3DMed User Manual
Contents
1. Current selected image view is surrounded by a red rectangle The controls for slice location are shown as follows Slice Location 30 act I I 1 Play fo FPS thich olume headimed Drag the slider to locate the slice of the selected image view The middle number below the slider shows the index of current slice The right number shows the total number of slices in the selected view l lz J0 Press the button Play to show the slices continuously You can control the frame speed via changing the number in the edit box beside the Play button Press this button again will stop playing Flay f20 FPS Stop fel FPS Use the combo box to select the volume hich Volume headime5d Adjusting Window Width Center The controls for adjusting the window width and window center level of the slice in selected image view are shown as follows 3DMED USER MANUAL Width Level and Color Width faoss Level jog7 5 Color Gray All Views Reset W L Enter new value into the edit boxes beside label Width and label Level to change the window width and window center Press Enter will apply the changes Width a095 Level 2047 5 Width fen Level 1o00 3DMED USER MANUAL Use the combo box to decide whether the changes will apply to all image views or just selected view a1 Views Selected View Unly el Views Press the button2. gt Load Volume and several submenus appeared Each submenu is corresponding to a supported format in 3DMed Now 3DMed supports the loading of BMP JPEG TIFF DICOM RAW IMO data files The submenus ate showed in below Load BMP Files Load DICDM Files Load IMO File Load JPEG Files Load Raw Volume Data Load TIFF Files When you loaded a dataset to 3DMed 3 Dimensional View will display the result of volume rendering and 2D Image View will display the slices In the Document panel New Document listview will add a volume in its Volumes listitem It is shown in the following figure Yolumes prod Surfaces Contents in Wol lew amp Yolumes z001 Surfaces 3DMED USER MANUAL To save a data in memory to disk you select the menu File gt Save Volume and several submenus appeared Each submenu is corresponding to a supported format in 3DMed Now 3DMed supports the writing of BMP JPEG TIFF DICOM RAW IMO data files The submenus are showed in below Write BMP File Write DICOM File Write IMO File Write JPEG File Write Raw File Write TIFF File Image Format Converting 3DMed supports many formats of data so you can use 3DMed as a image format converter You can load a data in the format that 3DMed supports and save it to a different format that 3DMed supports With th
3. 14 3DMED USER MANUAL Information in Status Bar When mouse cursor is moving on the image view the 3 dimensional coordinates and RGB value of the mouse cursor s current position are shown in the status bar at the bottom of main window im 3DMed i laj xj File Edit View Filter Segmentation Registration Visualization Option Help DLE Bees Document Image Display Surface Rendering Volume Rendering 3D Measurement 3D Cutting Display Object Slice Location I I I I I 1 30 58 Play 30 FPS Which Volume headimg58 x Width Level and Color Width 4095 Level 2047 5 Color Gray v z Reset W L Arrow Cursor Display Arrow Cursor Layout Selection C 1 3 2 2 aes Ae th e a n Dah 0 1402 95 311 2 29 06 67 g 67 b 6 15 3DMED USER MANUAL surface Render ing Surface rendering is a process after segmentation It will use the result of segmentation and the source volume data to build a 3 dimensional surface of the volume and then render this surface E Threshold Segmentation Form 2 x Source Image destination Image Slice Number In segmentation interface press OK to begin surface reconstruction after segmentation process has finished If the reconstruction process is done successfully you will see the result in the 3 dimensional view of the main window as follows 16 3DMED USER MANUAL ial 3DMed l x File
4. And the point will become the first point of your polygon Select the second point by clicking on left button of your mouse on another point in the Source Image The same is to the third and forth point of yout polygon 44 3DMED USER MANUAL File Edit View Filter Segmentation Registration Visualization Option Help ee eee ee ee Conte E S Yo Interactive Segmentation s Source Image destination Image A Slice Number ae GE A ee NS S N 1 1 69 When you want to end the polygon click the right button of your mouse It will automatically link the last point to the first point to form a polygon And the inter area of the polygon will be segmented The result of the segmentation will be showed in the Destination Image File Edit View Filter Segmentation Registration Visualization Option Help Conte Su Yo W ee Interactive Segmentation ae Source Image destination Image Slice Number a a ee 1 x 128 1 69 Pelee Linnea Uy ee Ube 0 45 3DMED USER MANUAL You have to segment the volume slice by slice Use the Slice Number Slide to change the current slice When you finish segmenting the whole volume click the OK button to save the segmentation result and close the dialog Click the Cancel button to close the dialog without saving the result File E
5. Reset W L to reset the window width and center to default value Reset W L Arrow Cursor Click the check box to show or hide atrow cursor Arrow Cursor F Display Arrow Cursor 3DMED USER MANUAL Arrow Cursor r Display Arrow Cursor Magnifier When mouse cursor is moving on the image view a rectangle area around the cutrent mouse position of the slice is magnified and shown at the left bottom of main window En l8 x File Edit view Filter Segmentation Registration Visualization Option Help Oo Al Bea Document Image Display Surface Rendering Volume Rendering Display Object m Slice Location 15 56 1 Play Bo ooo FPS Whi ch Yolume headings Width Level and Color Width foss Level 2047 5 Color Gray Reset W L Arrow Cursor E Display Arrow Cursor Layout Selection 1 3 C 2x2 x 248 163 2 Ltt 1108 g 1108 D 1108 0 Layout Selection Click the radio button in Layout Selection group box to select the layout of the views including three image views and one 3 dimensional view 1 3 layout 10 3DMED USER MANUAL Layout Selection EE 3DMed l x File Edit View Filter Segmentation Registration Visualization Option Help aaa E DZ EMBE Document Image Display Surface Rendering Volume Rendering T 3 Dimensional View isplay Object Slice Location 1 15 58
6. EEE Gr eer Plue i i f Ambient Color f Diffuse Color C Specular Color i Emission Color f Edge Color Red rr eer Blue b s o Alpha fo4 Alpha bo Sper Power Opacity Line Width A 1 Os LOUNA Point Size naa a emee p Note i The value of specular power is between 0 0 and 128 0 ii The value of opacity is the same as the alpha value of diffuse color and these two value will be changed together In wire frame representation you can adjust the edge color and line width The result is magnified 26 3DMED USER MANUAL Representation Surface Wire Frame Points Interpolation C Flat Smooth Properties f Ambient Color f Diffuse Color Specular Color Emission Color f Edge Color Red y Blue eee Alpha PEPEIPEEEPEP Ptr Spec Power _ 1 AATETETITTIIIUTINI Opacity PETE UEP rb rrr Line Width _ i 1 ee ee ee MOUNA Point Size yere p ee pr _ ye p oe p Sit r Reverse Hormals In points representation you can only adjust the size of point The color of points is decided by the surface materials The result is magnified 27 3DMED USER MANUAL Representation Surface Wire Frame Points Interpolation C Flat Smooth Properties f Ambient Color f Diffuse Color Specular C
7. Focus leave the edit box or Enter is pressed will apply the changes The way to adjust specular power and opacity is the same as above 24 3DMED USER MANUAL Diffuse Color 3 Ambient Color f Emission Color Specular Color a Edge Color Red 0 T1 PIPPI III III II dd ee ee Green io 74 Prrrrrrirtrbrrrrrrirrdide r r Elue s 0 8 Alpha C Ambient Color Specular Color Edge Color Red sr e eT Blue Alpha i i cn a f Diffuse Color Emission Color a 1 E Ambient Color Diffuse Color Emission Color f Specular Color f Edge Color Red l o reer Te Un Alpha EIN Uae cui ange iy ee Ong ff Ambient Color Specular Color Edge Color Red GY GeIL Blue Alpha If the value of opacity is below 1 0 the result will be translucent Ambient Color Diffuse Color i 0 Specular Color Emission Color r f Edge Color ee Red nn es GY eer Se S Blue y Alpha C Ambient Color Specular Color i Diffuse Edge Color Red GY GeIL Blue Alpha 25 TE f Diffuse Color f Emission Color Color Emission Color if ming i i 3 DME D USER MANUAL E Ambient Color f Diffuse Color C Specular Color Emission Color f Edge Color Red
8. Edit View Filter Segmentation Registration Visualization Option Help DPA HHE a Document ra Surface Rendering 3D Measurement Q Image Display Volume Rendering 3D Cutting m Representation nce a pans Surface Rendering Panel imoran Interpolation C Flat Smooth Properties Ambient Color Diffuse Color Specular Color Emission Color Surface Rendering Result Edge Color D TU OOOO Oe oo E E E OOO ETE E E E Y EEES IEEEEEEEEIEEEEEEE EEES EEEEEEEEEEETETET PELEUEEEEECEOOOOe eee PEEEUEEEEECGOOGeo eee Reverse Normals x 4 a irae a 0 g 0 b 0 0 Then press Surface Rendering button in the left to raise the surface rendering panel With this panel and mouse you can manipulate the rendering of the surface model Rotation parallel movement and zoom Keep the left mouse button down and drag on the 3D view to rotate the surface model freely Keep the middle mouse button down and drag on the 3D view to move the surface model in the scene 17 3DMED USER MANUAL Keep the right mouse button down and drag on the 3D view to make the model zoom in of Zoom out 18 3DMED USER MANUAL Representation of the model In the top of panel three kinds of representation are provided surface wire frame and points Surface is the default representation of the surface model shown above You can take this
9. Image View Contents in Yol View Volumes Surfaces Function Panel see Des AA MO Wa SR ee tee eee ane Menu Bar The Menu Bar shows all of the menus of 3DMed you can click one menu to call its function The Filter Segmentation Registration Visualization menus are dynamic menu And their contents depend on the dynamically loaded plunins Tool Bar The Tool Bar provides some frequently used general functions and you can access it quickly to click its icon Function Buttons and Function Panel The Function Buttons groups the functions provided by 3DMed Each button has a corresponding Function Panel to provide the user interface to access this function The Document button and its panel provide the management of the input data and the management of the displayed contents in 3 Dimensional View The Image Display button and its panel provide the function of 2D image processing please see chapter 2 to get more details 3DMED USER MANUAL The Surface Rendering button and its panel provide the function of surface rendering please see chapter 3 to get more details The Volume Rendering button and its panel provide the function of volume rendering please see chapter 4 to get more details The 3D Measurement button and its panel provide the function of 3 dimensional measurement In this alpha version of 3DMed this function is no
10. as the final result of the surface rendering i Peer 19 3DMED USER MANUAL In wire frame representation all the sides of triangles of the surface will be shown in the scene The result is magnified Representation Surface 0 Wire Frame Points a a lg ST aor ar i gt meee eae A ang aaa erma ies J 7 ay Sa a k a al ee ae te oe T Pattee Lee a ett Pe k T r 5 Bint i ea SE tee EELS ra 7 o re bs PU ras aD ig eal i aa Pee eat Pol See ee ee ee Foal is Bacal Eo Se a Fas ae ee a Se NS mares See sigh in RAS i Ses ae toca Sa seins eset a aa eo ee e a r 4M ae m ae 2 ec wean ra a EEEE EDERE E Eai g ee a eter enaere SPP 1 a r Tiape SBP E EErEE Peta 1 Macrae Weir USS Sai CEEI YIVO ILL h Men i i BE ae a Mie er TTT a In points representation all the vertices of the surface model will be shown in the scene The result is magnified Representation C Surface Wire Frame 0 Foints 20 3DMED USER MANUAL If the surface model is very big it will take long time to render in surface representation and mouse responses will be very slow In this condition you can do mouse manipulation rotation parallel movement and zoom in points representation and see the result in surface representation 21 3DMED USER MANUAL Interpolation modes There are two interpolation modes in surface representation flat an
11. eee nD FPS Which Volume headings x Width Level and Color Width joss Level 2o75 Color Gray v eset O I Arrow Cursor 7 Display Arrow Cursor X Y Image View Y Z Image View X Z Image View t Selection or E A Bo n E ee Seek e r 1034 g 1034 b 1034 0 2 2 layout Layout Selection ES fe Se 11 3DMED USER MANUAL ial 3DMed 18 x File Edit View Filter Segmentation Registration Visualization Option Help De Fl vx Hel S Document Image Display vN Surface Rendering Volume Rendering X Y Image View 3D Measurement S 3 Dimensional View Display Object m Slice Location 1 30 58 Play Bo ooo FPS Which Volume headims8 Width Level and Color Width faoss o Level 2047 5 Color Gray x Reset W L m Arrow Cursor V Display Arrow Cursor beyqut Selection X Z Image View 1 3 2 2 x 257 245 2 29T 1760 g 1760 D 1760 0 Mouse Manipulation for Image View Parallel movement Keep left mouse button down and drag on the image view 12 3DMED USER MANUAL Adjusting window width and window center Keep the middle mouse button down and drag on the image view Vertical movement for window center and horizontal movement for window width After adjusting 13 3DMED USER MANUAL Zoom Keep the right mouse button down and drag on the image view Zoom in Zoom out
12. 1 2 3 Stopping Value 6850 Clear Result Fast Marcing Segmentation Slice Number sc Scere Leas E AE OEA vee dl bee ee ee 50
13. 3D MEDICAL IMAGE PROCESSING AND ANALYZING SYSTEM Med User Manual 3DMed User Manual Medical Image Processing Group Institute of Automation Chinese Academy of Sciences Web site http www 3dmed net Corresponding person Professor Jie Tian E mail tian doctor com 3 DME D USER MANUAL Overview 3DMed stands for 3D Medical Image Processing and Analyzing System It is developed by the Medical Image Processing Group Institute of Automation the Chinese Academy of Sciences This software system is developed to provide medical imaging community another available software to process and analyze the medical image datasets It is an free software and can be downloaded from www 3dmed net freely In functions it combines all the functions of Data I 0 Data Format Converter 2D Image Processing Surface Rendering Volume Rendering Image Segmentation Image Registration 3D Virtual Cutting and 3D Measurement The segmentation and registration functions are provided via the plugins For more details please visit our web site www 3dmed net Main Interface The main interface of 3DMed is shown in the following figure 3DMED USER MANUAL Z 3DMed 68860 File Edit View Filter Segmentation Registration Visualization Option Help ten Bar DZA BEES 2 4m rin Document Image Display Surface Rendering Volume Rendering 3D Measurement 3D Cutting New Document Volumes z001 Surfaces 3 Dimensional Vier 2D
14. ake the model zoom in mouse move up or zoom out mouse move down See the following figures for zoomed images Zoom in Zoom out 32 3DMED USER MANUAL Selection of Transfer Function To select the transfer function click the Volume Rendering button in the Function Buttons This will bring the volume rendering panel to the front panel in the Function Panel The volume rendering panel is shown in the following figure Document Image Display sutace Rendering Volume Rendering IU Measurement 30 Cutting scalarOpacity Transfer Function scalar Opacity Fresets Ramp l z cala olor Transter Function Scalar F G Fresets Gray scale GradientUpacity Transter Function O On Gradient Opacity Fresets Mo Edge Detection In the volume rendering panel there are two tabs One is Transfer Function and the other is Shading To select the transfer function click the Transfer Function tab The tab is shown in the following figure 33 3DMED USER MANUAL Transfer Function Shading oc alarOpacity Transter Function scalar pacity Fresets Ramp l z scaler Color Transter Function scalar R G Fresets Gray scale Gracdientlpacty Transter Function O On Gradient pacity Presets Mo Edge Detection In this tab you can select the scalar opacity scalar color gradient opacity transfer functions Each transfer function has some preset
15. ay sutace Rendering volume Rendering JO Measurement O Enable Clipping Flane Clipping Add Plane Initial Orientation oy Plane Add Flane Manipulation which Plane 7 Translate Rotate s Ue Rotate amp Rotate lt amp Cube Clipping Reserve Cube Lube Manipulation Let DMM Rigt e 36 3DMED USER MANUAL The Enable Clipping check box is used to control if the cutting clipping 1s enabled If you check this option then the cutting clipping is took effect Otherwise there is no cutting clipping in the volume rendering process When the cutting clipping is turned on the Plane Clipping and Cube Clipping radio button is enabled You can turn Plane Clipping on turn Cube Clipping on or turn both on When the Plane Clipping is turned on you can add a clipping plane by click the Add button The initial direction can be selected in the Initial Direction listbox The following figure show a Yoz plane clipped image When the Cube Clipping is turned on you can control the size of the cube by adjusting the slider position of Left Right Bottom Top Front and Back slider The Reserve Cube and Cut Cube in the listbox are used to control which part is cutted The following figure show a Reserve cube clipped image the part of the specified cube is reserved The following figure sho
16. d smooth In wire frame and points representation the selection of interpolation modes is disabled Flat interpolation mode uses a simple interpolation method to render the surface Compared with smooth mode the result is rough but the rendering process is a little faster e 22 3DMED USER MANUAL Smooth interpolation mode uses a complicated interpolation method to render the surface The result is smooth but the speed is slow Interpolation f Flat i Smooth 23 3DMED USER MANUAL Material properties Representation i Surface U Wire Frame Points Interpolation i Flat f Smooth peiperties f Ambient Color f Diffuse Color C Specular Color U Emission Color Edge Color ee 1 sr OTL i hl f 1 Blue Alpha p aM Opacity es ane Ws ath i eee i PETE PEPE P Prd eed Point Size i Reverse Hormals enact Eevee PEPEEEEEP PPP reba joo 1 l In this area you can adjust the material color properties of the surface model In surface representation you can adjust ambient color diffuse color specular color emission color specular power and opacity of the surface To adjust color click the radio button of the color you want to adjust and then drag the slider beside Red Green Blue or Alpha to change the value of each channel You can also enter the value directly into the edit box to change the value between 0 0 and 1 0
17. d the right arrow changes the High Thresh value After you change these values the Destination Image will show you the result after segmentation 41 3DMED USER MANUAL ea Am TH AQ RO IAD RRA BOM Ea x OHSA 416 E o BT oos EMF v Garamond lt A FIB Z i i EEA gt Bie Threshold Segmentation Fora 2 z Faarao TE dectication EE a Slice Number 1541 1521 1501 1481 1461 i44 1421 1401 1381 1361 134 1321 1301 1281 1261 124 1221 120I orje Ill ggi Bazal gt 6 i 6 8 10 fw 17 4BK 977 42 Fl we Sm Ox If you are satisfied with the result and want to save it click the OR button to close the dialog otherwise you can click the Cancel button to close the dialog without saving the result of the segmentation SE AO THM BMAD ERO TAM RRA BOW HRW x s FA A o Bl 100 2 ENF v Garamond 7A B 7 2 i gt 2 4 lI i i 4 x E EA Threshold Segmentation Fora Source Image destination Image as r Slice Number a L 1541 1521 1501 1481 1461 i44 1421 1401 1381 1361 134 1321 1301 1281 1261 124 1221 1201 orje Ill ggi 6em 6 8 10 fw 17 4BK 977 42 J Ae Sm Ox 42 3DMED USER MANUAL Interactive Segmentation Click the Interactive Segmentation item in the Segmentation submenu and then you can begin the interactive segmentation process Os
18. dit View Filter Segmentation Registration Visualization Option Help a Interactive Segmentation Jeg Source Image destination Image Conte BSu Yo Slice Number UU AS CT POISE PSU UWS VSS TT TES SUS CCD Pg WC ESD ST Vest TORT Wes i SUES SLE SUIS SL URS SC STS Theat a PIU Le SUS SUES best Des se Ut hy A Les 1 63 r keas ROEE er D e a a ee ee LU cy sea A E Fast Marching Segmentation Click the Fast Marching Segmentation item in the Segmentation submenu and then you can begin the Fast Marching segmentation process 46 3DMED USER MANUAL ME Jag File Edit View Filter Segmentation Registration Visualization ption Help 3 l Fast Marching Segmentation Lo p 7 4 g Segm ay Interactive Segmentation Surface Rendering Volume Rendering Slice Location Yv EA VOR e OR SAA IE TA S EN heel AS E A tied a a U AS O S Ti R SSE Te ER 1 129 256 Which Volume whitegray v Width Level and Color Width 255 Level 127 5 Color Gray v All Views v Reset W L Arrow Cursor Display Arrow Cursor Layout Selection 1 3 O 2 2 L Fast Marching Segmentation After the Fast Marching Segmentation item is clicked there will appear a dialog and you can proceed the Fast Marching segmentation in this dialog File Edit View Filter Segmentation Registration Visualization Option Help re AR ah gt Fast Marching Segmentation e Source Image Destinition I
19. e adding of new data I O pulgins 3DMed will support more and more data formats and its format converting function will get more and more applications 3DMED USER MANUAL 2D Image Processing 2 Dimensional image processing functions include examining all the slices along z axis x axis and y axis X Y Image Y Z image and X Z Image playing the slices continuously adjusting the window width and window center of the selected images displaying the arrow cursor and magnify the area around the center of the cross changing the layout of the views a x File Edit View Filter Segmentation Registration Visualization Option Help VA Sees OD Als EES g Document mage Display C nsee Displey Surface Rendering Volume Rendering TATE i A Image Display Panel 3 Dimensional View 1 30 58 j Play 30 FPS thi ch Volume headimg58 v j Width Level and Color Slice Location Width 4095 Level 2047 5 Color Gray All Views Reset W L L m rrow Cursor M Display Arrow Cursor X Y Image Y Z Image X Z Image m Layout Selection i 143 So L k 241 y 256 2 29 r 1066 g 1066 b 1066 0 After loading a volume click Image Display to enter the panel of 2D image processing functions Browsing Slices In the right bottom of the main window there are three kinds of image views of the volume you can browse shown as follows 3DMED USER MANUAL
20. entation Registration Visualization Option Help ly em A Th gt Threshold Segmentation Form a PEET og Source Image Destination Image Surf Source Image destination Image Which Widt Width Level Color All V rroj g Column Diagram Layo 1x O 2 4 ii Slice Number Slice Number Slide There two images on the top of the dialog The left image is the source image which represents the original image before segmentation The right image is the destination image which represent the result image after segmentation The 40 3DMED USER MANUAL Column Diagram is in the middle of the dialog It shows you the pixel information of the original image The Slice Number Slide is on the bottom of the dialog You can use it to change the current slide number among the volume You can drag the left or right arrow below the Column Diagram to select your interest area Me ee THM RAM ELO TAD RA BOW HAW Xx 6 DO naan 4 4 Eo o BC 0 o o ERRE Garamond AM r Bs Zl ii EEA ETES Threshold Segmentation Fora 2 L Source Image destination Image Be i C IH Z Slice Number 2 E Oeil le aon ie a y Te AVS at Sp ee ate S A iin A L el te I AE St N EE 1 10 33 z fe a e 3 gt 6 e 3 9 fie 7 6K 547 15l RSE OX The left arrow changes the Low Thresh value an
21. for choice For example Scalar Color Transfer Function provides two preset for the user choice They are Gray scale and Rainbow If you select Gray scale the volume rendered image will be a gray image as is shown in the following figure AY ay 34 3DMED USER MANUAL And if you select Rainbow the volume rendered image will be a color image as is shown in the following figure Control of shading parameters To control the shading parameters click the Shading tab in the volume rendering panel The tab is shown in the following figure Transfer Function O Enable Shading Ambient Diffuse specular Power Preset Material Bright 35 3DMED USER MANUAL The Enable Shading check box is used to control if the shading is calculated If you check this option then the shading calculation is took effect Otherwise there is no shading calculation in the volume rendering process When the shading is turned on you can control the shading parameters by setting the ambient diffuse specular power or by selecting a preset material from the Preset Material listbox Cutting of Volume Rendered Image To cut or clip a volume rendered image click the the 3D Cutting button in the Function Buttons This will bring the 3d cutting panel to the front panel in the Function Panel The 3d cutting panel is shown in the following figure Document Image Displ
22. ima Jag File Edit View Filter Segmentation Registration Visualization Option Help D F i Fi Fast Marching Segmentatio om L Interactive Segmentation DL gt R Teda Sementation Surface Rendering Volume Rendering E J Ciorine New Document Volumes gorret Surfaces n Contents in Vol View Surfaces gorrc Volumes Interactive Segmentation ein SOGOFOC a o a After the Interactive Segmentation item is clicked there will appear a dialog and you can proceed the Interactive segmentation in this dialog 43 3DMED USER MANUAL File Edit View Filter Segmentation Registration Visualization Option Help D Source Insee Source Image Destinition Image destination Image Conte Sw Vo Slice Number m eae RRO ear Penns RCS RT 1 1 69 Slice Number Slide oer AE deny tot Her SOO eee Sell er Pte LD There two images on the top of the dialog The left image is the source image which represents the original image before segmentation The right image is the destination image which represents the result image after segmentation The Slice Number Slide is on the bottom of the dialog You can use it to change the current slide number among the volume You can select your interest area in the Source Image by drawing a polygon You can begin drawing the polygon by clicking the left button of your mouse on a point of the Source Image
23. mage Source Image destination Image Which Widt Width Level Color All Arr oj Dis Layo 1 3 2 4 ij Stopping Value Clear Result H Fast Marcing Segmentation Slice Number 1 1 1 Slice Number Slide There two images on the top of the dialog The left image is the source image which represents the original image before segmentation The right image is the destination image which represents the result image after segmentation The 47 3DMED USER MANUAL Slice Number Slide is on the bottom of the dialog You can use it to change the current slide number among the volume First you should define the stop value by enter it into the Stop Value text edit Then check the Fast Marching Segmentation check button to tell the computer that you ate going to proceed the segmentation Click the left button of your mouse on one point of your interest area in the Source Image the result of your segmentation will be showed in the Destination Image File Edit View Filter Segmentation Registration Visualization Option Help Fast Garching Segmentation Fors Jeg Source Image destination Image Stopping Value 850 Clear Result Fast Marcing Segmentation Slice Number 7 1 1 To S y OS eae E an You can also click the left button of your mouse on the point of your another interest area The result of the
24. olor Emission Color Edge Color Red Blue ee Alpha Spec Power _ r PETE PEPE P rb rrr Opacity Line Width 1 1 es to ee LEUI Foint Size _ yere p Se ar _ ane p gee pr emee E Reverse Hormals 28 3DMED USER MANUAL Reverse Normals It is a tool to correct the wrong direction of the normals calculated by the reconstruction algorithm Sometimes the direction is opposite to the right direction and results in an abnormal display You can press this button to get a proper display One abnormal display 29 3DMED USER MANUAL The proper display after reversed the normals 30 3DMED USER MANUAL Volume Render ing Volume rendering is a process to render a volume to an image directly When you loaded a volume into 3DMed the result of volume rendering will be display in the 3 Dimensional View automatically You can control and manipulate the process of volume rendering in various ways Rotation translation and zooming Keep the left mouse button down and drag on the 3D view to rotate the volume rendered image freely See the following figure for a rotated image Keep the middle mouse button down and drag on the 3D view to translate the volume rendered image in the scene See the following figure for a translated image 31 3DMED USER MANUAL Keep the right mouse button down and drag on the 3D view to m
25. previous segmentation will be accumulated 48 3DMED USER MANUAL File Edit View Filter Segmentation Registration Visualization Option Help am el i e Fast Garching Segmentation Fore Ze Source Image destination Image Which Widt Width Level Color All Arr oj Dig Layo 1x O 2x3 Stopping Value 850 Clear Result Fast Marcing Segmentation Slice Number 7 1 1 1 x Seo OS teenie ecb If you are not satisfied with the result click the Clear Result button the segmentation result will be cleared and the destination image return to the original one File Edit View Filter Segmentation Registration Visualization Option Help O 2 PF el h So ES Fast Harching Segmentation Fora BJE Source Image destination Image Stopping Value 850 Clear Result Fast Marcing Segmentation Slice Number 7 1 1 T S y 0 z aa Note that the segmentation is carried out in 3 dimensions When you finished the segmentation you can click the OK button to save the result and close the 49 3DMED USER MANUAL dialog You can also close the dialog without saving the result by clicking the cancel button a x File Edit View Filter Segmentation Registration Visualization Option Help Fast Garching Segmentation Fors Jeg Source Image destination Image Which Widt Width Level Color All Arroj Dis Layo
26. t provided and it will be provided in later version The 3D Cutting button and its panel provide the function of 3 dimensional virtual cutting please see chapter 4 to get more details The functions of segmentation and registration are also provided by 3DMed The Segmentation menu in Menu Bar provides the segmentation function The system will load segmentation plugins at startup If there is any segmentation plugin a submenu will be added in the menu Segmentation Please see chapter 5 to get more details about the segmentation functions provide by 3DMed In this alpha version of 3DMed the registration plugins are not provided so the Registration menu will has no submenu 3 Dimensional View The 3 Dimensional View provides a view for displaying the result of surface rendering or volume rendering please see chapter 3 and chapter 4 to get more details 2D Image View The 2D Image View provides a view for displaying the medical dataset slice by slice please see chapter 2 to get more details Status Bar The Status Bar provides a position for displaying some information for example the image value in the mouse position progress information etc Please see chapter 2 to get more details 3DMED USER MANUAL Image Input Output 3DMed supports many formats of data and new format can be supported by adding a plugin To load a medical dataset to 3DMed you select the menu File
27. w a Cut cube clipped image the part of the specified cube is cutted 37 3DMED USER MANUAL 38 3DMED USER MANUAL After loading the volume you can click the Segmentation item in the main menu to begin the segmentation process There are several items in the submenu of Segmentation Each of them represents a different segmentation method Jo O 3Died File Edit View Filter Segmentation Regist ation Visualization Option Help p r j i egmentation kay D B gt Ze nteractive Segmentation 8 Document Threshold Segmentation m A CO sin cmi Hew Document Volumes Mhai Surfaces Contents in Yol View Surfaces ghai Volumes i PR Gay a Threshold Segmentation Click the Threshold Segmentation item in the Segmentation submenu and then you can begin the threshold segmentation process 39 3DMED USER MANUAL O sinea Jog File Edit View Filter Segmentation Registration Visualization Option Help 7 Fast Marching Segmentation bis k d D 2 E L eractive Segmentation f Threshold Segmentation Surface Rendering th olume Rendering New Document Volumes g ad Surfaces Contents in Vol View Surfaces g ad Volumes a CO ANEA Threshold Segmentation After the Threshold Segmentation item is clicked there will appear a dialog and you can proceed the threshold segmentation in this dialog File Edit View Filter Segm
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