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3DMed User Manual

1. ES Edge Color Red A O LI Ke VILILLULLILI bs A O O O O O LILI ji Green O Tal VIULELLELELELILEULLLIL LI LI H mmm Blue 5 JU 47 PPEPrirrirrrrirrrrirdrridrddi ij Alpha lo 4 3 DME D USER MANUAL f Ambient Color fe Diffuse Color C Specular Color Emission Color Edge Color Red Sr eer JE _ __ooo FF FHHHH PPrPrrrirrrirrtrrrrrrirddrdd Blue i 0 5 0 47 Ambient Color f Diffuse Color Specular Color fe Emission Color O Edge Color Red Sr eer Elue nl 4 Net por xa po J po po Alpha Alpha ORI EPP rrr opec Power JE caaaaaaaaaaaaaaaaaaama Opacity o Line Width a A Point Size 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 3DMED USER MANUAL hich Surface ctheadMesh v Representation Interpolation E Flat fe Smooth Properties Fresets Default v f Ambient Color f Diffuse Color f Specular Color 7 Emission Color fe Edge Color It LILI LI LI IO Z 1 IL E 1 Red I ot LILI LI t ft bt bt ML tod Se It t tol Green I ot LILI LI LIO LI M tt ML O 1
2. Source Image destination Image Slice Number Mer 1401 1381 1361 1341 1321 1301 1281 1261 1241 1221 1201 1181 1161 1141 1121 1101 181 161 14 F em 6 8 9 ME T 6E 547 153 we Sm Ox The left arrow changes the Low Thresh value and the right arrow changes the High Thresh value After you change these values the Destination Image will show you the result after segmentation 3DMED USER MANUAL a THE ee MAW RAG RXO TAM RRA BOW BO Y X S 0g nNaa 8 4 gt A o 15471108 gt gt ERS Garamond 40M 18 7 ce el A gt gu Threshold Segmentation Form ajx L Source Image destination Image a Slice Number oO mle METERSE 1541 1521 1501 1481 1461 1441 1421 1401 1381 1361 1341 1321 1301 1281 1261 1241 1221 1201 em 6 8 10 ME 17 AE 97 23 RE E Ox If you are satisfied with the result and want to save it click the OK button to close the dialog otherwise you can click the Cancel button to close the dialog without saving the result of the segmentation cal THO REO WEW MAD KO IAW Rw BOM WAW 5 s 0egdnfasa 8 la E o BE 10 2 EXXF gt Garamond A SEB li i eee i ae 6 ase Threshold Segmentation Form Jeg AAA L Source Image destination Image al OL Humb K Sacre umber AA AXEL 1541 1521 1501 1481 1461 1441 1421 1401 1381 1361 1341 1321 1301 1281 1261 1241 1221 12
3. Blue Rm VLILLILELI DELILI I LILI IH Spec Power m Opacity A Line Width k y Tt A O A A O IMI O MU Point Sire A Kubi ae con Ma F ura m NES Background Color Reverse Normals 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 3DMED USER MANUAL thich Surface ctheadMlesh v Representation i Surface Wire Frame E Points poe TA AO Interpolation l Flat fa Smooth Properties Presets Default v O Ambient Color O Diffuse Color O Specular Color O Emission Color fe Edge Color It t t LI t ft ft LI bt tt a I ML Red o RET CRT m aT eA EREEN Blue sm Alpha Spec Power m VLELLELI LILI LI LI LILI HI MI Opacity EL ii a ei EI NE Ee a AAA ee Line Width oe Trtrtditttitdtttttitdit LILI MI H Point Size ya See pr atrija VUU RE y Background Color Reverse Normals Background Color Click this bottom and you can select a background color for the main window As shown in the following figure Original background 3DMED USER MANUAL Doc end Inis Displar For facu Eunderiog Volume Reoderiog 30 Faznuranant 4 Cutting vba ch Sor fece ctheadMesh E Dereser ati an fe Surface ire Frame 0 Points Interpol akti ca tf Flai fe Smoot
4. 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 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 your polygon 3DMED USER MANUAL Edit View Filter Segmentation Registration Visualization Option Help eee PP ee A za o 2 y Interactive Segmentation JE LJ Source Image Conte Sui Vo destination Image Slice Number p Y IAEA AE ASAS A AAA RIA ASA Cancel 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 Edit View Filter Segmentation Registration Visualization Option Help Kao ee 7 UUD zma 22 p LJ Interactive Segmentation ax Source Image destination Image Surf New D J
5. 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 Display surface Rendering volume Rendering JU Measurement O Enable Clipping Plane Clipping Add Plane Initial Orientation or Plane Add Plane Manipulation hich Plane Translate Rotate Rotate Y Rotate 2 S Lube Clipping Reserve Cube Lube Manipulation Let amp Right Bottom Top Front Back S 3DMED USER MANUAL The Enable Clipping check box is used to control if the cutting clipping is 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
6. 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 ni Use the combo box to select the volume Which Volume 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 a Views Reset WL 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 4095 Level 2047 5 Width 200 Level 1000 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 gt JA Views Press the button 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 arrow cursor Arrow Cursor z 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 current mouse position of the slice is magnified and shown at the left bottom of main window CEM p l l x File Edit View Filter Segmentation Registration Visualization Option Help n
7. 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 show a Cut cube clipped image the part of the specified cube is cutted 3DMED USER MANUAL 3DMED USER MANUAL Segmentation 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 MU Se Comercial eed A Esla Edit War Filta agua no pi riratjon Vimjali rutica plis Help El Fari A A MT Cy pa e Intare Sapa ele 7 F a un zni Cee Deere on So ata lud ar Lag Lava Fara Epari a D hermun Bigio Gros Tye La on Thrashed Aparra a xX Conlara an Nod Vilar ETE Surfacaa 2 Fact Barching Sagmentati zu x 2b MW oc LE rug amp kli ba Ihreshold Segmentation Click the Threshold Segmentation item in the Segmentation submenu and then you can begin the threshold segmentation process 3DMED USER MANUAL Ma Mon Commercial 20ted peal x Fila Eli Tica Filtar Segmentation Pagistration Vizmlirutisn Opilon Help Py oj Jz Fi A Fact Merchiog Semintation jie pa sa Ioni eiir Sagres ati ra 7 eeart Leveled Sementalian Surface Henderina Live Virs Segmentstion ZU Phaarormnant Pea gi sn a erst uti ok Thr rhal ig apar
8. Vo Sul Conte Su Vo Slice Number 4 v fot VEESI ERT NISI AA SU REG a Rete SA A Rott ten lada SV TDI feten taker beter TEKA AESI EEA ES it 1 1 69 xi 146 49 241 072 OTS Sre IES AU RN 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 Edit View Filter Segmentation Registration Visualization Option Help Interactive Segmentation JE Source Image destination Image O Va AA Y zz ME oro INTA Ud O Fast Marching Segmentation Click the Fast Marching Segmentation item in the Segmentation submenu and then you can begin the Fast Marching segmentation process 3DMED USER MANUAL ll Non Comnreercial 20rted Ella Edi Fica Filtar Semantati an Hhsistreatioo Visgalitation Goiien Help are i Fact archipg Segnentaiian Diz Je Inisrucilva Bagel ski ra Uoerarani Levelei Seenentation Surface Henderina Livs Vira Zagmantation Z Beacoranent kiglon ro Sagraini uki Xu Tkrurhald agmantatira Her Dororent Velnnaz L S Paces vb O X Cantante in Vol Tic H Fic te Sor facea Faai Sar ckiTy dugivnialiin m l sr TE s 132 peotra D D b re Af
9. can also enter the value directly into the edit box to change the value between 0 0 and 1 0 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 3DMED USER MANUAL fe Ambient Color C Diffuse Color f Emission Color C Specular Color Edge Color Red HN Greer AO SEO AR bordo Blue Sern MEN Alpha A ee nm Ambient Color C Diffuse Color f Emission Color Specular Color Edge Color Red OV Green Blue se O Alpha s nm C Ambient Color fe Diffuse Color Emission Color O Specular Color Z Edge Color Re J IILILLILILI A VIUILELILI LI bs PPrrirrrrirriri errirdgddgdbdgdd r Green 1 0 T9 VIIDLLLLLILI TILI LILI LI H Blue i lu 47 VIIDLILLLLI LI TILI LILI LI H j Alpha i Ambient Color C Diffuse Color Specular Color s Emission Color Edge Color Red Sr eer Alpha If the value of opacity is below 1 0 the result will be translucent fe Ambient Color C Diffuse Color O Emission Color C Specular Color f Edge Color Red IILILILI LILI LI x IUILILI fom PPrirrirrrrririrdribierrirdgddd beded j Greer i OI TA VILILLILLI LILI LI LILI LIH Blue IK 0 8 Alpha gt Ambient Color Diffuse Color f Emission Color C Specular Color
10. scene The result is magnified Representation Surface fe Wire Frame Points SANA Rac SE IME mea E a ena aa PERE a ae parace oa Puce bil ont se A A AI Ga HEH A Po y IS la GNP aig Ka ie E TE E i E 5 a A ls a OE Se a ra Za HE ALLE PE HAT In points representation all the vertices of the surface model will be shown in the scene The result is magnified Representation O Surface Wire Frame s Points 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 Interpolation modes Representation fa Surface Wire Frame Points abiterpolati on C Flat Smooth oOo iin Prope Fresets Default v f Ambient Color i Diffuse Color f Specular Color Emission Color f Edge Color Red Green Blue Alpha VILLELILIEITLI LI LILI I LILI IL HI Opec Power m j Line Width lA A UE II A A A STi Point Size joo Backeround Color Reverse Normals A Ap E 3DMED USER MANUAL There are two interpolation modes in surface representation flat and smooth In wire frame and points representation the selection of interpolation modes is disabled Flat inter
11. the 3D view to translate the volume rendered image in the scene See the following figure for a translated image Keep the right mouse button down and drag on the 3D view to make the model zoom in mouse move up of zoom out mouse move down See the following figures for zoomed images Zoom in 3DMED USER MANUAL Zoom out 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 3DMED USER MANUAL Document Image Display surface Rendering Volume Rendering JU Measurement JU Cutting scalarOpacity Transfer Function scalar Opacity Presets Ramp U Z calar olor Transter Function Scalar R 3 Fresets Gray scale GradientUpacity Transter Function O On Gradient Opacity Presets 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 3DMED USER MANUAL Transfer Function Shading ocalar Jpacity Transter Function scalar pacity Presets Ramp U2 scalar Color Transter Function Scalar R G Fresets Gray scale Gracdientlpacty Transter Function O Un Gradient Op
12. 01 E al 1 1 I 1 Y I I 1 1 1 1 1 1 1 I I 1 i I i Cancel 10 a T z 8 gov y EGE za gt em 6 a10 A 17 4E 94 423 REE Ox 3DMED USER MANUAL Interactive Segmentation Click the Interactive Segmentation item in the Segmentation submenu and then you can begin the interactive segmentation process ll Mon Corn rmercial IDEA ol x Fila pli Fica Filtar Segmentation Eagistratiooa Visgalitatiin pilon Help k E je El m Fact Marchiog Semantnilan je e nire fra Egresado silo lutitas Deemer t vel on Surface Benderime Live Wirs Segmentstioo ZU Beacoranent Faglon Griat Sagraini uti ca Phorechald agmartati ca Her Docurent z Vedran oe EE H Loe Paces Cantants in Vol Tica Tu Volumes Soe Fuca Interactiva 5egneniaiLan x Zi yi TE r 12 1300 b O ri After the Interactive Segmentation item is clicked there will appear a dialog and you can proceed the Interactive segmentation in this dialog 3DMED USER MANUAL Destinition Image destination Image Slice Number a SE E SES KEM ER ES a es e age ao cea cea owl esc a pom o ar od eta yo 1 1 69 Slice Number Slide Ni Rote Bie apt ana the go zbiti 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
13. 3D MEDICAL IMAGE PROCESSING AND ANALYZING SYSTEM 3DMed 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 mitk net freely In functions it combines all the functions of Data I O 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 mitk net Main Interface The main interface of 3DMed is shown in the following figure fl Non Commercial 3DMed p zle x File Edit View Filter Segmentation Registration Visualization Option Help E aaa 2 a O Fi Be in Z IR Tool Bar Document Image Display Surface Rendering Volume Rendering Function Buttons Hew Document Volumes Function Panel Conten
14. acity 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 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 Y 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 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
15. es abt ANOS r 0 ge 0 b 0
16. ev As sama z Document Image Display Surface Rendering Volume Rendering Display Object m Slice Location 1 15 58 Play so FPS Which Volume headimgsg y Width Level and Color Width 4095 Level 2047 5 NE eset Arrow Cursor Display Arrow Cursor Layout Selection e 1x3 O 2 2 x 248 y 163 z 14 r 1108 g 1108 b 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 3DMED USER MANUAL Layout Selection 181x File Edit View Filter Segmentation Registration Visualization Option Help D2 Als BES z z Document Image Display Surface Rendering Volume Rendering ni 3 Dimensional View isplay Object m Slice Location 1 15 58 Play so FPS Whi ch Yolume headimg59 y Width Level and Color Width a095 Level 2047 5 Color Gray EERE Reset n L Arrow Cursor J A E Y Display Arrow Cursor X Y Image View Y Z Image View X Z Image View a j 7 aps rej ir no ne r 1034 g 1034 b 1034 0 l 2 2 layout Layout Selection 143 fe 2x2 3DMED USER MANUAL mi 3DMed zle x File Edit View Filter Segmentation Registration Visualization Option Help E E z Di Als Ie Se A Document Image Di
17. h Prap ilat Presets Jefanlt r E Aruba sad Celer f Dif uxa Calar O Epaculur Calar O Emi mina Color ca Pi Z x dbdikiiliijidhiilddi di oni pac Par r a Pritt dilii dili di dd Opacity A A DEN E f Chosen background Document Inage Dixplap Surface Henderi ng Vilma Eandaring Y Passanant 4 Conting Which Sor feces ths A m Espreasaistian ja Sorface f Fire Fra o Points Interpolation Flat 7 Zpacih BErapavii sz Presets ES C avbient Color TM Diffuse Coler Specolar Colar C Exissiin Color T Edge Cela Earl plus NJEN OJ OJ pers A o CI Alpha Cuim solora es ATT e a Useckegranmd Celer Reverze Narrmala W m a li ui por 3DMED USER MANUAL Reverse Normals thich Surface ctheadMesh v Representation a Surface Wire Frame Points Interpolation Ir Flat a Smooth Properties Presets Default C Ambient Color E Diffuse Color O Specular Color 7 Emission Color f Edge Color Red oh Blue Alpha HA opec Fower Line Width s MAM MI NIN V ME MIR MI NM MIN IM V MI eal EO a vee pir zo poz yo YO RE y Backeround Color Reverse Normals It is a tool to correct the wrong direction of the normals ca
18. hich Volume headime58 y Width Level and Color Width lanas Level 2047 5 Color Gray nat z Reset W L Arrow Cursor Display Arrow Cursor Layout Selection O 1x3 e 22 x 402 y 311 z 29 r 67 g 67 b 67 papas a de NA ri 67 g 67 b 67 Tools 3DMED USER MANUAL Image Tools Image Tools je dh Ki zht Reverse gt o ho 4d Inverse Original image 3DMED USER MANUAL Left will rotate the image that has been chosen to the left with a angle of 90 degrees result as shown in the following figure Right will roate the image that has been chosen to the right with a angle of 90 degrees Reverse will reverse the image that has been chosen as shown in the following figure 3DMED USER MANUAL figure Hist will tell the information about scalar of each point of the current image as shown in the following figure 3DMED USER MANUAL MM Non Commercial Histogram Box Slice Ho FE Channel Channel 0 w Exclude Background Histogram bers O Current Value Max 65024 Amount Mean 11205 9 Percentage S D 12604 T Total Pixels 65536 Widgets Widgets E ze o Line Angle Pseudo Rect Poly Ellipse 0 Line click one time and the bottom is on then you can make a line in the image that you have chosen with the aid of the cross and the length of the line will be shown on the panel with the u
19. k the left button of your mouse on the point of your another interest area The result of the previous segmentation will be accumulated 3DMED USER MANUAL rm le Edit View Filter Segmentation Registration Visualization Option Help ur FSlic it P 4 s fai m Eh l Fast Garching Segmentation Form 2JE Source Image destination Image S Sl figa 1 Which Widt Width Stopping Value 850 Clear Result Fast Marcing Segmentation Slice Humber y 1 1 1 xi esses Wi rilo Sre ees U 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 otiginal one destination Image Stopping Value 850 Clear Result Fast Marcing Segmentation Slice Number y 1 1 xi 188 9 9 Wi rl ore ee 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 3DMED USER MANUAL dialog You can also close the dialog without saving the result by clicking the cancel button un T File Edit View Filter Segmentation Registration Visualization Option Help Fast Marching Segmentation Form 2JE Source Image destination Image All Y E Arrol Dis Layo 1 3 O 2 3 Stopping Value 650 Clear Result Fast Marcing Segmentation Slice Number ALIS LO F
20. l EEE eS Sor bide Batea Kali Mi Ferderirej O PE ee Se ET F mi m JE eres TE Copier Ber hnm mi Talp Dr ion p q D x E Cavin ir Yel Ti ue rimar After click 3DMED USER MANUAL Lila His Wire Falter paperii Hugiriruiisu Mima me fia JE E Bi Bl w TENE ab EA bim Hus ECC ICC 1 Bsc raza L La Bes foci Sol mame Cosita in Bo Pia Show information will show some information about the data which has been loaded as shown in the following figure Filter demai Leg A BEA Geli LITET Pol arin E Niurariniri E iing Hom foreman oH ges Delete will delete the data which has been loaded shown in the following figure Before click 3DMED USER MANUAL Mir Crear dl Mi a A A DEE bee jis zm ipi lsira ica i sr far Lara Palma kurdarirg Ti Errr su Ti iine Pie Da pagi zlet miwn s V X Laimis im E User wesw Sarl ett After click i Pinar EH fede Fila Fait Sige Fitur aprista pu P je Eel z A TT j ihe i E Erin E alla fen Armei Al e UTE q IMT k ITE as shown in the gt Remove will delete the 3D image in the main window following figure Before click 3DMED USER MANUAL Mir Crear dl That DF As pee da zm ipi lsira ica i sr far Lara Palma kurdarirg Th A seat Ti iine Mia Tea pa our wit s V X Lrmimis i
21. lculated 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 3DMED USER MANUAL The proper display after reversed the normals Volume Rendering 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 fl Non Commercial 3DMed 18 x File Edit View tS Segmentation Registration Visgelizetion Option Help DEN BEA z Document Image Display Surface Rendering qd Volume Rendering ji 3D Measurement Transfer Function Shading ae p auae ty Transfer Function Scalar pe Opacity fo 0294118 0294118 Presets Ramp 0 2 f 0 2 m Scalar Color Transfer Function Sedap fo o00 efo af az Presets MENJE m Gradi ent Opacity Transfer Function On Gradient Opacity Presets No Edge Detection pt a DO za lev Oe Db o 0 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 3DMED USER MANUAL Keep the middle mouse button down and drag on
22. m Pal ura s meri wesw ari etd After click Fila Fit Sige Klar aiii Mairrsiimi Find Eon fel bv Soe z remi W ieir faii lij Palas Pr iij E fio i bAi m Foros Fal te ie 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 3DMED USER MANUAL Bay Docent E Ysl ELE UE v O X Contents in Fol Vier E Yolonas Sur Ewes 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 the 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 Dimensio
23. n the 3D view to move the surface model in the scene 3DMED USER MANUAL Keep the right mouse button down and drag on the 3D view to make the model zoom in Of ZOOM out Surface select You can choose different surface from and then make transacts to it thich Surface ctheadMesh m Representatif IN Tr er E g dedi aa A ee E om ict dlesni RO UN i oni 1E os Ne aa CRA NV NI momen PEEP eee eee eee A 3DMED USER MANUAL Representation of the model aA presentation ifa Surface Wire Frame Points a hm Mn o OO OO OOO Le e il Interpolatii Flat Smooth Properties Presets Default v fe Ambient Color 7 Diffuse Color f Specular Color 7 Emission Color O Edge Color Red Green Blue _ EN EN te EO m sf O O O O LI LI LILI O O A Spec Power m y s UVLLILLIEL LILI LILI LILI LI H Opacity E p a IMA dood od obo od A IIA Line Width ta FPR LS CI Te TS II a A S TE SEY 501 1105 V Ti Point Sire Background Color Reverse Normals 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 as the final result of the surface rendering Representation Surface Wire Frame Points 3DMED USER MANUAL In wire frame representation all the sides of triangles of the surface will be shown in the
24. nal 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 Mi Hus lummercial Eai PE lila dit Jiss Filter Sapusntadica Bagietwation Wiegalisetion lpilan Help Ieai GerEecs Barrlaring Falma Jade Alica Lecetim l Play zij FFS Thich Tolma EZE w Fidthe Laval snd Celar Width paan Laval ET Tolar nar il MI Vier s errar ir mar E Di splav irrar Cursor Layani Selection lso a y j xy image idad x 123 v JB c LE r ETE g HE k 241 m 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 Current selected image view is surrounded by a red rectangle The controls for slice location are shown as follows Slice Location 1 1 100 hich Yolume os od 5 ae 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 1 1 100 Press the button
25. ng 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 3D View The 3D 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 3DMED USER MANUAL 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 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 gt Load Volume and several submenus appeared Each submenu is corresponding to a sup
26. nit of mm click a second time and the on bottom is off and then you can choose a line the line will change it s color and then you make move change it s leneth and even delete to the line as shown in the following figure 3DMED USER MANUAL 133 968mm Angle click one time and the bottom is on the you can make a angle in the image that you have chosen with the aid of the cross and also the degree of the angle will be shown on the panle with the unit of degree click a second time and the on bottom is off and then you can choose a angle the angle will change it s color and then you can make move change it s degree and even delete to the angle as shown in the following figure 131 187 Pseudo click the bottom draw a rect and the image in the chosen aera will be transferred from scalar image into RGB image as shown in the following figure 3DMED USER MANUAL Rect click the bottom you can make recrangles in the image that you have chosen with the aid of the cross as shown in the following figure 129 648mm 25 916mm Poly click the bottom you can make polyangles in the image that you have chosen with the aid of the cross as shown in the following figure 3DMED USER MANUAL 13052 032mm Ellipse click the bottom you can make ellipse in the image that you have chosen with the aid of the cross as shown in the following figure Surface Rendering Surface rendering is a
27. polation 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 Interpolation fe Flat Smooth Smooth interpolation mode uses a complicated interpolation method to render the surface The result is smooth but the speed is slow Interpolation Flat fe Smooth 3DMED USER MANUAL Material properties Representation s Surface Wire Frame Points Interpolation Flat a Smooth fe Ambient Color 7 Diffuse Color f Specular Color 7 Emission Color f Edge Color Red Green Blue Alpha O a a a a a a a a a Spec Power m Opacity e Line Width TEAL sal PA NI MU RI Wile A RI 501 1105 O Tit Point Sire Background Color In this area you can adjust the material color properties of the surface model From the menu you can choose different objects such as default bone skin and muscle and then make transacts to it Properties CRETE TOUCTEOOereererceeceececrrecrereccrererrrcrerrrrrererrrcrerrcrrererrrererrrrrererys s 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
28. ported format in 3DMed Now 3DMed supports the loading of BMP JPEG TIFF DICOM RAW IMO data files The submenus are showed in below File Edit View Filter Segmentation Registration Visualiz D Hew Document CtrltH as IZ Open Document Ctrlti save Document Ctrlts Save Document As Close Document Ctrl ti Load Volume d Load BMF Files Fr Save Volume A Load IMO le Load JPEG Files Load Surface b net a v a ooo PO Load Raw Volume Data Exit Load TIFF Files File Edit View Filter Segmentation Registration D Hew Document Cir1 H E E Fas Open Document Ctrlto Image Display 5 IH t Ctrlts Se her s Volume Rendering cave Document As AS Close Document Ctrlti Load Yolume F Save Volume F Load Surface d Load PLY File JE 0 CIG Kima Darro av A k Also you can left click Document panel then right click Volumes and there will be the same submenus appeared and you can do the samething as shown in the following figure 3DMED USER MANUAL he Yo anes ha Su P Load Volume Load EMP Files Load JPEG Files Load Raw Volume Data Load TIFF Files When you loaded a dataset to 3DMed Add to view will display the result with a 3D image in the main window shown as following figure Before click Bide dad Mam Bybee a parida ljapobruismo Digi pte Bala DA EBEG aos i kami I Hi gp
29. 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 21x Source Image destination Image ee Humber 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 3DMED USER MANUAL la rer Commerdal Had E Fils dit Fiss Piltar eT AA Bagi ciradilon Vi egali rati ca ptica Help iG TE s DPA Elsa nu Teas Display EJEN Surface Reader ing gt ra surface rendering panel Thich Sur IATA ispreaentaLion i Surface U Wire Frame Points j rtarpol ati m E Flai F Znicik a a mm Frasaka Dafoe fe inbiat olar O Ticos Color O 3pacolar Calor O inim Calor M l n Eeler surface rendering resault ee ee ogn xaf m 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 o
30. splay Surface Rendering Volume Rendering X Y Image View ua 8 3 Dimensional View Di splay Object m Slice Location 1 30 58 Play ET FPS Which Volume headin x Width Level and Color Width foss Level 2047 5 Color Gy lews Reset L Arrow Cursor Y Display Arrow Cursor Eraut Selection Y Z Image View X Z Image View C 1x3 a 2x2 x 257 y 245 z 29 r 1760 g 1760 b 1760 0 Mouse Manipulation for Image View Parallel movement Keep left mouse button down and drag on the image view 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 3DMED USER MANUAL Zoom Keep the right mouse button down and drag on the image view Zoom in Zoom out 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 ate shown in the status bar at the bottom of main window imi 3DMed la x File Edit View Filter Segmentation Registration Visualization Option Help OPA Bao Document Image Display Surface Rendering Volume Rendering 3D Measurement 3D Cutting Display Object Slice Location I v I y I 1 30 58 Play 30 FPS W
31. ta ti ca Her Dornen mn 5 Nelenar i land H Life faces Cantants in Vol Fica pro Volamas y bl lo facen o Thushold opina lion m l s TS a 117 cd gad ki On After the Threshold Segmentation item is clicked there will appear a dialog and you can proceed the threshold segmentation in this dialog Edit View Filter Segmentation Registration Visualization Option Help rm FE Eh gt Threshold Segmentation Fors E ost ao SC g a Source Image Destmation Image Source Image Pa destination Image Z gt JE Arro Dis Layol O 1x3 O 2x3 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 3DMED USER MANUAL destination image which represent the result image after segmentation The 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 m KRE REO MB HAD RO TAM REA BOW HEA Y x a b gt fel ja ti amp la v B KI v a E 100 bd a JEM Garamond gt M BZ i EE gu Threshold Segmentation Form
32. ter the Fast Marching Segmentation item is clicked there will appear a dialog and you can proceed the Fast Marching segmentation in this dialog ajx Fast Marching Segmentation Source Image Destinition Image Sur Source Image j i destination Image Stopping Value Slice Number 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 3DMED USER MANUAL 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 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 rm Fast Barching Segmentation Fora 2JE Source Image destination Image ur FSlic it P S SI pa 1 Which Widt Width Stopping Value 650 Clear Result Fast Marcing Segmentation Slice Humber 1 1 1 x 485495 Wi rors Deeb U You can also clic
33. ts in Vol View Volumes i el cthead Surfaces 3DMED USER MANUAL 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 ate 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 3D View The Image Display button and its panel provide the function of 2D image processing please see chapter 2 to get more details 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 not provided and it will be provided in later version The 3D Cutti

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