seed points on or in the label from which volumes are grown The growth is determined by dataset values The two growth regions will meet in the least dense value in the dataset usually a crack Starting point for this example is a label obtained from Segmentation Wizard Edit View Help Slice Position amp Orientation Ox Or Oz Ote Segmentation Reduction Analysis 2 Labels
9. EBS User s Manual 2 1 0 1 User s Manual 2 User Interface CONTENTS 20 c Modes surre eet ee o Ru Pes P ee 2 2 Command neu ee eds Heer Sapa wu AR RR Sx ATE 2 37 o mem su E nM pese s enis Widget uu pese ROS i ale ae RS pA AL obe RI a E 23 NIEW ATCA cs o us t wea e Be Boh Seg fe sns 2 53 17 cMIEWTyDeS co ruere Bae OE ne er De he Re oe eee 2 5 1 1 Multiplanar Reconstruction View 2 5 1 2 Intensity Projection View 2 5 3 Volume View e ee URS ah ROS 29 14 Surface VIEW o ocr Bat REN RUE Yon a ex UE desc 2 5 1 5 X Ray Simulation View 2 5 16 Cutaway View ug uox RORIS RUE 25920 CAD VIEW 2555 Supe ale a EORR I Red AU 4 2 6 u te RRR Sh Bole eee e RE Sce eue mu egets ROM Wie Ww TO0lDOX 2 2 2 2 5 Aue voie Sr eec ee eh De RC de phe eno Retos 2 6 1 1 Select Tool ERR eine 2 0 1 2 View Pan Tool 4 4 ee RR ww TRU 2 6 1 3 Zoom 0 2 6 14 ViewRotate Tool 2 6 1 5 Reset 2 6 1 6 Region Of Interest 0 2 6 1 7 Lookup Table Edit Tool ZOS Sli
10. Of Interest ROI Processing time increases with dataset size In case only part of dataset contains structures of interest it is possible to ignore irrelevant parts by defining sub region of the dataset where on which filtering is performed ROI ROI is used in Segmentation and some other filters 3 1 4 Segmentation Segmentation tags parts of dataset image which contain tissue of interest Bone extraction is done with value thresholding followed by optional post processing Segmentation tool is activated with Segment Tool button With segmentation parts of dataset are selected which contain image Simple thresholding is used to define areas There are also three options for object post processing 3 1 5 Further Processing Before reconstruction can start bone fragments have to be separated so they can be manipulated indepen dently Full set of functions available for that purpose is in Segmentation Toolbox 3 2 Reduction Reduction is done by moving the bone fragments and adding implants in form of fixation plates and screws The tools for reduction are available in Reduction Toolbox Ekliptik EBS CHAPTER FOUR ACTIVATION To access full functionality EBS requires to to be activated Following features are not available without activation Creation of new document Saving of existing document Export EBS can be activated by filling out a form under Help Activate menu The dialog will appear whith follow ing informati
11. Toolbox Coo amp 9 A 2 tebets 1 9 o Split Tool Marker x y 1 103 225 T3 Add Marker Delete 1 Select a label to work on This can be done by clicking on the item in Objects list or by activating the Select Tool and clicking on the desired label in 3D view 2 Select Split Tool The Split Tool panel will appear bellow The panel contains list of all markers buttons for editing markers and a button for applying the filter Ekliptik EBS 22 User Interface 3 Select one of the markers in the markers list Double click will navigate Dataset view to that marker 4 Click on the part which should become a separate label This can be done either in 3D view or in Dataset view When working in former the point might be moved from click location as to find the optimum placement based on the Dataset Verify that point is still on or inside the part you clicked on 5 New markers can be added by pressing Add Marker and 6 defining the marker as presented in step number 4 Repeat steps 5 and 6 for each part which should be separated 7 Press Apply Depending on label and dataset size filter processing may take some time Ekliptik EBS 2 6 Toolbar 23 8 Sometimes the Split Tool doesn t separate some parts as expected Solution is to either Undo the step and position the markers better or in this case where part has split into two labels
12. bone3 bone4 process it further Select the bones which belong together and 9 click on Merge button This will merge only the two labels Ekliptik EBS 24 User Interface In the image above is the final result It shows merged labels If some part of the label was split incorrectly it can always be fixed by merging the labels and re applying the split tool only on that particular label Also the label can be further divided by using the Split tool on it even without the Merge 2 6 3 9 Cut Tool Illustration This is a step by step example of Cut Tool usage on a case of splitting existing pelvis label into two new labels creating an artificial posterior column fracture Cut Tool can be used to cut away parts of label The cut is made by defining a single or multiple dividers drawn in 3D view Starting point for this example is a label obtained from Segmentation Wizard Ekliptik EBS 2 6 Toolbar 25 1 Select a label to work on This can be done by clicking on the item in Objects list or by activating the Select Tool and clicking on the desired label in 3D view 2 Select Cut Tool The Cut Tool panel will appear bellow The panel contains list of all dividers buttons for editing dividers setting the selected volume and a button for applying the filter 3 Rotate and align the view Cut will be made perpendicular to view direction 4 Draw the first divider by clicking points in the view area Divider wil
13. ce Tool ded b Be BE nr eS 2 6 1 9 Delete Command oo nu A A A t CONTENTS 2 7 2 8 2 9 2 10 2 6 2 Segmentation Toolbox 18 2 6 2 1 Segmentation Wizard 18 2 022 22 Filter GREG ERG Re ER 18 2 6 43 Segmentation 19 2 0 3 Babels Toolbox Reno a S E Square 19 2 63 New Label 220 EV wee Sm S 19 2 0 3 2 Merge Labels ee TP ceto mr ips mis 19 2 6 3 3 Tool i anne GERE AUR OE Ie 20 2 60 34 Fill Hole Tool 2 koh 058 REOS RM 20 2 6 3 5 Separates bs elie Eum Rue HE uum pud 20 2 6 3 6 Spit Tool node gebe ES Seb gsm 20 20327 Cut I00P uoce etre UE dy na eR US qe n au ehe ny 21 2 6 3 8 Split Tool Illustration 21 2 6 3 9 Cut Tool Illustration 24 2 6 4 Reduction Toolbox 30 2 6 4 1 Translate TOO 525506 Ban URS eee es 30 2 6 4 2 Pivotlool 4 0 22 2 2 xA RR a ea o ES 31 2043 Rotate Tool 4 2 2 deb an a VERG mM Bee 32 2 04 4 A A Ee RD ee 33 2 6 4 5 Add Sciew Tool s s ooo RR A ET 33 2 6 46 Add Fixation Plate 0 34 20 47 Measure Tool 522255 5 6 A Sede Ue
14. clicking in the items in Objects box in the toolbox 2 6 1 2 View Pan Tool 7 Shortcut X Click and drag to pan the view This tool can be temporarily activated by holding Alt middle mouse button 2 6 1 3 View Zoom Tool A Shortcut C Click and drag to zoom the view This tool can be temporarily activated by holding Alt left and middle mouse button 2 6 1 4 View Rotate Tool e Shortcut V Click and drag to rotate the 3D view In dataset view this tool changes view projection Ekliptik EBS 2 6 Toolbar 17 Figure 2 14 Viewpoint widget Viewpoint widget can also be used to to change the viewpoint click on surface to rotate the viewpoint to one of the predefined view orientations or drag to rotate freely This tool can be temporarily activated by holding Alt left mouse button 2 6 1 5 View Reset Command rs Click to reset the selected view to default 2 6 1 6 Region Of Interest Tool 4 Define region of interest ROI volume which is used in further processing ROI can be defined by manually by entering coordinates in tool panel or by dragging a mouse in dataset view Drawing region in dataset view will modify only two dimensions of ROI dimensions which are displayed in the view with the third one depth left unmodified To draw all three dimensions bounding box has to be drawn in two dataset views displaying different orientation Region is indicated by red rectangle
15. ecked Name Color Color can be changed by clicking on the color button Surface status for labels or object icon for fixation plates and screws 3Surface status shows the status of surface object in relation to the voxel data of a label There are 4 status icons Mesh is build and it reflects current state of the label Label does not contain enough voxels to build mesh from it Mesh is not build or contains old state of the label Build is required Build process can be started by clicking on the icon D Mesh is being built Mesh is already build building collision detection mesh Ekliptik EBS 38 User Interface 2 6 6 Selection Properties Name screw Length 10 655 Figure 2 22 Properties for selected Screw Selection contains properties of selected object or objects Some of the properties can be modified by typing in new value 2 7 Main Menu 2 7 1 File New Create anew document Dialog will be displayed to select dataset files location Open Load existing EBS document EBS documents have ebs extension Save Save document under existing name Save As Save document under a different name Export Geometry Export surfaces into 3D mesh file Following two file formats are supported COLLADA COLLAborative Design Activity is an interchange file format for interactive 3D applications COLLADA is managed by the Khronos Group When COLLADA is selected as export format all visible screws fixati
16. endicular to the normal at new entry point when screw direction has been previously manipulated Holes in all fixation plates elements contain placement handle When clicked screw will be placed in fixation plate hole 2 6 4 9 Fixation Plate Widget Figure 2 20 Fixation Plate Widget Fixation plate widget is a widget for editing fixation plate placement It is displayed for every selected fixation plate in a form of set of arrows The arrows act as a handles and can be clicked on and dragged with the mouse Indigo colored arrows annotate existing placement points By dragging them on a bone fixation plate will change the shape Dragging the placement arrow off the object will delete it Clicking and dragging the green arrow will add a new placement point at the position of the arrow This can be used to extend the fixation plate without changing the existing shape when clicking on arrows on either extreme or to control placement more precise when clicking one of the inner arrows Ekliptik EBS 2 6 Toolbar 37 2 6 5 Objects 123 v bone 2 Ho v bone 3 HO v bone 4 HO v bone 5 HO v bone 6 v bone 7 HO v bone 8 HO v bone 9 HO V bone 10 v Figure 2 21 Objects list Objects box contains list of all labels fixation plates and screws in the document Each object is represented by one row in the list and contains following information Visibility Object is visible when check box is ch
17. enter will move the object parallel to the screen surface 2 6 4 2 Pivot Tool s Shortcut E Click and drag on handles to change center of rotation Ekliptik EBS 32 User Interface Figure 2 16 Pivot Widget Pivot widget can be used in following ways Dragging one of the lines will move object in the direction of the line Dragging cube in the center will move the pivot to the surface of the object below the mouse cursor Dragging near the center will move the pivot parallel to the screen surface 2 6 4 3 Rotate Tool e Shortcut Click and drag the handles to rotate selected object Ekliptik EBS 2 6 Toolbar 33 Figure 2 17 Rotation Widget Rotate widget can be used in following ways Dragging one of the circles will rotate object in the axis of that circle Dragging the outermost circle will rotate the object in the axis perpendicular to the screen Dragging near the center of the widget will rotate object freely 2 6 4 4 Reset Reset Transformation 2 6 4 5 Add Screw Tool Click on scene to add a new screw Once screw is created Screw Widget can be used to edit its placement Ekliptik EBS 34 User Interface 2 6 4 6 Add Fixation Plate Tool Click on scene to add a new fixation plate Once fixation plate is created Fixation Plate Widget can be used to edit its placement 2 6 4 7 Measure Tool Click on scene to draw measure line At each vertex on the line ang
18. isplay Scale to 1 1 by selecting this option fixation plate is displayed on screen in real size Display scale can be calibrated in Options dialog Ekliptik EBS 2 6 Toolbar 15 2 6 Toolbar Figure 2 13 Toolbar on the left hand side Toolbar contains functions tools commands and properties for controling display and to edit the docu ment Functions are logically grouped into a few distinct toolboxes The top of the Toolbar is always occupied by View Toolbox View Toolbox contains tools and commands for changing view properties Properties of selected view are displayed directly underneath Below the selected view properties is a task selector which shows additional toolboxes based on task selected Segmentation Segmentation Toolbox Labels Toolbox Reduction Reduction Toolbox Other panels in Toolbox are Object List displays list of objects in the document Selection attributes display when object with exposed properties is selected Some tools display additional property panels when they are activated Ekliptik EBS 16 User Interface 2 6 1 View Toolbox View Toolbox contains tools and commands for modifying view properties such as eye point zoom and slice position 2 6 1 1 Select Tool 4 Shortcut Click on label in Dataset 3D view to select it Hold Shift while clicking to add to selection or Ctrl to remove object from selection An alternative way to select objects is by
19. l 1 v Pelvis Cut Tool 7 Rotate view to Anterior position 8 Click on Add Divider to add another divider 9 Draw the divider Ekliptik EBS 2 6 Toolbar 29 Ele Edit View Help vO Slice Position amp Orientation Ox OY Oz ONone Label Opacity a Segmentation Reduction Analysis Segmentation Toolbox 2 0508 Labels Toolbox coe amp s Objects E label 8 E label 1 v Pelvis Cut Tool Curve Nr Points 10 The two dividers divide space into 4 volumes To specify which of the four volumes should be separated click on Set button and 11 define the point in the volume which should be separated by clicking on it in the 3D view The element is marked with green sphere 12 Press Apply button Final result is displayed in the image below Ekliptik EBS User Interface 869 Labels Toolbox 0 2 2 6 4 Reduction Toolbox 2 6 4 1 Translate Tool Shortcut W Click and drag on handles to translate a selected object Ekliptik EBS 2 6 Toolbar 31 Figure 2 15 Move Widget Translation widget can be used in following ways Dragging one of the arrows will move object in the direction of the arrow Dragging cube in the center will move the selected object to the surface of the object below the mouse cursor Dragging near the c
20. l split the label Existing points in the divider can be moved however it is currently not possible to remove them Entire divider has to be re drawn use Delete followed by an Add Divider to start drawing divider from scratch Ekliptik EBS 26 User Interface Segmentation Toolbox 4 0 Labels Toolbox c m 5 Objects E label 8 Patton Nr Points 5 Divider plane can be seen on a viewpoint change Note that divider can be modified only in initial view for the specific divider In in case one of the divider points is clicked view will be changed back to initial view for that divider Double click on the divider in the divider list in tool panel will also activate the divider initial view Ekliptik EBS 2 6 Toolbar 27 6 Image above shows what would happen in case Apply button was pressed at this moment Do not press the Apply button Left side was split together with right posterior column One way to proceed would be to select the white label and apply separate on it Since parts we are interested in are not touching each other they will split just fine After that desired parts can be merged using Merge For the purpose of this example we will proceed in another way Ekliptik EBS 28 User Interface Segmentation Toolbox Labels Toolbox wo amp 0 Objects label 8 labe
21. lation does not give physically accurate image as it is based on following assumptions objects are of homogeneous material Attenuation depends only on thickness Visualization is based on sufaces It does not include data that is present in the original dataset but has not been captured by segmentation Fissures than have not been captured in the process of segmentation will not be visible Ekliptik EBS 12 User Interface Figure 2 10 X Ray Simulation View Additional properties for X Ray Simulation View include Power Negative Implants In Color renders screws and fixation plates in color assigned to object Draw Selected Object Edge renders object edge 2 5 1 6 Cutaway View Cutaway view display section trough the 3D model following the screw axis A screw has to be selected for this view to work Ekliptik EBS 2 5 View Area 13 Figure 2 11 Cutaway View Additional properties for Cutaway View include Lock Cut Direction fixes current section plane so that it doesn t move with camera anymore 2 5 17 CAD View 599 CAD view shows fixation plate from different sides in orthographic projection This view be used as reference for bending the plate A fixation plate has to be selected for this view to work Ekliptik EBS 14 User Interface Figure 2 12 CAD View Properties for CAD View Lock D
22. le between linear segments is displayed At the end of the line total line length is displayed Line is cleared by right mouse click or reset button in toolbox While tool is active angle between selected two screws is displayed as well With Automatic Measures some of the measures are made and displayed automatically Moved Rotated Fragments draws a line between label original position and label curent position for all moved or rotated lables Additionally distance and angle are displayed as a label over the line Angle Between Selected Screws shows angle between selected screws Angle is measured between first two screws in selection 2 6 4 8 Screw Widget Screw widget is a widget for editing screw length and its placement It is displayed for every selected screw in form of arrows and balls Those act as a handle and can be clicked and moved with the mouse Ekliptik EBS 2 6 Toolbar 35 Figure 2 18 Direction Handle When ball above the entry point arrow is clicked direction indicator is shown enabling change of direction Screw will automatically adjust the length to the new exit point Figure 2 19 Screw widget Ekliptik EBS 36 User Interface When screw exit point arrow is dragged screw exit point is changed When screw entry point arrow is dragged entry position is changed and either direction is changed so that exit point remains the same when exit point has been previously manipulated direction is perp
23. nd in specified folder selection dialog box will appear prompting to select one of the available datasets Once dataset is loaded it can be viewed in dataset views DICOM metadata such as more detailed patient info and scanning parameters are available trough the menu File Show Metadata Menu File DICOM Files Show Info displays short info about the state of dataset and where the images were loaded from This might be useful moving ebs documents to a different location Location of DICOM files is stored in ebs document as a relative path reference When document is saved to different device or media user must take care that DICOM files which document references are moved too To modify the path to DICOM files File DICOM Files Set Dataset Path can be used There are two utility commands to copy or move referenced DICOM files to user specified folder under FIle DICOM Files 44 Tasks 3 1 2 Filtering Dataset Based on scanning protocol used data might contain too much noise to proceed with segmentation By filtering dataset high frequency noise is removed More the data is smoothed easier will it will be to process further but possibly important details might be lost Filter dialog is shown by clicking the Filter Dataset button There are three smoothing filters available Recursive Gaussian Gradient Anisotropic Diffusion Curvature Anisotropic Diffusion Please consult ITK documentation about filter details 3 1 3 Region
24. ne oe PRO RE Teo ed do doe es Ie qb Mi pete uet 44 4 Activation 45 A Terminology 47 Ekliptik EBS CHAPTER ONE USER S MANUAL EBS is a software application for preoperative planning of bone fracture medical procedures based on a real patient data EBS contains a powerfull DICOM viewer with built in surgery planning simulation and analysis module In addition to standard medical views like MPR MIP MinIP IntIP Volume SSD it supports simulated X Ray which Cutaway and CAD view Simulation mode makes it possible to move bone fragments and fixate them using screws and fixation plates Various measurements can be made on so prepared reduction plan This manual is a guide through the concepts and building blocks of the EBS It also serves as a reference for a standard application procedures It starts off by describing User Interface and then moves on to a standard Tasks Terminology is located at the end Note that to access full functionality EBS has to be activated User s Manual Ekliptik EBS CHAPTER TWO USER INTERFACE EBS main window comprises of a document view area on the right hand side a toolbar on the left hand side and main menu at the top of the window Document viewing and editing is done by executing commands available from toolbar and menu using the tools activated from toolbar or by manipulaing widgets inside views directly 2 Mode EBS has different modes which determine how
25. objects are displayed and which tools and commands are available The mode can be selected on the top of the toolbar Segmentation is a process of labeling dataset and creating 3D model When in segmentation mode all objects will be as found labeled on dataset It is not possible to move objects in this view and implants are not shown Reduction contains simulated view and thus shows moved bone fragments It also shows all the implants Dataset in reduction view is calculated from original dataset taking into account all possibly moved parts Top right hand side corner of view contains a description of simulated parts e g Sumulated Reduction Implants is to be interpreted as the view contains fregments which have been moved and there are also some implants inserted 2 2 Command Command is executed as soon as button is clicked or menu item selected For the commands which work on objects the target object has to be selected before command is triggered To delete an object the object has to be selected first and only than should delete button be clicked Objects can be selected in Object List or in any of the views by using Select Tool 4 User Interface 2 3 Tool is an input mode which defines what action is triggered when mouse is clicked or dragged dragged over the view tool may support only certain view types Only one tool can be active at the time To distinguish between tool and command buttons tool buttons have a
26. ommand Clear Undo Buffer This command will release memory used by undo steps It will also revert filtered dataset to initial state This command can not be undone Due to large size of data EBS might sometime not be able to perform operation for the lack of memory To release unused memory use Clear Undo Buffer and try to execute operation again Options Display options dialog 2 7 3 View Layout Submenu item selects one of the available view layouts Pane Contents Submenu item selects one of the available view types for the selected view pane Grid Lines Toggle grid line overlay Onion Skin Onion skin displays original position and orientation of moved lables in Shaded Surfave Display as a transparent shape Stereo Toggle anaglyph stereo view Menu has a check box when stereo is enabled Ekliptik EBS 40 User Interface Eye Separation Commands under this menu can be used to change the stereo eye separation Build Surfaces Update surfaces for all the labels that have been modified since the surface was last build Rebuild Surfaces Rebuild surfaces for all the labels 2 7 4 Help Contents Display help contents Activation Activate EBS by sending serial number to the EBS activation service To access full feature set EBS has to be activated About Display application information 2 8 Objects 4 2 gt v bone 2 ne v bone 3 v bone 4 HO v bone 5 HO
27. on Computer ID is unique id of a computer EBS runs on The data is prefilled and can not be modified Software has to be activated on each computer separatelly Serial Number is a serial number provided to you by Ekliptik Name Company are the custom data describing user and company Email is the address which will be used to send activation notification Once all of the above data are entered pressing Get Activation Key will connect to EBS activation service and request activation key After a few moments key is automatically filled in and EBS is activated In case activation fails error message box appears In case the activation error persists please contact customer support support ekliptik si Activation requires an active Internet connection No other data then the data visible in the Activation dialog is transfered to activation service during activation 46 Activation Ekliptik EBS APPENDIX A TERMINOLOGY Dataset Medical examination comprising of a stack of slices Label A set of voxels in dataset Labels are used to represent elements of interest e g bone fragment Label shape can be visualized in 3D Slice Two dimensional image containing cross section trough the body Voxel A single pixel cell in the slice grid DICOM Digital Imaging and Communications in Medicine ROI Region Of Interest LUT Lookup table SSD Shaded Surface Display
28. on plates and labels with built surface representation will be exported The unit of exported scene is millimeter STL is a file format native to the stereolithography CAD software created by 3D Systems STL is widely used for rapid prototyping and computer aided manufacturing Each of meshes for selected labels will be exported into separate file In case there is more than one label selected a separate file with name of the label appended to the selected file name will be used for each label Export DICOM Save currently displayed dataset In Reduction mode simulated dataset with moved bone fragments will be exported Print Print currently displayed image in selected view For CAD view fixation plate bending angles are printed DICOM Files Show Info Show status of dataset file with source location of dataset files Ekliptik EBS 2 7 Main Menu 39 DICOM Files Set Dataset Path Set location of the dataset files Available only in cases when the dataset path specified in document is invalid DICOM Files Copy Dataset Files Copy dataset files referenced in the document to arbitrary folder DICOM Files Move Dataset Files Move dataset files referenced in the document to arbitrary folder Show Metadata Display DICOM metadata defined in currently loaded dataset DICOM metadata contain information about the patient and examination details Exit Exit the application 2 7 3 Edit Undo Undo command Redo Redo undone c
29. op left hand side corner of the view Alternativelly view type can be chosen by selection one of the options in Views Pane Contents menu Figure 2 5 View type icons Properties for selected view are displayed underneath the View toolbox inside the toolbar The Selected view properties can be expanded or minimized by clicking on the title Diffrent properties are displayed based on selected view type Some common properties shared among multiple views include The views which display dataset slices Multiplanar Reconstruction View Shaded Surface View and Cut away View Slice Section which can be a dataset orientation oblique or user defined path Slice orientation is described in a bit more detail in Multiplanar Reconstruction View section The slice position slider located underneath slice orientation radio buttons is is used to move among the slices perpendicular to view orientation Label opacity controls how labels are displayed inside the slice view A slider controls label opacity Opacity of the label mark can be modified from 0 to 100 In case of 100 no dataset image will be shown underneath the label area Fill selects if closed contour on the edge of the label or as a filled shape is used to denote label The 3D views all except Multiplanar Reconstruction 3D Orthographic projection selects between ortographic and perspective projection In perspective projec tion size of the objects changes with distance from the view
30. operation of hole filling i e filter is clearing the label Hole filling VotingBinaryIterativeHoleFillingImageFilter followed by GrayscaleFillholeImageFilter It is recomended to Select at least one opening filter as this will remove small isolated fragments which are usually artifacts of thresholding Clear all existing labels will remove labels that are already there before the filter is run 2 6 3 Labels Toolbox Labels are parts of whole volume which are of interest For the most part labels can be interpreted as bone fragments EBS offers tools to create and manipulate labels Initial label is usually created with Segmentation Tool 2 6 3 4 New Label Q Create new empty label 2 6 3 2 Merge Labels Merge selected labels into a new label Ekliptik EBS 20 User Interface 2 6 3 3 Paint Tool Manually paint selected label Painting is done in Dataset view The tool shows options box with following settings Paint over defines which objects to paint over Clear label when set painting will clear the label Size defines size of paintbrush in voxels 3D when selected the painting is done in multiple slices at once Isotropic takes voxel physical size in each direction into account when size is defined Round or Square defines a brush shape 2 6 3 4 Hole Tool Click on hole to fill it The tool works only on a single slice The tool will not perform when hole is not closed 2 6 3
31. tion View with Integrate transfer function Additional properties for Intensity Projection View are Clip low level is available only with Integrate projection function When checked integrating function will ignore all sample values which are below specified low threshold value Enabling this will display bone fragments with better contrast Overly Implants will overlay fixation plates and screws on top of the Intensity projection image Since the Intensity Projection always displays state as determined by examination implants might be in wrong location if the bone fragments have been moved after reconstruction With Display Implants in color checked the color property of implant will be used to render implant instead of value based on lookup table assigned to view Ekliptik EBS 10 User Interface 2 5 1 3 Volume View Volume View displays direct volume render of dataset A ray is cast for each pixel in output image in view direction to create a shaded version of dataset The apperance of output image greatly depends on selected transfer function Transfer function can be selected and modified using Lookup Table Edit Tool Figure 2 8 Volume View 2 5 1 4 Surface View Surface View displays shaded surfaces generated from dataset in a segmentation process Ekliptik EBS 2 5 View Area 11 Figure 2 9 Surface View 2 5 1 5 X Ray Simulation View X Ray view displays X Ray simulation based on surfaces X Ray simu
32. view might decrease color saturation of certain objects to enhance the stereoscopy effect 2 10 4 Collision Detection Collision detection prevents moving surfaces into each other To enable special processing has to be done on mesh objects The processing step is done in parallel to building mesh For collision detection to work NVIDIA PhysX system software hass to be installed http www nvidia com object physx 9 09 0408 whqgl html Note that no spe cial hardware is required to run this software 2 10 5 3D Connexion mouse EBS supports 3DConnexion input devices for changing viewpoint and moving objects in the 3D scene See the 3DConnexion web site for for details on available models http www 3dconnexion com Ekliptik EBS CHAPTER THREE TASKS EBS workflow comprises of following steps Importing examination and creation of surfaces Segmentation Reduction and fixation using surface representation Reduction 3 1 Segmentation Segmentation is a process of building a 3D surface model from examination represented as volumetric image stack of image slices Steps of segmentation are outlined below 3 1 Importing Examination A first step is to import examination data stored in DICOM format Examination is loaded by selecting File New menu and pointing to folder with examination With option Include Sub Folders all sub folders of selected folder will be scanned for images In case there is more than one dataset fou
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