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3D-DOCTOR User`s Manual

1. seen Pese eese ae eese 227 10 4 3DBASIC GENERAL COMMANDS ee ee eee eene eese en oeste ense etta see seen ases teen se eese ense 229 10 4 1 REM STATEMENT oa as A EE 229 10 4 2 ZEOGBIEE STATEMENT 4 229 10 4 3 INTEGER STATEMENT eere hene ern hieme ERIS 231 10 4 4 BEOAT STATEMENT nene Ru eene eB ER 231 TO A STRING STATEMENT rhe hene hiec ERIS 232 10 46 IMAGE3D STATEMENT eI Ier Rer eR 232 10 4 7 ASSIGNMENT STATEMENT c cscccccockcusceocscohcvccttcsteccbeceseccecestecdecdeceecbecedeecbedeceodbdnsdnodacdhceeceeee 233 10 4 S PRINT STATEMENT exp Eu 233 10 4 9 INPUT STATEMENT cec ce tee e 234 10 4 10 GOTO STATEMENT ceteri EXP de ER REP GREEK Exe teva 234 10 411 IE STATEMENT cte tei deduce tede e teet 235 10 4 12 FOR LOOP STATEMENT eene cere desee ene pte acere rene dne EET eee PUR 235 10 4 13 GOSUB AND RETURN STATEMENTS eee e n e n n nnn nnn nnn nnn n nnn n nne n nn np pana aua 236 10 4 14 END STATEMENT iet teet eet acere ine dece eee tede exe dete oce iret rex ETE ERE PEU 236 10 5 IMAGE OG LODUL DU FE 237 10 5 1 OPENIMAGE STATEMENT e nnn 237 10 5 2 SAVEIMAGE rtr rtr r rtr r r r r
2. enne 209 8 13 5 USE IMAGE PLANES COMMAND esee enne 209 TABLE OF CONTENTS 8 13 6 CREATE MOVIE COMMAND ener enne nn entrer innen tnr sese rennen nn rr eser entere nne 210 8 14 SURFACE INFO COMMAND TOOLS 211 8 15 3D VOLUME CALCULATION AND MEASUREMENT COMMANDS eee 211 8 15 1 CALCULATE VOLUMES COMMAND TOOLS MENU 211 8 15 2 MEASURE AND MEASURE REPORT COMMANDS TOOLS MENU eene 212 8 15 3 MEASURE ANGLE TOOLS 212 8 15 4 SET AS CONTOUR COMMAND TOOLS MENU 212 8 15 5 CONTOUR REPORT COMMAND TOOLS 213 8 16 SURFACE MODEL PROCESSING COMMANDS e ee ee eren eren eene eo netos etna etas ta seta seta sno 213 8 16 1 CROP OBJECT COMMAND TOOLS MENU esee 213 8 16 2 SIMPLIFY SURFACE COMMAND TOOLS MENU eese 214 8 16 3 SMOOTH SURFACE COMMAND TOOLS MENU enne enne enne nre nennen 214 8 16 4 REVERSE NORMAL COMMANDS TOOLS MENU enne enne 214 8 16 5 CUTTING PLANE AND SPLIT OBJECT COMMANDS TOOLS MENU eee 214 8 16 6 REFINE MODELS COMMAND TOOLS 215 8 17 SELECT COMMAN
3. 237 10 5 3 SAVEIMAGEPLANE STATEMENT tetr rtr tetr nnne aaa a p nnn ep apap nua 237 10 5 4 SETIMAGEPLANE STATEMENT eene e e I n n anna n n nnne nna 238 10 5 5 IMAGEDIM STATEMENT ranan rr ICI 238 10 5 6 GETPIXEL STATEMENT err 239 10 5 7 SETPEXEID STATEMENT a exerce ERR cBenINIR EUIS 240 10 5 8 SHOWIMAGE n n nn n n nnn a n n nan nn n ann ee 240 10 5 9 CLOSEIMAGE STATEMENT eene e e enn n nnn a nnn nnn 241 10 5 10 6517 8 25 n enn 241 10 5 11 SIZEIMAGEDOWN 2 242 10 5 12 ROTATEIMAGEX AND ROTATEIMAGEY STATEMENTS 242 10 5 13 CROPIMAGE STATEMENT n nnn nnn a a n nasa n n s n nn p 243 10 5 14 RESEICB STATEMENT eere eene US 243 10 5 15 SMOOTHAVE nn n nnn nnn n n e a eese snap aaa 244 10 5 16 SMOOTHMED STATEMENT eee n e e n n n nnn 244 10 5 17 ROTATEIMAGE 245 10 5 18 NEGATEIMAGE STATEMENT eec e e e nee n n n nnn nnn nn nnn nne a ann nh anna p 245 10 5 19 SHARPEN STATEMENT se i eceicecteceeet eot rete 246 10 5 20 STATEMENT eene n n
4. eese 107 3 7 7 2 Delete All Boundaries command Boundary Editor submenu esses 107 3 7 8 BOUNDARY SMOOTHING COMMANDS essere eene en entrer 108 3 7 8 1 Smooth Boundary command Boundary Editor submenu cree 108 3 7 6 2 Smooth Parameter command Boundary Editor submenu esee 108 3 7 9 BOUNDARY ATTRIBUTE COMMANDS eeeeeeeeee eene rennen 108 3 7 9 1 Set Plane Value command Boundary Editor submenu eese 108 3 7 9 2 Assign Plane Value command Boundary Editor submenu esse 109 3 7 9 3 Set Object command Boundary Editor submenu eere 109 3 7 9 4 Show Info command Boundary Editor submenu eene 110 3 7 9 5 Histogram command Boundary Editor submenu eene 111 3 7 10 UNDO COMMAND BOUNDARY EDITOR SUBMENU 111 3 7 11 DONE COMMAND BOUNDARY EDITOR SUBMENU eese enne enne nennen enne 111 3 8 BOUNDARY REPORT COMMAND EDIT 112 3 9 BOUNDARY PROCESS EDIT MENU e eere ee eese testen setate tosta seta se toas ease ease ease tasto soo 112 3 10 POINT EDITOR EDIT MENU 4 eee ee eese eese tn seta seta sta setate tss to setae ease tas tassa sna 113 3 1
5. The Transparent mode sets all visible image planes to be displayed transparently while the Opaque mode sets them opaque The Scale parameter adjusts the display of the image scale to match the scale of current 3D models being displayed A number greater than 1 will increase the image display size while a number smaller than 1 decreases the display size The Move By parameters are used to move the default location of image planes by shifting the specified amount in all 3 dimensions The Resolution parameter allows you to use a lower resolution of the original image This parameter downsizes the dimensions using the scaling factor within each image plane and has no effect on the Z dimension For example 1 1 will use the same image resolution while 1 2 uses half the resolution that is 50 lower Lower resolution results in coarse display but will increase the display speed and use less system memory If you do not have many image slices you can use the full resolution display Resolution 1 1 Click to apply the settings or Cancel to go back to the previous settings 204 SURFACE WINDOW COMMANDS The display of image planes can be turned on and off by using the View Image Planes command 8 11 Background command View Menu Use this command to define the background color A Color dialog box appears to allow the selection of a color for the background 8 12 Overlay Commands View Menu 8 12 1 Axes
6. e eeee esee ee eene neto aetas etas etas eta sean 126 4 9 NEXT PLANE COMMAND VIEW 4 ee eeee 127 4 10 ANIMATE COMMANDS VIEW MENU eec ee ee esee ease ease tosta sno 127 4 10 1 ANIMATE PLANES COMMAND ANIMATE SUBMENU eese nennen nennen 127 4 10 2 ANIMATION PACE COMMAND ANIMATE SUBMENU eene nennen enne enne 127 4 10 3 CREATE MOVIE COMMAND cc sccessssceceesececeeseecessaeeecsessececseneeceesaeeecsesaecesseeesessaeeeesenaeees 128 4 11 IMAGE PALETTE COMMANDS VIEW 4e eee eres eren eene n etna etna staat ta seta sea sno 129 4 11 1 PSEUDO COLOR COMMAND IMAGE PALETTE SUBMENU eene eene 129 4 11 2 RED COMMAND IMAGE PALETTE SUBMENU csesscceessececseseeceesaeeeceeseecesseeeeeesseeecsenaeees 129 4 11 3 GREEN COMMAND IMAGE PALETTE SUBMENU eese 129 4 11 4 BLUE COMMAND IMAGE PALETTE SUBMENU cssscccesssececseseecessececeesaececsnseeeessaeeecsenaeess 129 4 11 5 GRAY SCALE COMMAND IMAGE PALETTE SUBMENU sees eren enne enne 129 4 11 6 USER COMMAND IMAGE PALETTE SUBMENU 129 4 11 7 NEXT PALETTE COMMAND IMAGE PALETTE SUBMENU seen ener 129 4 11 8 DEFINE PALETTE COMMAND IMAGE PALETTE SUBMENU ccssesceceeseceeeeseeeessseeeensaeers 130 4 12 IMAGE CONTRA
7. 38 OVERVIEW AND TUTORIAL Once an image is displayed you can then use the image functions to process the image or use the segmentation functions to generate boundary data Boundary data are displayed as polygon lines in the IMAGE PLANE WINDOW and by default only lines for the current plane are displayed The following flow chart shows the steps needed to segment a 3D image to get boundary data and then create a 3D surface and a 3D volume rendering Segmentation and 3D Rendering t Object Setting to Define Multiple Object USE Edit Boundary Editor to create boundaries Draw a region of manually interest ROI USE Auto USE 3D USE 30 Segment Rendering _ Renderin command Interactiv Segment Segment Create boundary Boundary processing Data editing USE 3D USE 3D Rendering Rendering USE 3D Surface Surface Rendering Rendering Rendering Volume Simple Surface Complex Rendering command Renderin command command Surface rendering display Volume rendering display 39 OVERVIEW AND TUTORIAL In 3D DOCTOR a default object group named Default always exists and can be used as an object because it contains boundary data You can use the Edit Object Settings command to define new object groups and set it to current if you want to add boundary lines to this group If a group does not need to be seen in the IMAGE PLAN
8. Image Mosaic Dialog x Mosaic Matrix Layout Image Overlap Has Overlap Number of Images in a Row Left 5 eft Number of Rows i Top 9 Number of Images Added 4 D images3d Microscopy New Folder tissue1 tif D images3d Microscopy New Folder tissue2 tif D images3d Microscopy New Folder tissue3 tif D images3d Microscopy New Folder tissue4 tif Add Images Remove Help u e Create Cancel x m Mosaic Matrix Layout ire Number of Images in a Row 3 gt P sl Number of Rows Number of Images Added Add Images Remove Help 2 nd Cancel 160 IMAGE MENU COMMANDS the best edge matching to create seamless image mosaic You can also use the Image Crop Image Crop Region command to remove the overlap and then create a mosaic Once the mosaic image is successfully created use the File Save Save Image As command to save it to a file 5 11 Smooth Commands Image Menu 5 11 1 Median Filter command Smooth submenu The Image Smooth Median Filter command smoothes the current image display using a median filter If your image is a multi plane image the new image will be saved to a file and can be displayed using the File Open command 5 11 2 Average Filter command Smooth submenu The Image Smooth Average Filter command is used to smooth the current image display using an average filter 3x3 It can be applied multiple times if nee
9. eee enean nentes netto toto tata 251 10 10 1 DECONVNN STATEMENT ceeeeeeeeneeener trennen eaei Cohrs osor 251 10 10 2 DECONVMAX STATEMENT eec nenne nene nennen 252 10 10 3 RECONITER STATEMENT citet iet oo eneit e eeen a e Eio eo tee eei de inte 252 CHAPTER 11 WINDOW MENU COMMANDS eeeeeees este tatnen tatnen sn sn stata tais enses eee soto toto uo 254 11 1 NEW COMMAND WINDOW MENU eee ee esee teet tn sesto neto setas etas 254 11 2 CASCADE COMMAND WINDOW MENU eere eese totos tota tata 254 11 3 TILE COMMAND WINDOW MENU eese eene netto totos tata tatnen tuta sn 255 11 4 TILE HORIZONTAL COMMAND WINDOW 255 11 5 TILE VERTICAL COMMAND WINDOW 255 11 6 WINDOW ARRANGE ICONS COMMAND csssssssssssssssssesssesssessssssssssesesssesesesssssesnsnsesnses 255 11 7 1 2 COMMAND WINDOW 255 CHAPTER 12 HELP MENU COMMANDS ccscsssssssscccscscscscscsesssssccssscsesenecsseessessoesssssesssessees 256 12 1 HELP TOPICS COMMAND HELP 256 12 2 ABOUT COMMAND HELP MENU eese eene entente tasa sn sn 256 12 3 CONTEXT HELP COMMAND eeeeeeenenenenen
10. subtract And OR transparent Max Min etc If you have two images from a single source for example a CT image and an MRI image for the same patient using the registration and fusion functions you can create a brand new image with information you could never visualize before Chapter 5 Image Menu Commands e 3D Volume Image Reconstruction Create parallel cross section volume images using x ray images taken at angles around the object This allows you to turn your 25 OVERVIEW AND TUTORIAL x ray machine into a full CT Computed Tomography system using 3D DOCTOR Section 5 14 Reconstruction command e 3D Image Restoration by Deconvolution 3D DOCTOR provides two highly efficient deconvolution methods for 3D image restoration and reconstruction a fast nearest neighbor algorithm and an iterative maximum entropy algorithm If you have a 3D image acquired from a device where the point spread function PSF is known then you can easily get a restored image with much higher quality using 3D DOCTOR s restoration functions Chapter 8 Deconvolution Commands e 3DBasic Scripting support makes it easy to combine 3D DOCTOR functions for complicated batch mode processing and software customization 3DBasic is easy to learn because it uses standard Basic like syntax and provides full support for flow control and different types of variables Chapter 11 3DBasic Menu Commands The 3D DOCTOR tutorial section provides step by
11. OK The calibration parameters are used by the Edit Measuring Tool commands for calculating the physical measurements of the image including distance length area surface area and volume It is also used to adjust the distance between slices when creating surface renderings and volume renderings The pixel intensity is calibrated using a linear transform defined by the slope and intercept values Calibrated Pixel Value Slope Pixel Value Intercept If the slope and intercept values are not available you can calculate them using pixels that have known calibration Pixel Calibration m Enter Pixel and Calibration T able Entry 1 of 1 Pixel Value Calibrated Value Prey Delete Nex Add m Calibration Parameters Correlation Coef 0 0000 Slope 0 0000 Intercept 0 0000 Calculate Apply Cancel p X pen Save 80 EDIT MENU COMMANDS values for example phantom or step wedge pixels in a film Click the Calculate button to bring up the Pixel Calibration dialog box Enter the Pixel Value and its Calibrated Value The pixel value can be obtained using the Edit Image Editor Show Pixel Value command for an individual pixel or the Edit Boundary Editor Show Info command for a region enclosed by a boundary You can use the Save button to save the entered values to a text file or the Open button to open an existing file Use the Calculate button to
12. e Add new points e Move a point e Delete a point e Delete all points within a selected region e Label the points with a specified plane value When objects are defined it s highly suggested to leave only the object you are working with on and turn the rest of the objects off When objects are turned on all point data in these objects will be available to the editing functions 3 10 1 Add Point command Point Editor submenu Use this command to add new points to the current object The cursor will change to a Cross Cursor Point the cursor at an image location and click the left mouse button A new point will be added to the current object Repeat this step to add more points to the object You can switch to a different editing session by selecting another option from the Point Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Point Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 10 2 Move Point command Point Editor submenu Use this command to move a point to a new location The cursor will change to a Move Cursor Point the cursor at a point and hold down the left mouse button to move When the point is moved to the desired location release the left mouse button to confirm it You can switch to a different editing session by selecting another option from the Point Editor submenu or from
13. 6 2 2 Smooth command Boundary Process submenu This command will smooth boundary x lines using a B Spline algorithm When the Edit Boundary Distance Between Nodes Process Smooth command is started the Smooth Line Dialog box appears fio ay See Figure Curent Image Plane OK The dialog box allows you to enter C All Image Planes Cancel the pixel Distance Between Nodes NM and in which image planes you want the smoothing applied to 6 2 3 Simplify command Boundary Process submenu This command checks all boundary lines that are present and corrects the non simple boundary lines A non simple boundary line normally has some line segments intersecting with its own line segments This may cause problems during 3D rendering Non simple boundary lines can also be corrected using the Edit Boundary Editor 176 BOUNDARY PROCESS COMMANDS 6 3 Boundary Removal Commands 6 3 1 Delete By Length command Boundary Process submenu This command removes boundaries that are within pee Delete Boundaries By Length user specified length range When the Edit Boundary Process Delete By Length Max mman is sel he Cancel command elected t NN m Delete Boundaries By Length dialog box appears in which you can specify the Minimum and Maximum threshold values See Figure The min and max threshold values are the length of an entire line Boundary Length 6 3 2 Delete By Plane
14. A detailed report for boundary data can be generated easily using the Boundary Report function for quantitative analysis Section 3 8 Boundary Report command e Editors for Image Point Markers and Annotation The Image Editor allows pixel value editing displaying and mapping to other values Section 3 5 Image Editor Point markers are used to mark locations in a 3D image and are controlled using the Point Editor Section 3 10 Point Editor Annotations are easily created using the Annotation Editor Section 3 12 Annotation Editor e Image Measurements Area surface area volume distance profile and an image region histogram can all be calculated in 3D DOCTOR With the Measuring Tool you can quickly measure the length area of a region image density in a region and view the pixel histogram Section 3 4 Measuring Tool e 3D Image Reslicing With a single command you can reslice a 3D image along the X axis Y axis or an arbitrary axis defined by a 3D angle Resliced images allow you to make more accurate measurement or examination of certain objects that have different orientations Section 5 3 Reslice Commands e 3D Image Registration Auto Alignment and Fusion Easily register two images that are related by specifying 4 or more control points in 3D DOCTOR Once a pair of images are registered you can create an image fusion by combining the two images in any of the methods supported including add
15. BEGIN XI YI ZI H JI END 3D contours can be obtained from 3D surface models using the Tools Surface Contours commands Section 9 14 1 Surface Contours command 197 SURFACE WINDOW COMMANDS 8 4 2 Export Contours command Contours submenu Use the File Contours Export Contours command to save contours to a contour file ctr You can also save the contours to DXF and IGES format A contour file is an ASCII file that stores a group of 3D contour lines Each contour starts with the keyword BEGIN and finishes with the keyword END Each data line stores one point that includes six values the location X Y Z and the normal at the vertex I J K The following shows the contour file format BEGIN XI YI ZI IH JI Ki X2 Y2 Z2 12 J2 K2 Xn Yn Zn In Jn Kn END BEGIN XI YI ZI H JI END 3D contours can be obtained from 3D surface models using the Tools Surface Contours commands Section 9 14 1 Surface Contours command 8 5 Move Viewport command View Menu Use this command to move the viewport for x display of 3D surface Horizontal Location models You can move the viewport left right up Left o Right Refresh and down When this command is selected a Vertical Location Viewport Dialog box i appears See Figure Battom lt lt _ gt Top Gace The Viewport Dialog box allows you to move your 3D surface model around in the 3D SURFA
16. Remove Boundaries 187 Remove Plane 177 remove slices 141 INDEX Report objects 84 85 report surface contours 213 resize image 149 Resize volume 149 Resize Volume 241 resize workspace 81 RESLICE image 243 reslice volume 144 Reslice X Axis 143 Reslice Y Axis 143 reslice uneven spacing 140 reslicing image 25 RETURN 236 Reverse direction 214 Reverse normal 214 reverse slice order 141 ROI 22 186 ROI file TPS 72 ROI from boundaries 146 ROL boundaries 87 ROL clear 87 ROI deflate 87 ROI from boundaries 22 ROL inflate 87 ROI move 86 Rotate 138 Rotate boundary 103 Rotate By X Axis 51 Rotate By Y Axis 51 rotate volume 144 Rotate Volume 144 Rotate Volume Image 51 Rotate object 208 ROTATEIMAGE 245 ROTATEIMAGEX 242 ROTATEIMAGEY 242 RTViz Vox format 30 S Save As dialog box 68 Save Image As 69 Save Project 70 Save Surface File 196 save volume 222 Save Window 70 SAVEBOUNDARY 249 SAVEIMAGE 237 SAVEIMAGEPLANE 238 SAVEPROJECT 3dbasic 248 scale object 208 scan film 147 SCANIMAGE 251 Scanner scan image 222 Scanner select 76 267 Scanner TWAIN compatible 76 scientific data 55 Segment 186 Segment Current 186 segment object 21 49 Segment object 22 186 191 192 segment interactive 21 segmentation 24 247 Segmentation 22 191 192 segmentation training area 49 SEGMENTIMAGE 247 select a portion model 215 S
17. 10 4 4 FLOAT statement Syntax FLOAT Y yl where X1 Y and 1 are the names of float variables Example LOGFILE FLOAT X Y INPUT Enter X X Y X 25 0 PRINT X X Y Y END 231 3D BASIC COMMANDS 10 4 5 STRING statement STRING is used to declare variables that are text string Syntax STRING Namel note name2 where 1 note and name2 are text strings Example LOGFILE cNoutput log STRING Namel Note INPUT Enter Name Namel Note The name is Namel Note Namel PRINT New string is Namel END 10 4 6 IMAGES3D statement IMAGE3D is used to declare 3D image variables IMAGE3D variables can contain image data boundary data and other types of data created using 3D DOCTOR s processing functions Syntax IMAGE3D imagel Imagel0 T1 where imagel Image10 and 1 are images Example LOGFILE c output log IMAGE3D imagel OPENIMAGE image c 3ddoctor head3d tif SHOWIMAGE imagel END 232 3D BASIC COMMANDS 10 4 7 ASSIGNMENT statement Assignment statements are used to assign a value to a declared variable which can be an integer float or string Syntax Variable Expression Example LOGFILE STRING Note INTEGER N FLOAT F1 F2 Note This is the value for Note 200 1 1 2 N 2 N PRINT Note F2 END 10 4 8 PRINT statement PRINT
18. Contour Increment f 0 intersection between a 3D object and a m Contour Normal Calculation defined cutting Refresh plane The contours Calculate True Surface Normal generated can be C Calculate Normal Within Plane Get Contours used for analysis or i sent to a m Contour Smoothing manufacture LE machine for rapid Number of Existing Points To Be Used prototyping Number of Vertices Added Between Points 10 o applications scc Surface contours can also be used for making measurements of complex 3D shapes To measure the area and length or perimeter of a 3D object use this command to acquire surface contours first and then use the Surface Contours command to calculate the area and length for all existing contours After this command is selected a Cutting 3D Contours dialog box appears for defining the Cutting Plane Location and Output Contour File Name See Figure The Cutting Plane is defined using a 3D point and the normal direction of the plane Use the arrows to adjust the position of the cutting plane You can enter the values and use the Refresh to apply If you need contours to be smoothed you can check the B Spline box in the Contour Smoothing section of the dialog box and specify the proper parameters for the processing This step can be done later using the Tools Surface Contour B Spline Contours command in the 3D SURFACE WINDOW Once the cutting pla
19. Control Point submenu Use this command to switch to the Check control point mode This option checks a control point by comparing its entered destination coordinate to the calculated base 95 EDIT MENU COMMANDS value on all defined control points PRSPTITETITT The residual error is displayed Higher residual error indicates the 1 A Source X 122 572998 Y 73 503502 2 54 000000 Destination X 122 572998 Y 73 503502 2 54 000000 poor quality of the control point Residual Error X 0 0 Y 0 02 0 0 selection To check a control point point at the control point and click the left mouse button to show the residual error 3 6 7 Pick Point command Control Point submenu Use this command to switch to the Pick Point mode for picking a location in the target image where a new control point will be added in the source image To use this option you need to open both the source image and the target image at the same time Start the Control Point Editor for both images Switch to the Pick Point mode for the target image and to the New control point mode for the source image Move the cursor to a location in the target image that is also visible in the source image click the left mouse button to pick the location A temporary marker is placed in the target image Once a location is picked up for the target image switch to the source image You should be in the New control point mode now Move the cursor to the location that matc
20. GETPIXEL 239 3DBasic GOSUB 236 3DBasic GOTO 234 3DBasic IF 235 3DBasic IMAGE3D 232 3DBasic IMAGEDIM 239 3DBasic INPUT 234 3DBasic INTEGER 231 3DBasic introduction 227 3DBasic LOGFILE 229 261 3DBasic NEGATEIMAGE 245 3DBasic NEXT 235 3DBasic OPENBOUNDARY 248 249 3DBasic OPENIMAGE 237 3DBasic PRINT 229 233 3DBasic RECONBACKPROJ 246 3DBasic RECONITER 252 3DBasic REM 229 3DBasic RESLICE 243 3DBasic RETURN 236 3DBasic ROTATEIMAGE 245 3DBasic ROTATEIMAGEX 242 3DBasic ROTATEIMAGEY 242 3DBasic run 226 3DBasic Run 225 3DBasic SAVEBOUNDARY 249 3DBasic SAVEIMAGE 237 3DBasic SAVEIMAGEPLANE 238 3DBasic SAVEPROJECT 248 3DBasic SCANIMAGE 251 3DBasic SEGMENTIMAGE 247 3DBasic SELECTSCANNER 251 3DBasic SETIMAGEPLANE 238 3DBasic SETPIXEL 240 3DBasic SHARPEN 246 3DBasic SHOWIMAGE 240 3DBasic SIZEIMAGEDOWN 242 3DBasic SIZEIMAGEUP 241 3DBasic SMOOTHAVE 244 3DBasic SMOOTHMED 244 3DBasic STRING 232 3DBasic SURFCOMPLEX 250 3DBasic SURFSIMPLE 250 3DBasic THEN 235 3DBasic TO 235 3D DOCTOR mailing list 27 3D DOCTOR tutorial 36 3DS 23 3ds 3D Studio 196 8 bit palette 166 8 bit Palette gt Gray Scale 166 About 256 1 120 Add Files 40 59 add new control points 94 Add new object 184 INDEX add new points 113 Add Node 101 Add slices 142 Add Surface 196 Align image 152 alig
21. If the image slices are stored in separate files you need to create a stack first using the File New Stack command and then open the image When the Image Auto Alignment command is started an Automatic Image Slice Alignment box will appear See Figure r Image Planes To Be Aligned 3 Maximum Interations From 0 3 200 C Always Match to the Current Plane Match to the Neighbor Plane OK Use the Save Image As option to define an output file name to store the image Please note the current image is not changed There are two options that control how the alignment works The first is Always Match to the Current Plane and the second is Match to the Neighbor Plane The first option is best used for aligning image planes that are similar to the current plane The second option is used when all planes are to be aligned and similarity can only be found between neighbor planes In either case the current plane is used as the starting point and will not be changed during the process It is recommended to select the image plane that does not need to be aligned as the current plane before starting this command The parameter Maximum Iterations limits the number of iterations the software uses to find the best match A smaller value can be used to make it faster when only minor alignments are needed for the image If only a certain range of image planes n
22. Multiple objects 21 N Negate 162 NEGATEIMAGE 245 Network 62 69 New control point 94 new object selected portion 215 new stack 40 46 New Stack 20 28 40 59 New Stack multiple files 20 New Window 254 NEXT 235 Next Palette 129 next plane 127 Next Plane 186 node 102 Nodes delete in group 102 normal surface 218 number of iterations 171 O OBJ Wavefront 196 object 21 Object 21 Object Animation 209 Object counting 112 Object rendering 174 INDEX Object Report 84 85 Object setting 184 Object Setting 82 object settings 21 Object Settings 46 Object 3D cropping 213 object animate 208 object boundaries 21 Object Boundary lines 109 Object current 184 Object material 201 Object modify 184 object move by 208 Object new 184 object report 175 object rotate 208 object scale 208 object split 30 Objects Boolean operation 83 Objects combine 83 Objects define 46 Open Image 41 44 61 open volume 222 OPENBOUNDARY 248 249 OPENGL 17 OPENIMAGE 237 Overlay Annotations 133 Overlay Boundaries 132 Overlay Boundary Nodes 133 Overlay Control Points 133 Overlay image 132 Overlay Line Ends 133 Overlay Object Names 134 Overlay points 133 palette color 61 palette color image 166 palette image 165 palette define 130 Pick point control point edit 96 plane fusion image 159 Plane next 127 Plane
23. The View Image Palette Define Palette command creates a custom color palette for the tmage display Color Palette Dialog x When the Color Palette Draw rectangle to select entries and Pick Color to change Dialog box appears the current color palette is displayed Hold down the left mouse button and drag to draw a rectangle to select new colors Once the color entries are selected click the Pick Color button to pick a new color that will be assigned to all selected colors Image Greyscale Range 19 1707 Cancel Apply Pick Color Open Palette Save Palette EE ERI ESI zum Click the Apply button to use the defined palette for the current image display Click the Save Palette button to save the palette entries to a file and click the Open Palette button to read palette entries from a file 130 VIEW MENU COMMANDS 4 12 Image Contrast Commands View Menu 4 12 1 Contrast command Image Contrast submenu The View Image Contrast Contrast command will prompt the Image Contrast dialog box This allows the user to interactively adjust Grayscale Range the contrast of the image display This 369 Full Renge command is only used for grayscale images To increase or decrease the bright range Update image pixels adjust the scroll bar for the bright range Adjust the dark range scroll bar if the dark range pixels need to be adjusted Center The pixel gray levels betw
24. This command works similarly as the 3D Rendering Auto Segment command Syntax AUTOSEGMENT image numobjects AUTOSEGMENT image 4 where IMAGE3D image INTEGER numobjects Example IMAGE3D imagel OPENIMAGE imagel c 3ddoctor head3d tif AUTOSEGMENT imagel 3 SAVEPROJECT imagel c 3ddoctor head3d prj SHOWIMAGE imagel END 10 6 2 SEGMENTIMAGE statement This command segments an image using specified low and high thresholds The generated object boundary lines are stored in the IMAGE3D variable and can be used by surface or volume rendering commands This command works similarly as 3D Rendering Interactive Segment command Syntax SEGMENTIMAGE image low high alllines SEGMENTIMAGE image 50 189 0 where IMAGE3D image INTEGER low high INTEGER alllines 0 only outline 1 all boundaries Example IMAGE3D imagel OPENIMAGE imagel c 3ddoctor head3d tif SEGMENTIMAGE imagel 50 189 0 SAVEBOUNDARY imagel c Nobjectl bnd SHOWIMAGE imagel END 247 3DBASIC COMMANDS 10 7 Project and Boundary Commands 10 7 1 SAVEPROJECT statement This command saves object boundary and other processed information associated with an IMAGE3D variable into a project file This command is similar to File Save Project command Syntax SAVEPROJECT imagevar filename SAVEPROJECT imagevar filename where IMAGE3D imagevar STRING filename Example IMAGE3D imagel OPENIMAGE image c 3ddoctor head3d tif AUTOSEGMENT im
25. button to confirm and an ellipse will be created based on the bounding rectangle A square bounding rectangle will result in a circle boundary Repeat this step to add more boundaries If an exact circle is to be drawn hold down the SHIFT or the CONTROL key while drawing and release when finished To undo the last boundary use the Edit Undo option or CONTROL Z Use the function keys F5 or F6 to go to another image plane for more editing 100 EDIT MENU COMMANDS You can switch to a different editing session by selecting a different option from the Boundary Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Boundary Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 7 2 Boundary Node Editing Commands 3 7 2 1 Add Node command Boundary Editor submenu Use this command to add a node to an existing line The cursor will change to a Cross Cursor Point the cursor at an image location where you want to add a node to a line and click the left mouse button to add The node should be close to a line so the system knows which line to add the node to If you need to add a node that is not close to the line you should add a node close to the line first and then use the Move Node option to move it to the desired location To undo the previous edit use the Edit Undo option or CONTROL Z Use the function
26. c Nobjectl bnd SHOWIMAGE image END 249 3DBASIC COMMANDS 10 8 3D Rendering Commands 10 8 1 SURFSIMPLE statement This command performs a simple surface rendering using boundary data stored in an IMAGE3D object It is similar to the 3D Rendering Simple Surface Rendering command but the surface modeling data is saved directly to a file instead of displaying in a window Syntax SURFSIMPLE imagevar filename SURFSIMPLE imagevar filename where IMAGE3D imagevar STRING filename Example IMAGE3D imagel OPENIMAGE imagel c 3ddoctor head3d tif SEGMENTIMAGE image 50 189 0 SURFSIMPLE imagel c 3ddoctor head3d suf END 10 8 2 SURFCOMPLEX statement This command performs a complex surface rendering using boundary data stored in an IMAGE3D object It is similar to the 3D Rendering Complex Surface Rendering command but the surface modeling data is saved directly to a file instead of displaying in a window Syntax SURFCOMPLEX imagevar filename SURFCOMPLEX imagevar filename where IMAGE3D imagevar STRING filename Example IMAGE3D imagel OPENIMAGE image c 3ddoctor head3d tif SEGMENTIMAGE image 50 189 0 SURFCOMPLEX imagel c 3ddoctor head3d suf END 250 3DBASIC COMMANDS 10 9 Scanner Commands 10 9 1 SELECTSCANNER statement This command selects the scanner source for scanning an image Syntax SELECTSCANNER Example IMAGE3D imagel SELECTSCANNER SCANIMAGE imagel SAVEIMAGE
27. command Overlay submenu Axes Boundary Cube Use this command to toggle the display of the X Axis the Y Planes Axis and the Z Axis on and off of the 3D surface model The Faster menu item is checked when the display is turned on Paint As Cross 8 12 2 Boundary Cube command Overlay mua submenu Point Color Contours Use this command to toggle the display of the volume boundary cube on and off The menu item is checked when the display is turned on Contour DIGITUS 8 12 3 Planes command Overlay submenu Use this command to toggle the display of the original image plane locations on and off Each image plane or slice is shown as a cross of X and Y axes at the Z location image slice location The first plane and last plane are labeled in the display The menu item is checked when the display is turned on 8 12 4 Points command Overlay submenu Use this command to toggle the display of points on and off when available The menu item is checked when the display is turned on 8 12 5 Point As Cross command Overlay submenu Use this command to display points as crosses The size of the crosses can be changed using the View Overlay Point Size command The color of the crosses can be changed using the View Overlay Point Color command 205 SURFACE WINDOW COMMANDS 8 12 6 Point As Sphere command Overlay submenu Use this command to display points as spheres The size of the spheres
28. many different 3D displays x Color Properties Ambient Diffuse Specular Backside Color Shine Red j Green 000 RE Pick Color Apply You can change the color properties by clicking the Color button in the 3D Object 200 SURFACE WINDOW COMMANDS Setting dialog box Selecting the Color button will bring up the Color Properties dialog box See Figure The following explains the terms used to define the material display properties Ambient Ambient light is light that doesn t come from any particular direction Objects illuminated by ambient light are evenly lit on all surfaces in all directions Diffuse Diffuse light comes from a particular direction but is reflected evenly off a surface Even though the light is reflected evenly the object surface is brighter if the light is pointed directly at the surface Backside Color This defines the backside color of an object Normally the backside is not visible since it blocked by the front side However when a model is split using the Tools Split Object command the backside may become visible To split a model first create the model using the Surface Rendering command Start the Tool Cutting Plane command to show the cutting plane The normal of the cutting plane is always the viewing direction perpendicular to the screen Use the left mouse or the LEFT RIGHT key on the keyboard
29. 3 3D DOCTOR MAIN FUNCTIONS eeeeeeen nn n n n n n 24 1 4 TECHNICAL SUPPORT AND UPGRADES eere ee ee eee ee eee eo oeste to se ee etta ases 27 1 4 1 3D DOCTOR INTERNET MAILING LIST eee nnn nnn annua 27 1 5 USER 28 1 5 1 IMAGE PLANE WINDOW AND MONTAGE WINDOW 28 1 5 2 VOLUME VIEW WINDOW 29 15 33D SUREACE WINDOW roses a there erepti NES 30 T54 PLOT a ae ee ea een ever hene PS 32 P55 32 1 5 6 THE FLOATING POP UP MENU 33 1 5 7 HE MOUSE eee cene reU ueniedt ei ete mie 33 1 528 THE KEYBOARD nce RES en ean ad awh ew wna nee US Dea ead ewe hue 33 1 5 9 DRAW A SELECTION RECTANGLE AND MEASURE DISTANCE eee ee n nennen nnn nnne nnn 34 1 5 TO TOOLBARS 4 Beeneaamtexteutere eer iR 35 1 6 GETTING STARTED iss 36 1 6 T FHEBASICS EER odds te teet eere rir eere edt 36 1 6 2 CREATING A 3D STACK FROM 2D IMAGE SLICES eeeceeeeeee n e enn n nnne nnn nnn nnne nnn 40 1 6 3 IMPORTING RAW OR NON STANDARD IMAGE FILES eee 41 1 6 4 DEFINING VOXEL SIZE AND SLICE THICKNESS FOR CALIBRATION eee eene 44
30. 54 OVERVIEW AND TUTORIAL 1 6 12 3D Volume Rendering for 3D Scientific Data For 3D scientific data that do not have distinguishable object boundaries 3D DOCTOR provides an easy way to create 3D volume rendering for visualization and analysis The following are the steps for creating 3D Volume Rendering for Scientific Data Step 1 Open the 3D image If each image slice or plane is stored in a separate file use the File New Stack command to create a 3D stack list Step 2 If you want to render only a portion of the volume you can use the ROI Editor to define a region of interest If you already generated object boundaries through the Segmentation commands the object boundaries will be used to define the volume to be rendered Step 3 If the three dimensions have different scaling factors for example the spacing between slices or pixels is not even use the Edit Calibrations command to enter the scaling factor so the scales can be used to correct the display of the 3D rendering Step 4 Use the 3D Rendering Volume Rendering command to do the 3D rendering Use the options under the View menu while in the VOLUME VIEW WINDOW display to select the desired rendering mode and adjust the display 1 6 13 Automatic Alignment of Image Slices When objects move during the imaging process or you are working with images taken at different times image slices may not be aligned properly and this can affect the accuracy of the image an
31. 7 2 Delete All Boundaries command Boundary Editor submenu Use this command to delete all 3D DOCTOR existing boundary lines or all the lines within a selected if a Delete all boundaries within the selected rectangle selection rectangle exists in the IMAGE PLANE WINDOW To get a selection rectangle hold down the SHIFT key and drag the left mouse button to draw the selection rectangle The system will prompt a 3D DOCTOR dialog box to confirm this operation You can cancel this operation by clicking the No button in the confirmation dialog box Caution The Delete All Boundaries command will delete all the boundaries within the selected region or the entire image and all boundary data will be lost if it is not saved to a file Be careful when using this command You should save the lines to a file using the File Boundary and Point Export Boundary command in case you want to get the data back after deleting 107 EDIT MENU COMMANDS 3 7 8 Boundary Smoothing Commands 3 7 8 1 Smooth Boundary command Boundary Editor submenu Use this command to apply the B Spline smoothing to a selected boundary The cursor will change to a cross cursor Move the cursor to a boundary and click the left mouse button to smooth the boundary Use the Edit Undo command to recover a line previously deleted You can switch to a different editing session by selecting another option from the Boundary Editor submenu or from the floating p
32. IMAGE MENU COMMANDS 5 4 4 Crop Film command Crop Image submenu This command is used to crop multiple image slices from scanned image films using a user adjustable template If you get CT or MRI images on film this command simplifies the process of separating image slices into individual files so they can be used for 3D volume and surface rendering Your film can be scanned using an image scanner If you have multiple films the scanning resolution should be the same For most films 200 to 600 DPI dots per inch scanning resolution is enough The scanned image should be saved as an 8 bit or a 16 bit grayscale image in TIFF format When the Image Crop Image Crop Film command is selected the Crop Multiple Image Slices dialog box appears See Figure Crop Multiple Image Slices E m Template Layout Num in Row a Left Start at fi 0 Start Num in Column 5 Top Start at 10 afe Cancel m Image Slice Size Distance Between Slices Width 256 pl Horizontal fi 0 4 gt Height 256 EE Vertical fi 0 EE Fixed Slice Size Output Image Sequence Starts At fi Save Image As Browse x Save Template Open Template TERE Apply The following explains the parameters in the dialog box that are used to define the cropping template The template can be saved to a file to crop other films of the same scan All parameters except the number of slices are measured in image
33. MENU COMMANDS Edit menu commands data layers can be edited using the editors or editing commands descnbed in this chapter With commands under the Edit menu you can Set image calibration parameters used by the measurement tools Define multiple objects and edit object attributes and settings Define regions of interest Measure object length area surface area and volume View 2D and 3D image density profiles and image histograms Edit current image plane and see pixel values using the image editor Edit and define control points Edit boundary lines Edit points Edit image annotations 79 EDIT MENU COMMANDS 3 1 Calibration and Workspace commands Edit Menu 3 1 1 Calibrations command Edit Menu Use this command to edit system calibration parameters including the pixel size for X Y and Z dimensions X and Y are the pixel size within an image plane or slice and the Z parameter is the slice thickness plus the distance gap between image slices or planes The unit used when acquiring the image should also be entered Select the Edit Calibrations command to open the Image Calibration Parameters dialog box See Figure X Y 2 Voxel Resolution Pixel Rescale X voxel width 09375 Slope Y voxel height 09375 Intercept Z slice thickness Unit hu rawvalue Unit cm mm Calculate XY NewPixel Slope RawPixel Intercept Calculate Cancel Ld
34. Node command Boundary Editor submenu eee 101 3 7 2 3 Move Section command Boundary Editor submenu eee 101 3 7 2 4 Delete Node command Boundary Editor submenu eene 102 3 7 3 BOUNDARY MOVING COMMANDS rennen en 103 3 7 3 1 Move Boundary command Boundary Editor submenu ees 103 3 7 3 2 Rotate Boundary command Boundary Editor submenu esses 103 3 7 3 3 Mirror Vertical Horizontal command Boundary Editor submenu 104 3 7 4 BOUNDARY COPYING COMMANDS eese enne enne enne entres r erre 104 3 7 4 1 Copy Boundary command Boundary Editor submenu eee 104 3 7 4 2 Paste command Boundary Editor submenu eee trennen 105 6 TABLE OF CONTENTS 3 7 5 SPLIT AND MERGE BOUNDARY COMMAND BOUNDARY EDITOR SUBMENU 105 3 7 5 4 Split Boundary eet pP ee e d Rr rer eee t 105 3 7 5 2 Merge Boundaries o as m ree 106 3 7 6 CLOSE BOUNDARY COMMAND BOUNDARY EDITOR SUBMENU eee ener 106 3 7 7 BOUNDARY DELETE COMMANDS 107 3 7 7 1 Delete Boundary command Boundary Editor submenu
35. Pace function to change the elapse time between frames Click the Stop button to stop the recording The AVI file records the animation until the Stop button is pressed Select Finish to exit You can use an AVI file viewer to play the movie by opening the created AVI file Note When using the Full Frames Uncompressed encoding to create an animation you may get a movie AVI file that s quite large There are several things you can do to reduce the file size 1 Before you start the animation reduce the window size The smaller the window the less storage it takes 2 Useacompression based encoding For example using the Microsoft Video 1 encoding can reduce the size significantly But be careful not to choose one that s not installed on your machine 128 VIEW MENU COMMANDS 4 11 Image Palette Commands View Menu The commands under the Image Palette submenu are used to change the palette used for image display There are 6 types of predefined palettes available to use for displaying a grayscale image Other image types have a fixed color palette that cannot be changed using these commands 4 11 1 Pseudo Color command Image Palette submenu The View Image Palette Pseudo Color command switches the current image palette to a pseudo color palette Use the View Image Palette Define Palette command to define a customized palette for image display 4 11 2 Red command Image Palette submenu
36. Patient V 1ID 2006 01 18 rando mock 222222 2006 09 29 WILLIAMS 12345 19000300 F 2006 03 09 TEST 8888888868 1 BirthDate 2007 02 00 SOONIFOL 12345 19580000 M 2006 09 05 NYMAN RO 12345 19470000 M 27 2005 12 21 LastName 12345 ST 2006 09 07 KISSEL DO 12345 19000000 F 98 2007 01 25 Head MR 12345 20051201 Male te 2007 03 14 ESPINOSA 5 12345 19000000 M 1 2006 02 25 CARR JANEC 12345 19440000 F 40 PE 2005 12 16 20053331 12345 23 1999 11 22 ram 1999 11 23 2000 01 05 Save List 2000 06 09 2000 07 12 pen List 2000 07 21 If you have projects that are not on the list you can use the Search button to find and add them to the list To open a project select the entry from the list and then click the Open Project button 2 16 1 2 3 4 command File Menu This command can be accessed from the IMAGE PLANE WINDOW only Use the numbers and filenames listed at the bottom of the File menu to open the last four images you closed Choose the number that corresponds with the image you want to open 77 FILE MENU COMMANDS 2 17 Exit command Use the File Exit command to end your 3D DOCTOR session You can also use the Close command on the application Control menu 3D DOCTOR prompts you to save documents with unsaved changes Shortcuts Mouse Double click the application s Control menu button Keys ALT F4 Allows you to exit 3D DOCTOR 78 EDIT
37. Rectangle Draw Circle Add Node Move Node Move Section Delete Node Move Boundary Rotate Boundary Split Boundary Merge Boundaries Close Boundary Delete Boundary Copy Boundary Paste Smooth Boundary Smooth Parameter Mirror Vertical Mirror Horizontal Set Object Set Plane Value Assign Plane Value Inflate Deflate Show Info Histogram Undo Done EDIT MENU COMMANDS e Delete all boundary lines within a selected region or entire image e Set current plane value for line labeling and assign the current defined plane value to a boundary e Seta selected boundary to the current object e Show information and measurements related to the selected boundary e Calculate the image histogram from the selected boundary When editing is finished select the Done option from the pop up menu or select Edit Boundary Editor On Off again to exit the editing mode 3 7 1 Manual Boundary Tracing Commands 3 7 1 1 Trace Boundary command Boundary Editor submenu Use this command to start the object boundary drawing mode The cursor will change to a Cross Cursor Point the cursor at an image location and click the left mouse button A new line segment will be added to the current line and a rubber band line will follow the current cursor location to indicate the line segment to be selected Repeat this step to draw the entire line until all the segments are drawn When the Snap to Edges option is ON the intel
38. Segment function you need to select this command from the command list first Move the cursor to the Select New Shortcut Key box hold down the Ctrl key and press the A key to enter Select the Assign button to assign it to the Auto Segment command The Remove button removes an existing shortcut key The Reset All button removes all defined shortcut keys 3 15 Undo Can t Undo command Edit menu The Undo command is supported for certain operations such as the Boundary Editor operations Use this command to reverse the last editing action if supported Shortcuts Keys CTRL Z 120 VIEW MENU COMMANDS View Menu Commands Control the display of data layers zoom in and out in an image windon 09 on and of graphics adjust image contrast change image display palette and sunt to different image planes With commands under the View menu you can Show or hide the tool bar and status bar Create a montage view of a 3D volume image Zoom in and zoom out Change to different image planes Change image palette Adjust image contrast by using square root or log functions for image display Toggle image pixel interpolation on and off Control graphics overlay by toggling the following items on and off image boundaries boundary nodes and endpoints points control points annotations Show all boundaries in the current image plane Change 3D display viewing direction to left right up an
39. Transpa Wire Frame Wireframe To define the animation Texture sequence first select an Texture Opaque object from the list on the Transpa left and then choose a wireframe display action to show the object in the desired form Use the Hide button to make the object invisible in a frame Texture H 8 Remove ras Click OK to keep the animation sequence EME Cancel The Use Object Reis command toggles on and off tl ACTION 8 13 5 Use Image Plane This command turns on and o Planes is ON image planes sequentially Hide OPO yw al an lw MN You can use the View Image and animation SURFACE WINDOW COMMANDS 8 13 6 Create Movie command The View Animate Create Movie command captures screen actions into an AVI movie file When you select this command the Create AVI Movie dialog box will appear See Figure Create AVI Movie First enter an AVI filename using the Browse button and adjust the peer eee Frames Per Second The frame rate defines how many frames per second fis will be generated for the movie Frames Persecond kj Because it takes time to generate each frame image it s recommended to Start reduce the size of your image window cus i so the movie file will have a smoother Stop Finish transition from frame to frame Click the Start button to start recording The animation p
40. Use the Edit Object Settings command to turn on or off objects for 3D rendering 3 2 3 Object Manipulation command Edit Menu Use this command to copy or move boundary point and Object Manipulation annotation data between Data Items objects When you select the zu Edit Object Manipulation bal zd Point command an Object Manipulation dialog box will Text appear Objects can then be defined and updated using the Edit Object Setting command Cancel X 83 EDIT MENU COMMANDS 3 2 4 Object Report command Edit Menu Use this command to create a report for all currently active objects Objects must have their boundaries defined to calculate the parameters for the report Object Report Dialog When Edit Object Report command is selected the Object Report dialog box appears See Figure This command allows you to view a Detailed Report or a Summary Report The reports include values for the Total Number of Pixels the Object Center the Total Intensity of all Pixels the Minimum and m Report Type Summary C Detailed Report Apply Pixel Calibration Cancel Maximum Value of Pixels the Mean Pixel Value and the Variance of Pixel Values When the Detailed Report option is selected calculations for each image plane will be included and summed up for all image planes If an image plane has multiple boundaries for the same object the
41. WINDOW You can also use the function key F5 or F6 to move to the previous or next image plane Step 4 Move the cursor to a place on the edge of the object For Free Hand Tracing you must hold down the left mouse button to draw For piecewise line segments click and release the left mouse button to trace Once the first point is drawn move the cursor to the next point along the boundary Click the left mouse button again to confirm the point Repeat this step to draw more points along the boundary If a point is not correctly defined use the BACKSPACE key to undo the point With the BACKSPACE lt key you can undo multiple steps When you are close to the starting point hit the SPACEBAR key on the keyboard to close the boundary You now 52 Split Boundary Merge Boundaries Close Boundary Delete Boundary Copy Boundary Paste Smooth Boundary Smooth Parameter Mirror Vertical Mirror Horizontal Set Object Set Plane Value Assign Plane Value Inflate Deflate Show Info Histogram Undo Done OVERVIEW AND TUTORIAL have a finished boundary for the object in this image plane Although you can use the same process in this step to draw a new boundary for another image plane we find it easier to copy the current boundary to the next plane and modify the new boundary instead In this tutorial we ll use the copy to the next plane approach Step 5 Click the right mouse button to show the Boundary Editor
42. and by image motion as well as noise due to electronic and photometric sources The aim of image restoration is to bring the image toward what it would have been if it had been recorded without degradation When the source of degradation blurring and noise can be characterized and modeled as a point spread function PSF then their effects can be subsequently removed or reduced with a deconvolution process with the PSF and the degraded image 3D DOCTOR provides two types of deconvolution to restore degraded 3D images one is a fast nearest neighbor deconvolution and the other one is an iterative maximum entropy deconvolution method The Image Deconvolution Maximum Entropy command performs a 3D image restoration using an Iterative Maximum Entropy deconvolution algorithm The 3D Image Deconvolution Using Maximum Entropy dialog box requires the Source Image File Name the Point Spread Function PSF Image File Name an Output File Name where the restored image will be saved a Feedback Factor and the Number of Iterations See Figure 170 IMAGE MENU COMMANDS Source Image Browse Preview Use Synthetic PSF Spread Function PSF Image Browse Preview 3D Image Deconvolution Using Maximum Entropy Number of Iterations fi 0 Feedback Factor 1 100 50 Output Image Bess Cancel If no PSF is given an estimated synthetic PSF will be used You can use the Image Deconvolution S ynthetic PSF
43. and their Starting and Ending Positions are displayed in the Calculation Results dialog box You can save the data to a text file or use the Copy button to copy and paste the data into another program EDIT MENU COMMANDS Calculation Results x Image Measurements Total Length 534 99 Area 11038 02 Average Pixel 837 47 Variance Segment Pointl Y Point2 X Y Lenath 71 22 58 79 242 10 127 89 184 327 242 10 127 89 2208519432 69 741 220 85 194 32 42 44 94 46 204 457 42 44 94 46 70 33 59 68 44 576 70 33 59 68 54 84 59 24 15 501 54 84 59 24 71 22 58 79 16 386 Click the right mouse button to show other measurement options 3 4 3 Angle command Measuring Tool submenu The angle is 53 773121 degree When the Angle option is toggled on the cursor changes to the Angle Measurement Cursor Click the left mouse button to draw an anchor point move the mouse to a location and click to draw the first line Move the cursor to a second location to form the second line for the angle Click the left mouse button to confirm this location and a message box will appear See Figure to show the angle between the two lines Click the right mouse button to show other measurement options 89 EDIT MENU COMMANDS 3 4 4 2D Profile command Measuring Tool submenu When the 2D Profile option is toggled on use the mouse to draw a line or polygon in the image window When you ar
44. by the 3D Rendering Interactive Segment command belong to the current object Use the Edit Object Setting options to add new objects or modify the attributes of an object If you want to limit the segmentation process to within a region of interest you need to turn on the Edit Region of Interest ROI Tool On Off This allows you to define the regions of interest before segmentation You can define a rectangular circular or polygon type region of interest or use a combination of the shapes The regions of interest defined by the ROI Editing Tool apply to all image slices during the segmentation process If you have boundaries for an object and plan to do segmentation for a new object within this object you can use the Edit Regions of Interest ROI by Boundaries command This command defines the ROI based on the boundary of the current object Make sure you change the current object back to the object you are going to get boundaries for in the Object management dialog box before you start the Interactive Segment command After this command is selected the Interactive Segmentation dialog box appears See Figure Interactive Segmentation Set Image Thresholds Use Calibrated Value Prev Thresholds Color Refresh Show Image m Select Boundary Type C Outline Only All Boundary Lines Skeleton Boundary r Segment Image Planes Segment All Smooth Image Prev Plane Set Object Segment
45. can be changed using the View Overlay Point Size command The color of the spheres can be changed using the View Overlay Point Color command 8 12 7 Point Size command Overlay submenu x Enter Point Radius When this command is selected the Point Size ps5 05 Cancel dialog box appears See Figure This dialog box allows you to specify the point radius 8 12 8 Point Color command Overlay submenu When this command is selected the Define Value Color dialog box appears to allow you to choose a specific color for a range of values associated with points 8 12 9 Contour command Overlay submenu Use this command to toggle the display of contours on and off 3D contours can be obtained from 3D surface models using the Tools Surface Contours command The color of contours can be changed using the Tools Contour Color command The menu item is checked when the display is turned on 8 13 Animation Commands View Menu 8 13 1 Animate command Animate submenu This command is available to the 3D SURFACE WINDOW and starts the surface model animation process The animation sequence can be defined and controlled using the View Animate Animation Control command The animation will continue until the Animate command is selected again or the ESC key is pressed 8 13 2 Animation Pace command Animate submenu Animation Pace Control Ed Selecting the View Animate Animation Pace Enter Elapse Ti
46. can be obtained from 3D scanners or other instruments Select the File Sparse Points Import Points to Surface Model command A file Open dialog box appears to allow the entering of the 3D point data file name Select the data file and click to read the data in A 3D sparse data set must be stored in an ASCII file without any header Each data line contains four items XI ZI VALUE X2 Y2 Z2 VALUE2 Xn Yn Zn VALUEn Where X Y and Z are the location of a point in 3D space and VALUE is the intensity or value of the point The VALUE field is not used when creating a surface model from the points The delimiter between items is a single space and other characters should not be used The data items can be either integer or floating point Empty data lines are not allowed in the file Once the 3D points are read in successfully a 3D surface model is created and displayed Volume and surface area can be calculated from the model The 3D model can be exported to one of the supported 3D formats including DXF IGES STL VRML 3DS Wavefront OBJ and others 73 FILE MENU COMMANDS 2 10 3 Points To Contours command Sparse Points Import submenu Use the File Sparse Points Import Points to Contours command to convert a sparse data set of 3D points to 3D contours for 3D modeling and rendering 3D sparse points can be obtained from 3D scanners or other instruments After this command starts a file Open dialog box appea
47. can then install the network license key on one PC and install the license manager there This PC must be connected to the same local area network License manager is only needed for the PC that has the license key installed Installation for all PCs In Windows insert 3D DOCTOR installation CD into your CD ROM If the installation does not start automatically use Start and Run setup exe from the CD ROM The installation program will create a 3D DOCTOR program group add an icon for 3D DOCTOR software an icon to Install PC License an icon to Install License Manager and an icon for the REAME TXT file Following steps are required only when the license key driver is not installed automatically during the installation process You can click on the Install PC License icon or use the following steps For Windows NT 2000 XP Vista you need to login as a system administrator account or your account has all the system administrator rights to install device drivers Start and Run c Program Files 3D DOCTORnet hdd32 exe 16 OVERVIEW AND TUTORIAL Note c Program Files 3D DOCTORnet is the path to the 3D DOCTOR program folder please change it accordingly if you have installed 3D DOCTOR to a different folder Network License Manager Installation Only on one PC where the license key is installed Click on the icon Install Server License Manager and choose the Install the Service option Network License M
48. command Boundary Process submenu This command removes boundary lines within a specified range of 2u image planes When the Edit Boundary Process Delete By Plane command is started the Starts From To E Delete Boundaries by Plane ID Bol E Define Plane Range To Delete dialog box appears See Figure Within the dialog box you can specify in which planes you want to delete the boundaries 6 3 3 Delete Replica command Boundary Process submenu This command checks the boundaries of currently active objects to find replicated boundaries and removes them Replicated boundaries can cause strange and unexpected results in volume rendering and 3D surface rendering When replicated boundaries are used to create a surface model incorrect 3D volume calculations can result After the Edit Boundary Process Delete Replica command is selected you will be prompted about how many replicated boundaries have been found among the currently active objects Select Yes to remove all replicated boundaries Select to cancel the operation 6 3 4 Remove Plane command Boundary Process submenu This command removes boundary lines within the current image plane 177 BOUNDARY PROCESS COMMANDS 6 3 5 Delete Holes command Boundary Process submenu This command deletes all holes and islands from the currently active boundaries This command will improve the performance of rendering functions where holes
49. current mouse position is displayed in the Status Bar at the bottom of the IMAGE PLANE WINDOW If the image has calibration parameters for the pixel value for example DICOM files or calibration parameters entered through the Edit Calibration command the calibrated value is displayed as well Make sure the Status Bar is visible when using this tool The Status Bar can be toggled on and off by using the View Toolbars Status Bar command Section 4 3 Status Bar command The pixel value displayed by the Show Pixel Value option is only the pixel value in the current image plane To see pixel values of another image plane simply double click the corresponding plane in the MONTAGE WINDOW or use the F5 key to go to the previous plane or the F6 key to go to the next plane 3 5 3 Draw Pixels command Image Editor submenu This tool is used for raster image editing and repairing When this tool starts a Define Pixel Value to Draw dialog box appears to allow you to define the Pen Size in pixels and the Color to be painted See Figure Use the Edit Image Editor Show Image Pixel Value command to determine a pixel color value if you are not sure what color to use The pen size determines how large of an area is to be painted 92 EDIT MENU COMMANDS Once all the parameters are set properly you are ready to draw the selected color into the image The Paint Cursor will appear in the IMAGE PLANE WINDOW Move the cursor to a location wh
50. file prj a stack of images through the stack list file 150 an image file tif dic dcm jpg hdr png a surface model file suf dxf igs stl obj wrl or a volume file vol A display window will be created to show the image You can open multiple files and use the Window menu to switch between windows If your 2D image planes or slices are stored in separate files for example DICOM and TIFF files you need to create a stack list first using the File New Stack command then use the File Open command to open the images for 3D display and analysis If the image is in 3D form you will see 2 windows one window displays a single plane IMAGE PLANE WINDOW and another window displays the montage of all image planes MONTAGE WINDOW If your files are still stored separately only one window will appear displaying the image itself For a single 2D image file you can use the File Open command to display and perform 2D processing The image file formats supported are DICOM dcm dic TIFF tif Windows Bitmap bmp JPEG jpeg jpg and other raw image formats that can be configured using a 3D DOCTOR header file hdr The TIFF format used by 3D DOCTOR can store both 2D and 3D images The currently supported image types include 8 bit and 16 bit grayscale 1 bit bi level 4 bit palette 8 bit palette color and 24 bit true color Some image processing functions are specific to certain image
51. image 3D DOCTOR displays the Save Image Dialog box so you can name your document Use the Browse button to define the file name and file type for the image output If your image is a 3D volume with multiple slices you can save the current slice a range of slices or all slices 68 FILE MENU COMMANDS Save Image Dialog Browse m Image Planes To Be Saved Current Plane C All Planes iios From jo To o em 2 7 2 File Save As dialog box The File Save As dialog box will appear when certain commands are selected It allows you to specify the name and location of the file you re about to save File Name Type a new filename to save a document with a different name A filename can contain up to eight characters and an extension of up to three characters 3D DOCTOR adds the tif extension in the Save As Type box Drives Select the drive in which you want to store the document Directories Select the directory in which you want to store the document Network Choose this button to connect to a network location assigning it a new drive letter 69 FILE MENU COMMANDS Save in T1 Brain e t File name Save as type Windows BMP Files bmp Cancel 2 2 7 3 Save Window command Save submenu Use this command to save the current image window to a Bitmap bmp file 3D DOCTOR displays the Save As dialog box for you to define a file name 2 7 4 Save Project and Save P
52. image to a file Use the File Open command to open the new image file for processing 1 6 10 Creating Object Boundaries Using the Boundary Editor Although 3D DOCTOR provides several ways of automatic or semi automatic image segmentation functions sometimes when an object is complex and does not have a distinguishable edge it is necessary to create the boundaries manually using the Edit Boundary Editor menu Manual boundary editing may seem to take a longer time but once you are familiar with the editing functions it is easy to do and faster than you would think The following steps are suggested to draw boundaries y Trace Boundary for an object Section 3 7 Boundary Editor Ii Step 1 If multiple objects are going to be used for 3D Draw Rectangle rendering you should define your new object before the Dus Code boundaries are drawn Use the Edit Object Settings command to add a new object and set it as the Current Add Node object Move Node Move Section Step 2 Select the Edit Boundary Editor On Off command to start the Boundary Editor The default DERE ESSE drawing mode is Trace Boundary which allows you to Move Boundary draw a closed polygon for the object in the current image plane Click the right mouse button to bring up the floating pop up menu for other editing options Step 3 To switch to a specific image plane you can double click your left mouse button on an image pane in the MONTAGE
53. in a region 102 delete points 220 delete selected portion 216 density 110 despeckle image 161 DICOM 37 61 185 DICOM files 41 59 DICOM compressed 63 DICOM JPEG 63 DICOM sort 167 DICOM sort by image number 167 DICOM sort by image position 167 DICOMDIR 41 59 Diffuse light 201 digitize points 220 Directories 62 69 display image planes 203 draw new boundary 99 draw pixels 92 Draw Pixels 92 Drives 62 60 DXF 23 31 196 E edge detection 163 INDEX Edit bar 122 Edit image pixels 92 Edit menu 79 ellipse boundry 100 Exit 78 exit line editor 111 Export Boundary 107 249 Export Contours 198 Export Surface 196 F5 function key 126 F6 function key 127 feedback factor 171 file format 3D sparse points 73 file format DXF 23 File menu 58 File Name 62 69 File Open dialog box 62 File Save As dialog box 69 file contour 218 Fill Boundaries 134 Film scan 222 film scan and crop 24 FLOAT 231 Floating Popup Menu 33 focal planes fusion 158 Focus Fusion 158 FOR 235 Format vol 30 Format Vox 30 Format XYZ 30 Full View 126 Function key F5 126 Function key F6 127 Function keys F1 F2 F3 F5 F6 32 fusion 50 155 Fusion 157 fusion color 158 Fusion focal planes 158 fusion image 25 fusion image plane 159 G GETPIXEL 239 GOSUB 236 GOTO 234 gradient magnitude 163 gray scale 61 165 1
54. keys F5 or F6 to go to another image plane for more editing You can switch to a different editing session by selecting another option from the Boundary Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Boundary Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 7 2 2 Move Node command Boundary Editor submenu Use this command to move a node on a boundry The cursor will change to a Move Cursor Point the cursor at a node and hold the left mouse button to move When the node is moved to the desired location release the left mouse button to confirm it Repeat this process to move another node If a location on a line does not have a node you need to add a node first using the Add Node option and then move it to the desired location using the Move Node command To undo the previous edit use the Edit Undo option or CONTROL Z Use the function keys F5 or F6 to go to another image plane for more editing 3 7 2 3 Move Section command Boundary Editor submenu Use this command to move a section on a boundary The cursor will change to a Move Cursor Point the cursor at a location on the boundary and hold the left mouse 101 EDIT MENU COMMANDS button to move When the section is moved to the desired location release the left mouse button to confirm it Repeat this process to move anot
55. make it active 1 3 2 Terminology Many imaging terms have been used by 3D DOCTOR Some are standard image processing terms and some are 3D DOCTOR specific To make it easier to understand we provide a list of definitions in this section for the commonly used terminology Some words are used as the names of certain data items such as boundary object and image Other words are used as the names of commands or processing functions such as segmentation and surface rendering Some different words may have the same meaning such as image plane and image slice The best way to understand the terms and commands is to work with the software If you are not sure about a command try it and see what it does e 2D Image Image Slice Image Plane A single slice of an image is a 2D image One slice of a volume image can be called a 2D image For example when you scan a film and save the scanned image to a TIFF or JPEG file it s a 2D image When you open a 2D image single slice in 3D DOCTOR you only see the IMAGE PLANE WINDOW that displays the single image and no MONTAGE WINDOW e 3D Image Volume Image A 3D volume image includes a stack of 2D images A 3D volume image can be stored in a single image file or multiple files where each file contains one image slice or plane In 3D DOCTOR when a 3D image is opened you will see two display windows The IMAGE PLANE WINDOW shows a single slice with full details and the MONTAGE WINDOW shows all of th
56. manuals and any partial or whole copies within thirty days of purchase to the party from whom you received it for a refund subject to our restocking fee Use of the Software 1 Able Software Corp Able Software grants the original purchaser Licensee the limited rights to possess and use the Able Software Corp Software and User Manual Software for its intended purposes Licensee agrees that at any one time the Software will be installed on a single computer only If the software is installed on a networked system or on a computer connected to a file server or other system that physically allows shared access to the Software Licensee agrees to provide technical or procedural methods to prevent use of the Software by more than one user 2 One machine readable copy of the Software may be made for BACK UP PURPOSES ONLY and the copy shall display all proprietary notices and be labeled externally to show that the back up copy is the property of Able Software and that use is subject to this License Documentation may not be copied in whole or part 3 Use of the Software by any department agency or other entity of the U S Federal Government is limited by the terms of the below Rider for Governmental Entity Users 258 SOFTWARE LICENSE AGREEMENT 4 Licensee may transfer its rights under this license PROVIDED that the party to whom such rights are transferred agrees to the terms and conditions of this License and writ
57. n e n n n nnn 246 10 6 SEGMENTATION COMMANDS eere ee ee eee reet see seen sese eaa 247 10 6 1 AUTOSEGMENT STATEMENT eene n e n n n npa pau 247 10 6 2 SEGMENTIMAGE 247 10 7 PROJECT AND BOUNDARY COMMANDS eere ee eee ene eo ose ee eese enses ee 248 10 7 1 SAVEPROJECT STATEMENT n n n nnn nnn nnn nnn nnn nn n n a a n np pne 248 10 7 2 OPENPROJECT STATEMENT 248 10 7 3 OPENBOUNDARY STATEMENT ececete e e e e e n n n n n ann a 249 10 7 4 SAVEBOUNDARY 249 10 8 3D RENDERING COMMANDS eee ee eee toes ea nose ee eese seen esee ena 250 10 8 TT SURESIMPEE STATEMENT 5 Ite e ERE OUI UII 250 10 82 SURFCOMPLEX STATEMENT eee Idein arie pli er erae 250 10 9 SCANNER COMMANDS teresa eos so Seer a ee ae DR MEER 251 TABLE OF CONTENTS 10 9 1 SELECTSCANNER STATEMENT eei itte tit torret het iir rep irte ne 251 10 9 2 SCANIMAGE STATEMENT rE rsrs rete rete petri er tede pH E pent 251 10 10 DECONVOLUTION COMMANDS
58. o pde tes Fes Pls ee 78 CHAPTER 3 EDIT MENU COMMANDS eere eene enne stia sets stesso setas etas e ease ta seta sesso 79 3 1 CALIBRATION AND WORKSPACE COMMANDS EDIT MENU A eeeeee teen enne 80 3 1 1 CALIBRATIONS COMMAND EDIT ener 80 3 1 2 RESIZE WORKSPACE COMMAND EDIT 81 3 2 OBJECT COMMANDS sicasssssssssesssusssncssasesczenns 82 TABLE OF CONTENTS 3 2 1 OBJECT SETTINGS COMMAND EDIT 82 3 2 2 OBJECT COMBINATION COMMAND EDIT enne nennen nennen enne 83 3 2 3 OBJECT MANIPULATION COMMAND EDIT MENU eese ener enne nnns 83 3 2 4 OBJECT REPORT COMMAND EDIT enne 84 3 2 5 OBJECT HISTOGRAM COMMAND EDIT MENU nennen enne nennen eren 85 3 3 REGION OF INTEREST ROI EDIT eeeeeeee eene eene tn aeta seta 85 3 3 1 REGION OF INTEREST TOOL ON OFF COMMAND REGION OF INTEREST SUBMENU 85 3 3 2 ROI BY BOUNDARIES COMMAND REGION OF INTEREST SUBMENU eeeeerene een 87 3 3 3 INFLATE REGION COMMAND F7 REGION OF INTEREST SUBMENU 87 3 3 4 DEFLATE REGION COMMAND F8 REGION OF INTEREST SUBMENU eere 87 3 3 5 CLEAR ROIS COMMAND EDIT MENU ccc scessescecessneceeeesececsesaecesu
59. opened by 3D DOCTOR two display windows are created the IMAGE PLANE WINDOW and the MONTAGE WINDOW If the image is initially displayed only in the IMAGE PLANE WINDOW it indicates the image has only a single slice and you may need to use the File New Stack command to put multiple slices together into a 3D image for processing After the stack list is created you can use it directly to open the 3D image Once you have boundaries and other data you can save all data to a project file A project file contains all processed data such as objects boundaries point markers annotations and the file path to the image file Image data itself is not saved in the project file When you move your project file to a new location make sure the image file is moved as well The IMAGE PLANE WINDOW displays one image plane at a time with the plane ID displayed at the top left corner of the window The IMAGE PLANE WINDOW is the main display and analysis window for a 3D image where all image processing functions editing functions measurement tools and segmentation functions are used Function keys F5 and F6 move the display to the previous slice or next slice respectively 28 OVERVIEW AND TUTORIAL The MONTAGE WINDOW displays all image planes that are organized sequentially in one window Each image plane is displayed as a pane with a plane ID in a MONTAGE WINDOW Double clicking in an image pane within the MONTAGE WINDOW will display the sele
60. pixel intensities within the polygon The cursor will change to an Arrow Cursor Point and hold down the left mouse button at a line to see the display change in the Status Bar at the bottom of the IMAGE PLANE WINDOW Release the left mouse button to restore the display of the selected line You can switch to a different editing session by selecting another option from the Boundary Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Boundary Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 110 EDIT MENU COMMANDS 3 7 9 5 Histogram command Boundary Editor submenu Use this command to Calculation Results x show a histogram of an image region enclosed by Boundary Histogram Report a boundary Object Name brian y Image Plane 54 Center lt Y 153 577240 105 660858 Length 534 872314 Area 7438 643464 square While in this editing Pixel Value Calibrated Value Number of Pixels channel 0 mode click the left mouse 25 25 000000 1 button on a boundary line 28 28 000000 1 and a Calculation Results 43 43 000000 1 45 45 000000 1 dialog box will appear 48 48 000000 2 with the histogram d displayed J ump to another 57 57 000000 1 image plane if you need to 53 63 000000 1 get the histogram of a 64 64 000000 1 72 72 000000 1 different region covered 78 78 000000 3 by anot
61. pixels 147 IMAGE MENU COMMANDS Parameter Name Meaning Number of Slices in Defines the number of slices in the row direction left to right for example in a 4x6 matrix the number of slices in the row direction is 4 Number of Slices in Defines the number of slices in the column direction Column top to bottom for example in a 4x6 matrix the number of slices in the column direction is 6 Left Start At The left starting point of the entire template Top Start At The top starting point of the entire template Image Slice Width The width of an individual image slice This must be kept the same for all image slices to be used in an image stack or for any 3D visualization Image Slice Height The height of an individual image slice This must be kept the same for all image slices to be used in an image stack or for any 3D visualization Horizontal Distance The horizontal distance between two slices Between Slices Vertical Distance The vertical distance between two slices Between Slices Output Image The starting number appended to the base file name for Sequence Starts At image slice output files The increment is 1 for each additional file You can use the arrow keys to adjust each parameter The template is displayed in the image window so you can move it to the exact location for all slices Once the template is adjusted properly you can select the Save Template button to save the template to a file
62. press the SPACE BAR on the keyboard to close the polygon Repeat the process to define more polygons Step 4 Interactive Segmentation This starts the Interactive Segmentation command Adjust the thresholds and segment the image to generate object boundaries for 3D rendering Step 5 Edit Boundaries This step starts the Boundary Editor Now you can move to the image window to edit the boundaries Click the right mouse button to bring up the editing options and switch between them Use F5 and F6 to go to the previous image slice or the next image slice Step 6 Create 3D Model by Surface Rendering When boundaries are edited select this command to create 3D models using the Simple Surface Rendering 182 3D RENDERING COMMANDS command You can choose other rendering commands by selecting them from the main menu Repeat the above steps to process additional objects There are many other processing functions that are not listed in this wizard such image pre processing functions and boundary post processing functions You can use these functions together with the 3D Wizard The 3D Wizard can start automatically when an image is open This option can be turned on and off by using the File Auto 3D Wizard command When Auto 3D Wizard menu item is checked the wizard auto start is on 7 2 Auto Segment command 3D Rendering Menu This command automatically segments the current image and traces the boundaries for a specified num
63. previous 126 Planes 3d display 205 plot window 20 32 PNG 24 PNG image format 37 40 41 59 62 point marker 113 point report 116 Point Report 220 point spread function 56 57 Point add 113 point assign plane 114 266 Point delete 114 Point move 113 point set object 115 points as crosses 205 points to contours 74 points to surface model 73 points 3D digitizing 220 points delete 220 previous plane 126 Previous Plane 186 PRINT 229 233 Print Window 76 profile plot 32 project file 28 47 Project file 70 Project List 77 pseudo color palette 129 R radiographs 147 Rapid prototyping 217 Raster image editing 92 raw image file import 42 Raw Image File Import 42 Raw Image File Import Multiple Files 66 Raw Image File Import Single File 63 raw image import 41 Raw triangle file 196 RECONBACKPROJ 246 RECONITER 252 reconstruction 26 Reconstruction 164 reconstruction back projection 164 reconstrution iterative 164 rectangle boundary 100 rectangle draw 100 red color palette 129 Reduce Nodes 176 region of interest 186 Region of Interest 22 Region of Interest 85 Region of interest crop image 146 Region of Interest define 184 Region of Interest move 86 Regions of Interest from boundaries 184 register image 154 registration 50 154 155 Registration 153 154 registration image 25 REM 229 Remove background 162
64. recently added contour 3D contours can be obtained from 3D surface models using the Tools Surface Contour Surface Contours command 8 18 7 Delete Contour Surface Contour submenu Use this command to start the Delete Contour editing mode The menu command is checked when this editing mode is on Click this command again will turn off the editing mode While the editing mode is on you can move the cursor to a contour and click the left mouse to delete 3D contours can be obtained from 3D surface models using the Tools Surface Contour Surface Contours command 219 SURFACE WINDOW COMMANDS 8 19 3D Points Commands Tools Menu 8 19 1 Digitize Point Tools Menu This command turns on and off the 3D point digitizing tool and allows you to digitize 3D points on a 3D surface model The command is checked when the point digitizing tool is on To digitize a point move the cursor to a surface location of a 3D object and click the left mouse button to pick the point A point marker is displayed when the point is digitized You can use the Delete Point command to delete existing points You can use the Point Report command to get a report of point coordinates 8 19 2 Delete Point Tools Menu This command turns on and off the 3D point deleting tool and allows you to delete 3D points on a 3D surface model The command is checked when the point deleting tool is on To delete a point move the cursor close to the point to be deleted an
65. resized image will be doubled in all three dimensions This command is similar to Image Resize Volume command Syntax SIZEIMAGEUP imagevar filename 2 SIZEIMAGEUP imagevar filename scalar where IMAGE3D imagevar STRING filename INTEGER scalar Example IMAGE3D imagel OPENIMAGE imagel c 3ddoctor head3d tif SIZEIMAGEUP imagel c size2 tif 2 END 241 3DBASIC COMMANDS 10 5 11 SIZEIMAGEDOWN statement This command reduces the size of an image by a specified scaling factor For example if scaling factor is 2 then the resized image will be scaled down by 2 in all three dimensions This command is similar to Image Resize Volume command Syntax SIZEIMAGEDOWN imagevar filename 2 SIZEIMAGEDOWN imagevar filename scalar where IMAGE3D imagevar STRING filename INTEGER scalar Example IMAGE3D imagel OPENIMAGE imagel cN3ddoctorviead3d tif SIZEIMAGEDOWN imagel c size2 tif 2 END 10 5 12 ROTATEIMAGEX and ROTATEIMAGEY statements The ROTATEIMAGEX and ROTATEIMAGEY commands rotate a 3D volume around the X Axis and Y Axis respectively They are similar to Image Reslice X and Image Reslice Y commands Syntax ROTATEIMAGEX imagevar filename ROTATEIMAGEX imagevar filename ROTATEIMAGEY imagevar filename ROTATEIMAGEY imagevar filename where IMAGE3D imagevar STRING filename Example IMAGE3D imagel OPENIMAGE imagel cN3ddoctorviead3d tif ROTATEIMAGEX imagel c Nopview tif ROTATEIMAGE
66. resizing and image rotation The 3DBasic scripting tool makes it easy to create Basic like sophisticated 3D imaging programs Get 3D DOCTOR today and visualize your images in 3D 3D DOCTOR is cleared by FDA US Food and Drug Administration 510K clearance for medical imaging and 3D visualization applications 3D DOCTOR s user interface is similar to other Windows software programs You can use the menu items or toolbars to start the processing commands You can use the keyboard to scroll an image display window up down left and right and to rotate a 3D display to different angles You can use the mouse to draw a selection rectangle within an image window or perform data editing functions The right mouse button is used to bring up a floating pop up menu with available editing options when in an editing mode 3D DOCTOR has 5 main types of display windows 1 Single IMAGE PLANE VIEW to show a single image slice at a time 2 MONTAGE VIEW to display all slices from a 3D image The view can display the slices in a mosaic form or a single slice as a side profile or top profile view 19 OVERVIEW AND TUTORIAL 3 VOLUME VIEW to display volume rendered images 4 SURFACE VIEW to display 3D surface models 5 PLOT WINDOW to display histograms and measurements Each window has its own set of commands to open and save files edit and process data associated with the display window You can click the left mouse button within a window to
67. set must be stored in an ASCII file without any header Each data line contains four items XI ZI VALUE X2 Y2 Z2 VALUE2 74 FILE MENU COMMANDS Xn Yn Zn VALUEn Where X Y and Z are the location of a point in 3D space and VALUE is the intensity or value of the point The delimiter between items is a single space and other characters should not be used The data items can be either integer or floating point Empty data lines are not allowed in the file Once the 3D points are read in successfully a 3D image file is created and can be displayed using the File Open command 2 11 3DBasic File Menu This command can be accessed from the IMAGE PLANE WINDOW the MONTAGE WINDOW the 3D SURFACE WINDOW and the VOLUME VIEW WINDOW See Chapter 10 3DBasic Menu Command for details on using the 3DBasic scripting tool and commands 75 FILE MENU COMMANDS 2 12 Select Scanner command Scan submenu 3D DOCTOR supports the standard TW AIN interface for film and image scanners If a scanner is TWAIN compatible it can be used to scan images into 3D DOCTOR for processing To select a scanning device 1 Under the File menu click Select Scanner 2 Click the scanner you want to use and confirm 2 13 Scan command Scan submenu 3D DOCTOR supports the standard TW AIN interface for film and image scanners If a scanner is TWAIN compatible it can be used to scan images into 3D DOCTOR for processing Once a film image is sc
68. show the correlation coefficient slope and intercept values Select Apply to confirm the calibration parameters The calibration file is a simple ASCII text file that can be created using a text editor such as the Notepad This file does not have any header and stores each pair of original pixel and calibrated values in a text line The first value is always the raw pixel value and the second is the calibrated value Since this calculation is based on general regression and a correlation algorithm you can use it to do a correlation analysis for other types of data Simply enter your 2 column data into a text file Open it in 3D DOCTOR s Pixel Calibration dialog box and use the Calculate button in the Pixel Calibration dialog box to get the results The pixel intensity calibration is used by the Edit Object Report function The 3D Rendering Interactive Segment function can display the calibrated values for thresholds 3 1 2 Resize Workspace command Edit Menu Use this command to change the current workspace dimensions including the range for column min and max X row min and max Y and the total number of planes Once the dimensions are adjusted the display will be refreshed accordingly This command is available when there is no image in the workspace When boundary lines exist in the workspace the adjustment of the workspace dimension will not affect the boundary line data and scale It only changes the relat
69. statement prints values of variables expressions and text strings to the file defined by the LOGFILE statement Syntax PRINT parameters Example INTEGER I FLOAT STRING note 1 25 25 0 note Just a note PRINT Test Print note I F END 233 3D BASIC COMMANDS 10 4 9 INPUT statement The INPUT statement allows interactive assignment of values to variables Syntax INPUT Variable INPUT Prompt Text Variable Example INTEGER I FLOAT STRING note INPUT Enter I I INPUT Enter INPUT Enter Note note PRINT Test Input note I F END 10 4 10 GOTO statement The GOTO statement is one of several ways implemented in 3DBasic to control program flow Syntax GOTO lt Label gt where the Label is numeric value indicating the line where the program continues 3DBasic does not require a Label for each line Only a line that is a target line of a GOTO statement must have a label Example INTEGER I INPUT Enter I I GOTO 200 Iu 200 1 1 PRINT T END 234 3D BASIC COMMANDS 10 4 11 IF statement The IF statement implemented in 3DBasic is slightly different from the standard Basic format The ELSE statement is not supported and only lt gt and can be used as an operator Syntax IF Expression Operator Expression THEN lt LineLabel gt Example INTEGER I INPUT Enter I I IF I gt 10 THEN 200
70. step instructions on topics such as creating a 3D stack from single image files how to define objects how to create object boundaries using segmentation how to create 3D surface and volume rendering and image registration and fusion 26 OVERVIEW AND TUTORIAL 1 4 Technical Support and Upgrades At Able Software we make every effort to provide you with the best technical support possible Don t hesitate to contact us 1f you need assistance of any kind For technical support bug reports or to submit comments and suggestions please contact us by email support ablesw com Fax 781 862 2640 or Phone 781 862 2804 or by regular mail Customer Support Department Able Software Corp 5 Appletree Lane Lexington MA 02420 2406 USA On Able Software s Web Site http www ablesw com 3d doctor we have pages dedicated to technical support and upgrade information Please visit our site to get the latest information on new releases and availability of new upgrades The latest 3D DOCTOR upgrades are normally available to users under service contract at our web site http www ablesw com 3d doctor You can also contact the distributor from whom you purchased the software for both technical and other information 1 4 1 3D DOCTOR Internet Mailing List We have set up an Internet mailing list for 3D DOCTOR users and those who are interested in 3D image processing and rendering technologies We regularly post news about new release
71. the MONTAGE WINDOW 124 VIEW MENU COMMANDS Fable Software 09 00 tert m ax 9 Fil ie map ST tad hie HV El3le 1 xul Dix die i ir epe e re e al fnew Bo xl ieda jelo 5 4 4 3 Full Resolution command View Menu This command creates a full resolution display of the SIDE VIEW FRONT VIEW and MONTAGE VIEW images 4 4 4 Vertical Flip command View Menu This command flips vertically the SIDE and FRONT VIEW image The image data is not changed by this command 125 VIEW MENU COMMANDS 4 5 Zoom In command View Menu To zoom in on an image area hold the left mouse button to drag a selection rectangle in the image window Then use the View Zoom In command to display the zoomed region When the cursor is not an arrow the selection is not directly available because it is currently in an editing session such as editing lines or selecting control points To get a selection rectangle during an editing session hold down the SHIFT key and the left mouse button to drag a selection rectangle in the image window If no selection rectangle is present the area around the cursor is zoomed Shortcuts Keys F2 4 6 Zoom Out command View Menu This command will zoom out the current window to a lower level This allows the window to display a larger image area Shortcuts Keys F3 4 7 Full View command View Menu Use this command to display the entir
72. the image has a single plane or creates a new image file to store multiple planes if it has multiple planes The original image file is not affected by this processing In the multiple plane case you can save the modified image to a new file when the Save As dialog box appears after the command is selected 5 2 3 Rotate command Rotate submenu This command is used to rotate the image planes by a user defined angle This X changes the raw image data or creates a new image file When the Rotate Image Com Cckwin dialog box appears enter the angle in 5 degrees and select the rotation direction Clockwise for either counter clockwise clockwise Cancel You use Edit Measuring Tool Angle command to check the angle for rotation Rotation Angle in Degrees This changes the image data in memory if the image has a single plane or creates a new image file to store multiple planes if it has multiple planes The original image file is not affected by this processing In the multiple plane case you can save the modified image to a new file when the Save As dialog box appears after the command is selected 138 IMAGE MENU COMMANDS Use the File Open command to display the newly created image file 5 2 4 Transpose command Rotate Submenu This command is used to transpose or rotate the image 90 degrees This changes the image data in memory if the image has a single plane or creates a new image f
73. the mouse to 2151 xi 3D Profile draw a polygon in the IMAGE PLANE WINDOW When you are finished press any key to close the polygon Once the line is completed 3D DOCTOR will show the 3D image density profile for pixels within the area in a PLOT WINDOW See Figure Click the right mouse button to show other measurement options 91 EDIT MENU COMMANDS 3 5 Image Editor Edit Menu 3 5 1 Image Editor On Off command Image Editor submenu This command starts the Image Editor The Image Editor supports the following options Show Pixel Values Draw Pixels and Map Pixel Values The Image Editor can be used to show image pixel values modify pixel values by drawing in the image with a specified pen and map pixel values to new Show Pixel Value ones When the image has multiple planes or slices Draw Pixels only the current plane is affected by the editing If Map Pixel Values you need to save the modified image use the File Save Save Image As command If the image is not saved the changes will be lost when you switch to a different image plane Image Editor On Off The options can be selected by using the Image Editor submenu or the floating pop up menu brought up by clicking the right mouse button 3 5 2 Show Pixel Value command Image Editor submenu When this option is selected you can show pixel values by holding down the left mouse button and moving to the pixel locations The pixel value at the
74. to be used for other scanned films If you have a saved template from a previous operation use the Open Template button to open the template The parameters from a previous template may not apply perfectly to the current image but you can easily adjust their position using the ARROW KEYS Be very careful with the mage Width and Image Height parameters as they must be kept the same for all image slices if they are going to be used together for 3D 148 IMAGE MENU COMMANDS rendering Don t change the width and height if you are using a previously defined template for image cropping If you enter the parameters directly use the Apply button to update the template display in the IMAGE PLANE WINDOW Use the Browse button to locate the directory and the base filename to save the cropped image slices The starting number defines the position of the first image slice in the sequence The increment is 1 for each additional image You can change the file names later using the Windows File Explorer Once all of the parameters are defined select the Start button to crop the slices and save them to image files After all of the image slices are generated use the File New Stack command Section 1 6 2 Creating a 3D Stack from 2D Image Slices and Section 2 1 New Stack command to put them into a list and open the files for 3D applications 5 5 Resize Volume command Image Menu This command is used to resize the cur
75. to create headers for a group of image data files belonging to a 3D volume image When creating headers for multiple files an image stack list file 150 can be created as well which will be used by 3D DOCTOR to open the volume image Once the header file is created correctly you can then use the header file hdr instead of the image data file to open the image and read the data into 3D DOCTOR The file will be treated the same as a directly supported file format like DICOM or TIFF The following are the steps needed to create a header file for a single non standard image file or a list file for an image volume stored in multiple files Step 1 Select File Raw Image Import Single File if dealing with only one raw image data file or File Raw Image Import Multiple Files command if working with multiple files for an image volume When this command is selected a Create Image Header File dialog box will appear to enter in a set of image parameters Section 2 4 1 Raw Image File Import Single File command and Section 2 4 2 Raw Image File Import Multiple Files command Both commands create a header or configuration file for each image data file which allows 3D DOCTOR to read a non standard or proprietary image data file directly The command for multiple files can also generate a list file for the volume image This provides a universal image reader capable of handling most uncompressed image file formats so you can bring your d
76. under the Edit Boundary Editor submenu or the Edit Boundary Process submenu You can then start over and create a new training area for segmentation The boundary lines can be edited using the Edit Boundary Editor options Use the File Boundary and Point Export Boundary command to save boundary data to a file 187 3D RENDERING COMMANDS 7 5 Surface Rendering Commands 3D Rendering Menu 7 5 1 Complex Surface command Surface Rendering submenu This command creates a complex 3D surface rendering using the boundary data generated from a 3D image The algorithm used for Complex Surface rendering normally has a longer processing time than the Simple Surface rendering algorithm and is suitable for a complex surface where branches and holes exist The Surface Smoothing function can be used to smooth surface models Complex Surface Rendering E Denseness of Triangle Mesh Recommended Settings X fi 4 Smaller value generates higher number of surface polygons and takes longer to process 1 ELE Larger value generates lower ber of surface polygons am numi Cancel The denseness parameters for the triangle mesh are used to control the final number of surface polygons 1 is the smallest value allowed which will use the maximum number of surface polygons Larger value will decrease the density and therefore lose some small details The initial Recommended Settings are estimated from the imag
77. value Cancel is increased by the increment value specified or decreased if the specified value is negative every time you label a point If the option is not selected all the points labeled will have the same plane value until you reset the value to a different value You can switch to a different editing session by selecting a different option from the Point Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Point Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 10 5 Assign Plane command Point Editor submenu Use this command to assign the current specified plane number to an existing point The cursor will change to an ID Cursor Point and click the left mouse button at a point to set the value Use the Edit Boundary Editor Show Info option to verify the plane value 114 EDIT MENU COMMANDS You can switch to a different editing session by selecting a different option from the Point Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Point Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 10 6 Set Object command Point Editor submenu Use this command to put points to the current object First select the object you want to use then move the mouse to a point and
78. very simplified user interface to make it easy to use To do a deconvolution you simply select the Image Deconvolution Fast Nearest Neighbor OR Maximum Entropy command to start The following explains the parameters in the 3D Image Deconvolution dialog box that appears See Figure and how to define them Chapter 8 Deconvolution commands 3D Image Deconvolution Using Maximum Entropy m Source Image Browse Preview Use Synthetic PSF m Point Spread Function PSF Image Browse Preview Number of Iterations 10 Feedback Factor 1 100 50 Output Image ae Cancel x The Feedback Factor is in the scale of 1 to 100 The larger the feedback factor the stronger the deconvolution will be applied during each iteration However if the original image is noisy a smaller feedback factor should be used to reduce the noise The Number of Iterations controls how many iterations the process will take If both the image and the Point Spread Function PSF are in good quality and do not have much noise a smaller number of iterations may be sufficient 56 OVERVIEW AND TUTORIAL 1 6 15 3D DOCTOR Command Line Options 3D DOCTOR provides command line options to run a 3DBasic script or do a surface rendering from boundary data from another program or from the operating system directly The following lists the command line syntax 3ddoctor 3dbasic d surfsimple bas Where 3ddoctor is the progr
79. you can Get information on an image including number of columns rows planes bits per pixel and image type Flip rotate and transpose your image Reslice a volume along an arbitrary axis for more accurate measurement and view Crop a 3D image volume Perform 3D image registration or geometric correction Combine two images to create a fusion or create color fusion from two or three images Negate despeckle and remove a dark background from your image Smooth image using either median or average filter Detect image edges Classify a color image into a fewer number of color classes Convert images from one image type to another image type 3D reconstruction from images taken with regular angles 136 IMAGE MENU COMMANDS When a 3D volume image is processed using one of the image processing functions under the Image menu only the current image plane is processed The resulting image is displayed in a new IMAGE PLANE WINDOW as a 2D image or a single plane image The original image is not changed You should save the modified image to an image file if you need to keep the result If an image is a single plane image the image itself is processed and can be saved to a new image file 5 1 Information command Image Menu When this command is selected Image Information dialog box appears See Figure ax The dialog box displays the parameters associated with the image displayed CRINES Plan
80. 0 1 ADD POINT COMMAND POINT EDITOR 0 113 3 10 2 MOVE POINT COMMAND POINT EDITOR SUBMENU iier enne enne nnne 113 3 10 3 DELETE POINT COMMAND POINT EDITOR SUBMENU eere eene nnne 114 3 10 4 SET PLANE VALUE COMMAND POINT EDITOR SUBMENU cscsscceeeescecesssececessseeecsseeeeeens 114 3 10 5 ASSIGN PLANE COMMAND POINT EDITOR SUBMENU eene enne enne nnne 114 3 10 6 SET OBJECT COMMAND POINT EDITOR SUBMENU cies eene en nnne nnne 115 3 10 7 DONE COMMAND POINT EDITOR SUBMENU en nennen nennen 115 3 11 POINT REPORT COMMAND EDIT 116 3 12 ANNOTATION EDITOR EDIT ee eeee esee ee ette sees 117 3 12 1 ADD TEXT COMMAND ANNOTATION EDITOR SUBMENU 117 3 12 2 DELETE COMMAND ANNOTATION EDITOR SUBMENU eese nennen enne 117 3 12 3 MODIFY COMMAND ANNOTATION EDITOR SUBMENU cicer eene enne enne 118 3 12 4 MOVE COMMAND ANNOTATION EDITOR SUBMENU 118 3 12 5 SET OBJECT COMMAND ANNOTATION EDITOR SUBMENU eene nennen 119 3 12 6 CONVERT TO BOUNDARY COMMAND ANNOTATION EDITOR SUBMENU 119 3 12 7 PROJECT NOTES COMMAND EDIT MENU cies 119 3 13 TEXT TO BOUNDARIES
81. 076 5102 0 153 0 204 0 255 0 Density 0 255 Cancel Apply 223 VOLUME WINDOW COMMANDS 9 3 Color command View menu Colors for Volume Rendering x The View Color command is available when the volume rendering uses the color rendering mode Use this command to change the colors uses by either the low intensity voxels or high intensity voxels Click on the Change buttons to define a new color Click the m Low Intensity Voxels Change High Intensity V oxels DK button to apply the new colors to the volume rendering 9 4 Viewing Angle Commands View Menu The commands under the Viewing Angle submenu in the VOLUME VIEW WINDOW allow you to change the view of the volume rendered image You can turn the volume right left up down clockwise CW and counter clockwise CCW Turn Right Tum Left Tum Up Tum Down Tum Cw Tum COW 9 5 Slice Selection Commands View Menu 9 5 1 Slice Range command View menu This command is used to select a range of slices in Volume Rendering Once a volume rendering is created use this command to enter the range of slices to be used You can use this function to create a rendering of a portion within the volume 9 5 2 Hide and Show Slices commands View menu The commands are used to hide and show slices at the front or the back of the volume One slice is hidden or shown at a time Y
82. 1 6 5 CREATING 3D MODEL USING SEGMENTATION eene ne nnn n nnn nnn nn nnn nnn nhan nana nua 46 1 6 6 CREATING 3D VOLUME RENDERING eene e e e e n n nnn rtr rtr rtr rtr r n app pap nua 48 1 6 7 3D IMAGE SEGMENTATION USING A TRAINING AREA eee n n en nnn nnn nnn nnn nnn nean 49 1 6 8 REGISTERING TWO IMAGE STACKS AND CREATING A FUSION IMAGE eere 40 1 6 9 RESLICING A 3D IMAGE ALONG AN ARBITRARY nennen nnn nnn nnne nun 51 1 6 10 CREATING OBJECT BOUNDARIES USING THE BOUNDARY EDITOR eee 52 1 6 11 CREATING A 3D RENDERING FROM 3D CONTOURS eeceeeeee 53 1 6 12 3D VOLUME RENDERING FOR 3D SCIENTIFIC e n n n nnn nnn nnn nnn 55 1 6 13 AUTOMATIC ALIGNMENT OF IMAGE SLICES eese 55 1 6 14 ONE STEP 3D IMAGE DECONVOLUTION eene n n n nen n n nnn n nnn nnn nnn 56 TABLE OF CONTENTS 1 6 15 3D DOCTOR COMMAND LINE OPTIONS esee eene eene en nennen rennen nennen 57 CHAPTER 2 FILE MENU COMMANDS eee ee eene enne ense tn seta setas to stie stesse toss ease tas etas etas e taste sea 58 2 1 NEW STACK COMMAND FILE 59 2 2 OPEN COMMAND FILE neta seta setas etna setas etse seta se tne tas 61 2 2 L BIEE OPEN DIALOG BOX
83. 12 OVERLAY COMMANDS VIEW MENU c esee esee ease tosta soo 205 8 12 1 AXES COMMAND OVERLAY ener enne nennen rennen nr rne enne 205 8 12 2 BOUNDARY CUBE COMMAND OVERLAY SUBMENU cessere enne ne 205 8 12 3 PLANES COMMAND OVERLAY SUBMENU innere rennes rennen enne 205 8 12 4 POINTS COMMAND OVERLAY SUBMENU 205 8 12 5 POINT AS CROSS COMMAND OVERLAY SUBMENU 205 8 12 6 POINT AS SPHERE COMMAND OVERLAY 0 206 8 12 7 POINT SIZE COMMAND OVERLAY SUBMENU 206 8 12 8 POINT COLOR COMMAND OVERLAY SUBMENU eese eren enne enne nnn nnne 206 8 12 9 CONTOUR COMMAND OVERLAY SUBMENU eese entren enne enne innen nnne 206 8 13 ANIMATION COMMANDS VIEW MENU ces eeee esee ette estote toss 206 8 13 1 ANIMATE COMMAND ANIMATE SUBMENU nennen rennen enne nennen nnne 206 8 13 2 ANIMATION PACE COMMAND ANIMATE SUBMENU cssssceceessececeescecessneeeceesaeeeesneeeeeens 206 8 13 3 ANIMATION CONTROL COMMAND ANIMATE SUBMENU 0 cccsssssceseescecesseececesseeeseneeeeeens 208 8 13 4 OBJECT ANIMATION COMMAND ceeseeeeeeerer enne
84. 15 1 Calculate Volumes command Tools Menu This command calculates 3D volumes of surface models for all objects The volume calculation is based on the current surface geometry and calibration parameters and the calculations may vary depending on the rendering method used When the Tools Calculate Volumes command is selected a 3D DOCTOR Report dialog box appears showing the Volume and Surface Area calculations See Figure 3D DOCTOR Report x Object Volume and Surface Area Calculations i Object Name Volume Volume Unit Surface Are Copy 669147 973130 cubic pixels 111166 402 1960351 351322 cubic pixels 111605 989 Print Save Hi 211 SURFACE WINDOW COMMANDS 8 15 2 Measure and Measure Report commands Tools Menu This command switches on and off the 3D measurement tool and allows measuring length between points on a 3D surface To make a measurement first change the orientation of a 3D surface model using the arrow keys so the region to be measured is visible Move the cursor to a location and click the left mouse button to pick a location A point marker is displayed at the location Repeat this step to pick more points The 3D coordinates of the current point and the cumulative length is displayed in the status bar at the bottom of the window When you have entered all points for the measurement use the Measure Report command to display the results You can use the ESC Escape key or the Cle
85. 2 5 13 3 REMOVE BACKGROUND COMMAND PROCESSING SUBMENU eere 162 5 13 4 SOBEL EDGE COMMAND PROCESS SUBMENU c sccesseseeceeseececseaececeeseecessueeecseaeeeenseaeens 163 5 13 5 GRADIENT MAGNITUDE COMMAND PROCESS SUBMENU cccsssssceseeseeceestececeeseeeesseeeens 163 5 13 6 MAP PIXEL V ALUES COMMAND PROCESSING SUBMENU cicer enne 163 5 14 RECONSTRUCTION COMMAND IMAGE 164 5 15 CONVERSION COMMANDS IMAGE 165 5 15 1 24 BIT RGB PALETTE COMMAND CONVERSION SUBMENU 165 5 15 2 24 BIT RGB GRAY SCALE COMMAND CONVERSION SUBMENU eene 165 5 15 3 8 BIT PALETTE RGB COMMAND CONVERSION SUBMENU eene een 165 5 15 4 8 BIT PALETTE GRAY SCALE COMMAND CONVERSION 0 166 5 15 5 8 BIT PALETTE 1 BI LEVEL COMMAND CONVERSION SUBMENU 166 TABLE OF CONTENTS 5 15 6 16 BIT GRAY SCALE 8 BIT COMMAND CONVERSION SUBMENU eere 166 5 15 7 8 BIT GRAY SCALE 24 BIT RGB COMMAND CONVERSION SUBMENU 166 5 15 8 1 BIT 8 BIT GRAYSCALE COMMAND CONVERSION SUBMENU eren 167 5 16 SORT SLICES COMMANDS IMAGE 167 5 16 L SORT BY IMAGE POSITIONS 2n RGB eaa D SAAR Dao Ii d M 167 5 162 SORT BY IMAGE NUMBER anh Gite ee Seth BAHL 167 5 17 DECONVOLUTION COMMANDS IMAGE 1
86. 3 Segment Object Step 1 It is highly recommended to define an ROI region of interest before this segmentation method is used A carefully defined region of interest will keep the region growing process staying in the proper image area and from jumping to other areas when image noise is present An ROI is defined using Edit Region of Interest and updated by using the ROI Editor Tool later Step 2 To start the process select the 3D Rendering Segment Object Draw Training Area command to get into the drawing mode The right mouse button will bring up the pop up menu of options you can use The training area is used to create a set of features for the 3D segmentation so it should be big enough to cover most of the typical features of the object Step 3 To draw a training area move the cursor to a location and click the left mouse button to define the first point Move the cursor to the next location and click the left mouse button again to define the line segment Repeat this process until you are close to the starting location Hit the SPACEBAR to close the polygon and the current image plane is segmented automatically The object boundary in the current image plane is displayed in the IMAGE PLANE WINDOW Step 4 If you want to continue the segmentation process to another plane use the 3D Rendering Segment Object Previous Plane or 3D Rendering Segment Object Next Plane option from the main menu or from the floating pop up menu
87. 3D DOCTOR User s Manual 3D Imaging Modeling and Measurement Software Quick Start Guide Tutorials View Controls Editing Tools 3D Model and Volume Rendering Able Software Corp http www ablesw com 1 1 2012 3D DOCTOR FOR WINDOWS User s Manual Able Software Corp 5 Appletree Lane Lexington MA 02420 2406 USA Phone 781 862 2804 Fax 781 862 2640 Email support ablesw com Web http www ablesw com 3d doctor Information in this document is subject to change without notice and does not represent a commitment on the part of Able Software Corp The Software described in this document is furnished under the Software License Agreement set forth in the back of this document The Software may be used or copied only in accordance with the terms of the License This User s Manual may not be reproduced stored in a retrieval system or transmitted in any form or by any means electronic or mechanical including photocopying and recording for any purpose other than the purchaser s personal use without the prior written permission of Able Software Corp c Copyright 1994 2012 Able Software Corp All rights reserved ASC 3DDR BN 120710 The following trade names are referenced throughout this manual Able Software 3D DOCTOR 3DBasic 3D DOCTOR for Windows 3D DOCTOR for Windows NT 3D DOCTOR for Windows 95 are trademarks owned by Able Software Corp MSDOS Windows Windows NT Microsoft Windows NT Windows 2000 Windows 2K Wi
88. 3D DOCTOR and its applications Please contact us if you would like to sign up for the training or need more information See contact information on the title page of this manual 18 OVERVIEW AND TUTORIAL 1 3 About 3D DOCTOR 1 3 1 Overview 3D DOCTOR is an advanced 3D modeling image processing and measurement software for MRI CT PET microscopy scientific and industrial imaging applications 3D DOCTOR supports both grayscale and color images stored in DICOM TIFF Interfile GIF JPEG PNG BMP PGM MRC RAW or other image file formats 3D DOCTOR creates 3D surface models and volume rendering from 2D cross section images in real time on your PC You can export the polygonal mesh models to STL ASCII and Binary DXF IGES 3DS OBJ VRML PLY XYZ and other formats for surgical planning simulation quantitative analysis finite element analysis FEA and rapid prototyping applications You can calculate 3D volume and make other 3D measurements for quantitative analysis 3D DOCTOR s vector based tools support easy image data handling measurement and analysis 3D CT MRI images can be re sliced easily along an arbitrary axis Multi modality images can be registered to create image fusions Misaligned slices can be automatically or semi automatically aligned using 3D DOCTOR s image alignment functions Other image processing functions include template based film cropping image reslicing to correct slices of uneven thickness volume
89. 66 green color palette 129 grey scale palette 129 H hardware key 16 264 Header File create 42 Help index 256 Help Index 256 Help menu 256 Histogram 111 histogram plot 32 histogram within a region 111 hollow object 180 Horizontal Flip 138 hot keys 32 I IBL format 72 identical boundaries 177 identical boundaries remove 177 IF 235 IGES 23 Image alignment interactive 151 image combination 161 Image Editor 92 Image Format PNG 37 Image fusion 161 image histogram 111 Image Information 137 Image menu 136 Image mosaic 160 Image Palette 129 image palette adjust 130 image pixel editor 92 Image Plane 20 Image Plane and Montage Windows 28 image plane window 29 image plane downsize 204 image plane opaque 204 image plane reverse order 141 image plane transparent 204 Image Planes display 204 image profile measure 90 image region crop 145 image registration 154 Image registration 50 155 image reslice 140 Image Settings 204 Image Slice 20 image slice alignment 55 image slice thickness variable 140 image slice reverse 141 image slices 147 image slices animation 209 Image smoothing 161 image types 24 image 3D 20 image alignment 150 image from points 74 INDEX image fusion 158 image resample 149 image resize 149 image reslicing 25 image restoration 168 169 170 Image Rotate By X Axis 51 Image Rot
90. 67 5 17 1 FAST NEAREST NEIGHBOR DECONVOLUTION COMMAND IMAGE DECONVOLUTION MENU 169 5 17 2 MAXIMUM ENTROPY COMMAND IMAGE DECONVOLUTION MENU eere 170 5 17 3 SYNTHETIC PSF COMMAND IMAGE DECONVOLUTION 172 CHAPTER 6 BOUNDARY PROCESS COMMANDS eee ee seen sete etta setas tta sata stas etos sense ena 173 6 1 BOUNDARY SPLIT MERGE AND ASSIGN OBJECT 174 6 1 1 SPLIT OBJECT COMMAND BOUNDARY PROCESS SUBMENU csssssceeesseecesseeeeeeesseeecesseeeeens 174 6 1 2 ASSIGN OBJECT COMMAND BOUNDARY PROCESS SUBMENU cernerent 175 6 1 3 MERGE BOUNDARIES COMMAND BOUNDARY PROCESS SUBMENU 175 6 2 SMOOTH BOUNDARY COMMANDS eese eese eese ee seta seta stats tosta aseo ense ease tassa soa 176 6 2 1 REDUCE NODES COMMAND BOUNDARY PROCESS SUBMENU cccsssseceeseseeeeesseeeessneeeeens 176 6 2 2 SMOOTH COMMAND BOUNDARY PROCESS SUBMENU ssssseceessececeeseecessneeecseaeeecsseeeenens 176 6 2 3 SIMPLIFY COMMAND BOUNDARY PROCESS SUBMENU cese enne nnne 176 6 3 BOUNDARY REMOVAL COMMANDS e eee esee esee essen states tots to neto setas etas taste eoo 177 6 3 1 DELETE BY LENGTH COMMAND BOUNDARY PROCESS SUBMENU eene eene 177 6 3 2 DELETE BY PLANE COMMAND BOUNDARY PROCESS SUBMENU eere ene 177 6 3 3 DELETE REPLICA COMMAND BOUND
91. 7 contours delete 219 contours delete last 219 220 Contours export 198 contours import 53 Contours import 197 Contrast 131 Contrast Adjustment Dialog Box 131 control point 94 Control Point Dialog Box 97 control point check 96 Control point pick point 96 control point residual error 96 control points 50 156 Convert 8 bit Palette to 1 bit bilevel 166 Copy Boundary 105 counting points 116 Create Header 41 create image mosaic 160 Create movie 128 210 Create Movie 128 210 Create 3DBasic 225 Crop film 147 Crop image 145 crop image by ROI 146 crop image region 145 Crop image ROI 146 Crop Object 3D 213 Crop Volume 145 CROPIMAGE 243 cube boundary 30 179 263 cube volume boundaries 48 customize palette 130 cutting contours 217 cutting plane 217 218 Cutting Plane 215 D DECONVMAX 252 DECONVNN 251 deconvolution 26 149 168 169 170 Deconvolution 56 57 Deconvolution Maximum Entropy 252 Deconvolution Nearest Neighbor 251 Define Object 82 Define ROI 87 deflate boundary 178 delete cursor 102 107 108 delete a point 113 114 Delete All Boundaries 107 delete all points within a selected region 113 Delete By Length 177 delete contour 219 delete contours 219 Delete control point 95 delete last contour 219 Delete last contour 219 220 Delete Line 107 Delete Lines By Plane 177 Delete Node 102 delete nodes
92. 9 See Figure Z Plane 27 Z Plane 27 When a new control point is Cancel added a control point mark red circle with a cross 1s displayed at its location m From Source To Destination 3 6 3 Move command Control Point submenu Use this command to switch to the Move mode for changing the location of an existing control point The cursor is changed to a Move Cursor in this mode To move an existing control point point at the mark hold down the left mouse button and drag to the new location This operation only changes the source location but the specified destination coordinates are not changed Use the Modify option to change the destination coordinates 3 6 4 Modify command Control Point submenu Use this command to switch to the Modify mode for changing the destination coordinates of existing control points The cursor is changed to a Cross Cursor in this mode To modify an existing control point point at the mark and click the left mouse button The Control Point dialog box will appear to allow changes to the coordinate values 3 6 5 Delete command Control Point submenu Use this command to switch to the Delete mode for deleting existing control points The cursor is changed to a Delete Cursor in this mode To delete an existing control point point at the mark and click the left mouse button The control point mark will disappear after it is deleted 3 6 6 Check command
93. 9 18 888476 10 brain 0 031021 1 136919 pixe 11 brain 0 137712 4 779604 pixe m N 14131 071192 470 609328 pixe 8 16 Surface Model Processing Commands 8 16 1 Crop Object command Tools Menu This command uses the currently entered measurement curve to crop all currently visible objects that intersect with the curve To make a measurement curve first change the orientation of a 3D surface model using the arrow keys so the region to be cropped is visible Move the cursor to a location and click the left mouse button to pick a location A point marker is displayed at the location Repeat this step to pick more points The 3D coordinates of the current point and the cumulative length is displayed in the status bar at the bottom of the window When you have entered all points for the measurement curve select the Crop Object command to crop the portions that s included by the measurement curve The cropping takes place in 3D space and it cuts into the object in the same direction as our viewing direction In other words it cuts straight into the computer screen using the current orientation of the visible objects 213 x SURFACE WINDOW COMMANDS After the cropping is completed the cropped object is displayed and the objects being cropped are made visible You can use the View Object command to make objects visible or invisible or change their display properties You can use the ESC Escape key to clear the current measurem
94. AND TUTORIAL 1 5 10 Toolbars oftware 3D File Edit View Image 3DRendering Window Help ite lt e 4 md mma kjo amp amp 9 4 ajulo ajap 5 e ial o At the top of the IMAGE PLANE WINDOW toolbars provide access to the more frequently used functions such as view controls editing tools and other functions If your cursor stops on a tool button for a few seconds a simple tool tip will appear to show you the command Turning on the specific editing mode can activate the toolbars Boundary Editor toolbars 5 2 aa ua a easuring Tool toolbars L3 e o ojojejeje Region of Interest ROI Tool toolbars Qal e 4 4 e Zooming and Rotating toolbars Brain Eo Brain Object List and Object Setting toolbar The drop down list allows you to quickly select one object and set it as current 35 OVERVIEW AND TUTORIAL 1 6 Getting Started 1 6 1 The Basics 3D DOCTOR is developed using object oriented technologies that make the software highly efficient to process and manipulate 3D images and other associated data items in an integrated environment 3D DOCTOR Work Flow see figure below l Open Image File Use the File New Stack command to put multiple slice image files into a 3D stack or the File Open command if multiple slices are stored in a sin
95. ARY PROCESS SUBMENU eere 177 6 3 4 REMOVE PLANE COMMAND BOUNDARY PROCESS SUBMENU esee nenne 177 6 3 5 DELETE HOLES COMMAND BOUNDARY PROCESS SUBMENU eere nene 178 6 3 6 DELETE ALL BOUNDARIES COMMAND BOUNDARY PROCESS SUBMENU 178 6 4 BOUNDARY SHAPE COMMANDS tasto seta sta seta sets eo seta setas etas etas tassa seta soa 178 6 4 1 CLOSE BOUNDARIES COMMAND BOUNDARY PROCESS SUBMENU eere 178 6 4 2 INFLATE COMMAND BOUNDARY PROCESS SUBMENU isses ener enne enne 178 6 4 3 DEFLATE COMMAND BOUNDARY PROCESS SUBMENU csssessecessececeeseecessneeecsesaeeeeseeeeens 178 6 4 4 ALIGN CENTERS COMMAND BOUNDARY PROCESS SUBMENU eere eene 178 6 5 BOUNDARY ORIENTATION COMMANDS ecce sees estes en sesso s tone tasso 179 6 5 1 REVERSE SLICES COMMAND BOUNDARY PROCESS SUBMENU cierre eene 179 6 5 2 FLIP VERTICAL COMMAND BOUNDARY PROCESS SUBMENU eerte ener 179 6 5 3 FLIP HORIZONTAL COMMAND BOUNDARY PROCESS SUBMENU ice eene 179 6 6 CUBE BOUNDARY COMMAND BOUNDARY PROCESS SUBMENU 179 6 7 HOLLOW OBJECT COMMAND BOUNDARY PROCESS 50 180 CHAPTER 7 3D RENDERING MENU en seen stent ta sets sess ta setas sena 181 7 1 3D WIZARD COMMAND 3
96. CE WINDOW 198 SURFACE WINDOW COMMANDS 8 6 Viewing Angle Commands View Menu Viewing angle can be adjusted using the mouse Hold down the left mouse button and move to rotate the object The mouse wheel is used to zoom in and out Hold down the right mouse button to move the object within the display window 8 6 1 Turn Right command Viewing Angle submenu Use this command to turn the current 3D object to the right 8 6 2 Turn Left command Viewing Angle submenu Use this command to turn the current 3D object to the left 8 6 3 Turn Up command Viewing Angle submenu Use this command to turn the current 3D object up 8 6 4 Turn Down command Viewing Angle submenu Use this command to turn the current 3D object down 8 6 5 Turn CW command Viewing Angle submenu Use this command to rotate the current 3D object clockwise 8 6 6 Turn CCW command Viewing Angle submenu Use this command to rotate the current 3D object counter clockwise 8 6 7 Setting command Viewing Angle submenu When the View Viewing Angle Setting command is selected a 3D Display Setting dialog box appears See Figure This dialog box allows you to interactively change the viewing angle of your 3D surface model 199 SURFACE WINDOW COMMANDS 8 7 Object command View Menu Use this command to change the object display properties such as color transparency ambient diffuse shine etc When the View Objec
97. COMMAND EDIT 119 3 14 SHORTCUT KEYS COMMAND EDIT 120 3 15 UNDO CAN T UNDO COMMAND EDIT MENU e eres eres eee enses sense tn seta setas ta sno 120 CHAPTER 4 VIEW MENU COMMANDS e eres eres enses etas tn asta seta setas stesse esse setas 121 4 1 TOOLBAR COMMAND VIEW MENU eere esten esee seen 122 4 2 EDIT BAR COMMAND VIEW MENU eere crees teen seen setenta sete sse tones tense toss enu 122 4 3 STATUS BAR COMMAND VIEW MENU 122 4 4 MONTAGE VIEW COMMANDS VIEW 123 4 4 1 MONTAGE VIEW COMMAND VIEW eene nnne nenne enne 124 4 4 2 ALL VIEWS COMMAND VIEW MENU tenen nennen nnne 124 4 4 3 FULL RESOLUTION COMMAND VIEW MENU isses ener enne enne rennen 125 7 TABLE OF CONTENTS 4 4 4 VERTICAL FLIP COMMAND VIEW 125 4 5 ZOOM IN COMMAND VIEW e eere ee seta setas etas 126 4 6 ZOOM OUT COMMAND VIEW MENU eese eee sees ette seats toss setas 126 4 7 FULL VIEW COMMAND VIEW cese eese eese te enean neto aetas etas e tasto seta seta sto 126 4 8 PREVIOUS PLANE COMMAND VIEW
98. COMMANDS 9 1 Volume File Commands 9 1 1 Open Volume command File Menu The File Open Volume command is accessible from the VOLUME VIEW WINDOW only Use the File Open Volume command to open a volume file created by the 3D Rendering Volume Rendering command The volume file vol is in binary format 9 1 2 Save Volume command File Menu The File Save Volume command is accessible from the VOLUME VIEW WINDOW only Use the File Save Volume command to save the current volume rendering data to a file The default volume file vol is in binary format 3D XYZ files xyz can be used to save the XYZ position of all voxels used in volume rendering Use the File Open Volume command to open a volume file 9 1 3 Save Stereo Pair command File Menu The File Save Stereo Pair command is accessible from the VOLUME VIEW WINDOW only Use the File Save Stereo Pair command to create a pair of images from the VOLUME VIEW WINDOW for stereo display When the Create Stereo Image Pair dialog box appears See Figure enter the Output Image File Name The letter L and R will be added to the name denoting the left and right images of the stereo pair If you need your output image to be a certain size you can Create Stereo Image Pair n x enter the Columns Width and Output Image File Name Rows Height The viewing angle between left and right Browse eyes Angle Between Image degree is normally set as 6 Dutpu
99. CT OPENPROJECT SAVEIMAGE SAVEIMAGEPLANE SETIMAGEPLANE GETPIXEL SETPIXEL SIZEIMAGEUP SIZEIMAGEDOWN ROTATEIMAGE RESLICE CROPIMAGE AUTOSEGMENT SEGMENTIMAGE IMAGEDIM OPENBOUNDARY SAVEBOUNDARY 227 3D BASIC COMMANDS DECONVNN DECONVMAX SURFSIMPLE SURFCOMPLEX and other commands are being implemented 3DBasic supports different variable types including INTEGER 32 bit long FLOAT 64 bit double STRING variable length text string and IMAGE3D a data container for 3D images boundaries and other data Following are some examples of often used 3DBasic programs Example for Image Segmentation LOGFILE c output log PRINT THIS IS A 3D SEGMENTATION EXAMPLE STRING FILENAME INTEGER X1 X2 Ad 51 2 186 1 INPUT Enter image file name FILENAME PRINT FILENAME OPENIMAGE imagel FILENAME AUTOSEGMENT imagel 2 SAVEPROJECT imagel c test prj SHOWIMAGE imagel PRINT FINISHED END Example for Simple Surface Rendering LOGFILE c output log PRINT THIS IS A SURFACE RENDERING PROGRAM STRING FILENAME IMAGE3D imagel INPUT Enter image file name FILENAME PRINT FILENAME OPENIMAGE imagel FILENAME REM Assuming boundary data has been generated OPENBOUNDARY imagel d test bnd SURFSIMPLE imagel d test suf CLOSEIMAGE image PRINT FINISHED END 228 3D BASIC COMMANDS Example for saving image slices to sep
100. Centers command Boundary Process submenu This command aligns the centers of boundaries to correct shifting caused by digitizing or by other circumstances While boundary locations will be moved based on the center location of their neighbor boundaries their shapes are not changed You 178 BOUNDARY PROCESS COMMANDS can use the Edit Boundary Editor to manually move boundary locations and change their shapes 6 5 Boundary Orientation Commands 6 5 1 Reverse Slices command Boundary Process submenu This command reverses the slice numbers of current boundaries The boundaries on the first slice will be moved to the last slice while the last slice is moved to the first slice This command is normally used to reverse the Z slice thickness direction for boundary data and therefore create an inverted 3D surface model by surface rendering 6 5 2 Flip Vertical command Boundary Process submenu This command flips the current boundaries vertically Use File Boundary Export to save boundaries to a file 6 5 3 Flip Horizontal command Boundary Process submenu This command flips the current boundaries horizontally Use File Boundary Export to save boundaries to a file 6 6 Cube Boundary command Boundary Process submenu This command defines rectangular boundaries for image slices The boundaries can be used for 3D Rendering functions Object Reports and Boundary Editor functions This command allows you to create bounda
101. D RENDERING 182 7 2 AUTO SEGMENT COMMAND 3D RENDERING 183 7 3 INTERACTIVE SEGMENT COMMAND 3D RENDERING MENU eere 184 7 4 SEGMENT OBJECT COMMANDS 3D RENDERING MENU e eeee eee ee nete ee enan 186 7 5 SURFACE RENDERING COMMANDS 3D RENDERING 0 188 10 TABLE OF CONTENTS 7 5 1 COMPLEX SURFACE COMMAND SURFACE RENDERING SUBMENU eerte 188 7 5 2 SIMPLE SURFACE COMMAND SURFACE RENDERING SUBMENU een 189 7 5 3 CONVEX SURFACE COMMAND SURFACE RENDERING SUBMENU eene 190 7 6 VOLUME RENDERING COMMANDS 3D RENDERING 191 7 6 1 SMOOTH RENDERING VOLUME RENDERING SUBMENU c ssesceeeessececeescececsnececeeaeeecssneeeeens 191 7 6 2 DIRECT VOLUME COMMAND VOLUME RENDERING SUBMENU 0 cccssseceesececeesteeeesseeeeeees 192 7 6 3 MULTIPLE COLOR RENDERING VOLUME RENDERING SUBMENU 193 7 7 SPLIT OBJECT COMMAND 3D RENDERING MENU cccscsssssssscscscscscssscssssssssesesens 194 CHAPTER 8 SURFACE WINDOW COMMANDS ccscssssscscssssssssccssscsssenecssecsscesecssesssessscssses 195 8 1 ADD MERGE MODEL COMMAND FILE 196 8 2 SAVE MODEL COMMAND FILE MENU ee eeeeee 196 8 3 EXPORT MODEL COMMAND FILE 196 8 4 CONTOURS COMMANDS
102. DS TOOLS eee esee eese ease ease tasto sno 215 S TTE SELECT COMMAND citu SR ne D an eH 215 8 17 2 NEW OBJECT COMMAND enne nennen tenes rentrer enters ren tene seen rennen enne 215 8 T7 3 DELETE COMMAND reist ess bliin ee A deret RES REQUE ERR 216 8 18 SURFACE CONTOUR COMMANDS TOOLS 217 8 18 1 CUT CONTOURS COMMAND SURFACE CONTOUR SUBMENU eerte eren 217 8 18 2 PLANE COLOR COMMAND SURFACE CONTOUR SUBMENU eee nennen enne 218 8 18 3 B SPLINE CONTOURS SURFACE CONTOUR SUBMENU iicet nennen nnne enne 218 8 18 4 CONTOUR COLOR SURFACE CONTOUR SUBMENU ssssssceeesececeeceececsnececeesaeeeceeeaeeeseneeeeneas 219 8 18 5 DELETE ALL CONTOURS SURFACE CONTOUR SUBMENU eerte enne nennen ener 219 8 18 6 DELETE LAST CONTOUR SURFACE CONTOUR SUBMENU eerte enne enne 219 8 18 7 DELETE CONTOUR SURFACE CONTOUR 0 219 8 19 3D POINTS COMMANDS TOOLS esee esee esee eese e esto neto setas etas e ense tuse ta sesso 220 8 19 1 DIGITIZE POINT TOOLS MENU 220 8 19 2 DELETE POINT TOOLS MENU 220 8 19 3 POINT REPORT TOOLS enne ener enne rennen nein nennen enne 220 CHAPTER 9 COMMANDS FOR VOLUME WINDOYWNV ee eeeeee esee ee seen s
103. Delete editing mode The Delete editing mode allows you to remove existing annotations The cursor will change to a Delete Cursor To remove a single annotation point the cursor within an annotation and click the left 117 EDIT MENU COMMANDS mouse button The annotation will disappear from the display window Repeat this step to delete other annotations To remove all annotations within a rectangle region hold down the SHIFT key and the left mouse button and drag the mouse to draw a rectangle When the region is selected release both the SHIFT key and the left mouse button Select the Delete option again from the floating pop up menu using the right mouse button or from the Annotation Editor submenu You can switch to another editing session by selecting a different option from the Annotation Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Annotation Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 12 3 Modify command Annotation Editor submenu This command switches to the Modify editing mode The Modify editing mode allows you to change the text of an existing annotation The cursor will change to a Cross Cursor during this editing session Point the cursor within an annotation and click the left mouse button The editing window will appear to allow you to modify the text Click outside the edit
104. E WINDOW use the Edit Object Settings command to turn it off Deleting an object will remove both the object group and all data associated with the object Boundary lines can be E gt Add image slices to the stack list Files should be added in the same order of edited or proces sed using the 3D sequence DICOM files can be sorted automatically o Cancel the Edit B oundary A Editor Save List c images3d HeadCTHalf HeadCT Ist Sort DICOM Files C Same Order No Sor menu or under the Add Files Add Folder went Delete By mage Position C Bylmage Number Edit Boundary Process DicamDir Preview Insert Ate Delete All Iv Split mage Series menu The boundary lines CXimages3dYHeadCTHeIN 1728337 C images3d HeadCTHalf 12283395 1 1 CAimages3diHeadCTHal 17283413 Sort By Name are organized as object 6 Vneges3 leedGTHONt 72847 Esse ie C images3d HeadCTHalf 1 7283449 Nol Files nine Stack 93 C images3d HeadCTHalf 172283467 groups for more effective C images3d HeadCTHalf 1 7283485 C images3d HeadCTHalf 1 7283503 management and more CAimages3dHeadCTHal 17283521 fl ibl b h C images3d HeadCTHalf 1 7283539 C images3d HeadCTHalf 1 7283557 ex1 e use y t e C images3dYHeadCTHalfi 17283575 C images3d HeadCTHalf 1 7283593 rendering functions C vmages3d HeadCTHelh 7283611 C images3d HeadCTHalf 17283629 CAimages3diHeadCTHalf 7283647 Cima leadCTHalfi 7283865 C images3d HeadCTHalf 1 7283683 Control p
105. EDIT MENU COMMANDS This command toggles the measuring tool on and off The v Measure On Off Measuring Tool is available to both the 2D IMAGE PLANE v Measure WINDOW and the VOLUME VIEW WINDOW Angle 2D Profile In the 2D IMAGE PLANE WINDOW the Measuring Tool Histogram supports the following options Measure Angle 2D and 3D 3D Profile Profiles and Histograms The options can be selected by using the main drop down menu or the floating pop up menu brought up by clicking the right mouse button The toolbars can also be used to select the options mt Ed ie In the VOLUME VIEW WINDOW created using the 3D Rendering Volume Rendering command the distance is calculated in 3D When measuring distance the line must be drawn on the object surface in order to get an accurate measurement 3 4 2 Measure command Measuring Tool submenu When the Measure option is toggled on use the mouse to draw a polygon or a polyline in the image window When you are finished press the key or press any other key to close the polygon Once the line is completed 3D DOCTOR will show the parameters related to this line or polygon in the Status Bar at the bottom of the IMAGE PLANE WINDOW The parameters include Length Area Volume Surface and Average and Variance of pixels in the polygon The pixel measurement values average and variance of pixel values are calculated only when the polygon is closed The Length of each line segment
106. ESSED IN THIS LICENSE ARE THE ONLY WARRANTIES MADE BY ABLE SOFTWARE AND ARE IN LIEU OF ALL OTHER WARRANTIES EXPRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO IMPLIED WARRANTIES OF MERCHANTABILITY AND OF FITNESS FOR A PARTICULAR PURPOSE THIS WARRANTY GIVES YOU SPECIFIED LEGAL RIGHTS AND YOU MAY ALSO HAVE OTHER RIGHTS WHICH VARY FROM JURISDICTION TO JURISDICTION SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION OR LIMITATION OF WARRANTIES SO THE ABOVE LIMITATIONS OR EXCLUSIONS MAY NOT APPLY TO YOU Term This License is effective as of the time Licensee receives the Software and shall continue in effect until Licensee ceases all use of the Software and returns or destroys all copies thereof or until automatically terminated upon the failure of Licensee to comply with any of the terms of this License 259 SOFTWARE LICENSE AGREEMENT General This License is the complete and exclusive statement of the parties agreement Should any provision of this License be held to be invalid by any court of competent jurisdiction that provision will be enforced to the maximum extent permissible and the remainder of the License shall nonetheless remain in full force and effect This License shall be controlled by the laws of State of Massachusetts and the United States of America Rider For U S Governmental Entity Users This is a Rider to the 3D DOCTOR for Windows SOFTWARE LICENSE AGREEMENT License and shall take precedence over the L
107. ETPIXEL imagel col row pix PRINT pixel col row pix NEXT END 239 3DBASIC COMMANDS 10 5 7 SETPIXEL statement This function sets a pixel value in the current plane of an opened image The image must be opened before this command is used To work on another image plane use SETIMAGEPLANE to set the plane as current first and then use this function Syntax SETPIXEL image col row value where IMAGE3D image INTEGER col row value the col and row defines the pixel location Example LOGFILE c output log IMAGE3D imagel INTEGER col row pix OPENIMAGE imagel cN3ddoctorviead3d tif SETIMAGEPLANE imagel 2 255 FOR col 20 FOR row 0 TO 20 SETPIXEL imagel col row pix NEXT END 10 5 8 SHOWIMAGE statement This command displays a currently opened image Syntax SHOWIMAGE imagevar where IMAGE3D imagevar Example IMAGE3D imagel OPENIMAGE imagel c 3ddoctor head3d tif SHOWIMAGE imagel END 240 3DBASIC COMMANDS 10 5 9 CLOSEIMAGE statement This command closes a currently opened image when it is no longer needed This will free up all memory allocated by the image Syntax CLOSEIMAGE imagevar where IMAGE3D imagevar Example imagel OPENIMAGE imagel c 3ddoctor head3d tif CLOSEIMAGE imagel END 10 5 10 SIZEIMAGEUP statement This command enlarges an image by a specified scaling factor For example if scaling factor is 2 then the
108. FILE MENU eese eee etes ette etes toss aetas etas ta seta seta soo 197 8 4 1 IMPORT CONTOURS COMMAND CONTOURS SUBMENU 197 8 4 2 EXPORT CONTOURS COMMAND CONTOURS SUBMENU ssssccceesecesesseecessseeeceeaeeeesseeeeeens 198 8 5 MOVE VIEWPORT COMMAND VIEW 198 8 6 VIEWING ANGLE COMMANDS VIEW 199 8 6 1 TURN RIGHT COMMAND VIEWING ANGLE 0 199 8 6 2 TURN LEFT COMMAND VIEWING ANGLE SUBMENU cce 199 8 6 3 TURN UP COMMAND VIEWING ANGLE SUBMENU eeeeererenneeren enne 199 8 6 4 TURN DOWN COMMAND VIEWING ANGLE SUBMENU ieeieeeeeeeeeeneeren nennen nennen enne 199 8 6 5 TURN CW COMMAND VIEWING ANGLE SUBMENU eere enne nnn rennen nnne 199 8 6 6 TURN CCW COMMAND VIEWING ANGLE SUBMENU cssssceceessececeeseecessnececeeaeeeeeseeeenens 199 8 6 7 SETTING COMMAND VIEWING ANGLE SUBMENU enne 199 8 7 OBJECT COMMAND VIEW MENU eee esee esee ee stessa stats toss aetas etas staat tasto soo 200 8 8 WIREFRAME COMMAND VIEW 202 8 9 IMAGE PLANES COMMAND VIEW 203 8 10 IMAGE SETTINGS COMMAND VIEW MENU eere ee etes enne enata aetas etas eta stiano 204 8 11 BACKGROUND COMMAND VIEW 205 8
109. GE MENU COMMANDS Crop 3D Image Volume Specify Range Crop Start End X Column 39 fi 97 Cancel Y Row 63 fi 25 2 Plane fo fi na C images3d 3dheadCrop ti Save As This command is often used to crop out a volume of interest from a bigger image sub volume is often smaller and requires less system resources to process 5 4 3 Crop ROI command Crop Image submenu This command is used to crop an image using the defined regions of interest ROI Image pixels inside or outside the regions of interest ROI can be changed to a constant color or linearly transformed using user defined parameters If your regions of interest ROI are drawn using the ROI Editing Tools the ROIs are applied to all image slices If the ROIs are derived from object boundaries using the Edi ROI ROI By Boundaries command then each image plane will be cropped by the ROIs within the plane Use the Browse button to define the output image file name If you need to save as DICOM you need to change the file extension to DCM The operation can be applied to image pixels either within the ROI or outside the ROI Choose an option to replace image pixels with a constant color or apply a scaling formula Use the Preview button to see how image will be changed after the processing If the image is a single plane image it is cropped in memory and can be saved using the File Save Save Image As command 146
110. Hit the SPACEBAR or select the Segment Current option to segment with the same training area or draw a new training area by clicking the left mouse button in the image The existing training area will automatically be removed when a new training area is defined Step 5 If the defined ROI and the training area are general enough for the entire volume image you can select Segment from the right mouse button pop up menu or from the 3D Rendering Segment Object submenu This command will apply the signatures generated from the training area to segment all image planes that have not been segmented If you want to remove the boundary lines from the current plane and restart the process use the Remove Plane command under the 3D Rendering Segment Object submenu or the floating pop up menu brought up by clicking the right mouse button 1 6 8 Registering Two Image Stacks and Creating a Fusion Image 3D DOCTOR provides the Image Registration command to geometrically transform or register a 3D stack image source image against another 3D image target image 49 OVERVIEW AND TUTORIAL using user defined control points The Registration command will create a new image from the source image that has the same orientation scale and dimension as the target image so they can fused or compared When you have two images from the same patient but acquired using different imaging devices for example a CT and MRI image of a head registerin
111. I I I PRINT I lt 10 I I I 200 1 1 1 PRINT gt I0 I I I END 10 4 12 FOR loop statement The FOR loop allows implementing sophisticated programs to repeat certain operations with different variable values Syntax FOR Control Variable Starting Value TO Ending Value Operations NEXT where the Control Variable will start with the Starting Value and run the program through the NEXT statement and then increment the Control Variable by 1 and repeat the operation until the Control Variable is the same as the Ending Value Example INTEGER I J FOR I 0 TO 100 PRINT J J NEXT END 235 3D BASIC COMMANDS 10 4 13 GOSUB and RETURN statements Same as the standard Basic the use of GOSUB and RETURN allows implementation of subroutines Syntax GOSUB Label Label Subroutine starts Subroutine body RETURN Example INTEGER I GOSUB 200 PRINT I I END 200 INPUT I RETURN 10 4 14 END statement This command indicates the end of the program Syntax END Example PRINT This is a test END 236 3DBASIC COMMANDS 10 5 Image Commands 10 5 1 OPENIMAGE statement This command opens an image or project file for processing It is similar to File Open function Syntax OPENIMAGE imagevar filename OPENIMAGE imagevar filename where IMAGE3D imagevar STRING filename Example IMAGE3D imagel OPEN
112. IMAGE imagel c 3ddoctor head3d tif SHOWIMAGE imagel END 10 5 2 SAVEIMAGE statement This command saves specified image planes to a file and both start and end plane are included The image must be currently open and the start and end planes must exist If the start plane is the same as the end plane then only this plane is saved This command is similar to File Save Image As command Syntax SAVEIMAGE imagevar filename startplane endplane SAVEIMAGE imagevar filename startplane endplane where IMAGE3D imagevar STRING filename INTEGER startplane endplane Example LOGFILE c output log IMAGE3D imagel OPENIMAGE imagel c 3ddoctor head3d tif SAVEIMAGE imagel c newfile tif 1 3 END 10 5 3 SAVEIMAGEPLANE statement 237 3DBASIC COMMANDS This command saves the current active image plane to a file An image plane can set active by using SETIMAGEPLANE command Syntax SAVEIMAGEPLANE imagevar filename SAVEIMAGEPLANE imagevar filename where IMAGE3D imagevar STRING filename Example LOGFILE c output log IMAGE3D imagel OPENIMAGE imagel cN3ddoctorviead3d tif SETIMAGEPLANE imagel 3 REM save image plane 3 to file SAVEIMAGEPLANE imagel c 3ddoctor plane3 tif END 10 5 4 SETIMAGEPLANE statement This command sets specified image plane as current for processing functions like GETPIXEL SETPIXEL and SAVEIMAGEPLANE The image plane number must exist Syntax SETIMAGEPLANE image planenum wh
113. Insert Location Before Slice f C After Slice 142 IMAGE MENU COMMANDS 5 3 6 Reslice X Axis command Reslice submenu This command is used to rotate the 3 D volume image around the X Axis to create a top view of the volume The new image is saved to an image file and the original image remains unchanged With this command you can easily overcome the limitation of an imaging device by cutting the image along a different axis Use the Image Reslice Reslice Y Axis command to create a side view of a volume image Use the File Open function to open the resliced image for processing and analysis 5 3 7 Reslice Y Axis command Reslice submenu This command is used to rotate the 3 D volume image around the Y Axis to create a side view of the volume The new image is saved to an image file and the original image remains unchanged With this command you can easily overcome the limitation of an imaging device by cutting the image along a different axis Use the Image Reslice Reslice X Axis to create a top view of a volume image Use the File Open function to open the resliced image for processing and analysis 143 IMAGE MENU COMMANDS 5 3 8 Reslice Volume command Reslice submenu This command is used to reslice or rotate a 3 D volume image at a defined angle After this command is selected the Rotate Volume Dialog box appears to allow the user to define the angle for reslicing See Figure The a
114. MMANDS IMAGE MENU eere esee ee eren en neto 157 5 9 1 FUSION COMMAND IMAGE FUSION SUBMENU esee eene 157 5 9 2 COLOR FUSION COMMAND IMAGE FUSION SUBMENU ssssceeeessececeeseecessneeeceesseeecssneeeeees 158 5 9 3 FOCUS FUSION COMMAND IMAGE FUSION SUBMENU sssccccessseeecesseececseeeeceesseeeeseneeenens 158 5 9 4 PLANE FUSION IMAGE FUSION 0 enne enne ner rennen 159 5 10 MOSAIC COMMAND IMAGE stia sts sets seas etas e eaae en 160 5 11 SMOOTH COMMANDS IMAGE MENU crece esee ee ette ente tons 161 5 11 1 MEDIAN FILTER COMMAND SMOOTH SUBMENU esee nennen eene entere enne 161 5 11 2 AVERAGE FILTER COMMAND SMOOTH SUBMENU eene nennen enne enne 161 5 11 3 DESPECKLE COMMAND SMOOTH SUBMENU cessere eene enne enne inneren enne 161 5 12 SHARPEN COMMAND IMAGE setas toss toss tna e en 161 5 13 PROCESS COMMANDS IMAGE MENDO eere sees seen stessa sos to netos etas e ease ease ease tasto sto 162 5 13 1 CLASSIFY COMMAND PROCESS SUBMENU eese ener ennt entente erinnern enne 162 5 13 2 NEGATE COMMAND PROCESS SUBMENU 16
115. Open command to open the aligned image file for display and processing The current image stack is not changed during the process If there is a strong correlation between image slices you can also use the Image Auto Alignment command to perform an automatic alignment of the image slices 152 IMAGE MENU COMMANDS 5 7 Tilt Correction command Image Menu This command is used to correct the image distortion caused by the gantry tilt during a CT scan Because of the tilted gantry the image slices are not perfectly perpendicular to the main axis See Figure below If the tilted image slices are not corrected distortion will be introduced in volume and surface rendering Image Slice This function uses the tilt angle stored in the DICOM header to compensate the tilt and generate image slices that are perpendicular to the main axis for segmentation and 3D rendering applications See Figure below If the corrected image appear to have more severe distortion the tilt angle may have a wrong sign You can reverse the sign 14 5 to 14 5 and correct the image again Image Slice 15 5 IMAGE MENU COMMANDS 5 8 Image Registration commands Image Menu 5 8 1 Register Image command Image Menu This command is used to interactively register the current image against a target image by adjusting the orientation location and scale The current image and the target image should have multiple slices Current
116. PLANES COMMAND OVERLAY SUBMENU ener en 134 4 13 11 NEIGHBOR BOUNDARIES COMMAND OVERLAY SUBMENU eene 134 4 14 SELECTION RECTANGLE COMMAND VIEW 135 4 15 CALIBRATED COORD COMMAND VIEW 135 CHAPTER 5 IMAGE MENU COMMANDS eerte eee eese e etna tn seta seta seta sete stesse esses etas e tassa 136 5 1 INFORMATION COMMAND IMAGE MENU eee 137 5 2 ROTATE COMMANDS IMAGE MENU eere ee eese eese te stans tons toss toss tas 138 5 2 1 VERTICAL FLIP COMMAND ROTATE SUBMENU eese eere 138 5 2 2 HORIZONTAL FLIP COMMAND ROTATE SUBMENU eese ener enne enne nennen 138 5 2 3 ROTATE COMMAND ROTATE SUBMENU cssssscecssseececseseecesaeeecsenaececseeeecesaeeecseaeeesseeeeens 138 5 2 4 TRANSPOSE COMMAND ROTATE SUBMENU cccsssscecseseeceessececsssaececseseeeseseeeeeneaeeeenneaeens 139 TABLE OF CONTENTS 5 3 RESLICE COMMANDS IMAGE eee esee eese 140 5 3 1 RESLICE COMMAND RESLICE SUBMENU eeeeeeereeenneee enne enne nennen inneren entere nnne nns 140 5 3 2 REVERSE SLICE COMMAND RESLICE SUBMENU esee enne 141 5 3 3 MOVE SLICES TO COMMAND RESLICE 0 141 5 3 4 DELETE SLICES COMMAND RESLICE SUBMENU ccssssseceessececsene
117. Plane Delete Plane Use Connectivity Next Plane Finish The current image window display is changed to show pixels within the Minimum and Maximum Threshold range as red and the rest of the image remains the same You can change the display color to other colors using the Color button Use the Min and Max scroll bars to increase or decrease the pixel range 184 3D RENDERING COMMANDS There are three different types of segmentation options Outline Only All Boundary Lines and Skeleton Boundary Use the Outline Only option to segment only outlines In this case no holes or islands will be kept Use the All Boundary Lines option to segment all possible boundaries including holes and islands Use the Skeleton Boundary option if you are interested in the skeleton of a structure in the image Once the thresholds are set for the current image plane click the Segment Plane button to extract object boundaries for this plane Boundary lines will be displayed in both the IMAGE PLANE WINDOW and the MONTAGE WINDOW if present You can remove the boundaries from the current plane using the Delete Plane Seg button If the regions within the selected threshold range look fragmented you can check the Smooth Image box to apply smoothing when the image is segmented You can use the Prev Previous Plane and Next Plane buttons to move to the previous or next image plane for segmentation Use the current thre
118. S The Cutting Plane command is used to define the cutting plane location for splitting object and cut surface contours After this command is selected the cutting plane is displayed in the 3D surface window The cutting plane is initially in the direction of facing the viewer perpendicular to the screen This direction will be fixed until you redefine the cutting plane by turning it off and on again Since the orientation of the cutting plane is selected based on the viewing direction it is recommended to adjust the object orientation first and then call this command You can use the Up Down arrow keys 7 to adjust the depth of the cutting plane Once the cutting plane is in the correct position you can use the Tools Split Object command to cut the object The split object is displayed while the original object is made invisible in the process You can use the View Object command to make objects visible or invisible or change their display properties The cutting plane can be defined and then used by the Surface Contour Cut Contours command 8 16 6 Refine Models Command Tools Menu This command enhances a surface model resolution by increasing the number of surface triangles Each triangle is split into 4 new smaller triangles The model is smoothed during the process You can use the View Object command to change the display properties 8 17 Select commands Tools Menu The select commands are used to select a portion that
119. ST COMMANDS VIEW MEND eee ee eee eene enne tassa seta setas ta seta ato 131 4 12 1 CONTRAST COMMAND IMAGE CONTRAST SUBMENU eese eene rennen enne 131 4 12 2 LOG SCALE COMMAND IMAGE CONTRAST SUBMENU csse nennen nennen 131 4 12 3 SQUARE ROOT SCALE COMMAND IMAGE CONTRAST SUBMENU eeeeeerenn eene 131 4 12 4 INTERPOLATION COMMAND IMAGE CONTRAST SUBMENU 131 4 13 OVERLAY COMMANDS VIEW MENU eee ee esee teet tese eost neto setas sense 132 4 13 1 IMAGE COMMAND OVERLAY SUBMENU csssssecesssseeceessececseceecesaeeecseseeessseeeensaeeeeeeeeeens 132 4 13 2 BOUNDARIES COMMAND OVERLAY SUBMENU cccsssseceeeesceceesaececeeeaecessnececnsaeeecsnneeens 132 4 13 3 BOUNDARY NODES COMMAND OVERLAY SUBMENU ccsssssecesssececeeseeeeeseeeeeeesaeeeeseneeees 133 4 13 4 BOUNDARY ENDS COMMAND OVERLAY SUBMENU cessere nennen nennen 133 4 13 5 POINTS COMMAND OVERLAY SUBMENU enne 133 4 13 6 CONTROL POINTS COMMAND OVERLAY SUBMENU eene enne ener entere 133 4 13 7 ANNOTATIONS COMMAND OVERLAY SUBMENU 222 133 4 13 8 OBJECT NAMES COMMAND OVERLAY SUBMENU csssssceeseeecesssececeesaececsnseeeesseeeeneaaeees 134 4 13 9 FILL BOUNDARIES COMMAND OVERLAY SUBMENU eere nennen 134 4 13 10 BOUNDARIES IN ALL
120. Single File command This command creates a header or configuration file to direct 3D DOCTOR to read a vendor proprietary image file format or raw image file This command provides a universal image reader capable of handling most uncompressed image file formats so you can bring your data directly into 3D DOCTOR for processing and rendering The Create Image Header File dialog box appears as follows Create Image Header File xj r Header File Name OK 3 441a hdr Cancel r Image File Name Save D images3d vhuman Hunter a_1 441 a raw Browse Step 2 Iv Little Endian parameters Image Configuration listed in the Photometric Display of Columns X 2048 of Rows Y 1216 dialog box C Min is White must be of Slices 2 f Bits Per Pixel 8 16 8 C Min is Black correctly i JEEE Number of Bytes To Skip Before Image Data enter or entered in 1 if not sure order for the software 0 read the image data correctly If you do not know the parameters you should contact the vendor or source where you received the file about those parameters 64 FILE MENU COMMANDS Enter the following parameters Bytes To Skip Image Data File Name Use the Browse button or enter directly the file name where the image data is stored Enter the file name exactly the way it appears because it is used by 3D DOCTOR to find the ima
121. T SUBMENU eese enne 94 3 6 3 MOVE COMMAND CONTROL POINT SUBMENU enne enne enne enne 95 3 6 4 MODIFY COMMAND CONTROL POINT SUBMENU nennen enne enne 95 3 6 5 DELETE COMMAND CONTROL POINT 0 95 3 6 6 CHECK COMMAND CONTROL POINT SUBMENU sssscceceesseceseeseecessececsesaecesseseeeneseeeenenaes 95 3 6 7 PICK POINT COMMAND CONTROL POINT SUBMENU ccce 96 3 6 8 OPEN CONTROL POINTS COMMAND CONTROL POINT SUBMENU eee 96 3 6 9 SAVE CONTROL POINTS COMMAND CONTROL POINT SUBMENU eene 96 3 6 10 CONTROL POINT DIALOG 97 3 7 BOUNDARY EDITOR EDIT neto toss ta seta seta seta sete sesto ase 98 3 7 1 MANUAL BOUNDARY TRACING COMMANDS cessent ener nennen nennen nter rennen reser nnns 99 3 7 1 1 Trace Boundary command Boundary Editor submenu eee 99 3 7 1 2 Draw Rectangle command Boundary Editor submenu eee 100 3 7 1 3 Draw Circle command Boundary Editor submenu eee 100 3 7 2 BOUNDARY NODE EDITING COMMANDS cicer nennen enne 101 3 7 2 1 Add Node command Boundary Editor submenu eee 101 3 7 2 2 Move
122. The View Image Palette Red command switches the current image palette to a red color palette Use the View Image Palette Define Palette command to define a customized palette for image display 4 11 3 Green command Image Palette submenu The View Image Palette Green command switches the current image palette to a green color palette Use the View Image Palette Define Palette command to define a customized palette for image display 4 11 4 Blue command Image Palette submenu The View Image Palette Blue command switches the current image palette to a blue color palette Use the View Image Palette Define Palette command to define a customized palette for image display 4 11 5 Gray Scale command Image Palette submenu The View Image Palette Gray Scale command switches the current image palette to a gray scale palette Use the View image Palette Define Palette command to define a customized palette for image display 4 11 6 User command Image Palette submenu The View Image Palette User command switches the current image palette to a user defined palette Use the View Image Palette Define Palette command to define a customized palette for image display 4 11 7 Next Palette command Image Palette submenu The View Image Palette Next Palette command changes the current image palette to the next available palette on the list 129 VIEW MENU COMMANDS 4 11 8 Define Palette command Image Palette submenu
123. U cessere 72 2 9 4 EXPORT POINT COMMAND BOUNDARY AND POINT SUBMENU cce 72 2 10 SPARSE POINTS IMPORT FILE ecce esee seta sete stes 72 2 10 1 DISPLAY COMMAND SPARSE POINTS IMPORT SUBMENU cccssseeceesssceceenececseseeeesseseeenses 73 2 10 2 POINTS TO SURFACE MODEL COMMAND SPARSE POINTS IMPORT 0 73 2 10 3 POINTS CONTOURS COMMAND SPARSE POINTS IMPORT 0 74 2 10 4 POINTS TO IMAGE COMMAND SPARSE POINTS IMPORT SUBMENU 2 74 2 11 3DBASIC FILE MENU 4e eee eese eerte to setas toss toas ease 75 2 12 SELECT SCANNER COMMAND SCAN 50 76 2 13 SCAN COMMAND SCAN SUBMENU eee reset teer ee ees eo neto setas setas 76 2 14 PRINT FILE MENU et 76 2 14 1 PRINT SCREEN COMMAND PRINT 0 76 2 14 2 PRINT WINDOW COMMAND PRINT SUBMENU cccessssceceesececseeeecessneeeeneaeeecseseeeesseseeenes 76 2 15 PROJECT LIST FILE ssesesssesessesseseosoesessossesoessesoesoesessossesoessesoesoesessossessossesoessesessossee 77 2 16 1 2 3 4 COMMAND FILE MENU esee esee ta seta sete 77 217 EXIT COMMAND
124. X ray images 3D reconstruction 164 XYZ 23 221 Z Zoom In 126 INDEX Zoom Out 126 269
125. Y imagel c sizeview tif END 242 3DBASIC COMMANDS 10 5 13 CROPIMAGE statement This command crops a sub volume from an image and save the volume to a new image file This command is similar to Image Crop Volume command Syntax CROPIMAGE imagevar filename x1 x2 yl y2 7172 CROPIMAGE imagevar filename x1 x2 yl y2 7172 where IMAGE3D imagevar STRING outputfile INTEGER x1 x2 y1 y2 z1 Z2 defines the volume Example IMAGE3D imagel OPENIMAGE imagel c 3ddoctor head3d tif CROPIMAGE imagel cNcrop tif 10 50 10 50 1 15 END 10 5 14 RESLICE statement This command reslices or rotates a volume image along a defined direction and saves the volume to a new image file This command is similar to Image Reslice Volume command Syntax RESLICE imagevar filename xAngle yAngle zAngle RESLICE imagevar filename x Angle yAngle zAngle where IMAGE3D imagevar STRING filename FLOAT xAngle yAngle zAngle defines the angle Example imagel OPENIMAGE imagel c 3ddoctor head3d tif RESLICE imagel c 3ddoctor votate tif 90 0 0 0 0 0 CLOSEIMAGE imagel OPENIMAGE imagel c N3ddoctorvotate tif SHOWIMAGE imagel END 243 3DBASIC COMMANDS 10 5 15 SMOOTHAVE statement This command smooths a volume image using the low pass averaging filter and saves the processed image to a new image file Syntax SMOOTHAVE imagevar filename SMOOTHAVE imagevar filename where IMAGE3D imagevar STRING
126. a new model Other 3D data file formats include AutoCAD DXF STL 3DS and ASCII raw triangle file The Raw Object file is in ASCII format with one line at the beginning of the file specifying the name of the object and each following line specifying one 3D triangle face Each triangle face has 3 points x y z for the 3 corners If you need to access the 3D surface data directly from your own program this raw format may be the simplest to read and write A surface file contains 3D surface data created from the surface rendering commands The surface file is in binary format and is used internally by 3D DOCTOR If you need to export the 3D data to other systems you can use the File Export Model command For a complete list of 3D data file formats supported by 3D DOCTOR for import and export refer to Section 1 3 3 3D DOCTOR Main Functions 8 2 Save Model command File Menu This command can be accessed from the 3D SURFACE WINDOW only Use this command to save surface model data to a surface model file suf A surface file contains 3D surface data created from the surface rendering commands The surface file is in binary format and is used internally by 3D DOCTOR If you need to export the 3D data to other systems you should use the File Export Model command 8 3 Export Model command File Menu This command can be accessed from the 3D SURFACE WINDOW only The File Export Model command exports the triangular 3D surface data t
127. age Planes command View Menu This command turns on and off the image plane display in the surface window See Figure When the original image planes are displayed the command is checked in the menu If you need to change the display properties such as transparency mode and choose individual planes for display then use the View Image Settings command If you need to change the size location or orientation of an object you can use the View Object command to do so E 3D Surface ct pelvis prj 203 SURFACE WINDOW COMMANDS 8 10 Image Settings command View Menu This command allows you to change the display properties Image Plane Properties of image planes An Image Image File Plane Properties dialog box P images3d ctpelvs t appears with the current display settings See Figure The Image File field shows the current image source Ep You can use the Change button switch to a different image to displayed the 3D Image Display Move By tn B m 0 EG Resolution 1 2 M n4 SURFACE WINDOW E Transparent Opaque On OK Off Cancel The Display field shows the display status of each image plane The On status indicates a plane is visible while the status hides it To turn one or more image planes on or off select them first in the list then click the On or Off buttons to change the status di
128. age data correctly If you do not know the parameters you should contact the vendor or source where you received the file about those parameters Enter the following parameters 66 FILE MENU COMMANDS Non Standard Image Data Files Use the Add Files button to add more data files to be imported to the list Make sure the files are added in the same order as they exist in the volume image When the file Open dialog box appears you can select multiple files by holding down the SHIFT key and the left mouse button The file Open dialog box has a limit on the number of files to be selected so don t select too many files each time Bytes To Skip List File Name Use this button to define an image stack list file name to save the list of the files to be imported If the list file name is not defined then only header files are created Number of Columns This field refers to the number of pixels in the X or column direction in one image plane or Planes 2 slice Number of Rows This field refers to the number of pixels in the Y or row direction in one image plane or slice Number of Image Planes or Slices This is the number of image planes or slices in the file Number of Bits Per Pixel This tells the size of each image pixel If the number of bits is 8 then each pixel is one byte in size and can store up to 256 levels If the number of bits is 16 then each pixel has 2 bytes of data and can store up to 65536 l
129. agel 4 SAVEPROJECT imagel c 3ddoctor head3d prj SHOWIMAGE imagel END 10 7 2 OPENPROJECT statement This command opens a project file and stored object boundaries and other associated information into an IMAGE3D variable This command is similar to File Open command Syntax OPENPROJECT imagevar filename OPENPROJECT imagevar filename where IMAGE3D imagevar STRING filename Example IMAGE3D imagel OPENIMAGE image c 3ddoctor head3d tif OPENPROJECT imagel c 3ddoctor head3d prj SURFSIMPLE imagel c 3ddoctor head3d suf SHOWIMAGE imagel END 248 3DBASIC COMMANDS 10 7 3 OPENBOUNDARY statement This command loads object boundary data into an IMAGE3D variable from a boundary file This command is similar to File Import Boundary command Syntax OPENBOUNDARY imagevar filename OPENBOUNDARY imagevar filename where IMAGE3D imagevar STRING filename Example IMAGE3D imagel OPENIMAGE imagel c 3ddoctor head3d tif OPENBOUNDARY imagel c 3ddoctor head3d bnd SHOWIMAGE imagel END 10 7 4 SAVEBOUNDARY statement This command saves object boundary data into a boundary file This command is similar to File Export Boundary command Syntax SAVEBOUNDARY imagevar filename SAVEBOUNDARY imagevar filename where IMAGE3D imagevar STRING filename Example IMAGE3D imagel OPENIMAGE imagel c 3ddoctor head3d tif SEGMENTIMAGE imagel 50 189 0 SAVEBOUNDARY imagel
130. alysis 3D DOCTOR s Image Auto Alignment command uses a maximum likelihood algorithm to align slices automatically and accurately across the stack The following are the steps for Auto Alignment Section 5 7 Auto Alignment command Step 1 Open the 3D image If each image slice or plane is stored in a separate file use the File New Stack command to create a 3D stack list Step 2 Define an image region using the left mouse button An image region is an area with strong contrast visible patterns and variations Step 3 Select the Image Auto Alignment command When this command is started the Auto Image Alignment Dialog box will appear Adjust the matching parameters if needed and define an output file name Select OK to start the process A properly aligned image is created and saved as a new image file Step 4 Use the File Open command to display the new image file 55 OVERVIEW AND TUTORIAL 1 6 14 One Step 3D Image Deconvolution Image deconvolution is used to remove or reduce degradations caused during the imaging process These include the blurring introduced by optical systems and by image motion as well as noise due to electronic and photometric sources 3D DOCTOR provides two types of deconvolution to restore degraded 3D images one is a Fast Nearest Neighbor deconvolution and the other is an iterative Maximum Entropy deconvolution method Although the deconvolution process is quite complex 3D DOCTOR provides a
131. am name 3dbasic flag indicates a 3DBasic script is provided in the file specified by the next parameter d surfsimple bas To use an image and start 3D DOCTOR use the following command 3ddoctor f d Nmagestack lst Or 3ddoctor f dN NDICOMDIR To create rendering from boundary data use the following formats 3ddoctor simple i d Ncontours bnd o d Nsimpsurf suf Where 3ddoctor is the program name simple indicates using the simple surface rendering method i flag indicates a boundary file for input while the o for the output 3D surface file 3ddoctor complex i d contours bnd o d Ncompsurf suf Where 3ddoctor is the program name complex indicates using the complex surface rendering method i flag indicates a boundary file for input while the o for the output 3D surface file 57 FILE MENU COMMANDS File menu commands Open and save data files inclucing images boundary knes pohgons points and mockls in 3D DXF STL VRML OB IGES With commands under the File menu you can e Open an image file for display and processing e Save an image to a file in any 3D DOCTOR supported format e Create a stack list to handle a 3D image stored in multiple files e Import raw or non standard image data files by creating header files e Import 3D sparse point data and create 3D volume images for processing e Save generated data to a 3D DOCTOR project file e Import and export object boundary and point fil
132. an switch to a different editing session by selecting another option from the Boundary Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Boundary Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 106 EDIT MENU COMMANDS 3 7 7 Boundary Delete Commands 3 7 7 1 Delete Boundary command Boundary Editor submenu Use this command to delete an existing boundary line The cursor will change to a Delete Cursor Point the cursor at a location that is close to the line to be deleted and click to remove the line The system will always remove the closest line to the location clicked When deleting a line try to be as close as possible to avoid deleting the wrong line If you need to delete a group of boundaries within a region you can hold down the SHIFT key and the left mouse button to draw section rectangle for the region Choose this command Delete Boundary from the main menu or the popup edit menu to delete Use the Edit Undo command to recover a line previously deleted You can switch to a different editing session by selecting another option from the Boundary Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Boundary Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 7
133. and The View Overlay Annotations menu item is checked when annotations are displayed The menu item is grayed out if no annotations are detected 4 13 8 Object Names command Overlay submenu The View Overlay Object Names command toggles on and off the user defined object names This option is for display only and it will not affect any data or processing Objects can be added using the Edit Object Setting command The View Overlay Object Names menu item is checked when object names are displayed The menu item is grayed out if no object names are detected 4 13 9 Fill Boundaries command Overlay submenu The View Overlay Fill Boundaries command toggles the boundary fill mode on and off When this option is on a hatch pattern defined for an object is used to draw the region enclosed in the object boundary 4 13 10 Boundaries In All Planes command Overlay submenu By default only boundaries related to the currently active image plane are displayed in the IMAGE PLANE WINDOW The View Overlay Boundaries In All Planes command resets the default so boundaries on all image planes can be displayed in the IMAGE PLANE WINDOW This command toggles this option on and off 4 13 11 Neighbor Boundaries command Overlay submenu By default only boundaries of the current image plane are displayed in the window The View Overlay Neighbor Boundaries command displays the boundaries in the previous and next image plane This co
134. and Boundary and Point submenu This command reads point data from a point file in the PNT or XYZ format The point data loaded is automatically put into the current object 2 9 4 Export Point command Boundary and Point submenu This command saves currently active point data in the IMAGE PLANE WINDOW to a point file You can use either the PNT format or XYZ format Point data in all active objects are saved to the point file You can turn off the objects temporarily using Edit Object Settings if their data do not need to be exported 2 10 Sparse Points Import File Menu This command can be accessed from the IMAGE PLANE WINDOW the MONTAGE WINDOW the 3D SURFACE WINDOW and the VOLUME VIEW WINDOW 72 FILE MENU COMMANDS 2 10 1 Display command Sparse Points Import submenu The File Sparse Points Import Display command brings up the file Open dialog box This command allows you to display the 3D points directly in a window The viewing angle can be adjusted as well as color shape and other attributes If the XYZ points have a value field the points will be displayed using a spectrum color palette to reflect the value range Use the View Overlay Point Color command to change or adjust the colors used for point display 2 10 2 Points To Surface Model command Sparse Points Import submenu Use this command to convert a data set of 3D sparse points to a 3D surface model for 3D modeling and rendering 3D sparse points
135. and islands are not important 6 3 6 Delete Boundaries command Boundary Process submenu The Edit Boundary Process Delete All Boundaries command will delete all boundaries that are currently active in all of the image planes 6 4 Boundary Shape Commands 6 4 1 Close Boundaries command Boundary Process submenu This command checks all active boundaries and closes open ended boundaries 6 4 2 Inflate command Boundary Process submenu This command inflates the current object boundaries by a user defined distance in pixel unit The Edit Boundary Process Inflate command is often used to increase the size of boundary lines generated from the 3D Rendering Interactive Segment functions for different rendering uses 6 4 3 Deflate command Boundary Process submenu This command deflates the current object boundaries by a user defined distance in pixel unit The Edit Boundary Process Deflate command is often used to decrease the size of boundary lines generated from the 3D Rendering Interactive Segment functions for different rendering uses Boundary lines generated from segmentation are normally right on the edge of an object When performing a Volume Rendering the edge pixels are used in the display and often vary quite significantly from one slice to another Using the Deflate command to deflate the boundary line by a small amount will greatly improve the quality of the volume rendered image display 6 4 4 Align
136. and to change the color of lines for each object or turn some objects on and off the display If lines are turned off from the active object set they will not be used in the rendering process You can use the 3D Rendering Surface Rendering commands to create 3D models and calculate the volume for all of the objects You can use the Edit Object Report or Edit Boundary Report commands to get statistical reports for boundaries and objects 6 1 3 Merge Boundaries command Boundary Process submenu This command merges overlapped boundaries Overlapped boundaries that belong to the same object can be merged with the Edit Boundary Process Merge Boundaries command You can use the Edit Object Manipulation command to combine multiple object boundaries into one and then merge the overlapped ones 175 BOUNDARY PROCESS COMMANDS 6 2 Smooth Boundary Commands 6 2 1 Reduce Nodes command Boundary Process submenu When this command is selected the Reduce Mann x Reduce Nodes dialog box appears See Figure The Edit Boundary Enter Threshold Proces Reduce Nodes command n performs a global smoothing to remove Apply extra nodes within a specified threshold The Threshold is a distance in pixels between a node and its line When the C Alllmage Planes distance between a node and its line is less than the threshold the node is removed from the line Current Image Plane OK Cancel di
137. anned you can use the Image Crop Image Crop Film command to separate the slices and use the File New Stack command to put slices into a stack for 3D rendering and visualization applications To acquire a new image document 1 Under the File menu click Scan 2 Follow the instructions on the screen See your scanner or camera documentation for more scanner specific information 3 The scanned image will be displayed in an IMAGE PLANE WINDOW for cropping and processing 2 14 Print File Menu Under the File Print menu a number of options are available You can adjust your print setup Print Setup you can preview an image or other data file Print Preview you can print your images or data files Print you can print an entire 3D DOCTOR screen Print Screen and print a 3D DOCTOR window Print Window 2 14 1 Print Screen command Print submenu Use this command to print a screen dump on your default printer Make sure the printer is turned on and set up properly before using this function 2 14 2 Print Window command Print submenu Use this command to print the current active image window on your default printer Make sure the printer is turned on and set up properly before using this function 76 FILE MENU COMMANDS 2 15 Project List File Menu This command displays a list of recently created projects Every time you save a project file an entry is added to the list 3D DOCTOR Project List
138. ar Measure command to clear the current measurement curve before starting another measurement 8 15 3 Measure Angle Tools Menu This command switches on and off the 3D angle measurement tool It allows measuring angle a 3D surface model After the tool is switched on click 3 points on the surface model to form an angle for measurement The measured angle is then displayed 8 15 4 Set As Contour command Tools Menu Use this command to turn the current measurement curve into a contour so you can export to a file and perform further analysis See the previous section for more details on how to create a measurement curve 212 SURFACE WINDOW COMMANDS 8 15 5 Contour Report Command Tools Menu drea 3D DOCTOR Report 3D DOCTOR R t 3D DOCTOR Report dialog box Surface Contour Report Included in the report are the Area Length Contour Object Name Area unit Copy Number of Nodes and 0 brain 13506 446421 657 748596 pixe Center X Y Z location 1 brain 30 361274 28 961577 Print of all existing surface 2 brain 2 644976 9 416413 pixe contours See Figure 3 brain 6 938850 20 827115 pixe Save 4 brain 0 714814 7 959492 pixe The calculations use the 5 brain 1 790897 8 863716 pixe same scale and unit as 6 brain 1 970970 11 170018 the surface models from 7 brain 2 247591 10 044805 pixe which the surface 8 brain 5 502844 13 727270 pixe contours are generated 9 brain 14 20966
139. arate image files LOGFILE c output log INTEGER X STRING FILENAME NAME1 NAME IMAGE3D imagel NAME testimg INPUT Enter image file name FILENAME PRINT FILENAME OPENIMAGE imagel FILENAME REM saves image slice 1 to 10 to files testimagel to testimage10 FOR X 1TO 10 NAME NAME X PRINT NAMEI SAVEIMAGE imagel X X NAMEI NEXT END 10 4 3DBasic General Commands 10 4 1 REM statement This command indicates that the entire line following REM is only comment and will not affect the program execution Syntax REM comment text Example REM this is a sample comment REM PRINT This REM the above line will do nothing 10 4 2 LOGFILE statement This command defines the output file where it stores all information generated by the PRINT command Besides the PRINT command all error messages will also be saved to the log file Syntax LOGFILE c output log 229 3D BASIC COMMANDS LOGFILE outputname where STRING outputname This command can be used more than once in a program to define different log files for PRINT output 230 3D BASIC COMMANDS 10 4 3 INTEGER statement INTEGER is used to declare integer variables Syntax INTEGER I J K1 where I J and K are the names of integer variables An integer variable is 32 bit long and must be declared before it used in the program Example LOGFILE c output log INTEGER I J Ij 25 1 101 PRINT 1 J J END
140. asily 155 IMAGE MENU COMMANDS Step 2 For the source image select the Edit Control Points On command and switch to the New editing mode For the target image select the Edit Control Points On command and switch to the Pick Point mode Step 3 Go to the target image and move to an image slice where you can identify a point in both the source image and the target image For example the tip of the nose Move the cursor to the identified location and click the left mouse button red cross is displayed to show the point is picked up from the target image Step 4 Now move back to the source image and display the image slice where the identified point is located Move the cursor to the position and click the left mouse button in the source image to add a control point at this location The control point definition dialog box appears On the left From side the values of column row and plane are obtained from the source image The values on the right side To are the coordinates from the target image picked up in Step 3 Step 5 Repeat Step 3 and Step 4 until you have at least 4 control points for the source image Normally you should define more than 4 control points Make sure the control points are spread out within the volume They must not all be in a single image slice Step 6 Select the Image Registration command Enter the parameters required the output file name and the dimension of the output image use the same as th
141. ata directly into 3D DOCTOR for processing and rendering Step 2 All parameters listed in the dialog box must be correctly entered in order for the software to read the image data correctly If you do not know the parameters you should contact the vendor or source where you received the file to obtain these parameters The figure below shows how the parameters correspond to data stored in an image file 42 OVERVIEW AND TUTORIAL Enter the following parameters 1 Non Standard Image Data Files Multiple Files Use the Add Files button to add the data files to be imported to the list Make sure the files are added in the same order as they exist in the volume image When the file Open dialog box appears you can select multiple files by holding down the SHIFT key and the left mouse button The file Open dialog box has a limit on the number of files to be selected so don t select too many files each time Header files will be created when the button is pressed for all the data files Each data file will have a corresponding header file If the configuration is different from data file to data file then you should use the File Raw Image File Import Single File command to create header files for each individually Planes Z 2 List File Name Multiple Files Use this button to define an image stack list file name to save the list of the files to be imported If the list file name is not defined then o
142. ate Boundary mode The cursor will change to a Rotate Cursor Point the cursor at a boundary and hold the left mouse button down to rotate the boundary around its center When the boundary is rotated to the desired location release the left mouse button to confirm it Repeat this process to move another boundary To undo the previous edit use the Edit Undo option or CONTROL Z Use the function keys F5 or F6 to go to another image plane for more editing You can switch to a different editing session by selecting another option from the Boundary Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Boundary Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 103 EDIT MENU COMMANDS 3 7 3 3 Mirror Vertical Horizontal command Boundary Editor submenu Use this command to mirror a boundary vertically or horizontally This command is often used together with the Copy Boundary and the Move Boundary commands to create symmetrical boundaries The cursor will change to a Vertical Horizontal Mirror Cursor while in this editing mode To mirror a boundary line vertically or horizontally point the cursor at a line and then click the left mouse button to mirror it You can switch to a different editing session by selecting another option from the Boundary Editor submenu or from the floating pop up menu brought up b
143. ate By Y Axis 51 image sharpen 161 IMAGE3D 232 IMAGEDIM 239 Import Contours 197 Import non standard image file 41 import 3D sparse points 73 74 inflate boundary 178 INPUT 234 Installation 15 INTEGER 231 Interactive segment 22 Interactive Segment 191 192 247 Interfile 41 Interpolation 132 JPEG 37 40 59 61 63 JPEG DICOM 63 K keyboard 120 Keyboard 33 keyboard accelerators 120 keyboard shortcut keys 120 L label a point 113 Length Distance 34 License Agreement 258 List Files of Type 62 Log Scale 131 LOGFILE 229 loop control 209 lst stack list file 60 M Map pixel values 93 Map Pixel Values 163 mark 3D locations 113 material property 200 maximum entropy 171 Measure Distance 34 Measure 2D 88 Measure 3D 88 212 measure 3d object 213 Measure angle 89 measure profile 90 265 measurements 25 Measuring Tool 88 Median filter 161 merge boundaries 106 merge overlapped boundaries 175 minimum system requirements 17 Mirror boundary 104 Mirror vertical 104 Mirror vertical horizontal 104 model select 215 Modify control point 95 montage from images 160 montage window 19 29 mosaic images 160 Mouse 33 move cursor 101 move a point 113 Move boundary 103 move by object 208 Move control point 95 Move Node 101 Move Section 101 move slices 141 Move Viewport 198 multiple file stack 40 multiple image files 40
144. ber of foreground objects This command works with both color and grayscale images The segmentation algorithm is texture based and can separate up to 256 objects The segmentation command processes within the regions of interest ROD if they are present If you need to define certain regions to be processed instead of the entire image then use the Edit ROI Tools to define regions of interest before this command is called After you call the command a dialog box appears to ask you to enter the number of objects to be extracted This number should be determined based on the image For example if you see that an image may have 5 objects that show distinguishable texture and color you can enter 5 to start the segmentation You can use increase the number to divide objects into smaller regions or decrease the number to combine smaller regions into larger ones New objects are created from this process Use the Edit Object Settings command to rename or change their display status The boundary lines can be edited using the Edit Boundary Editor options Use the File Boundary and Point Export Boundary command to save boundary data to a file The boundary lines can be processed using commands under the Edit Boundary Process submenu 183 3D RENDERING COMMANDS 7 3 Interactive Segment command 3D Rendering Menu Use this command to do an interactive segmentation of the current 3D image to extract object boundaries The boundaries created
145. ce around until it is properly aligned with the previous slice To let the software align the current slice automatically click the right mouse button to show the tool menu and select the Auto Align option After the slice is aligned you still use the Move Slice and Rotate Slice to adjust manually If you need to rotate the image slice click the right mouse button to bring up the floating popup menu Select the Rotate Slice tool To rotate the slice simply hold down the left mouse button and move within the image to rotate Once the image slice is aligned release the left mouse button to confirm Use the F5 and F6 function keys to move to the previous and next plane to continue the alignment process Repeat Step 2 and 3 to align all image slices Even though the slices appear to be aligned at this point the alignment is for display only and the current image stack is not changed You ll need to follow the next step to save the aligned image stack to a new file for further processing 151 IMAGE MENU COMMANDS 6 Once all slices are properly aligned click the right mouse button to bring up the popup menu and select the Save Aligned Image command to save the results to a new image file The Save As dialog box will appear and you can enter the file name that is going to be used to store the new aligned image Click the button to start the alignment process When the process 15 finished use the File
146. ce rendering image or measuring a special image area In the following sections detailed steps will be given to explain how certain tasks are done Each type of graphical data such as images boundary lines point markers annotations and control points is treated as a layer in the main IMAGE PLANE WINDOW Once an image is opened in 3D DOCTOR an image plane is displayed in the IMAGE PLANE WINDOW while other planes are organized and displayed in the MONTAGE WINDOW You can double click in a plane in the MONTAGE WINDOW to switch the display to the corresponding image plane The following flow chart shows the steps needed to open a 3D image A 3D image can be stored as a single 3D file such as TIFF or 2D slices in various formats such as DICOM TIFF JPEG BMP PNG or a vendor proprietary format Additionally separate 2D image slices can be compiled into a 3D stack to create a single stack list file to access all image slices 37 OVERVIEW AND TUTORIAL Open Image File Slice format file Dicom slice image Unknown T Tiff slice image format 3D tiff file Bmp slice image image 2D header file USE Eile New USE Eile Baw Stack Image File Import command command Add slice Define image image to list file header file parameters Create list file Create header file 3D or 2D header file Open 3D tiff file Open 3D list file Open 3D header file USE File Open 2D slice and montage display
147. check the Little Endian box to set it as big endian Header File Name Use this field to enter a header file name to save the configuration parameters 3D DOCTOR will use this file name to read your image If you want to copy or edit all the information from an existing header file use the Browse button to open the existing header file All parameters will be read in for you to modify Step 3 Select to save all the information to the header file You are now able to work with your image data by using the File Open command and selecting the header file type hdr 65 FILE MENU COMMANDS 2 4 2 Multiple Files command Raw Image File Import submenu This command creates header or configuration files for a 3D image stack stored in multiple data files This allows 3D DOCTOR to read raw or non standard image files This command provides a universal image reader capable of handling most uncompressed image file formats so you can bring your data directly into 3D DOCTOR for processing and rendering The File Raw Image File Import Multiple Files command is used to create headers for a group of image data files which belong to a 3D volume image When creating headers for multiple files an image stack list file lst can be created as well Section 1 6 2 Creating a 3D Stack from 2D Image Slices which will be used by 3D DOCTOR to open the 3D image When an image file is not directly supported by the File Open command
148. click the left mouse button to set it You can switch to a different editing session by selecting a different option from the Point Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Point Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 10 7 Done command Point Editor submenu Use this command to exit from the Point Editor 115 EDIT MENU COMMANDS 3 11 Point Report command Edit Menu This command generates a report for all currently active points The report shows the Number of Points based on groups all points objects and image planes The information can be used for counting objects and can be brought to a spreadsheet program for analysis or plotting Report Window E x Statistical Report of Points Total Number Active Points 28 Number of Points by Object Object Count default 0 head 0 brain 28 Number of Points by Image Plane Plane _ Count n 00 4 m E x 116 EDIT MENU COMMANDS 3 12 Annotation Editor Edit Menu Use the Edit Annotation Editor On Off command to start the Annotation Editor tool With the Annotation Editor you can add new annotation items delete annotations modify existing annotations and convert an annotation to boundaries At the start of the editing a Font dialog box appea
149. command to create a Gaussian function based synthetic point spread function if getting an experimental PSF for an imaging device is difficult The Number of Iterations parameter needs to be specified in the dialog box The larger the number of iterations the longer the processing will take Because this algorithm performs iterative deconvolution to get the highest restoration quality it often is time consuming depending on the image size and your system performance The Feedback Factor 1 100 parameter needs to be specified in the dialog box The feedback factor is in the scale of 1 to 100 The larger the feedback factor the stronger the deconvolution that will be applied during each iteration However if the original image is noisy a smaller feedback factor should be used to reduce the noise The deconvolution functions require significant amounts of system memory because both the source image data and the PSF image are loaded in memory Since a Fourier transform is used for both the source image and the PSF additional memory is required for the processing A simple way to estimate the amount of memory required for this operation is to take the uncompressed file size of the source image or the PSF image whichever is bigger and multiple the size by 12 to get the required amount For example if your image size is IMB then 12MB is what it requires for this processing This is only a rough estimation and sometimes more memory may be nee
150. crop a region first define a x rectangle in the image by holding down the left mouse button and dragging Once the Left Right 197 rectangle is defined select the Image Crop Image Crop fes Bottom 125 Region command from the menu and the Crop Image Confirm or change crop rectangle Region dialog box appears m Result Image Dimension See Figure This dialog box URINE Columns La allows you to adjust the range E of the region and the FE 55 dimensions of the cropped p image If you are cropping subsections from a scanned film and going to use the sections to form a stack it is very important to crop all of the slices the same size for 3D visualization and analysis To keep using the selection rectangle for another region simply move your cursor within the rectangle hold down the left mouse button and move the rectangle to a new location Release the left mouse button to confirm 5 4 2 Crop Volume command Crop Image submenu This command is used to crop a sub volume from the current image and save the new image to a file To crop a volume first define a 2D image region by holding down the left mouse button and drawing a rectangle Once the rectangle is defined select the Image Crop Image Crop Volume command and the Crop 3D Image Volume dialog box appears to allow you to adjust the range of the 3D volume See Figure A file name is required to save the new image 145 IMA
151. ctangle Release the left mouse button and a rectangle boundary will be created Repeat this step to add more rectangles The Circle mode process is similar to the Rectangle drawing mode You need to draw the enclosing rectangle to define the circle Move the cursor to a position for the upper left corner of the rectangle Hold down the left mouse button and drag to a position marking the lower right corner of the rectangle Release the left mouse button and a circle or ellipse boundary will be created based on the bounding rectangle Repeat this step to add more circles To adjust an existing ROI select Adjust ROI option from the ROI submenu or the floating pop up menu Move the cursor to an ROI click and hold down the left mouse button to adjust the shape of the ROI To move an ROI select the Move ROI option from the ROI submenu or the floating pop up menu Move the cursor to an ROI click and hold down the left mouse button to move the ROI When finished select Done from the floating pop up menu to exit the ROI Editing Tool 86 EDIT MENU COMMANDS Use the Edit Region of Interest ROD Inflate Region F7 and the Edit Region of Interest ROD Deflate Region F8 options to increase or decrease the size of the ROI respectively The region of interest ROI can be removed using the Edit Clear ROIs command 3 3 2 ROI By Boundaries command Region of Interest submenu Use the Edit Region of Interest ROD ROI by Boundary comma
152. cted image plane in the IMAGE PLANE WINDOW The MONTAGE WINDOW provides a navigation tool among the 3D image planes and an overview of the 3D image structure Note in 3D DOCTOR we count image planes starting from If a 3D image has 256 planes or slices the first plane is plane 0 and the last plane is plane 255 3D DOCTOR generated data such as boundary lines point markers annotations and control points are displayed in the IMAGE PLANE WINDOW and are edited here as well Some data items may be displayed in both the IMAGE PLANE WINDOW and MONTAGE WINDOW but editing always takes place in the IMAGE PLANE WINDOW functions under the View menu can be used to control the display of the IMAGE PLANE WINDOW including zoom in zoom out pseudo color palette selection image contrast adjustment interpolation mode and histogram enhancement When the IMAGE PLANE WINDOW is in the zooming mode scroll bars will be displayed the ARROW KEYS PAGE UP and PAGE DOWN HOME and END keys can be used to scroll the image To zoom into a specific image region you can hold down the left mouse button and drag it to draw a select rectangle and then press the F2 key to zoom in The F3 key zooms out 1 5 2 VOLUME VIEW WINDOW 3D volume renderings are displayed in a VOLUME VIEW WINDOW The 3D rendered image is created using ray tracing algorithms and displayed at different user 29 OVERVIEW AND TUTORIAL selected angles The display can be animat
153. d The third time it is contained by a boundary of the same object it is included again Boundaries can be generated automatically using the Auto Segment 3D Rendering Interactive Segment or the 3D Rendering Segment Object command Section 1 6 5 Creating a 3D Rendering Using Interactive Segmentation and Section 1 6 7 3D Image Segmentation Using a Training Area You can manually define or update boundaries using the Edit Boundary Editor command Section 3 7 Boundary Editor Boundary data can also be imported from other digitizing devices and ASCII files Section 2 9 1 Import Boundary command 21 OVERVIEW AND TUTORIAL intersecting boundaries self intersecting boundary contained boundaries Region of Interest ROI User defined regions of interest are used to limit the image areas to be processed by the image segmentation functions After an image is open ROIs are defined using the Edit Regions of Interest command before segmentation is done for an object Section 3 3 Region of Interest ROD ROIs can be in several shapes or combinations of shapes such as polygons circles and rectangles ROIs defined using Edit Regions of Interest apply to all image slices and new ROIs may need to be defined when segmenting other slices If you already have a boundary for an object and would like to use the boundary as a temporary ROI for segmenting a new object within it then use the Edit Regions of Interest ROI by Boundaries com
154. d 116 All Planes 147 brain 91 All Planes 158 By Image Plane Print dd di OK 1 0 165 1 0 161 1 1 163 1 2 161 1 3 160 1 3 158 1 4 158 4 The parameters in the report include the Number of Boundaries Image Plane the Center X Y Z Mean and Variance of Boundary Areas Minimum and Maximum Area Mean and Variance of Length and Minimum and Maximum Length The information can be used to verify the boundary data processed by the Edit Boundary Process functions such as Smooth Simplify Merge Boundaries Delete By Length Delete By Plane etc The information can be used for counting objects and can be brought to a spreadsheet program for analysis or plotting 3 9 Boundary Process Edit Menu See Chapter 6 Boundary Process Commands for details of boundary processing commands 112 EDIT MENU COMMANDS 3 10 Point Editor Edit Menu Points can be defined in the 2D IMAGE PLANE WINDOW to mark 3D locations of interest When points are defined they will be used as location markers in the 3D SURFACE WINDOW and the 3D VOLUME WINDOW Use the Edit Point Editor Point Edit On Off command to start the Point Editor tool When the tool is started the cursor will change according to the editing mode Use the Point Editor submenu or the right mouse button to get the editing pop up menu An option is checked if the corresponding editing mode is currently active With the Point Editor you can
155. d click the left mouse button to delete the point You can use the Digitize Point command to add more points You can use the Point Report command to get a report of point coordinates 8 19 3 Point Report Tools Menu This command displays a report of all existing points You can use the Digitize Point command to add more points You can use the Delete Point command to delete existing points 220 VOLUME WINDOW COMMANDS Volume Window Commands Select volume rendering method and control volume rendering display 3D DOCTOR creates volume renderings by ray tracing the voxels defined by object boundaries Volume rendering creates a 3D display using both the 3D image and the boundaries Voxels are ray traced to show the image in a 3D space Volume rendering supports several rendering modes including transparency where voxels are treated as transparent direct object where only surface voxels are displayed and maximum density where only the brightest voxel is displayed along each ray Because volume rendering creates each view by ray tracing the entire volume it may take a longer amount of time to rotate when you have a larger image For 3D volume rendering you can save the data to a XYZ file where each voxel location is recorded as a point With commands under the VOLUME VIEW WINDOW menus you can e Open and save volume files e Choose a volume rendering method e Change display contrast e Change colors 221 VOLUME WINDOW
156. d down Switch rendering method Animate your 3D image 121 VIEW MENU COMMANDS 4 1 Toolbar command View Menu Use the View Toolbars Toolbar command to display and hide the Toolbar The Toolbar includes buttons for some of the most common commands like opening and saving files setting objects displaying layer controls image zoom in and out and help 5 s u gt elo ala mesa A check mark appears next to the menu item when the Toolbar is displayed B v Toolbar Edit Bar Status Bar Move your mouse to a Toolbar button and stay there for a few seconds to see the tool tip The tool tip tells what command is associated with the button 4 2 Edit bar command View Menu Use the View Toolbars Edit Bar command to display and hide the Edit Bar The Edit Bar includes buttons for some of the most common commands used when editing boundary lines points control points and other data layers A check mark appears next to the menu item when the Edit Bar is displayed ra n m 2 ua e o o o o RA Y Toolbar v EditBar Status Bar Move your mouse to an Edit Bar button and stay there for a few seconds to see the tool tip The tool tip tells what command is associated with the button 4 3 Status Bar command View Menu Use the View Toolbars Status Bar command to display and hide the Status Bar The Statu
157. ded If your image is a multi plane image the new image will be saved to a file and can be displayed using the File Open command 5 11 3 Despeckle command Smooth submenu The Image Processing Despeckle command is used to remove black and white noise pixels from a monochrome or binary image If your image is a multi plane image the new image will be saved to a file and can be displayed using the File Open command 5 12 Sharpen command Image Menu This command is used to sharpen an image using a sharpen filter This command works with both grayscale and color images If your image is a multi plane image the new image will be saved to a file and can be displayed using the File Open command 161 IMAGE MENU COMMANDS 5 13 Process Commands Image Menu The Process submenu includes commands for color image classification image negate remove dark background and edge detection 5 13 1 Classify command Process submenu This command is used to classify image pixels grayscale and color into separate color groups based on their color and texture information using a clustering algorithm You can specify the number of color classes based on the image and the number of iterations desired to run the algorithm When the Image Classify command is started the Image Classification dialog box appears In the current version the maximum Number of Classes to be used is limited to 255 and there is no limit on the Number of Itera
158. ded because of image padding for Fourier transforms Make sure your system memory plus swap space will provide enough space when using this function This figure shows the result of a 171 IMAGE MENU COMMANDS Hubble Telescope image restored using the Maximum Entropy deconvolution method E Eb Ed Ic 5 17 3 Synthetic PSF command Image Deconvolution Menu Use this command to create a synthetic point spread function for deconvolution This command uses a 3D optical density distribution function with user defined parameters to create a point spread function when an exact point spread function measurement is difficult to obtain for an imaging system Besides the image dimension parameters number of columns rows planes and bits per pixel the maximum intensity defines the maximum pixel value in the image The slice thickness and pixel width are physical parameters used by the modeling function and must be entered in the same units If these values are unknown simply use 1 for both The PSF image can be viewed using the File Open command 172 BOUNDARY PROCESS COMMANDS Boundary Process Commands Merge boundanes smooth and boundary ines delete boundaries by length or by image plane splat objects inflate and deflate boundaries With commands under the Edit Boundary Process menu you can Split and assign objects Reduce the number of nodes in a boundary Smooth and simplify boundary lines Merge b
159. density values are calculated by grouping the binaries within the image plane according to their topology For an object boundary topology such as holes and islands are used to include or exclude image pixels When the Summary Report option is selected calculations for the each object within the object boundary are calculated The following is a sample summary report created from the Edit Object Report command Statistical Report of Objects Object Plane Total Object Color Total Mean Variance Minimum Maximum Number of Center Density Density Density Density Pixels X Y Z head All 1977074 137 12 0 16762839 847 86 253963 07 2 0 4095 00 144 6 24 00 6 55 0 4 brain All 685196 111 59 0 68459870 999 12 78180 55 6 0 4095 00 158 7 6 00 2 54 7 0 The 3D DOCTOR Report dialog box for both the detailed and summary reports allows you to Save the data into a text file or Print the table You can also use the Copy option to copy the data to the clipboard and paste into other programs for plotting or analysis 84 EDIT MENU COMMANDS 3 2 5 Object Histogram command Edit Menu Use this command to calculate B an image pixel histogram for all currently active objects Object Histograms based on their boundaries in all image slices The Object default has no data histogram combines all image slices and displays be ed histogram for
160. ding to the editing function used The initial editing function is New Use the right mouse button to get the pop up menu for editing options or select the options from the Edit Control Point submenu A control point is displayed as a red cross with an outer circle if it lies in the current image plane or as an orange cross with an outer circle if it is not in the current plane With the Control Point Editor you can Add new control points New Move an existing control point Move Modify control point coordinates Modify Delete an existing control point Delete Check control point residual error Check Pick a point from a target image Pick Point Open an existing control point file Open Save control points to a point file Save 3 6 2 New command Control Point submenu Use this command to switch to the mode for adding new control points The cursor is changed to a Cross Cursor in this mode To add a new control point move the cursor to a location in the IMAGE PLANE WINDOW and then click the left mouse button The Control Point dialog box will 94 EDIT MENU COMMANDS appear for you to enter the From Source and the To Destination coordinates Among the 3 coordinate values X and Y are for the column and row directions respectively the Z is the image plane number x Column 530313 Column 530313 counting from 0 to the total Y R Y R number of planes minus 1 Row 381328 gt gt Row 38132
161. display control commands View editing commands Edit and processing commands 3D Rendering 82 EDIT MENU COMMANDS Use the Line Type button to select a line type and line width for boundary line display When an object is turned off using the On Off button all data within the object will not be visible and will not be affected by the editing and processing commands When working on a certain object it is highly recommended to turn the rest of the objects off so they will not be affected by commands you want to apply only to the current object Use the File Boundary and Point Export Boundary command to save the boundary and the defined object data to a file The File Save Save Project command is used to save all of the 3D data including the defined object data 3 2 2 Object Combination command Edit Menu Use this command to combine 3 E Combine Objects two objects together using a Boolean operation subtract _ First Object Second Object intersect union or negative head bone new object is created to store the combination At the Combine Objects Subtract Intersect Union C Negative dialog box select the First Bg d Object and the Second LA m Object from the list Select Boolean Operation the operation type and enter m New Object OK the name of the new object SottTissue Click to start the Cancel process
162. dit Undo option or CONTROL Z Use the function keys F5 or F6 to go to another image plane for more editing You can switch to a different editing session by selecting another option from the Boundary Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Boundary Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 102 EDIT MENU COMMANDS 3 7 3 Boundary Moving Commands 3 7 3 1 Move Boundary command Boundary Editor submenu Use this command to change to the Move Boundary mode The cursor will change to a Move Cursor Point the cursor at a boundary and hold the left mouse button down to move When the boundary is moved to the desired location release the left mouse button to confirm it Repeat this process to move another boundary To undo the previous edit use the Edit Undo option or CONTROL Z Use the function keys F5 or F6 to go to another image plane for more editing You can switch to a different editing session by selecting another option from the Boundary Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Boundary Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 7 3 2 Rotate Boundary command Boundary Editor submenu Use this command to change to the Rot
163. e image to create 3D volumes and surface renderings The boundary bnd file is an ASCII file recording the boundaries of a 3D object The boundaries can be created using the 3D Rendering Auto Segment command the 3D Rendering Interactive Segment commands Section 1 6 5 Creating a 3D Rendering Using Interactive Segmentation or the 3D Rendering Segment Object commands Section 1 6 7 3D Image Segmentation Using a Training Area 2 9 1 Import Boundary command Boundary and Point submenu The File Boundary and Point Import Boundary command is used to open an existing boundary file and display it in the current image window When the file Open dialog box appears use the Files of Type area to specify the file format Boundary File bnd DXF Hile dxf Point File pnt Slice File slc or 3D XYZ File xyz The boundary file is in ASCII text format and can store boundaries for a single object or multiple objects The format looks like this OBJECT ObjectName ColorCode S1 YO XI Xn Yn YO END S2 YO XI Xm Ym YO END Sk YO XI Xn Yn YO END END 71 FILE MENU COMMANDS Where S0 S1 Sk are the image slice number such as 0 1 34 Xi and Yi are the coordinates of points on the boundary polygon They can be integer or floating point numbers The polygon is closed so the last point is always the same as the first point The OBJECT keyword starts each ob
164. e many lines are overlapped you can use the Edit Object Settings command to change the color of the lines for each object or to turn some objects on and off the display If lines are turned off from the current object set they will not be used in the rendering process The Split Object command is useful for cutting an object to see a profile in a direct object rendered volume For example an image of a head can be cut into two sections and the inside of the brain can be visualized clearly when one section is used in direct object volume rendering By cutting an object several times the profiles of different sections can be seen in the volume rendered image 174 BOUNDARY PROCESS COMMANDS 6 1 2 Assign Object command Boundary Process submenu This command automatically groups the boundaries of the current objects into new objects using connectivity rules For example an image may have multiple objects that have similar characteristics and can be segmented into a single object In this case you can use the Edit Boundary Process Assign Object command to separate the boundaries into individual objects If boundaries in the neighbor image planes intersect or overlap they are grouped into the same object If not they are put into separate objects Boundaries in the current object will be replaced by boundaries that belong to the newly created objects and displayed with their specified color You can use the Edit Object Settings comm
165. e Registration dialog box appears you need to specify an name to store the registered eve image This file should be x different from your original image Save The size for the new image New Dimension Current Dimension must be specified the Columns 256 Columns 256 Number of Columns Number of Rows and the Number of Image Planes Normally if Planes 109 Planes 109 you register one image to a target image you should use Rows 256 Rows 256 the same size as the target Fiel Interpolation Cancel image in the New Dimension parameters This ensures that the two images will have the same image size and can be combined by the Image Fusion functions When you have two images from the same patient but acquired using different imaging devices for example a CT and an MRI image of a head registering the two images to the same coordinate system will allow you to compare them more accurately and to create fusion images using one of the image fusion commands In addition a fusion image created by combining multi modality images will display more information about the source studied The following steps are used to register a 3D image against a target image and create a fusion image from two registered images Step 1 Open the target image stack and the source image stack that is going to be registered Now move the windows away from each other so they can be accessed e
166. e dialog box specify the folder where the compressed DICOM files are located and the folder you want to output the uncompressed DICOM files If the Overwrite Existing Files is checked uncompressed file will replace the compressed file If not you should store the uncompressed files in a separate folder so the uncompressed image series and studies don t mix together with original files Click Start to uncompress them It is recommended to make a backup copy of your original files 2 4 Raw Image File Import File Menu This command can be accessed from the IMAGE PLANE WINDOW the MONTAGE WINDOW the 3D SURFACE WINDOW and the VOLUME VIEW WINDOW 2 4 1 Single File command Raw Image File Import submenu 3D DOCTOR supports various image file formats directly including DICOM TIFF JPEG PNG and BMP For other image file formats such as raw binary files or a vendor proprietary image file format 3D DOCTOR provides a function to create an image header file for an image data file when its configuration or file structure is known Once the header file is created correctly you can then use the header file hdr to open the image file and read the data into 3D DOCTOR The file will be treated the same way as a directly supported file format like DICOM or TIFF 63 FILE MENU COMMANDS The following are the steps needed to create a header file for an unsupported image data file type Step 1 Select the File Raw Image File Import
167. e finished press the N key or press any other key to close the polygon Once the line is completed 3D DOCTOR will show the image density profile along the line in a PLOT WINDOW See Figure 2015 Image Profile Intensity 2581 0000 0 28 0000 Pixels 0 00 170 00 The PLOT WINDOW can take multiple profile curves Simply keep the current PLOT WINDOW open and repeat the line drawing process When you are finished a new density profile will be added to the display of the current PLOT WINDOW Click the right mouse button to show other measurement options 90 EDIT MENU COMMANDS 3 4 5 Histogram command Measuring Tool submenu When the Histogram option is toggled on use the mouse to draw a line or polygon in the IMAGE PLANE WINDOW When you are finished press any key except the N key to close the polygon Once the polygon is closed 3D DOCTOR will show the histogram for the defined region in a PLOT WINDOW See Figure The PLOT WINDOW can OE ____ _ 10 xl take multiple profile curves Simply keep the current Histogram PLOT WINDOW open and repeat the line drawing 2 0000 m process When done a new histogram curve will be added to the display of the current PLOT WINDOW Click the right mouse button 0 0000 I PixelLevel to show other measurement 17 00 2387 00 options 3 4 6 3D Profile command Measuring Tool submenu If the 3D Profile option is toggled on use
168. e formats 47 OVERVIEW AND TUTORIAL 1 6 6 Creating 3D Volume Rendering 3D volume rendering is easy to do in 3D DOCTOR The following explains the process of performing a 3D volume rendering Step 1 Open the 3D image using the File Open command If the image has multiple slices you should see two windows one window displays a single slice and a second window displays a montage of all the slices If you don t see the MONTAGE WINDOW and the image plane number is not displayed in the IMAGE PLANE WINDOW then you ll need to use File New Stack to put the 2D image files into a 3D stack first Step 2 If you want to use the entire image for the rendering then use the Volume Rendering Smooth Rendering command Use the View Opacity command to adjust the tissue opacity range for the display Or Step 3 If you want to render a portion of the volume within the single IMAGE PLANE WINDOW start Edit ROI Editor Regions of Interest Click the left mouse button to draw a region of interest and press the SPACEBAR to finish Step 4 Use the Volume Rendering Smooth Rendering command to create 3D volume rendering Once the VOLUME VIEW WINDOW is displayed all the view control and settings can be adjusted using commands under the View menu 48 OVERVIEW AND TUTORIAL 1 6 7 3D Image Segmentation Using a Training Area The following steps are used to segment an object in a 3D volume image based on a user defined training area Section 7
169. e hollow boundaries can then be used to create a solid shell with empty core for the new object For objects with thin walls you can use the Interactive Segmentation to trace solid boundaries single outline for the object first and then use this function to create a hollow object The thickness can be specified in pixel unit The hollow boundaries work well for objects oriented perpendicular to the image planes If you see holes added to your 3D object when doing a 3D surface rendering you should use the Boundary Editor to either make the inside boundary smaller or simply delete the inside boundary to restore the surface area on these image planes 180 3D RENDERING COMMANDS 3D Rendering Menu Commands Perform 3D image senentation create 3D volumes and 3D surface renderings With commands under the 3D Rendering menu you can e Segment a 3D image to get object boundary lines using the interactive segmentation algorithm e Segment a 3D image using the automatic segmentation algorithm e Segment a single 3D object by providing a training area e Create 3D surface rendering e Create cubic boundaries for the entire image volume e Create 3D volume rendering e Split Objects with a user defined line 181 3D RENDERING COMMANDS 7 1 3D Wizard command 3D Rendering Menu This command is used to simplify the process of creating 3D rendering and models from a 3D image Start the 3D Wizard command after your image is open T
170. e image in the image window The image window will be resized to adjust to the image aspect ratio 4 8 Previous Plane command View Menu This command switches to the previous image plane available in the MONTAGE WINDOW For example if the current image plane being displayed is plane 5 then the previous plane to be displayed is plane 4 If the first image plane has been reached it will then loop back to the last plane The View Previous Plane command works only when an image has multiple image planes A better way to jump to a certain image plane in 3D DOCTOR is by double clicking in a specific pane in the MONTAGE WINDOW Shortcuts Keys F5 126 VIEW MENU COMMANDS 4 9 Next Plane command View Menu This command switches to the next image plane available in the MONTAGE WINDOW For example if the current image plane being displayed is plane 5 then the next plane to be displayed is plane 6 If the last image plane has been reached it will then loop back to the first plane image plane 0 The View Next Plane command works only when an image has multiple image planes A better way to jump to a certain image plane in 3D DOCTOR is by double clicking in a specific pane in the MONTAGE WINDOW Shortcuts Keys F6 4 10 Animate Commands View Menu 4 10 1 Animate Planes command Animate submenu This command is available to the IMAGE PLANE WINDOW and the VOLUME VIEW WINDOW The software will display image planes con
171. e image slices within the 3D image You can simply open the image to see if it is properly organized as a 3D image or still a single 2D slice You can think of a 2D image as an individual sheet in a book and you need to stack all the sheets up in the correct order to make a 3D volume In 3D DOCTOR the File New Stack command is used to put single image slices together to form a 3D image for processing and analysis Section 1 6 2 Creating a 3D Stack from 2D Image Slices e Calibration For a 3D image the voxel size image resolution must be provided to 3D DOCTOR This ensures that the 3D rendered image will have the correct 20 OVERVIEW AND TUTORIAL scale in all 3 dimensions and result in calibrated computation for all the reporting functions Calibration parameters for voxel resolution include the size of a pixel in a slice for example 1 mm and the slice thickness The slice thickness is the sum of the image slice thickness plus the gap distance between two neighbor slices For DICOM images these parameters are normally provided in the header but you may need to adjust the slice thickness if not all the slices are used Calibration parameters for voxel values can also be entered and used by reporting and quantitative analysis functions when available Section 1 6 4 Defining Voxel Size and Slice Thickness for Calibration e Object In 3D DOCTOR an object contains the boundaries and the image pixel data within the boundaries Whe
172. e is entered The new slice thickness is the value to be used for image reslicing If this value is smaller than the current slice thickness between two slices additional slices will be added using interpolation If the new thickness is bigger then some existing slices will be ignored in the new image Use the Browse button to define the output image Reslice Image Dialog X New Thickness Planes Thickness 1 000000 1 000000 1 000000 Save Spacing 1 000000 1 000000 Open Spacing 1 000000 1 000000 ox 1 000000 n E ance Save New Image File As P images3d Newimage tif file name The new image will have even spacing between all slices Use the File Open command to display the resliced image file 140 IMAGE MENU COMMANDS 5 3 2 Reverse Slice command Reslice submenu This command is used to reverse the order of image slices This command works only with multi plane or multi slice images If the image planes are stored in a stack list file a new list file 150 is created with the reverse order of image planes The original image data files are not changed in this case When the image planes are stored in other types of image files a new image file is created with the reverse order of image planes or slices 5 3 3 Move Slices To command Reslice submenu This command is used to move a range of image slices to a new location within the image stack This command works only wi
173. e size and the object boundary data You can change them to smaller or larger values based on the image size and how much computing resources you have Because a large number of surface polygons require more system memory and longer time to process you may consider lowering the denseness by increasing the number when processing a large size image For example when creating a surface model from an image of 512X512 with 1000 slices you can use 2 for Z to reduce the density along the Z axis Object boundaries must be defined before using the 3D Rendering Surface Rendering Full Complex Surface command Use either the 3D Rendering Interactive Segment command or the 3D Rendering Segment Object commands to generate boundary lines automatically You can also use the Edit Boundary Editor options to draw boundaries manually Depending on the quality of the original 3D image the boundary lines generated using the image segmentation functions may need to be edited to get better rendering results The Edit Boundary Editor provides functions to 188 3D RENDERING COMMANDS edit boundary lines easily and quickly Functions under the Edit Boundary Process submenu can also be used to perform global boundary line processing such as Smooth Delete By Length Delete By Plane and other processing commands Once a 3D surface is created from the boundary data a new 3D SURFACE WINDOW appears with the surface image displayed A 3D menu bar is assoc
174. e target image if fusion is going to be done Click on the OK button to start the process When the process is done a new registered image is created and saved to the name as specified Step 7 If image fusion or color fusion needs to be done select the Image Fusion or Image Color Fusion command Enter the file names and select the required image combination option and then click on to start 156 IMAGE MENU COMMANDS 5 9 Image Fusion Commands Image Menu 5 9 1 Fusion command Image Fusion submenu The Image Image Fusion Fusion command is used to combine two registered images together using a user specified operator to create a new fusion image file name is required to save the output image When the Fusion command is started the 3D Image Fusion dialog box appears See Figure 3D Image Fusion x m First Image D images3d PETCT ctl tif Browse r Second Image D images3d PETCT pet tif Browse Preview r Fusion Operations C ADD C AND C XOR C SUBTRACTC COR TRANSPARENT C MIN m Output Image OK D images3d PETCT ctpet tif Browse Cancel The combination operators include ADD SUBTRACT MIN MAX AND OR and TRANSPARENT 157 IMAGE MENU COMMANDS 5 9 2 Color Fusion command Image Fusion submenu The Image Image Fusion Color Fusion command is used to combine two or more images together to create a color com
175. each color Pixel Value Calibrated Value Number of Pixels 0 0 000000 5775 channel separately when an 1 10000mn 3909 image is an RGB color image 2 000000 4098 3 000000 5417 4 000000 6261 The histogram includes 3 5 000000 5717 columns the Raw Pixel Value 6 000000 7040 the Calibrated Pixel Value 7 000000 6573 8 000000 7843 using the parameters entered 3 000000 8296 by the X Edit Calibration 10 000000 7154 d d the Numb 11 000000 8488 command and the Number of 12 000000 8561 Pixels at this value If a pixel 13 000000 7343 value does not exist in the object it is not listed in the histogram output OK The Report Window dialog box allows you to save the data into a text file or use the button to copy the data to the clipboard and paste the data into other programs for plotting or analysis The following is a sample histogram report created from this command Object Histograms Object tumor Pixel Value Calibrated Value Number of Pixels 11 989 000000 1 15 985 000000 1 17 983 000000 3 2 18 982 000000 3 3 Region of Interest ROI Edit Menu 3 3 1 Region of Interest Tool On Off command Region of Interest submenu Use the Edit Region of Interest ROD ROI Tool On Off command to start the ROI Editing Tool 3D DOCTOR supports multiple regions so you can define an ROI as a 85 EDIT MENU COMMANDS separate area or as an area with islands or holes When multiple region boundaries are defin
176. ececseseecesseeecssaesessneeeens 141 5 3 5 ADD SLICES COMMAND RESLICE SUBMENU ccssssccecsesceceesececseaececseseecnsseeeceeaeeeenneaeens 142 5 3 6 RESLICE X AXIS COMMAND RESLICE SUBMENU cessent 143 5 3 7 RESLICE Y AXIS COMMAND RESLICE SUBMENU enne enne 143 5 3 8 RESLICE VOLUME COMMAND RESLICE SUBMENU eene enne enne nnne 144 5 4 CROP IMAGE COMMANDS IMAGE 145 5 4 1 CROP REGION COMMAND CROP IMAGE SUBMENU enne nennen 145 5 4 2 CROP VOLUME CROP IMAGE SUBMENU cessere 145 5 4 3 CROP ROI COMMAND CROP IMAGE SUBMENU eese eene ener enne nennen ne 146 5 4 4 CROP FILM COMMAND CROP IMAGE SUBMENU cicer enne ener enne nien nnne 147 5 5 RESIZE VOLUME COMMAND IMAGE 149 5 6 IMAGE ALIGNMENT eese ee seta sten stato natos toss setas etas e ease ease tasto 150 5 6 1 AUTO ALIGNMENT COMMAND IMAGE MENU nennen enne enne nnne 150 5 6 2 ALIGN SLICES COMMANDS IMAGE eene nennen inneren inneren 151 5 7 TILT CORRECTION COMMAND IMAGE 153 5 8 1 REGISTER IMAGE COMMAND IMAGE MENU seen ene enne nennen rennen entere nnne 154 5 8 2 REGISTRATION WITH CONTROL POINTS IMAGE 155 5 9 IMAGE FUSION CO
177. econstruct or restore a 3D image using fast nearest neighbor deconvolution e Reconstruct or restore a 3D image using iterative maximum entropy deconvolution 168 IMAGE MENU COMMANDS 5 17 1 Fast Nearest Neighbor Deconvolution command Image Deconvolution Menu Image restoration is used to remove or reduce degradations that were incurred while the image was being obtained These degradations include the blurring introduced by optical systems and by image motion as well as noise due to electronic and photometric sources The aim of image restoration is to bring the image toward what it would have been if it had been recorded without degradation When the source of degradation blurring and noise can be characterized and modeled as a point spread function PSF then their effects can be subsequently removed or reduced with a deconvolution process using the PSF and the degraded image 3D DOCTOR provides two types of deconvolution to restore degraded 3D images one is a fast nearest neighbor deconvolution and the other one is an iterative maximum entropy deconvolution method The Image Deconvolution Fast Nearest Neighbor command performs a 3D image restoration using a Fast Nearest Neighbor deconvolution algorithm The 3D Image Deconvolution dialog box requires the Source Image File Name the Point Spread Function PSF Image File Name and an Output Image File Name where the restored image will be saved See Figure 3D Image Deconv
178. ed caution must be taken to ensure a region is to be included or excluded The parity rule is used to determine if an area is inside the ROI or outside It works like this count the number of boundaries you encounter from the inside of the area to the outside of the area If the number is odd then the area is inside if the number is even then it is outside Section 1 3 2 Terminology Boundary Contour Tool On Off Once you are in the ROI editing mode you can use the right v Rectangle mouse button to display the floating pop up menu to switch Circle to a different drawing mode or you can use the commands Move ROI under the ROI submenu See Figure There are three types of drawing modes Rectangle Circle and Polygon The default ROI By Boundaries mode is Polygon The selected drawing mode is checked Inflate Region F7 Deflate Region F8 When in the Polygon drawing mode move the cursor to a position and click the left mouse button to start drawing Move to the next position and click the left mouse button again to confirm the line segment Repeat this process to draw the entire region The BACKSPACE lt key will undo one step Hit any other key on the keyboard to close the region When in the Rectangle drawing mode move the cursor to a position for the upper left corner of the rectangle Hold down the left mouse button and drag to a position for the lower right corner of the re
179. ed along a certain viewing angle using the View Animate command Section 4 10 Animate The screen image can be saved to an image file in TIFF format using the File Save Image As command If no object boundary has been defined you can draw a selection rectangle in the IMAGE PLANE WINDOW and use the 3D Rendering Cube Boundary command to define boundaries for a cube volume and then perform Volume Rendering When boundaries are defined volume rendering can be used directly You can use 3D Rendering Split Object to slice object boundaries into 2 parts and then use the split object for volume rendering The 3D volume can be saved to XYZ or 3D DOCTOR s own VOL file formats The VOLUME VIEW WINDOW has a set of display control functions in the View menu to zoom in zoom out use pseudo color palette and adjust contrast and other display controls 1 5 3 3D SURFACE WINDOW 3D surface models created by surface rendering functions are displayed in the 3D SURFACE WINDOW The 3D surface models are in 3D polygon mesh form 30 OVERVIEW AND TUTORIAL represented by surface triangles and polygons The models can be viewed from any selected angle and can be animated along a certain viewing path The data created by surface rendering methods can be saved to a vector based 3D graphics file format such as DXF format to be used by other 3D modeling or graphics software packages The data can also be saved in STL format for rapid prototyping ap
180. ed in real time according to the current threshold selection When pixels that belong to the intended object are displayed in red color you can click the Segment Plane button to extract the boundaries for the current image plane Use the Next Plane or Prev Plane button to go through other planes to segment them individually If the threshold values are applicable to all slices you can click on the Segment All button to extract boundaries for all image slices Click Finish to leave the interactive segmentation function Step 6 Now you can repeat Steps 2 to 4 to segment boundaries for other objects Step 7 The boundary lines can be edited using the tools provided by the Edit Boundary Editor If you need to split the object into two sub objects then use the 3D Rendering Split Object command to do it Use the File Save Save Project command to save the boundaries and other data to a project file Step 8 Once the boundaries are defined you are ready to create 3D surface models This can be accomplished using the 3D Rendering Simple Surface Rendering or the 3D Rendering Complex Surface commands You can also create 3D volume rendering using the 3D Rendering Volume Rendering command Step 9 When the 3D SURFACE WINDOW appears use commands under the View menu to change the viewing angles and other controls Step 10 Use the File Export Model command to save your surface model to a STL file or other supported 3D fil
181. ee ee ie 62 2 3 UNCOMPRESS DICOM COMMAND FILE 63 2 4 RAW IMAGE FILE IMPORT FILE MENU 4 eese esee setate sesto uae 63 2 4 1 SINGLE FILE COMMAND RAW IMAGE FILE IMPORT SUBMENU 222 63 2 4 2 MULTIPLE FILES COMMAND RAW IMAGE FILE IMPORT SUBMENU cceeeren eee 66 2 5 OPEN MODEL COMMAND FILE MENU eese eee ette setenta seta setas stone setas etes 68 2 6 CLOSE COMMAND FILE 68 2 7 SAVE FILE MENU iie seseeeeseeso esos seoseb es vh sos sesssussussesssvessensanesaa sess sssossecasoasssasecassassensdoossuaseuass 68 2 7 1 SAVE IMAGE AS COMMAND SAVE SUBMENU 68 2 1 2 PIEESAVE AS DIALOG ete ee ede hs Ge OI RI eH 69 2 7 3 SAVE WINDOW COMMAND SAVE 0 entrer inneren entere seen enne 70 2 7 4 SAVE PROJECT AND SAVE PROJECT AS COMMANDS SAVE SUBMENU eene 70 2 8 NEW WORKSPACE COMMAND FILE MENU 4 eee seen eene 70 2 9 BOUNDARY AND POINT FILE MENU e ee eese esee ee entes en setas etas ta 71 2 9 1 IMPORT BOUNDARY COMMAND BOUNDARY AND POINT SUBMENU cere 71 2 9 2 EXPORT BOUNDARY COMMAND BOUNDARY AND POINT SUBMENU cene 72 2 9 3 IMPORT POINT COMMAND BOUNDARY AND POINT SUBMEN
182. eed to be aligned you can change the plane number in the From and To edit boxes Both numbers are included in the alignment 150 IMAGE MENU COMMANDS process If the range is not continuous you can use this command again to define a new range for the alignment process 5 6 2 Align Slices Commands Image Menu When image slices planes are not properly aligned you can use the image slice alignment tools get all slices properly aligned The commands under the Image Align Slices submenu allow you to move or rotate image slice around until it is aligned to the neighbor slice The image slice alignment should be done first before doing segmentation 3D rendering or other processing The following steps explain how to use the Align Slices commands to align the slices of a multi plane image 1 Open the image stack using the File Open command You should see two windows the IMAGE PLANE WINDOW and the MONTAGE WINDOW If you have not created an image stack list you can use the New Stack command to do so Select Image Align Slices Start Alignment to start the alignment tool The current image slice is turned transparent and displayed on top of the previous slice For example if your current image plane is 55 then image plane 54 is displayed together with 55 Both are displayed transparent The initial tool is Move Slice Hold down the left mouse button and move the cursor within the image window to move the current image sli
183. eeecseaueeecnesaeeesseseeenenaes 87 3 4 MEASURING TOOL EDIT MENU eee esee esee testen 87 3 4 1 MEASURE ON OFF COMMAND MEASURING TOOL SUBMENU csssssceceesteeecseseeeessteeeeneaaes 87 3 4 2 MEASURE COMMAND MEASURING TOOL SUBMENU csssscceceeceececseececeesaeeeceeseeeessneeeensaaes 88 3 4 3 ANGLE COMMAND MEASURING TOOL SUBMENU eese nennen ener 89 3 4 4 2D PROFILE COMMAND MEASURING TOOL SUBMENU cerent nennen nennen erret 90 3 4 5 HISTOGRAM COMMAND MEASURING TOOL SUBMENU cerent enne ener enne 9 3 4 6 3D PROFILE COMMAND MEASURING TOOL SUBMENU esee enne enne 9 3 5 IMAGE EDITOR EDIT MENU eee esee ee sees seen setenta toss to aetas etas e ease ta seta 92 3 5 1 IMAGE EDITOR ON OFF COMMAND IMAGE EDITOR SUBMENU 92 3 5 2 SHOW PIXEL VALUE COMMAND IMAGE EDITOR SUBMENU eee enne 92 3 5 3 DRAW PIXELS COMMAND IMAGE EDITOR 0 enne nnns 92 3 5 4 MAP PIXEL V ALUES COMMAND IMAGE EDITOR SUBMENU enne 93 3 6 CONTROL POINT EDITOR EDIT MENU ee eeeee ee eee eene 94 3 6 1 CONTROL POINT EDITOR ON OFF COMMAND CONTROL POINT SUBMENU 94 3 6 2 NEW COMMAND CONTROL POIN
184. een the lower threshold dark and the upper threshold bright will be displayed using the full Width dynamic range of the display device for fe example 256 levels on an 8 bit display device Note This command does not change the raw image pixel values it only affects the Cancel 2238 display Shortcuts Keys F4 4 12 2 Log Scale command Image Contrast submenu The View Image Contrast Log Scale command applies a log function to scale the image histogram for image display This command does not change the image itself it only affects the image display 4 12 3 Square Root Scale command Image Contrast submenu The View Image Contrast Square Root Scale command applies a square root function to scale the image histogram for image display This command does not change the image itself it only affects the image display 4 12 4 Interpolation command Image Contrast submenu The View Image Contrast Interpolation command toggles image interpolation on and off for the IMAGE PLANE WINDOW This command is for display control only The option will stay on until it is toggled off 131 VIEW MENU COMMANDS When interpolation is on you can see a much smoother image display because a nearest neighbor algorithm is used to create a fine display for the region of interest This command creates an extremely smooth display when you zoom in closely in a small image region You can toggle this option
185. elect Scanner 251 Select tool 215 selection rectangle 107 179 Selection Rectangle 34 135 separate boundaries 175 Set Object 109 115 Set Plane Value 108 114 SETIMAGEPLANE 238 SETPIXEL 240 Shape 200 SHARPEN 246 sharpen image 161 shell 3D 180 shortcut keys 120 Show Info 110 Show Pixel Value 92 SHOWIMAGE 240 side view montage window 124 Simple Surface rendering 188 single image plane window 19 SIZEIMAGEDOWN 242 SIZEIMAGEUP 241 slc slice file 72 slice file slc 72 slice thickness 44 slices add 142 slices move 141 Slices remove 141 Smooth Boundary 176 Smooth Surface 214 SMOOTHAVE 244 SMOOTHMED 244 Software License Agreement 258 sparse points file format 73 Specular light 201 Split Boundary 105 split object 201 Split Object 174 Square Root Scale 131 stack list file 42 stack list file format 60 Status Bar 122 INDEX STL 23 31 STRING 232 sub volume 179 surface contours 217 Surface file 68 open 68 Save 70 surface image window 31 surface model 22 25 surface model from points 73 surface normal 218 Surface normal reverse 214 surface rendering 22 31 47 Surface rendering 46 Surface Rendering Complex 250 Surface Rendering Simple 250 surface view 20 Surface add file 196 surface contours 213 Surface smooth 214 SURFCOMPLEX 250 SURFSIMPLE 250 system display setting 17 system requirements 17 Technica
186. enanata senes esent soto totos ts ts ento tatnen sn 256 APPENDIX A SOFTWARE LICENSE AGREEMENT ecce scene eene eene eene eost tn 258 INDEX 261 14 OVERVIEW AND TUTORIAL 3D DOCTOR Overview and Tutorial 3D DOCTOR basc concepts data structure and data types object definitions user interface UI dems and simple steps to get started 1 0 Installation Guide 3D DOCTOR has multiple licensing options including a license using a software key a hardware USB key or a network floating license with a USB network license key Please use the following guide to install and validate your license 1 0 1 Installation Guide for License Using a Software Key If the PC has multiple user set up please logon as the user who will use R2V on this PC 3D DOCTOR license works only with the user profile that has installed validated the license If you have a software installation CD please insert the CD to start the installation process You can also download the installation file from this link skip this step if you already have the trial version installed http www ablesw com 3d doctor 3dsetup exe Run 3dsetup exe and follow the on screen instructions to install The first time you run 3D DOCTOR a License Validation dialog box will appear Please use the Validate License button to email the user key f
187. ent curve 8 16 2 Simplify Surface command Tools Menu The Tools Simplify Surface command will smooth surface models based on the 3D geometry of an object When this command is selected the Smooth Decimate Surface dialog box appears The percentage of vertices to be reduced is AMI xi the parameter that affect amount of Vertices To Be Reduced 34 smoothing to the surface models A bigger value will result in more surface triangles 40 to be reduced and simpler model 6 When the process is finished the newly simplified models will be displayed while nam the original models are set inactive in display The original models are kept unchanged and you can use the View Object command to turn the display on 8 16 3 Smooth Surface command Tools Menu The command is used to smooth 3D surface models based on their surface geometry This command can be used repeatedly to get a smoother model For rapid prototyping applications a complex but smooth model can be generated using the Full Complex Surface Rendering command and smoothed using this command 8 16 4 Reverse Normal Commands Tools Menu This command is used to reverse surface normal direction for 3D models It is used to correct the display of some models that have a reversed normal direction counter clockwise or clockwise when created outside 3D DOCTOR 8 16 5 Cutting Plane and Split Object Commands Tools Menu 214 SURFACE WINDOW COMMAND
188. er For non DICOM images 40 OVERVIEW AND TUTORIAL make sure the order of the files to be added corresponds to the order of their 3D position within the image stack If the DICOMDIR file is available with the DICOM image files you can use the Load List command to open it and then select an image series from the Patient Study Series list The Load List command can also load images from an existing stack list file The Delete button allows you to delete a file from the current list Select a file from the list first and then press the Delete button If you need to take a look at an image file added in the list select the file name in the list and then press the Preview button The image will be displayed in the preview window If the image cannot be previewed then you may have a problem with the file or the file format used You may have to use 3D DOCTOR s File Raw Image File Import function to configure the file first Step 3 Once the files are added to the list you can save the list to an image list file by pressing the Save List button You can also open an existing list of files for editing by pressing the Open List button Step 4 Click the Open button to open the 3D image list you just created In the future you can use the File Open command to open the list file directly All files stored in the list will be treated as an image plane within the 3D image 1 6 3 Importing Raw or Non sta
189. ere IMAGE3D image INTEGER planenum Example LOGFILE c output log imagel OPENIMAGE imagel c 3ddoctor head3d tif REM set image plane to 3 SETIMAGEPLANE imagel 3 REM save image plane 3 to file SAVEIMAGEPLANE imagel c 3ddoctor plane3 tif END 10 5 5 IMAGEDIM statement 238 3DBASIC COMMANDS This function retrieves the image dimension values including the number of columns number of rows and number of planes The image must be opened before this command is used This command is similar to Image Information but with less parameters Syntax IMAGEDIM image x y Z where IMAGE3D image INTEGER xyz Example LOGFILE c output log IMAGE3D imagel INTEGER cols rows planes OPENIMAGE imagel cN3ddoctorviead3d tif IMAGEDIM imagel cols rows planes PRINT Cols cols Rows rows Planes planes END 10 5 6 GETPIXEL statement This function retrieves a pixel from the current plane of an opened image The image must be opened before this command is used To work on another image plane use SETIMAGEPLANE to set the plane as current first and then use GETPIXEL function Syntax GETPIXEL image col row value where IMAGE3D image INTEGER col row value the col and row defines the pixel location Example LOGFILE c output log imagel INTEGER col row pix OPENIMAGE imagel cN3ddoctorviead3d tif SETIMAGEPLANE imagel 2 FOR col 20 FOR row 0 TO 20 G
190. ere you want to start drawing and hold down the left mouse button to draw Release the left mouse button to stop Repeat this process to draw a different image area If you need to change the color and pen size select the Edit Image Editor Draw Pixels Define Pixel Value To Draw command again from the Image Editor submenu The image type is grayscale Graylevell or the floating pop up menu and the Define Pixel Value to Draw dialog box appears You can Pen Size in pixels change the parameters and start to draw with the Current Pixel Value new color and pen size Graylevel 0 If you want to keep the changes you should save Define the current plane to a TIFF tif file with a Eum different file name from the original image using the File Save Save Image As command Cancel 3 5 4 Map Pixel Values command Image Editor submenu This command maps all pixels with the same value in an image plane to a new specified value If the image has multiple planes only the currently active plane is affected by this command If you want to save the changes you should save the current image plane to a new image file using File Save Save Image As command Map Pixel Values xj r Use Pixel Value Range Old Value Range To New Value Min Max ww p p Cancel r Use Lookup T able File Browse c image lookuptable txt When the Map Pixel Value dialog box appears specify the Map Pixel Values and t
191. es e Open and save surface files e Export 3 D Rendering Data to DXF IGES 3D Studio VRML and Wavefront OBJ file formats e Script and run your own 3D Basic programs e Select image or film scanner to scan your images into 3D DOCTOR e Adjust your printer setup preview images print images print the screen and print a window As discussed in Section 1 5 User Interface there are a number of windows that can be viewed and active in 3D DOCTOR Each window has its own set of commands under the File menu bar Some commands are unique to one specific window s File menu while other commands can be found in more than one or all of the window s File menus To avoid repetition the commands will only be described once but the windows in which the command is available will be identified 58 FILE MENU COMMANDS 2 1 New Stack command File Menu This command can be accessed from the IMAGE PLANE WINDOW the MONTAGE WINDOW the 3D SURFACE WINDOW and the VOLUME VIEW WINDOW Use this command to create or edit a new stack list in 3D DOCTOR When each image plane or slice is stored in a separate file you need to create a stack list file This file should include the names of all the files that make up the 3D image so 3D DOCTOR can process the image as a 3D volume instead of a single slice When your 2D image slices are very large in size and are stored in separate files in a format supported by 3D DOCTOR such as DICOM TIFF BMP JPEG I
192. es delete a line delete all lines move a line to another plane add a node to a line move a node within a line delete a node from a line etc When the tool is started the cursor will change to a different style according to the editing mode Use the right mouse button to get the editing pop up menu or use the toolbars for editing options An option is checked if the corresponding editing mode is currently active When multiple objects are defined it is highly suggested to leave only the object you are working with on and turn the rest of the objects off If some objects are left on all lines belonging to those objects will be available to the editing options and can be affected or modified by the editing functions To undo previous editing use the Edit Undo command CONTROL Z or the Undo option from the floating pop up menu brought up by clicking the right mouse button With commands under the Boundary Editor you can e Draw anew boundary line in the current image plane Draw rectangle type boundaries Draw circle or ellipse type boundaries Add a node to an existing line Move a node of an existing line Delete a node from an existing line Move a boundary to a new location Split an existing line into two separate ones at a selected location Close a line to make it a closed polygon e Make an identical line from an existing line e Delete an existing boundary 98 d d Trace Boundary Snap To Edges Draw
193. es po Bits Per Pixel fie The parameters include the Number of Columns Phelwid 0390625 Sice Thickness I Image Width the Number of Rows Image Image Type Grayscale Height the Number of Bits Per Pixel the FieName 3 172839839 Number of Image Planes Slices the Image Display Type the Voxel Size and Slice Rios thickness Patient Name Frstname LastName Patient ID fi 23456799 When available Patient Name Study ID Study BwhDae 19380814 Sex Date Series Number and the Modality will also Study fi be displayed If some of the information items StudyDate fags SSCS are not available you can enter them here so they can be used when saving the image to the aye DICOM files Cancel 137 IMAGE MENU COMMANDS 5 2 Rotate Commands Image Menu This submenu includes commands for image orientation adjustments 5 2 1 Vertical Flip command Rotate submenu This command is used to flip the image vertically This changes the image data in memory if the image has a single plane or creates a new image file to store multiple planes if it has multiple planes The original image file is not affected by this processing In the multiple plane case you can save the modified image to a new file when the Save As dialog box appears after the command is selected 5 2 2 Horizontal Flip command Rotate submenu This command is used to flip the image horizontally This changes the image data in memory if
194. es are in degrees in counter clockwise direction around the X Y and Z axis respectively Move By You can move the object from the current location to a new location by entering the distance in the X Y and Z fields The distance is in model space unit Both positive and negative values can be used positive value will move the object along the axis direction while a negative value moves it to the opposite direction Scale The object can be scaled up or down in all three dimensions by multiplying to the X Y and Z scaling factors The initial scaling factors are derived from calibrations and the original image sizes when the surface model is created The scaling factors will affect both the display and the calculation of volume and surface areas To decrease the size you need to use a scaling factor less than 1 For example when the value is 0 5 the object will shrink by half from the original model size in the dimension specified while a factor of 2 doubles the size Click the Reset button to restore the shape parameters to the default values 8 8 Wireframe command View Menu This command turns on and off the wireframe display of current 3D surface models The View Wireframe command is checked when the wireframe display mode is on This display mode applies to all currently visible models If you need to set the wireframe display mode of an object then use the View Object command 202 SURFACE WINDOW COMMANDS 8 9 Im
195. evels Number of Bytes to Skip Before the Image Data Array Some image files have a fixed length header for storing vendor specific information The length or the size of this header must be provided so the software knows to skip it in order to read the image data correctly If this value is unknown or it varies from image to image then enter 1 to let the software estimate the value automatically using the image size and the file size Little Endian or Big Endian This parameter only matters when the number of bits per pixel is greater than 8 for example when an image is in 16 bit For most images created on a PC the file is stored as little endian default If your image is created on a Macintosh or a Unix workstation it is possible the pixel is stored as big endian You can tell right away if the image does not display correctly for example discontinuous gray levels In this case uncheck the Little Endian box to set it as big endian Step 3 Header files will be created when the OK button is pressed for all the data files Each data file will have a corresponding header file If the configuration is different from data file to data file then you should use the command File Open Raw Image File Single File to create header files individually You are now able to work 67 FILE MENU COMMANDS with your image data by using the File Open command and selecting the list file type Ist or header file type hdr for each image p
196. filename Example IMAGE3D imagel OPENIMAGE imagel c 3ddoctor head3d tif SMOOTHAVE imagel cN3ddoctorNsmooth I tif SHOWIMAGE imagel END 10 5 16 SMOOTHMED statement This command smooths a volume image using a median filter and saves the processed image to a new image file Syntax SMOOTHMED imagevar filename SMOOTHMED imagevar filename where IMAGE3D imagevar STRING filename Example IMAGE3D imagel OPENIMAGE imagel c 3ddoctor head3d tif SMOOTHMED image c N3ddoctorNsmooth I tif SHOWIMAGE imagel END 244 3DBASIC COMMANDS 10 5 17 ROTATEIMAGE statement This command rotates an image with a user defined angle and saves the processed image to a new image file The rotation is done within each slice and will rotate counterclockwise if the angle is positive and clockwise if negative Syntax ROTATEIMAGE imagevar filename 5 6 ROTATEIMAGE imagevar filename angle where IMAGE3D imagevar STRING filename FLOAT angle Example imagel OPENIMAGE imagel c 3ddoctor head3d tif ROTATEIMAGE image c 3ddoctor newimage tif 5 6 SHOWIMAGE imagel END 10 5 18 NEGATEIMAGE statement This command reverses the grayscale polarity of an image and saves the processed image to a new image file In the new image white pixel becomes black and vice versa Syntax NEGATEIMAGE imagevar filename NEGATEIMAGE imagevar filename where IMAGE3D imagevar STRING filename Examp
197. g Menu The 3D Rendering Segment Object commands segment a 3D image using texture information derived from a user defined training area The algorithm uses a region growing based method This command works on individual planes with different training areas or on all image planes with the same training area It is highly recommended to define an ROI region of interest before this segmentation method is used A carefully defined region of interest will keep the region growing process within the proper image area and from jumping to other areas when image noise is present An ROI is defined using the Edit Region of Interest ROD ROI Tool On Off and updated by using the ROI Editing Tool To start the segmentation process select the 3D Rendering Segment Object Draw _ Training Area command to get into the drawing mode The right Next Plane mouse button will bring up the pop up menu options Previous Plane you can use The training area is used to create a set of features for the 3D segmentation so it should be big enough to cover most of the typical features of the object Draw Training Area Remove Boundaries Segment Current Segment ll To draw a training area move the cursor to a location and click the left mouse button to define the first point Move the cursor to the next location and click the left mouse button again to define the line segment Repeat this process until you are close to the starting location Hit any ke
198. g the Done option from the floating pop up menu brought up by pressing the right mouse button 104 EDIT MENU COMMANDS 3 7 4 2 Paste command Boundary Editor submenu Use this command to paste boundaries that have been copied to memory using the Copy Boundary or Delete Boundary command This command is often used to copy boundaries from a different image plane when the shape are similar or the same between the image planes To paste the copied boundaries into the current plane first use the F5 or F6 key to switch to the image plane where you want to place the boundaries and then use the Paste Ctrl V command to paste 3 7 5 Split and Merge Boundary command Boundary Editor submenu 3 7 5 1 Split Boundary Use this command to split an existing boundary polygon into two separate polygons The cursor will change to a Cross Cursor Move the cursor to one side of the boundary click and hold down the left mouse button and drag it to draw a line to the other side of the boundary A rubber band line is displayed while you drag the mouse Release the left mouse button to split the boundary along the cutting line Repeat this process to split other boundaries To undo the previous edit use the Edit Undo option or CONTROL Z Use the function keys F5 or F6 to go to another image plane for more editing You can switch to a different editing session by selecting another option from the Boundary Editor submenu or from the floating pop up
199. g the two images to the same coordinate system will allow you to compare them more accurately When an image is acquired with some geometric distortion it can be geometrically corrected to its original shape when proper control points can be identified The following steps are used to register a 3D image against a target image and create a fusion image from two registered images Step 1 Open the target image stack and the source image stack that is going to be registered Now move the windows away from each other so they can be accessed easily Step 2 For the source image select the Edit Control Points On command and switch to the New editing mode For the target image select the Edit Control Points On command and switch to the Pick Point mode Step 3 Go to the target image and move to an image slice where you can identify a point in both the source image and the target image For example the tip of the nose Move the cursor to the identified location and click the left mouse button A red cross is displayed to show the point is picked up from the target image Step 4 Now move back to the source image and display the image slice where the identified point is located Move the cursor to the position and click the left mouse button in the source image to add a control point at this location The control point definition dialog box appears On the left From side the values of column row and plane are obtained from the source i
200. ge data Number of Columns This field refers to the number of pixels in the X or column direction in one image plane or slice Number of Rows This field refers to the number of pixels in the Y or row direction in one image plane or slice Number of Image Planes or Slices This is the Planes 2 number of image planes or slices in the file Number of Bits Per Pixel This tells the size of each image pixel If the number of bits is 8 then each pixel is one byte in size and can store up to 256 levels If the number of bits is 16 then each pixel has 2 bytes of data and can store up to 65536 levels Number of Bytes to Skip Before the Image Data Array Some image files have a fixed length header for storing vendor specific information The length or the size of this header must be provided so the software knows to skip it in order to read the image data correctly If this value is unknown enter 1 to let the software estimate it automatically using the image size and file size Little Endian or Big Endian This parameter only matters when the number of bits per pixel is greater than 8 for example when an image is in 16 bit For most images created on a PC the file is stored as little endian default If your image is created on a Macintosh or a Unix workstation it is possible the pixel is stored as big endian You can tell right away if the image does not display correctly for example discontinuous gray levels In this case un
201. gle image file Your image can also be processed using the commands under the Image menu Define Object and Object Boundaries Use the Edit Object Settings to add objects to your project Use the 3D Rendering Auto Segment to automatically detect object boundaries You can also use the Interactive Segment or Segment Object commands to generate object boundaries for the defined objects You can use Edit Boundary Editor to trace object boundaries manually 3D Surface Rendering and Volume Rendering You can export the 3D surface models using the File Export Model command to many commonly used formats and create advanced animation using the View Animation Control command 3D surface model is created by connecting boundaries from all image slices Orginal Image Boundaries are detected using image segmentation It is important to have a good understanding of how different types of data such as images boundary lines point markers control points and annotations are handled by the software and how they are generated displayed edited and saved in a file OVERVIEW AND TUTORIAL In a previous section we have explained the windows used to display image planes volume images and surface images In this section we will explain the relationship between different data types supported by the main IMAGE PLANE WINDOW and its associated functions This allows you to see how some tasks can get done quickly and easily such as creating a surfa
202. gorithms to create a 3D display of the volume image If your image is a grayscale image the contrast of the volume rendered image is related to the contrast set for the original image display You can use the View Image Contrast command to adjust the display contrast before doing volume rendering Object boundaries will be used by volume rendering when available Use either the 3D Rendering Interactive Segment command or the 3D Rendering Segment Object commands to generate boundary lines automatically You can also use the Edit Boundary Editor options to draw boundaries manually Entire image volume a portion defined by regions of interest ROI or image portions defined by object boundaries can be used to create volume rendering volume Rendering xj Rendering Mode Voxel Type ow OK Grayscale Opaque Cancel Color C Transparent The following lists the 3D volume rendering methods supported 1 Grayscale with Opaque Voxels Image voxels are treated as opaque and ray traced and shaded using grayscale values 2 Grayscale with Transparent Voxels Voxels are treated as transparent and ray traced to create 3D rendering 3 Color with Opaque Voxels Color shading is applied on opaque voxels in volume rendering 4 Color with Transparent Voxels voxels are treated as transparent in the ray tracing process and color shading is applied Colors can be changed interactively There are two shading methods you ca
203. hanced image from the original image using a Sobel edge detector This command works only with grayscale images Other image types such as color images must be converted to a grayscale image before this command can be used If your image is a multi plane image the new image will be saved to a file and can be displayed using the File Open command 5 13 5 Gradient Magnitude command Process submenu The Image Process Gradient Magnitude command creates an edge enhanced image from the original image by calculating the gradient magnitude of the image This command works only with grayscale images Other image types such as color images must be converted to a grayscale image before this command can be used If your image is a multi plane image the new image will be saved to a file and can be displayed using the File Open command 5 13 6 Map Pixel Values command Processing submenu The Image Processing Map Pixel Values command is used to convert a range of pixel values to a new value This command works with grayscale images or palette color images When the Map Pixel Values dialog box appears enter the range of pixel values to be mapped and the new value Click OK to start the process Use Pixel Value Range Old Value Range To New Value Min Max cu p 5 p Cancel Use Lookup T able File Browse c NimageMookuptable txt When the Map Pixel Value dialog box appears specify the Map Pixel Values and the Ne
204. has its own menu bar Some functions are common to all windows such as the print and help commands Some functions are specific to a certain type of image window and their availability depends on the current image type and processing status An image window must be activated to make its functions accessible When you have multiple windows you can click the left mouse button within a window to make it active Most of the options provided by Edit Boundary Editor Edit Point Editor and Edit Control Point Editor can also be invoked from the floating pop up menus Clicking the right mouse button within the IMAGE PLANE WINDOW brings up the floating pop up menu with some popular commands or editing options You can display a menu s option by clicking on its menu heading with the left mouse button or by holding down the ALT key and typing the underline letter of its menu heading You can also select a menu option with the function keys called hot keys for example F1 to get on line help F2 to zoom in and F3 to zoom out F5 and F6 set the current display to the previous or next image slice respectively Some menu options initiate commands directly while others include a floating pop up menu brought up using the right mouse button or use a dialog box to initiate 32 OVERVIEW AND TUTORIAL commands An ellipsis mark next to a menu heading indicates that there is a dialog box for that option In 3D DOCTOR all options under the editing t
205. he New Value to be mapped A lookup table can be used to map the pixel values The lookup table file is a text file where each line has two numbers The first number is the original pixel value and the second number is the desired value or the new value to be mapped to This command is often used for global image pixel editing on image types such as 8 or 16 bit grayscale and 8 bit palette color image 93 EDIT MENU COMMANDS 3 6 Control Point Editor Edit Menu Control points are used to register or geometrically Editing On Olf transform an image to another image coordinate system Each control point defines a pair of points X Y Z for New both the source image and the target image When you eus have more than 4 control points a linear transform can Biel be established between the two images The source Check image can be registered to become the same size and orientation as target image using Pick Point Image Registration function Once an image is Open Control Points registered it can be fused with the target image or Save Control Points compared in the same coordinate system 3 6 1 Control Point Editor On Off command Control Point submenu The Edit Control Point Editing On Off command is used to start the Control Point Editor The Control Point Editor selects or modifies control points for image registration Once the Control Point Editor is started the cursor will change accor
206. he 3D Wizard dialog is displayed see figure to remind you the processing steps needed The push buttons are used to start the process of a task The following explains how to use the 3D Wizard Steps for creating 3D rendering Step 1 Image Calibration The image m image calibration dialog box will appear to allow you to verify the calibration parameters and dl DEDE DICIS modify them when needed For DICOM images their calibrations are normally Al Draw Regions of Interest ROI stored in the image file and used automatically by 3D DOCTOR Other image files may require calibrations to be entered R Interactive Segmentation to Generate Object Boundaries N Edit Boundaries Create 3D Model by Surface Rendering Step 2 Define Objects When the Object gt Complex Surface Rendering Management dialog box appears enter a i new object name at the bottom and click Add to the object list Click OK to use this object as the current object for segmentation If you want to use an already defined object you can select the object from the object list and click the Current button to set it as the Current object Step 3 Draw Regions of Interest ROI Regions of Interest ROI define the image regions to be used for image segmentation Once the ROI button is clicked you ll be in the editing mode to draw a polygon for a ROI Click the left mouse in the image window to draw a polygon and
207. her boundary 73 000000 1 82 000000 1 83 000000 1 You can switch to a 84 000000 1 different editing session by selecting another option from the Boundary Editor submenu or from the floating pop up menu brought up by pressing the right mouse button s OK You can terminate the Boundary Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 7 10 Undo command Boundary Editor submenu Use this command to undo a previous editing operation The Undo command is available for a certain number of steps during the editing session from the start to the end Once the editing session is turned off or switched to another editor the undo data buffer is refreshed Note You should save the vector data to a file frequently by using the File Boundary and Point Export Boundary command if you are doing intensive editing 3 7 11 Done command Boundary Editor submenu Use this command to exit the Boundary Editor 111 EDIT MENU COMMANDS 3 8 Boundary Report command Edit menu This command generates a report for all currently active boundaries The report shows the statistics about boundary data based on Boundaries Objects and Image Planes 3D DOCTOR Report x Statistical Report of Object Boundaries Copy Num of Boundaries ImagePlane Cent Object Name All Boundaries All Objects 207 All Planes 152 By Object default 0 Save hea
208. her section To undo the previous edit use the Edit Undo option or CONTROL Z Use the function keys F5 or F6 to go to another image plane for more editing You can switch to a different editing session by selecting another option from the Boundary Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Boundary Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 7 2 4 Delete Node command Boundary Editor submenu Use this command to delete a node from an existing line The cursor will change to a Delete Cursor To delete one node point the cursor at a node and click the left mouse button to remove it The system will always remove the closest node to the location clicked When deleting a node try to be as close as possible to the node you want removed Hold down the left mouse to delete nodes continuously To delete nodes within a region hold down both the SHIFT key and the left mouse button to drag and draw a selection rectangle including the nodes to be removed Once the rectangle is in place release the SHIFT key and the left mouse button Select the Delete Node option again and you will be asked to confirm the removal If the answer is YES all nodes and ends within the selected rectangle will be removed Lines will not be split if both ends are outside the region To undo the previous edit use the E
209. hes the object location in the target image identical point on the object not coordinates and click the left mouse button to define a new control point The coordinate picked from the target image is used for the To Destination fields in the Control Point dialog box Edit the values if necessary 3 6 8 Open Control Points command Control Point submenu This command reads control points from an existing control point file A control point file is an ASCII text file that stores control point pairs used for image registration 3 6 9 Save Control Points command Control Point submenu This command saves defined control points to a control point file A control point file is an ASCII text file that stores control point pairs used for image registration 96 EDIT MENU COMMANDS 3 6 10 Control Point Dialog Box The Control Point dialog box allows you to specify the destination coordinates of a selected control point The selected control point location is displayed and be modified The X is equivalent to the horizontal direction and Y 1s the vertical direction The Control Point x To Destination coordinate is to be entered and used when generating a geometric transform for vector data registration 97 EDIT MENU COMMANDS 3 7 Boundary Editor Edit menu Use the Edit Boundary Editor On Off command to start the Boundary Editor With the Boundary Editor you can add new boundary lin
210. i plane image you will be asked to provide an image filename to save the converted image The new image can be displayed using the File Open command 165 IMAGE MENU COMMANDS 5 15 4 8 bit Palette Gray Scale command Conversion submenu This command is used to convert an 8 bit palette color image to an 8 bit grayscale image The color information is lost in this conversion If the image has only a single plane the processing is done in memory You can use the File Save Image As to save the modified image to a new file If your image is a multi plane image you will be asked to provide an image filename to save the converted image The new image can be displayed using the File Open command 5 15 5 8 bit Palette 41 bit Bi level command Conversion submenu This command is used to convert an 8 bit palette color image to a 1 bit bi level monochrome image A selection rectangle should be defined before using this command The selection rectangle is used to indicate the color to be extracted If the image has only a single plane the processing is done in memory You can use the File Save Image As to save the modified image to a new file If your image is a multi plane image you will be asked to provide an image filename to save the converted image The new image can be displayed using the File Open command 5 15 6 16 bit Gray Scale 8 bit command Conversion submenu This command is used to convert a 16 bit graysca
211. iated with the 3D SURFACE WINDOW and many options can be used to adjust the display angle color and other parameters 3D surface models can be exported to many 3D graphics format using the File Export Model command including DXF IGES 3DS OBJ STL and other formats 7 5 2 Simple Surface command Surface Rendering submenu This command creates a simple 3D surface rendering using the boundary data generated from a 3D image The algorithm used for the simple surface rendering is vector based and is normally faster than other algorithms 3D surface models generated by the 3D Rendering Surface Rendering Simple Surface command will have much less surface triangles and be more suitable for rapid prototyping and other applications that require a more simplified surface Object boundaries must be defined before using the 3D Rendering Surface Rendering Simple Surface command Use either the 3D Rendering Interactive Segment command or the 3D Rendering Segment Object commands to generate boundary lines automatically You can also use the Edit Boundary Editor options to draw boundaries manually Depending on the quality of the original 3D image the boundary lines generated using the image segmentation functions may need to be edited to obtain better rendering results The Edit Boundary Editor provides functions to edit boundary lines easily and quickly The functions under the Boundary Process submenu can also be used to perform global boundary
212. icense where a conflict occurs 1 The Software was developed at private expense no portion was developed with government funds is a trade secret of Able Software and its licenser for all purposes of the Freedom of Information Act is commercial computer software subject to limited utilization as provided in any contract between the vendor and the government entity and in all respects is proprietary data belonging solely to Able Software and its licenser 2 Government personnel using the Software are hereby on notice that use of the Software is subject to restrictions that are the same or similar to those specified above 260 INDEX INDEX 1 1 bit monochrome 166 2 24 bit RGB gt Gray Scale 165 24 bit RGB gt Palette 165 24 bit true color 165 2D Image 20 3 3D contours 198 217 3D formats XYZ 23 221 3D image 20 3D Image 20 3D image I O 40 3D measure report 212 3D profile 32 3D Profile 91 3D rendering from contours 53 3D Rendering menu 181 3D sparse points 73 74 3D Studio file 196 3D surface model 30 3D surface window 30 3d surface measure 213 3D volume calculation 211 3D Wizard 182 3D Wizard auto start on off 183 3DBasic 26 227 3DBasic menu 225 3DBasic Assignment 233 3DBasic CLOSEIM AGE 241 3DBasic Create 226 3DBasic CROPIMAGE 243 3DBasic DECONVMAX 252 3DBasic DECONVNN 251 3DBasic examples 228 3DBasic FLOAT 231 3DBasic FOR 235 3DBasic
213. ies Voxels are ray traced to show the image in a 3D space Section 7 5 Volume Rendering command Volume rendering supports several rendering modes including transparency where voxels are treated as transparent direct object where only surface voxels are displayed and maximum density where only the brightest voxel is displayed along each ray Because volume rendering creates each view by ray tracing the entire volume it may take a longer amount of time to rotate when you have a larger image For 3D volume rendering you can save the data to a XYZ file where each voxel location is recorded as a point 23 OVERVIEW AND TUTORIAL 1 3 3 3D DOCTOR Main Functions The following is a list of things you can do with 3D DOCTOR e Visualize Images In Most File Formats DICOM TIFF BMP JPEG Interfile PNG Raw Image Data and other 3D image formats are all supported in 3D DOCTOR Image files in various vendor specific formats can be easily imported using 3D DOCTOR s universal image import function 3D surface rendering data can be exported to AutoCAD DXF IGES STL for rapid prototyping VRML for Internet use 3DS for 3D Studio and WAVEFRONT OBJ and raw triangle objects to transfer 3D surface model to other programs 3D volume rendering data can be saved as volume or as 3D XYZ format The 3D XYZ format is compatible with many commercial 3D quantitative analysis and simulation programs e Process Most Image Types 3D DOCTOR can process 8 bit a
214. ile located in the 3D DOCTOR program folder to license ablesw com to receive a license key file Save the license key to your 3D DOCTOR program folder to complete the license validation process You can also access the License Validation dialog box using the Help License Validate License command Please note without a validated license 3D DOCTOR will run in demo mode and many file exporting functions will be unavailable 15 OVERVIEW AND TUTORIAL 1 0 2 Installation Guide for License Using a USB License Key The following steps are required to install the USB hardware key Label ZQBXR and its device driver to enable the software NOTE If you are using Windows NT 2000 or XP you need to login to the system as a system administrator or with all the ADMINISTRATOR permissions to install device drivers before you start the following steps The license key driver is normally installed automatically If not please install it using the following steps 1 You can use Start Programs 3D DOCTOR Install Hardware Key Driver to install the driver automatically Or you can run hdd32 exe from the 3D DOCTOR program folder directly 2 Plug the hardware key to the USB port on your PC 1 0 3 Installation Guide for Network License When using a network floating license first you need to install 3D DOCTOR on all PCs you plan to run 3D DOCTOR The PCs must be connected to the local area network to share the license You
215. ile to store multiple planes if it has multiple planes The original image file is not affected by this processing In the multiple plane case you can save the modified image to a new file when the Save As dialog box appears after the command is selected Use the File Open command to display the newly created image file 139 IMAGE MENU COMMANDS 5 3 Reslice Commands Image Menu This submenu includes commands for reversing image slices image reslicing for images with variable slice spacing and 3D reslicing along the X Y or a user defined axis 5 3 1 Reslice command Reslice submenu This command is used to reslice an image that has uneven slice thickness or spacing You can use this command to change the slice thickness of a multiple slice image by giving a different slice thickness When you have a multi slice image in which the slice thickness is different from the pixel resolution you can use this command to create a new image with a slice thickness that is the same as the pixel resolution by entering the pixel XY resolution Use the Edit Calibration command to check the XY resolution in the New Thickness field This command works only with multi plane or multi slice images After this command is selected the Reslice Image Dialog Box see Figure appears to allow you to enter the exact spacing the sum of slice thickness and distance between slices Check the spacing for all slices to make sure the correct valu
216. image files and then click the Open button to add them to the stack list Or you can use the Select All button to add all files to the list DICOM images can be sorted automatically by 3D DOCTOR according to their 3D positions stored in the file header For non DICOM images make sure the order of the files to be added corresponds to the order of their 3D position within the image stack 5 1 1 2 840 113619 2 5 1762855897 1313 959214259 If the DICOMDIR file is available with the DICOM image files you can use the Load List command to open it and then select an image series from the Patient 59 FILE MENU COMMANDS Study Series list The Load List command can also load images from an existing stack list file The Delete button allows you to delete a file from the current list Select a file from the list first and then press the Delete button If you need to take a look at an image file added in the list select the file name in the list and then press the Preview button The image will be displayed in the preview window If the image cannot be previewed then you may have a problem with the file or the file format used You may have to use 3D DOCTOR s File Raw Image File Import function to configure the file first Step 3 Once the files are added to the list you can save the list to an image list file using the Save List button You can also open a list to bri
217. imagel 3ddoctor Nmagefile tif END 10 9 2 SCANIMAGE statement This command selects the scanner source for scanning an image Syntax SCANIMAGE imagevar where IMAGE3D imagevar Example IMAGE3D imagel SELECTSCANNER SCANIMAGE imagel SAVEIMAGE imagel 3ddoctor Nmagefile tif END 10 10 Deconvolution Commands 10 10 1 DECONVNN statement This command performs a nearest neighbor deconvolution It is similar to the Restoration Fast Nearest Neighbor command Syntax DECONVNN sourcefile psffile outputfile areasize kernelsize scalar DECONVNN sourcefile psffile outputfile 32 11 0 0001 251 3DBASIC COMMANDS where STRING sourcefile psffile outputfile INTEGER areasize kernelsize FLOAT scalar Example LOGFILE DECONVNN c Nmage tif cNpsf tif cNoutput tif 32 11 0 0001 END 10 10 2 DECONVMAX statement This command performs a maximum entropy based deconvolution It is similar to the Restoration Maximum Entropy command Syntax DECONVMAX sourcefile psffile outputfile iterations feedback DECONVMAX sourcefile psffile outputfile 15 0 05 where STRING sourcefile psffile outputfile INTEGER iterations FLOAT feedback this value should be less than 1 Example LOGFILE c output log DECONVMAX c image tif c psf tif cNoutput tif 15 0 05 END 10 10 3 RECONITER statement This command performs the 3D reconstruction using the iterative recons
218. ine Contours Surface Contour submenu B Spline Smoothing Parameters x Use this command to smooth contours using the B Spline method Number of Existing Points To Be Used 25 px Number of Vertices amp dded Between Points 0 Cancel SURFACE WINDOW COMMANDS After this command is selected the B Spline Smoothing Parameters dialog box appears to define the following parameters Number of Existing Points To Be Used as control points This parameter is defined in percentage relative to the total number of points on the original contour A value of 25 means that a quarter 1 4 of the total points are used in the calculation Smaller values will result in more smoothing Number of Vertices Added Between Points This is used to add smoothing points between each pair of control points 3D contours can be obtained from 3D surface models using the Tools Surface Contour Surface Contours command 8 18 4 Contour Color Surface Contour submenu Use this command to define a color from the Color dialog box for the contours 3D contours can be obtained from 3D surface models using the Tools Surface Contour Surface Contours command 8 18 5 Delete All Contours Surface Contour submenu Use this command to delete all contours 3D contours can be obtained from 3D surface models using the Tools Surface Contour Surface Contours command 8 18 6 Delete Last Contour Surface Contour submenu Use this command to delete the most
219. ine image regions to be used by both volume rendering and surface model creation For each 3D image you can define multiple objects and change their status using the Edit Object Setting command After the objects are defined you can set one as Current and generate boundaries for it using one of the segmentation commands or the Boundary Editor Boundary data can also be imported from other sources or exported to other programs The following explains the process of generating boundary lines using image segmentation for 3D rendering Section 7 1 and 7 2 Segmentation commands Step 1 Open the 3D image using the File Open command If the image has multiple slices you should see two windows one window displays a single slice and another window displays a montage of all the slices If you don t see the MONTAGE WINDOW and the image plane number is not displayed in the IMAGE PLANE WINDOW you will need to use the File New Stack command to put the 2D image files into a 3D stack first Step 2 If you want 3D DOCTOR to detect object boundaries automatically simply select the 3D Rendering Auto Segment command and enter the number which indicates how many possible objects you d like to detect Click OK and wait for the boundaries to be detected If you are happy with the boundaries then go to Step 6 If you d like to segment the image planes interactively then follow Step 3 to Step 6 Step 3 Use the Edit Object Settings command to add new ob
220. information Image slices may not be ordered correctly using one method due to incomplete information stored in the image You can try to use another method to sort them 5 16 1 Sort By Image Position This function sorts the current image slices using the image position information stored in the DICOM image file 5 16 2 Sort By Image Number This function sorts the current image slices using the image number record stored in the DICOM image file 5 17 Deconvolution commands Image Menu Perform 3D image restoration by deconvolution Image restoration is used to remove or reduce degradations that were incurred while the image was being obtained These include the blurring introduced by optical systems and by image motion as well as noise due to electronic and photometric sources The aim of image restoration is to bring the image toward what it would have been if it had been recorded without degradation When the source of degradation blurring and noise can be characterized and modeled as a point spread function PSF then their effects can be subsequently removed or reduced with a deconvolution process using the PSF and the degraded image 167 IMAGE MENU COMMANDS 3D DOCTOR provides two types of deconvolution to restore degraded 3D images one is a Fast Nearest Neighbor deconvolution and the other one is an iterative Maximum Entropy deconvolution method With commands under the Image Deconvolution menu you can e R
221. ing area to confirm The updated annotation will be displayed in the IMAGE PLANE WINDOW Repeat this process to modify other annotations or text labels Use the Delete option to delete an existing annotation or the Add option to add a new annotation You can switch to another editing session by selecting a different option from the Annotation Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Annotation Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 12 4 Move command Annotation Editor submenu This command switches to the Move editing mode This editing mode allows you to move annotation text to a new location Click the left mouse button on an annotation and drag the mouse to move 118 EDIT MENU COMMANDS 3 12 5 Set Object command Annotation Editor submenu This command switches to the Set Object editing mode This editing mode allows you to change the object attribute of text to the Current object Click the left mouse button on an annotation to change 3 12 6 Convert to Boundary command Annotation Editor submenu This command switches to the Convert To Boundary editing mode This editing mode allows you to trace the annotation text into object boundaries The purpose is to use the text boundaries in surface rendering to create labels on a 3D model Normally the te
222. ion by selecting another option from the Boundary Editor submenu or from the floating pop up menu brought up by pressing the right mouse button 108 EDIT MENU COMMANDS You can terminate the Boundary Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 7 9 2 Assign Plane Value command Boundary Editor submenu Use this command to assign the currently specified plane value to an existing boundary line The plane value of a boundary line indicates the Z value in 3D space which is critical and very important in the volume and surface rendering processes If you use 3D DOCTOR s segmentation functions to get the boundaries normally you do not have to do anything in terms of the plane value as the software sets them automatically If you import your boundary data from somewhere else or it is created in other ways you need to use the Assign Plane Value function to adjust the plane value to make the boundary lines correct in 3D space The cursor will change to an ID Cursor Point and click the left mouse button at a line to set Once a line is selected it is highlighted to indicate the selection and the plane value is displayed in the Status Bar To assign the current plane value to a group of lines within a rectangle you need to hold down both the SHIFT key and the left mouse button to draw a rectangle and select the Assign Plane Value command again All lines that inter
223. is complete and not connected to other parts of the object set the selected portion as a new object or delete the portion from the object it belongs 8 17 1 Select command This command toggles the selection tool ON and OFF When the selection tool is on the menu item is checked To select a portion on an object first turn on the selection tool Move the cursor to an object click the left mouse button The selected portion will be highlighted To set the selected portion as a new object call the New Object command To delete the selected portion call the Delete command 8 17 2 New Object command This command sets the selected portion on an object to a new object Use the Select command to select a portion first and then use this command to set it as a new object 215 SURFACE WINDOW COMMANDS 8 17 3 Delete command This command deletes the selected portion on an object Use the Select command to select a portion first and then use this command to delete 216 SURFACE WINDOW COMMANDS 8 18 Surface Contour Commands Tools Menu 8 18 1 Cut Contours command Surface Contour submenu The command is Cutting 3D Contours used to obtain surface contours of m Cutting Plane Location X Y 2 all currently visible m 3D objects created BE D zi using the surface Cutting Plane Normal b a im b g rendering command contour is Number of Contours To Get calculated as the E
224. ist Ist Raw Image hdr Bitmap bmp JPEG Files jpeg File Name Type or select the filename you want to open This box lists files with the extension you selected in the Files of Type box List Files of Type Select the type of file you want to open The currently supported image file format is Stack List 150 3D DOCTOR Project prj TIFF tif Bitmap bmp JPEG jpeg jpg DICOM dcm dic Raw Image hdr PNG png and other image formats Other 3D formats such as surface file suf and volume image vol are also supported Drives Select the disk drive in which 3D DOCTOR stores the file that you want to open Directories Select the directory where 3D DOCTOR stores the file that you want to open Network Choose this button to connect to a network location assigning it a new drive letter 62 FILE MENU COMMANDS 2 3 Uncompress DICOM command File Menu This command is used to uncompress JPEG compressed DICOM images Compressed DICOM files cannot be opened directly into 3D DOCTOR If you have compressed DICOM files use this command to convert them to uncompressed DICOM first and then use them in 3D DOCTOR Uncompress DICOM Files x Uncompress DICOM Files In Folder Browse Include Sub Folders C Nimages3dNDICOM Compressed Browse Overwrite Exsiting Files C images3d DICOM Compressed Cancel r Output DICOM Files To Folder At th
225. itch to the rectangle boundary line drawing mode The cursor will change to a Cross Cursor To draw a rectangle in the current image plane point the cursor at an image location that will be the upper left corner Hold down the left mouse button and drag to a position for the lower right corner of the rectangle Release the left mouse button to confirm the rectangle boundary Repeat this step to add more rectangle boundaries If an exact square is to be drawn hold down the SHIFT or the CONTROL key while drawing and release when finished To undo the last boundary use the Edit Undo option or CONTROL Z Use the function keys F5 or F6 to go to another image plane for more editing You can switch to a different editing session by selecting a different option from the Boundary Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Boundary Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 7 1 3 Draw Circle command Boundary Editor submenu Use this command to switch to the circle ellipse boundary line drawing mode The cursor will change to a Cross Cursor To draw a circle ellipse in the current image plane point the cursor at an image location that will be the upper left corner Hold down the left mouse button and drag to a position for the lower right corner of the rectangle outline Release the left mouse
226. ive location of the boundary lines 81 EDIT MENU COMMANDS 3 2 Object Commands 3 2 1 Object Settings command Edit Menu Use this command to define new objects update existing objects or set the status of existing objects After this command is selected an Object management dialog box appears See Figure Object management 9 dd du rrent Current ul on Color Hatch LineT ype Delete gt a R Open Save 3D DOCTOR always defines a default object with the name default This object will always exist and cannot be deleted or changed When adding a new object to the current object list click the Add button and then click on the name in the object list to edit To define a color for an object you can click on the color of the object Or first select an object by highlighting it in the object list and click the Color button Choose a color from the Color dialog box to apply The color defined for the object will be applied to all the data within the object automatically Double click in the Status field of an object will set it as Current Or use the Current button to set a selected object as the current object if you are going to work within this object All data created will be put into the current object When one or more objects are turned on using the On Off button all data within those objects will be active to the
227. ject and is followed by the name of the object and the color code 2 9 2 Export Boundary command Boundary and Point submenu The File Boundary and Point Export Boundary command is used to save boundary data to a file The currently supported formats include Boundary Files bnd DXF CAD drawing exchange Files dxf ROI regions of interest file compatible with formats using Pinnacle treatment planning systems Files roi Slice File slc IBL for laser scanners or coordinate measuring machines Files ibl 3D XYZ saves boundaries as 3D points Files xyz and Point saves only the points data Files pnt The boundary file bnd saves the boundary data of the currently active objects The DXF file saves boundaries of all objects as well as points and text annotations If you need to export the points select the export file type to point file pnt to do so If the option to apply calibration is selected the output boundary and point data will be scaled using the calibration parameters entered in the Image Calibration Parameters dialog box Section 1 6 4 Defining Voxel Size and Slice Thickness for Calibration This option is used when boundary and point data are exported for analysis purposes in real physical unit Because the boundaries with calibration would not match the image coordinates you should not use this option if you intend to import the boundaries into another image 2 9 3 Import Point comm
228. ject names for this image When the Object management dialog appears enter a new object name in the edit box at the bottom and click the Add button to add to the object name list Highlight one object from the list and click the Current button This will set the new object as the current object and it will receive the boundary data generated from the segmentation process in Step 4 Click the OK button to finish this step 46 OVERVIEW AND TUTORIAL Step 4 Regions of Interest ROIs can be defined using the Edit Region of Interest ROD command to limit the image areas for the segmentation If ROIs are defined only pixels within the ROIs are processed for boundary extraction This is especially useful when segmenting objects with complex boundary lines across the image planes Once the ROI editing is you can click the left mouse button within the image to draw polygons Press the SPACEBAR to close a polygon ROIs are displayed as thick blue lines Step 5 Select the 3D Rendering Interactive Segment command Answer Yes when asked if you want to keep the current object for segmentation The Interactive Segmentation dialog box appears and the display of the single IMAGE PLANE WINDOW is changed The red color is used to show pixels that fall within the threshold range specified by the Minimum and Maximum values Use the slider bar to adjust the Minimum and Maximum values The display of the current image slice is updat
229. l Support 27 terminology 20 Texture 200 THEN 235 TIFF 61 Tile 254 255 Tile Horizontal 255 Tile Vertical 255 TO 235 tomography 26 Tool bar 122 tool bars 35 toolbars boundary editor 35 toolbars measuring tools 35 toolbars object 35 toolbars zooming and rotating 35 top view 19 training area draw 186 transparency 201 Transpose 139 treatment planning system ROI file 72 true color 61 turn clockwise 199 turn down 199 turn left 199 turn right 199 turn up 199 tutorial 36 268 TWAIN scanner 76 U uncompress DICOM 63 Undo 111 120 Upgrades 27 user interface 19 User Interface 28 user palette 130 V View menu 121 viewing angle 224 Viewport move 198 volume 110 Volume 211 Volume cut 174 volume image 20 Volume Image Window 30 volume rendering 23 25 30 47 55 221 Volume rendering 46 48 191 192 193 volume rendering color map 193 Volume rendering direct object 191 192 193 Volume rendering maximum density 191 192 193 Volume rendering surface casting 191 192 193 Volume rendering transparent 191 192 193 volume view 20 volume window 30 Volume open 222 Volume save 222 Voxel size 44 voxels 30 VRML 23 W Wavefront OBJ 196 web address 27 web browser 23 Window 1 2 254 Window Arrange Icons 255 Window menu 254 Windows 95 17 Windows NT 17 wireframe 202 Workspace resize 81 X
230. lane 2 5 Open Model command File Menu This command can be accessed from the IMAGE PLANE WINDOW the MONTAGE WINDOW the 3D SURFACE WINDOW and the VOLUME VIEW WINDOW Use this command to open a surface file A surface file contains 3D surface data created from the surface rendering commands The 3D DOCTOR surface file is in binary format and is used internally by 3D DOCTOR If you need to export the 3D surface data to other systems you can use the File Export Model command Other 3D data file formats for import include AutoCAD DXF STL 3DS and ASCII raw triangle file 2 6 Close command File Menu This command can be accessed from the IMAGE PLANE WINDOW the MONTAGE WINDOW the 3D SURFACE WINDOW and the VOLUME VIEW WINDOW Use this command to close all windows containing the active document 3D DOCTOR suggests that you save changes to your document before you close it If you close a document without saving you lose all changes made since the last time you saved You can use the File Save Save Image As command to save the modified image to a new file while the original image remains unchanged You can also close a document by using the Close icon on the document s window 2 7 Save File Menu This command can be accessed from the IMAGE PLANE WINDOW the MONTAGE WINDOW the 3D SURFACE WINDOW and the VOLUME VIEW WINDOW 2 7 1 Save Image As command Save submenu Use this command to save the currently active
231. le imagel OPENIMAGE imagel c 3ddoctor head3d tif NEGATEIMAGE image c 3ddoctor newimage tif SHOWIMAGE imagel END 245 3DBASIC COMMANDS 10 5 19 SHARPEN statement This command sharpens an image using a high pass filter and saves the processed image to a new image file Syntax SHARPEN imagevar filename SHARPEN imagevar filename where IMAGE3D imagevar STRING filename Example imagel OPENIMAGE imagel c N3ddoctorvhead3d tif SHARPEN imagel cN3ddoctorviewimage tif SHOWIMAGE imagel END 10 5 20 RECONBACKPROJ statement This command performs the 3D reconstruction using the filtered back projection algorithm and saves the reconstructed to a new image file Syntax imagevar filename 5 0 imagevar filename angle where IMAGE3D imagevar STRING filename FLOAT angle Example IMAGE3D imagel image2 FLOAT angle angle 5 0 OPENIMAGE image c 3ddoctor head3d tif RECONBACKPROJ image c 3ddoctor newimage tif angle OPENIMAGE image2 c 3ddoctor newimage tif SHOWIMAGE imagel SHOWIMAGE image2 END 246 3DBASIC COMMANDS 10 6 Segmentation Commands 10 6 1 AUTOSEGMENT statement This command segments an image using the Auto Segment command The generated object boundaries are stored in the IMAGE3D variable and can be saved to a project file or used by surface or volume rendering commands
232. le For simple reslicing along the X axis to create a side view of the image use the Image Reslice X Axis command For reslicing along the Y axis to create a top view of the image use the Image Reslice Y Axis command If you need to reslice the image along an arbitrary axis that is defined by a 3D angle then use the Image Reslice Volume command The Rotate Volume Dialog box appears for entering the 3D angle for the axis namely X up down angle Y left right angle and Z clockwise angle If you do not know the Rotate Volume Dialog x desired angle you can use the following steps to estimate it Section 5 4 Up Down 5 m Enter Rotation Angles In Degrees Reslice Step 1 Use the 3D p o Z Clockwise Step 2 Once the 3D Dutput File rendering is displayed use the ina e the Browse viewing angle control tool buttons adjust the volume orientation to the position you want to see in the new image after reslicing Step 3 Use the View Viewing Angle Angle Setting command to show the current viewing angle Click Save to remember the angle so they will be used by the Image Reslice Volume command automatically or write down the angle values X Y Z to enter manually 51 OVERVIEW AND TUTORIAL Step 4 Now start the Image Reslice Volume command and enter the angle values and provide a new Output File name Click OK to reslice and save the new
233. le image to an 8 bit grayscale image This command works with 3D volume images and saves the resulting image to a new file If the image has only a single plane the processing is done in memory You can use the File Save Image As to save the modified image to a new file If your image is a multi plane image you will be asked to provide an image filename to save the converted image The new image can be displayed using the File Open command 5 15 7 8 bit Gray Scale 24 bit RGB command Conversion submenu This command is used to convert an 8 bit grayscale image to a 24 bit RGB color image When a color palette is used the colors are used in the new color image This command works with 3D volume images and saves the resulting image to a new file If the image has only a single plane the processing is done in memory You can use the File Save Image As to save the modified image to a new file If your image is 166 IMAGE MENU COMMANDS a multi plane image you will be asked to provide an image filename to save the converted image The new image can be displayed using the File Open command 5 15 8 1 bit 8 bit Grayscale command Conversion submenu This command is used to convert a 1 bit monochrome image to an 8 bit grayscale image The new image is saved to a file specified 5 16 Sort Slices commands Image Menu The image slice sorting functions work with DICOM image files that store image position and image number
234. le opened windows in an overlapped fashion WINDOW MENU COMMANDS 11 3 Tile command Window menu Use this command to arrange multiple opened windows in a non overlapped fashion 11 4 Tile Horizontal command Window menu Use this command to vertically arrange multiple opened windows in a non overlapped fashion 11 5 Tile Vertical command Window menu Use this command to arrange multiple opened windows side by side 11 6 Window Arrange Icons Command Use this command to arrange the icons for minimized windows at the bottom of the main window If there is an open document window at the bottom of the main window then some or all of the icons may not be visible because they will be underneath this document window 11 7 1 2 command Window menu 3D DOCTOR displays a list of currently open document windows at the bottom of the Window menu A check mark appears in front of the document name of the active window Choose a document from this list to make its window active 255 Help menu commands The Help menu offers the following commands which provide you assistance with this application Help Offers you an index to topics on which you can get help Topics Displays the version number of this application 12 1 Help Topics command Help menu Use this command to display the opening screen of Help From the opening screen you can jump to step by step instructions for using 3D DOCTOR for Windows and various type
235. ligent edge tracing will be performed while the cursor is moving To keep the edges traced click the left mouse button at the current location This option can be turned on or off at any time using the right click popup menu or the main menu To trace continuously hold down the left mouse button to start tracing Release the left mouse button to finish the current section of the boundary When the drawing is completed hit the SPACEBAR key except the N key to close the polygon Repeat the above process to add another line If you have defined more than one object the current object is used automatically to hold the newly added boundary To undo the current point selection use the Edit Undo command or the BACKSPACE key Use the function keys F5 or F6 to go to another image plane for adding boundaries in other planes The boundary will have the Z value of the current image plane by default You can use the Edit Boundary Editor Assign Plane Value option to change the image plane You can switch to a different editing session by selecting a different option from the Boundary Editor submenu or from the floating pop up menu brought up by pressing the right mouse button 99 EDIT MENU COMMANDS You can terminate the Boundary Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 7 1 2 Draw Rectangle command Boundary Editor submenu Use this command to sw
236. line processing such as Smooth Delete By Length Delete By Plane and other processing commands Once a 3D surface is created from the boundary data a new 3D SURFACE WINDOW appears with the surface image displayed A 3D menu bar is associated with the 3D SURFACE WINDOW and many options can be used to adjust the display angle color and other parameters The surface can be displayed as either a solid surface which is the default setting in 3D DOCTOR transparent or as a Wire Frame 3D surface models can be exported to many 3D graphics formats using the File Export Model command including DXF IGES 3DS OBJ STL and other formats 189 3D RENDERING COMMANDS 7 5 3 Convex Surface command Surface Rendering submenu This command creates a simple surface model from the boundaries by ignoring all holes and islands This is suitable when your boundaries are clean without islands and holes 3D surface models can be exported to many 3D graphics format using the File Export Model command including DXF IGES 3DS OBJ STL and other formats 190 3D RENDERING COMMANDS 7 6 Volume Rendering commands 3D Rendering Menu 7 6 1 Smooth Rendering Volume Rendering submenu This command creates a 3D volume rendering by using voxels within defined object boundaries if present or a region of interest or the entire volume if no boundaries or regions of interest ROI are present The volume rendering uses ray tracing based al
237. ly opened image to be registered Target image this image will stay the same and not affected by the registration ne CEA EST ED ERES E E CEEE Step 1 Use the Open button to open the target image Both the current image and the target image are displayed in 3D The 3D view can be rotated Step 2 Define the transform by adjusting the orientation location and scale of the current image to fit the target image Step 3 Once the images fit each other use the Browse button to define the filename to store the registered image Click the Register button to create the registered image Target Image for Regiveaton Ow Display Transtorm Rotate n o ELI Move By Y o BD 2 0 dl Sene xh es vh zf sb M sedie PEUT Show Target image Only Show Beth Images o Sore Regeedinsg To Browse Soucelmage Head THal stack it Cancel Target Image lor Regearation Open Target Image ko Fegietation Bee E Gnopes3AFeginenC Thandie Display Transform Rotate in degoes Rotate m degrees a x e a Y p v fo zh s z e sj Mave By Move By x p BD 10 2 Sose
238. m This method checks all pixels at each pixel location of all image planes and keeps the biggest value for the final fusion image 159 IMAGE MENU COMMANDS Once the fusion image is successfully created use the File Save Save Image As command to save it to a file 5 10 Mosaic command Image Menu This command is used to create an image mosaic from multiple images or images with multiple planes Images with overlapped borders can be merged seamlessly After the Image Mosaic command is started the Image Mosaic Dialog box appears See Figure In the dialog box you can enter the Mosaic Matrix Layout Parameters and the Image File Names The Number of Images in a Row and the Number of Rows defines the layout of the image mosaic For example if you have 6 images to be merged together you can plan to have 3 images for each row and have 2 rows Use the Images button to add image files to the list The order of an image in the list determines its location in the final mosaic If an image has multiple planes each plane will be treated as an image and used in the mosaic The images have different sizes but they must be the same type for example 8 bit 16 bit grayscale or 24 bit RGB image Different image types can supported by this command The Image 1 Image 2 Image Image 4 Image 5 Imaget If the images have border ov roughly how much overlap exist the top When Has Overlap is
239. mage The values on the right side To are the coordinates from the target image picked up in Step 3 Step 5 Repeat Step 3 and Step 4 until you have at least 4 control points for the source image Normally you should define more than 4 control points Make sure the control points are spread out within the volume They must not all be in a single image slice Step 6 Select the Image Registration command Enter the parameters required the output file name and the dimension of the output image use the same as the target image if fusion is going to be done Click on the OK button to start the process When the process is done a new registered image is created and saved to the name as specified 50 OVERVIEW AND TUTORIAL Step 7 If image fusion or color fusion needs to be done select the Image Fusion or Image Color Fusion command Enter the file names and select the required image combination option and then click on to start 1 6 9 Reslicing a 3D Image Along an Arbitrary Axis 3D DOCTOR provides functions to reslice a 3D image along a user defined axis or simply the X or the Y axis of the current image coordinate system With these functions you can easily overcome the limitations of an imaging device and create image slices along any axis By reslicing a 3D image certain features that may be difficult to see in the original form can become more visible in the new image The resliced image is saved in a new image fi
240. mand to create an ROI from the existing object boundaries The existing object must be set as Current before you do this Segmentation Segmentation is an automated image processing function to extract or generate object boundaries 3D DOCTOR has several image segmentation functions For example the 3D Rendering Interactive Segment function uses the image s grayscale range to create boundaries The 3D_ Rendering Segment Object function uses a defined training area to help detect similar image regions The segmentation function can process all slices automatically Surface Rendering Surface rendering creates polygon based 3D surface models from defined object boundaries Section 7 3 Surface Rendering Surface 22 OVERVIEW AND TUTORIAL rendering displays the surface model and allows you to change the color and transparency properties of the rendered objects 3D volume and surface area can be accurately calculated from these surface models You can save surface models to 3D formats such as AutoCAD DXF and IGES Saving a surface model in VRML format allows for use over the Internet by web browsers with the necessary plug ins In addition 3DS format can be used for 3D Studio and STL format can be used for rapid prototyping applications The WAVEFRONT OBJ and raw surface triangles allow the transfer of data to other software packages e Volume Rendering Volume rendering creates a 3D display using both the 3D image and the boundar
241. me Between Frames command will bring up the Animation Pace Control dialog box See Figure 40 milliseconds Cancel 206 SURFACE WINDOW COMMANDS This dialog box allows you to control the amount of time in milliseconds between frames during the animation process 207 SURFACE WINDOW COMMANDS 8 13 3 Animation Control command Animate submenu This command allows you to define and control the animation sequence and movement of each object The 3D Animation Control dialog box appears See Figure 3D Animation Control Object Animation Control Viewing Angle Control Select an object from the listto edit After Each Loop Increment in Degrees brain C Return to Starting Point p The following defines the increment values Reverse Direction and the number of steps in a loop Y Left Right ght Rotate in degrees By 1 T scale x 0 x x D 7 Clockwise p Y Poo Y b 2 Z 7 Steps 0 Steps LN Steps o OK Cancel dui To define the movement of an object in the animation first select the object from the Object List and then enter the following parameters e Rotate in degrees The X Y Z are the increments in degree that changes the three angles that control the rotation of the object at each frame The X is for the angle that ro
242. menu brought up by pressing the right mouse button You can terminate the Boundary Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 105 EDIT MENU COMMANDS 3 7 5 2 Merge Boundaries Use this command to merge two boundaries into one The cursor will change to a Merge Boundary cursor in this editing mode Move the cursor to the first boundary click and hold down the left mouse button and drag it into the second boundary Release the left mouse button to merge Repeat this process to merge more boundaries To undo the previous edit use the Edit Undo option or CONTROL Z Use the function keys F5 or F6 to go to another image plane for more editing You can switch to a different editing session by selecting another option from the Boundary Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Boundary Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 7 6 Close Boundary command Boundary Editor submenu Use this command to create a closed polygon The cursor will change to a Cross Cursor when the Boundary Editor is in the Close Boundary editing mode To close a line point the cursor at a line and then click the left mouse button to close it The closed line is then displayed Repeat this step if more lines are to be closed You c
243. mmand You can turn on the displays of SIDE VIEW and FRONT VIEW by using the View All Views command This command is not available if an image has only a single plane 4 4 2 Views command View Menu This command toggles on the side and front profile views for the image This view mode shows the current slice position and the profile by looking from the side of the volume See Figure The SIDE VIEW displays a lower resolution column profile defined by a yellow vertical line in the IMAGE PLANE WINDOW You can move this line by holding down the left mouse button This allows you to display a different profile A yellow vertical line is displayed in the SIDE VIEW window to indicate the current image plane The plane ID is displayed at the upper left corner You can display a specific image plane in the IMAGE PLANE WINDOW by moving the yellow line within the MONTAGE WINDOW This FRONT VIEW window shows the current slice position and the profile by looking from the top of the volume The FRONT VIEW displays a lower resolution row profile defined by a yellow horizontal line in the IMAGE PLANE WINDOW You can move this line by holding down the left mouse button to display a different profile A yellow horizontal line is displayed in the FRONT VIEW window to indicate the current image plane The plane ID is displayed at the upper left corner You can display a specific image plane in the IMAGE PLANE WINDOW by moving the yellow line within
244. mmand toggles this option on and off 134 VIEW MENU COMMANDS 4 14 Selection Rectangle command View Menu The View Selection Rectangle command allows the user to define uu selection rectangle according to Current Selection Rectangle their needs Left 110 Right 110 pen When the command is selected A m Top 1 tom fi Define Selection Rectangle dialog se box appears See Figure of Columns 0 HofRows Q Apply 4 15 Calibrated Coord command View Menu The View Calibrated Coord command toggles the display of calibrated image voxel coordinates on and off By default 3D DOCTOR displays current voxel locations in the image coordinate system If the Calibrated Coord display option is selected then the user defined calibration parameters will be applied to scale the image voxel location to the user defined unit When using the Edit Measuring Tool options within an image window holding down the CONTROL key and the left mouse button will apply the calibration parameters to the calculation when the Calibration Coord option is turned on Otherwise only the voxel location is used This command affects the display only and it will not affect any data or processing 135 IMAGE MENU COMMANDS Image Menu Commands Funcions for image processing 3D volume image regstration and fuson image conversion color dassjfication With commands under the Image menu
245. n a boundary is drawn it always belongs to the current object For example a 3D image of a head can be separated into multiple objects including the outline of the head the skull and the brain Once boundaries are generated for each object the boundaries can be used for 3D rendering You can group objects together to create different 3D displays by turning them on or off For example if half of a head and the brain are selected as objects an image of an exposed brain will appear with the half of the head that was selected Objects are defined and updated using the Edit Object Setting command Section 3 2 1 Object Setting command Boundary Contour Boundaries are contours that define the area of a 3D object in each slice within a 3D image Because boundaries are used to tell which part of the volume image is included in 3D rendering and quantitative analysis they are required before 3D rendering can be done On each image plane one object can have any number of boundaries that are not self intersected or intersected to each other One boundary can be contained by another boundary of the same object to form a hole or island See Figure on the next page The polarity rule applies in boundary topology to indicate which part is included and which part is excluded For example when a voxel is first contained by a boundary it is included The second time it is contained by a boundary of the same object it is outside the object or exclude
246. n choose grayscale or color The grayscale mode uses the value from the voxels for the rendering The color mode uses user 191 3D RENDERING COMMANDS defined colors for shading Use the View Color command to change colors used for volume rendering Voxels can be treated as transparent or opaque in the rendering Volume data can be saved using the File Save Volume command to VOL XYZ and other formats 7 6 2 Direct Volume command Volume Rendering submenu This command creates a direct 3D volume rendering by using voxels within defined object boundaries The volume rendering uses ray tracing based algorithms to create a 3D display of the volume image If your image is a grayscale image the contrast of the volume rendered image is related to the contrast set for the original image display You can use the View Image Contrast command to adjust the display contrast before doing volume rendering Object boundaries will be used by volume rendering when available Use either the 3D Rendering Interactive Segment command or the 3D Rendering Segment Object commands to generate boundary lines automatically You can also use the Edit Boundary Editor options to draw boundaries manually 3D Rendering Volume Rendering includes several different rendering methods such as Maximum Density Transparent Direct Object and Surface Casting for creating different rendering effects of the 3D image There are three scales you can choose from fo
247. nd 16 bit gray scale images 8 bit and 24 bit color images and 1 bit black and white images Image type conversion functions are provided to change image types For example converting a 24 bit RGB color image to grayscale or converting a 16 bit grayscale image to an 8 bit grayscale image reduces the size of the image e Template Based Film Cropping If your CT or MRI images come on film then you can scan them using a film scanner or a regular image scanner with a transparency kit for 3D processing 3D DOCTOR s template based Image Crop Image Crop Film command can be used to crop image slices and save them to image files automatically Section 5 4 4 Crop Film command e Powerful Display Functions A 3D image is displayed in both an IMAGE PLANE WINDOW to show full details of a single image plane slice and a MONTAGE WINDOW where all image planes are displayed as thumbnail size panes to allow easy navigation between slices The 3D volume rendering and 3D surface rendering allows you to see the image in 3D AII display windows can be animated and saved to an AVI movie file using the movie creation function Section 4 10 3 Create Movie command You can switch the image plane display to another slice by double clicking on a pane in the MONTAGE WINDOW With the palette control functions you can change the palette to pseudo color red green or blue Section 4 11 Image Palette You can adjust the image contrast to enhance the image display o
248. nd to define image plane based regions of interest from object boundaries in the current object The regions of interest ROI will be visible and work on their own image plane The ROIs defined using the ROI Editing Tool will work for the entire image The two types of ROIs can be used together for image segmentation and cropping Use the Edit Region of Interest ROD ROI Tool On Off to define regions of interest for all image planes 3 3 3 Inflate Region command F7 Region of Interest submenu Use the Edit Region of Interest ROD Inflate Region command to increase the size of the currently defined regions of interest Use the Edit Region of Interest ROD ROI Tool On Off to define a new region of interest for image segmentation Use the Edit Region of Interest ROD Deflate Region command to decrease the size of the ROI 3 3 4 Deflate Region command F8 Region of Interest submenu Use the Edit Region of Interest ROD Deflate Region command to decrease the size of the currently defined regions of interest Use the Edit Region of Interest ROD ROI Tool On Off command to define a new region of interest for image segmentation Use the Edit Region of Interest ROD Inflate Region to increase the size of the ROI 3 3 5 Clear ROIs command Edit Menu Use this command to remove the currently defined regions of interest 3 4 Measuring Tool Edit Menu 3 4 1 Measure On Off command Measuring Tool submenu 87
249. ndard Image Files 3D DOCTOR supports various image file formats directly including DICOM TIFF JPEG Interfile PNG and BMP For other non standard image file formats such as a raw binary file or a vendor proprietary image file format 3D DOCTOR s raw image import function will create an image header file for the raw image data file when its configuration or file structure is known If an image is 256 by 256 uncompressed and 12 16 bits deep and hence usually stored as two bytes per pixel then the file is going to contain 256 256 2 131072 bytes of pixel data at the end of the file If the file is 145408 bytes long as all GE Signa 3X AX files are for example then you need to skip 145408 131072 14336 bytes of header before you get to the data If you are sure the pixel data is stored at the end of the file then you can enter 1 and let 3D DOCTOR calculate it automatically for you Because images can be stored either by row or by column the imported image orientation may be different or incorrect In this case the Image Flip or Image Transpose commands can be used to adjust the orientation 3D DOCTOR has two functions under the File menu for importing raw image files File Raw Image File Import Single File and File Raw Image Import Multiple Files 41 OVERVIEW AND TUTORIAL The first command is used to create a header file for a single image data file either stored as a 3D volume or as a 2D plane The second command is used
250. ndering Segment Object commands to generate boundary lines automatically You can also use the Edit Boundary Editor options to draw boundaries manually When the Volume Color Mapping dialog box appears use the Add button to add a new entry The Base group includes all pixel intensity range except those defined by the other entries in the table For each color map entry the From and To fields define the starting and ending values of a range The transparency value has a range from 0 to 1 0 means no transparency or total opaque while 1 means total transparent If it is defined as total transparent then it will be invisible in the rendering If it is opaque it will be visible but will block any voxels behind it Volume Color Mapping xi Add Save DK Delete Open di To pick a From or To value from the image preview highlight the value from the table first then move the cursor to the image and click to pick 193 3D RENDERING COMMANDS To enter a value manually highlight it and then type in a value To change the color click on the color and then use the Color dialog box to pick a color If you want to save your color map for other similar images use the Save button You can also open an existing color map file by using the Open button Click OK to create the volume rendering To change the colors after the volume rendering is created use the View C
251. ndows 95 98 Windows ME Windows XP and Vista are trademarks of Microsoft Corporation Pentium Pentium 4 and Pentium III are trademarks of Intel Corp Other brands or product names are trademarks or registered trademarks of their respective holders TABLE OF CONTENTS Table of Contents CHAPTER 1 3D DOCTOR OVERVIEW AND TUTORIAL eee ee eee eee enne eene eee tn seen 15 1 0 INSTALLATION GUIDE eh IY a tne ba eee a Tape ss 15 1 0 1 INSTALLATION GUIDE FOR LICENSE USING A SOFTWARE enn 15 1 0 2 INSTALLATION GUIDE FOR LICENSE USING A USB LICENSE KEY eee 16 1 0 3 INSTALLATION GUIDE FOR NETWORK LICENSE eeeeee n n n nen nnn nnn nnn nnn nnn nnne aun 16 Inst llation forall POS si i t qu etr HER 16 Network License Monitor crrr an e e eet eH dede Hep eere 17 USse NETHASP ini File ptiondl e etr iet e ette ette peres 17 1 1 MINIMUM SYSTEM REQUIREMENT ccsssssssssssccsssscccssssccccssssccscssscscssseccccssssccscssseeceses 17 1 23D DOCTOR TRAINING idees cose cse o nada soe ae tuna sesvsuvesesvsecasedvetsssoucdesssedecsiesctedssudedeestes 18 1 3 ABOUT 3D DOCTOIOR ovvisiscissensecscssssovivonsssssulensoesessascossecessvbeseosseducsosssbisssseeteossvesbeossceessdssbecsesenseeseses 19 OVERVIEW mentem EA 19 1 322 TERMINOLOGY E terree rete eripiet reu erp e e e Eee 20 1 3
252. ne is in the correct position click the Get Contours button to calculate the surface contours The calculated contours will be displayed in the 3D SURFACE WINDOW 217 SURFACE WINDOW COMMANDS Repeat this process by adjusting the location of the cutting plane to acquire more contours The contours can be saved to a contour file ctr using the File Export Contours command The contour file is an ASCII file with the following syntax for each line BEGIN XI YI ZI 1 Nyl 1 X2 Y2 Z2 Nx2 Ny2 Nz2 Xn Yn Zn Nxn Nyn Nzn END BEGIN END Where X Y Z are the locations of a node on the contour and Nx Ny Nz are the normal at this node location There are two options available for the normal calculation The key words BEGIN and END indicate the beginning and ending of a contour The color of the cutting plane can be defined using the Tools Surface Contour Plane Color command To adjust the scale you can use the View Object and then the Shape command to define the scaling parameters To get measurements of the contours use the Tools Contour Report command 8 18 2 Plane Color command Surface Contour submenu This command is used to define the color of the cutting plane used to calculate 3D object surface contours Select a color from the Color dialog box and click OK to confirm the selection The cutting plane is only displayed when the Tools Surface Contours command is used 8 18 3 B Spl
253. ng the list of files in for editing using the Open List button Step 4 Click Open to open the 3D image list you just created In the future you can use the File Open command to open the list file directly files stored in the list will be treated as an image plane within the 3D image If your DICOM files include several series the series will be separated automatically and new list files 150 will be created The names of the additional list files will use the same base name with a number attached to the end so you can use them to open these series The stack list file 150 is a simple ASCII text file that can be edited or created using a text editor such as the Notepad program The following is a sample stack list file STACK LIST FILE D NimagesNstudy INile 1 dcm D images study INile2 dcm DNimages study INile3 dcm DNimages study INile4 dcm D NimagesNstudy INile 128 dcm The first line STACK LIST FILE indicates this is a 3D DOCTOR stack list file and the rest of the lines list all the image files within the stack in the correct order You can open an existing document with the File Open command Shortcuts Toolbar Keys CTRL N directly opens the Create 3D Image Stack dialog box 60 FILE MENU COMMANDS 2 2 Open command File Menu This command can be accessed from the IMAGE PLANE WINDOW the MONTAGE WINDOW the 3D SURFACE WINDOW and the VOLUME VIEW WINDOW Use this command to open a project
254. ngle consists of 3 x values the X Up Down Start angle that rotates around the r Enter Rotation Angles In Degrees X axis the Y Left Right X Up Down fo ee angle that rotates around the Y axis and the Z Clockwise Y Left Right fo angle that rotates around the Z axis Z Clockwise fo If you are unsure about the angle definition you can first Output File create a 3D surface rendering of the current image using the 3D _Rendering Surface Rendering command and adjusting the angles so your viewing direction will be perpendicular to the slicing plane In the SURFACE VIEW WINDOW select the View Viewing Angle Angle Setting option to get the values of the three angles Enter these values as the angle to reslice the volume The new image is saved to an image file and the original image remains unchanged With this command you can easily overcome the limitation of an imaging device by reslicing the image along a different axis Use the File Open function to open the rotated image for processing and analysis 144 IMAGE MENU COMMANDS 5 4 Crop Image Commands Image Menu Crop Region Crop Volume Crop ROI Crop Film 5 4 1 Crop Region command Crop Image submenu This command is used to crop a 2D image region from the current image or image slice The cropped image is displayed in a new IMAGE PLANE WINDOW and can be saved to an image file for processing To
255. nly header files are created 3 Header File Name Single File Use this field to enter a header file name to save the configuration parameters This will be used again later in 3D DOCTOR to read your image If you want to copy or edit all the information from an existing header file use the Browse button to open the existing header file All parameters will be read in for you to modify 4 Image Data File Name Single File Use the Browse button or enter directly the file name where the image data is stored Enter the file name exactly the way it appears as it is used by 3D DOCTOR to find the image data 5 Number of Columns This is the number of pixels in the X or column direction in one image plane or slice 6 Number of Rows This is the number of rows or pixels in the Y direction in one image plane or slice 7 Number of Image Planes or Slices This is the number of image planes or slices in the file 43 OVERVIEW AND TUTORIAL 8 Number of Bits Per Pixel This tells the size of each image pixel if the number of bits is 8 then each pixel is one byte in size and can store up to 256 levels If the number of bits is 16 then each pixel has 2 bytes of data and can store up to 65536 levels 9 Number of Bytes to Skip Before the Image Data Array Some image files have a fixed length header for storing vendor specific information The length or the size of the vendor header must be provided so the software knows to ski
256. nment 150 all views full resolution 125 all views vertical flip 125 Ambient light 201 Angle Setting 134 angle measure 89 Animate 206 animate object 208 Animate plane 127 206 Animation Control 208 Animation pace 127 206 animation image planes 209 animation loop control 209 Animation objects 209 Annotation Editor 117 annotation Add 117 Annotation delete 117 Annotation modify 118 119 Arrange Icons 254 Assign object boundary 175 assign plane 114 Assign Plane ID 109 Assignment 233 auto alignment 150 Auto Alignment 55 Auto Segment 183 AutoCAD DXF 196 Average filter 161 AVI file 128 210 AVI create 128 210 B background color 205 basic concept 36 batch process 57 bi level 61 binary image 161 blue color palette 129 blue light 214 Boolean objects 83 Boundaries in all planes 134 Boundaries in neighbor planes 134 Boundaries Align boundaries 178 Boundaries flip vertical 179 Boundaries reverse slices 179 boundary 21 boundary cube 205 boundary editor 21 47 52 Boundary Editor 98 262 boundary line editing tool 98 boundary lines edit 98 Boundary Process commands 173 Boundary report 112 boundary add node 101 Boundary assign object 175 boundary circle 100 boundary close 178 boundary close a line 106 boundary deflate 178 boundary delete 107 boundary delete node 102 boundary delete replica 177 Boundary edit 185 bo
257. nterfile PNG GIF or a format that can be configured you need to put the files into a stack to do any 3D processing or analysis If your images are stored in DICOM format you can add the files to the list and 3D DOCTOR will separate the series if multiple series exist and sort each series using the image position or image number information stored in the header The following are the steps needed to create a stack list that can be used to open a whole 3D image Step 1 Select File New Stack The Create 3D Image Stack dialog box will appear See Figure Step 2 Use the Add Files button to add files to the stack list A file Open dialog box is used to get file names The file Open dialog box Create 3D Image Stack x Add Files to the 3D Image Stack Files should be added in the same Open Cancel order of the 3D sequence DICOM files can be sorted automatically Add Files Add Before Load List md Cie DES Ss Sort DICOM Files Delete Add After Save List C Same Order No Sort By Image Position C By Image Number D images3d Stanford 1 2 840 113619 2 5 1762855897 1313 95921 425 D images3d Stanford 1 2 840 113619 2 5 1762855897 1313 95921 425 D images3d Stanford 1 2 840 113619 2 5 1762855897 1313 95921 42E supports multiple file name selections so you can add several files in one group mages Senor 129071981925 70205908717 Hold down the SHIFTAey f or the CONTROL Key to a ee ee Rf highlight the
258. o a 3D file such as AutoCAD DXF dxf IGES igs 3D Studio 3ds VRML wrl Raw Triangular Objects tri STL stl Wavefront OBJ obj and 3D DOCTOR s binary surface file suf AutoCAD DXF and 3D Studio file formats are supported by AutoCAD as well as by other 3D graphics packages The VRML format is a standard graphics format for web viewing 196 SURFACE WINDOW COMMANDS The Raw Object file is in ASCII format with one line at the beginning of the file specifying the name of the object and each following line specifying one 3D triangle face Each triangle face has 3 points x y z for the 3 corners If you need to access the 3D surface data directly from your own program this raw format may be the simplest to read and write 8 4 Contours Commands File Menu The commands under the File Contours menu can be accessed from the 3D SURFACE WINDOW only 8 4 1 Import Contours command Contours submenu Use the File Contours Import Contours command to open a 3D contour file ctr or other formats such as DXF format A contour file is an ASCII file for storing a group of 3D contour lines Each contour starts with the keyword BEGIN and finishes with the keyword END Each data line stores one point that includes six values the location X Y Z and the normal at the vertex J The following shows the contour file format BEGIN XI YI ZI Il JI Kl X2 Y2 Z2 12 J2 K2 Xn Yn Zn In Jn Kn END
259. off when individual pixels need to be visualized and investigated 4 13 Overlay Commands View Menu 4 13 1 Image command Overlay submenu v Image The View Overlay Image command toggles on and off the Boundaries display of the image This option is for display only and Boundary Nodes will not affect any data or processing Boundary Ends Object Names The View Overlay Image menu item is checked when the Neighbor Boundaries image is displayed Ten 4 13 2 Boundaries command Overlay submenu Annotations Fill Boundaries The View Overlay Boundaries command toggles on and Boundaries In Ali Planes off the display of boundary lines This option is for display only and will not affect any data or processing The View Overlay Boundaries menu item is checked when lines displayed The menu item is grayed out if no boundary line data is available in the current session 132 VIEW MENU COMMANDS 4 13 3 Boundary Nodes command Overlay submenu The View Overlay Boundary Nodes command toggles on and off the display of node markers This option is for display only and it will not affect any data or processing The View Overlay Boundary Nodes menu item is checked when line node markers are displayed The menu item is grayed out if no boundary data is available in the current session 4 13 4 Boundary Ends command Overlay submenu The View Ove
260. oints are used C imagesad HeadCTHelh 7263701 C images3d HeadCTHalf 1 7283719 1 1 1 1 C images3d HeadCTHalf 1 7283737 primarily for registering C magesse HeedCTHeIN 720375 one image to another Control points are defined using the Control Points Editor Other data items such as points and annotations can be created using their own editing functions under the Edit menu 1 6 2 Creating a 3D Stack from 2D Image Slices Very often image planes or slices are stored in separate files in a format supported by 3D DOCTOR such as DICOM TIFF BMP JPEG PNG or a format that can be configured The following are steps needed to create a stack list file when image slices are stored in separate files The stack list file can be used as if it is a single image file Section 2 1 New Stack command Step 1 Select File New Stack The Create 3D Image Stack dialog box will appear See Figure Step 2 Use the Add Folder or Files button to add files to the stack list A file Open dialog box is used to get file names The file Open dialog box supports multiple file name selections so you can add several files in one group Hold down the SHIFT key or the CONTROL Key to highlight the image files and then click the Open button to add them to the stack list Or you can use the Select AII button to add all files to the list DICOM images can be sorted automatically by 3D DOCTOR according to their 3D positions stored in the file head
261. olor command 7 7 Split Object command SD Rendering Menu See Section 6 1 Split Object command Boundary Process submenu for more details about the Split Object command 194 SURFACE WINDOW COMMANDS Surface Window Commands Control surface rendering display adjust objet material properties and color of ight for rendering display When triangular mesh models of objects are generated and displayed 3D DOCTOR provides functions to make interactive adjustments for their display properties such as transparency ambient diffuse and shine background settings overlay options and the color of the light source to create different ways of 3D display With commands under the 3D SURFACE WINDOW menus you can Import and export 3D surface models Control surface window viewing options Change object rendering properties Change the color of the light source Calculate the 3D volume and surface area of 3D surface models Obtain surface contours from 3D models 195 SURFACE WINDOW COMMANDS 8 1 Add Merge Model command File Menu This command can be accessed from the 3D SURFACE WINDOW only Use this command to add 3D surface data stored in a surface file to the current dataset This command can merge the surface rendering data from multiple surface files Surface rendering data created using different rendering methods for example simple surface or complex rendering can be combined together to create
262. olution r Source Image Browse Preview Use Synthetic PSF Point Spread Function PSF Image Browse Preview r Control Parameters Image Area Radius 22 Scale Factor 0 0 9 0 05 PSF Area Radius n m Output Image Browse emea Cancel Because the Fast Nearest Neighbor algorithm uses information from the nearest image layers it deconvolves much faster than the Maximum Entropy method When 169 IMAGE MENU COMMANDS high restoration accuracy and quality is more important than speed the Maximum Entropy method is highly recommended If no PSF is given a synthetic PSF will be used for the deconvolution Among the control parameters the mage Area Radius specifies the width and height of the image window to be used in the convolution with the PSF The PSF Area Radius specifies the width and height of the PSF kernel to be used The Scale Factor 0 0 9 defines how much feedback is applied in the deconvolution process with 0 as the weakest and 0 9 the strongest The deconvolution functions require a significant amount of system memory because both the source image data and the PSF image are loaded in memory because of performance issues 5 17 2 Maximum Entropy command Image Deconvolution Menu Image restoration is used to remove or reduce degradations that were incurred while the image was being obtained These include the blurring introduced by optical systems
263. on soil2 tif Add Images Remove Create Cancel Enter the Source Image files using the Images button At least 2 images must be defined The Source Images should be a single slice If you have multiple slices stored in a single file you can open the image into 3D DOCTOR and use the File Save Save Image As command to save the slices into separate files and then use the Image Fusion Focus Fusion command to create the fusion The images can have different sizes but they must be the same type for example 8 bit 16 bit grayscale or 24 bit RGB image Different image types cannot be mixed in a fusion image All image types are supported by this command Once the fusion image is successfully created use the File Save Save Image As command to save it to a file 5 9 4 Plane Fusion Image Fusion submenu This command combines all image planes or slices from a currently displayed image stack into a single slice image The Image Plane Fusion dialog box appears See Figure Image Plane Fusion Dialog x The slices can be fused using one of Fusion Method the following methods C Minimum Minimum This method checks all Average pixels at each pixel location of all Preah image planes and keeps the smallest mem value for the final fusion image Average This method adds up all pixels at each pixel location of all image planes and calculates the average value for the final fusion image Maximu
264. onitor Run the Aksmon exe program in the Monitor folder to start the license monitor program on the server to see how many licenses are being used Use NETHASP ini File optional If 3D DOCTOR cannot find the License Manager Server automatically from a PC you can change the name of NETHASPtcp ini file to NETHASP ini and edit it using the NotePad program In the file please enter the IP address of the server where the license manager and license key is installed NH SERVER ADDR xx xx xx Xx 1 1 Minimum System Requirements e Operating Systems Windows XP Vista 7 or newer version Other operating systems including Macintosh and Unix are not currently supported e CPU Pentium Pentium compatible or better e RAM A minimum of 128 MB is required although 512 MB or more is highly recommended to provide better performance for processing larger images e HARD DISK 50 MB are needed for the software and additional space is needed to store your 3D images e DISPLAY At least a 16 bit color or better display with OpenGL support This normally requires setting up your Display using the device driver provided by the video board manufacturer Use the Start Settings Control Panel option or right mouse click on the PC screen and then use the Properties Settings option to set up or change the display settings 17 OVERVIEW AND TUTORIAL 1 2 3D DOCTOR Training We provide web based online training to get you up to speed on
265. ools can be invoked using either the main drop down menu or the floating pop up menu brought up by clicking the right mouse button within the IMAGE PLANE WINDOW 1 5 6 The Floating Pop up Menu ee Edit Boundary To select an option using the floating pop up Split Object menu while in an editing mode first use the Simpify Boundaries right mouse button to bring up the pop up menu and then use the left mouse button to Simple Surface Rendering select the option Fast Complex Surface Rendering Complex Surface Rendering 1 5 7 The Mouse Volume Rendering Save Project A two button mouse lets you position the cursor and select items on the screen The left mouse button is normally used to select menu options edit screen objects and draw a selection rectangle for zooming in and out Click the right mouse button to display a floating pop up menu that provides the most frequently used commands depending on the processing status and the current data type 1 5 8 The Keyboard The keyboard can be used to start commands and enter text such as file names and annotations The keyboard is also used with some editing tools for example the Boundary Editor and Measuring Tool When drawing a boundary polygon for an object boundary or region of interest hit the SPACEBAR to close the boundary and finish the current polygon Some short cut keys are also enabled for specific functions for example F1 for help F2 for zoom in and F3 fo
266. op up menu brought up by pressing the right mouse button You can terminate the Boundary Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 7 8 2 Smooth Parameter command Boundary Editor submenu Use this command to enter the smoothing threshold used for the B Spline smoothing As a rule of thumb bigger threshold will result in stronger smoothing applied to a larger segment on a boundary 3 7 9 Boundary Attribute Commands 3 7 9 1 Set Plane Value command Boundary Editor submenu Use this command to specify the current plane value Z to be used when assigning MDA SSIS the values to selected lines using the Assign Sat Pies E Plane Value option When the current plane value is set you can use the Assign Plane Value tool to simply point and click on lines 5 to move them to different image planes When you start the Set Plane Value command a Define Plane Value dialog box will appear See Figure If the Automatically Increase By option is selected then the current plane value is increased by the increment value specified or decreased if the specified value is negative every time you label a boundary line If the option is not selected the plane value will stay unchanged until you reset it to a different value Use this command to change or view the currently defined plane value You can switch to a different editing sess
267. options Select the Copy option and then click on the boundary to copy it and move to the next image plane to Paste it into that image plane You will not see the boundary for the next plane unless you have selected the View Overlay Neighbor Boundaries option However the copied boundary will be displayed in the MONTAGE WINDOW if one IS present Step 6 Click the F6 key to move to the next image plane To modify the boundary so that it fits the object in the current plane use the Add Node Move Node or Delete Node options within the Boundary Editor If you need to move some points first click the right mouse button to bring up the menu then select the Move Node option If you want to see the exact location of the points select the View Overlay Boundary Nodes command Move the cursor to a node hold down the left mouse button and drag it to a new location Release the left mouse button to confirm the new location Step 7 Repeat Step 5 and Step 6 to continue working on a plane by plane basis Once all boundary lines are created you can save the boundary lines to a boundary file and then create surface or volume rendering 1 6 11 Creating a 3D Rendering From 3D Contours When you have only object boundaries or 3D contours created from other programs or 3D measurement devices you can use 3D DOCTOR to edit and analyze the boundaries and create a 3D surface rendering for visualization The following are the steps for creating a 3D
268. ormation command shows that the number of columns for the image is 1000 the number of rows is 2000 and the number of slices is 50 The calibration parameters can then be calculated by dividing the physical size by the image size For this image X 200mm 1000 cols 0 2mm Y 400mm 2000 rows 0 2mm And the slice thickness Z 100mm 50 2mm You can then enter 0 2 0 2 and 2 for the X Y and Z fields respectively If you know the FOV field of view size you can obtain the XY resolution value by using the Calculate XY button Step 3 The parameters for the Pixel Rescale portion of the dialog box are used to calibrate pixel values to their physical units for example the Hounsfield unit used by 45 OVERVIEW AND TUTORIAL a CT image Two parameters Slope and Intercept are used to define a linear transformation between the pixel value and the calibrated pixel value NewValue PixelValue Slope Intercept If you do not have the parameters they can be calculated from the calibration step wedge in an image where pairs of pixel values and calibrated values are available Click the Calculate button to do this 1 6 5 Creating a 3D Model Using Segmentation 3D DOCTOR allows you to 3D surface models quickly from your cross section image To create 3D models you first need to generate boundary or contour lines for objects in the image and then use the surface rendering command to create the model The boundary lines def
269. ou can use the short cut key to remove a slice or to show a slice Angle Setting The orientation can be set using the Front to Back command When it s checked the slices at the front of the volume are used in the operation 9 5 3 All Slices command View menu This command resets the slice selection to use all slices in volume rendering 224 3D BASIC COMMANDS 3DBasic Commands The File 3DBasic menu offers the following commands to create and run 3DBasic programs Creates and edits new 3DBasic programs Run Execute a 3DBasic program 3D DOCTOR provides a command line option to run a 3DBasic script from another program or from the operating system directly in addition to running a 3DBasic script using the interactive user interface The following lists the command line syntax 3ddoctor 3dbasic d surfsimple bas Where 3ddoctor is the program name 3dbasic flag indicates a 3DBasic script is provided in the file specified by the next parameter d surfsimple bas 225 3D BASIC COMMANDS 10 1 Create command 3DBasic menu This command provides a dialog box to edit and create a 3DBasic script program 3DBasic is a Basic like scripting language implemented to allow programming with 3D DOCTOR s advanced image processing functions to perform sophisticated tasks in batch mode The Check Syntax button will test run the created program without executing any image related functions to see if any synta
270. oundary lines Delete boundary lines using a length threshold Delete boundary lines on certain image planes Delete replicated boundaries Remove boundaries within an image plane Delete holes and islands Inflate and deflate boundaries Align boundary centers 173 BOUNDARY PROCESS COMMANDS 6 1 Boundary Split Merge and Assign Object Commands 6 1 1 Split Object command Boundary Process submenu This command splits the current object defined by the object boundary lines into two new objects The Edit Boundary Process Split Object command divides the boundary with a user drawn straight line After this command starts the cursor is changed to a Cross Cursor Click the left mouse button to define the first point A rubber band line will appear when the mouse is moved Click the left mouse button again to define the second point Once the splitting line is defined the Split dialog box appears to prompt you to enter the image planes on which the boundaries are to be split See Figure This provides an option to control the TEENS xj splitting in the Z direction If you want to create only one object check the box From 0 Plane Only keep object on right Otherwise i Cancel two new objects on both side of the Ta Ro Plane splitting line will be kept Only ki bject on right The original object boundaries are kept T Un keep eben rl unchanged and displayed on the screen together with the new objects Becaus
271. p it in order to read the image data correctly Enter 1 if you want the software to estimate it 10 Little Endian or Big Endian This parameter only matters when the number of bits per pixel is greater than 8 for example when an image is in 16 bit For most images created on a PC the file is stored as little endian default If your image is created on a Macintosh or a Unix workstation it is possible the pixel is stored as big endian You can tell right away if the image does not display correctly for example discontinuous gray levels In this case uncheck the Little Endian box to set it as big endian Step 3 Select OK to save all the information to the header file You are now able to work with your image data by using the File Open command and selecting the header file type hdr If a list file is saved for an image volume it will be automatically opened 1 6 4 Defining Voxel Size and Slice Thickness for Calibration For a 3D image the voxel size image resolution must be provided so 3D rendering will have the correct scale in all 3 dimensions and can be used by the reporting and measurement functions If your image is stored in DICOM format the parameters may already exist in the file header and will be used automatically by 3D DOCTOR However you may need to adjust the slice thickness if some slices are not used when you create the 3D stack The following explains the parameters and how they are defined Your image mu
272. plane the processing is done in memory You can use the File Save Image As to save the modified image to a new file If your image is a multi plane image you will be asked to provide a new image filename to save the converted image The new image can be displayed using the File Open command 5 15 2 24 bit RGB Gray Scale command Conversion submenu This command is used to convert a 24 bit true color to an 8 bit grayscale image This command changes the image from a three band RGB color image to a single band grayscale image The color information is lost in this conversion If the image has only a single plane the processing is done in memory You can use the File Save Image As to save the modified image to a new file If your image is a multi plane image you will be asked to provide an image filename to save the converted image The new image can be displayed using the File Open command 5 15 3 8 bit Palette RGB command Conversion submenu This command converts an 8 bit palette image to a 24 bit RGB image Normally an 8 bit palette image is only good for display and not suitable for quantitative analysis as the colors are coded By converting it to a 24 bit RGB image it can be used for histogram analysis color classification and other applications If the image has only a single plane the processing is done in memory You can use the File Save Image As to save the modified image to a new file If your image is a mult
273. plications or in VRML format for display through the Internet The 3D SURFACE WINDOW has its own set of display control functions including zoom in zoom out viewing angle adjustment light source control animation and the use of different surface rendering methods The View Object command within the 3D SURFACE WINDOW is used to toggle an object display on and off change the color and its transparency mode 3D volume and surface area can be calculated from surface models using the Tools Calculate Volumes command within the 3D SURFACE WINDOW 31 OVERVIEW AND TUTORIAL 1 5 4 PLOT WINDOW One dimensional curves such as image pixel profiles image histograms and 3D image pixel profiles generated using Edit Measuring Tools commands displayed in a PLOT WINDOW 1 3D Profile The PLOT WINDOW allows the display of multiple lines The data can be saved to an ASCII text file in table form which can be used in a spreadsheet or other data analysis program The plot can also be printed to a printer The 3D image profile generated from the Edit Measuring Tool 3D Profile command is displayed in a 3D PROFILE WINDOW See Figure The plot can be printed to a printer or saved to a text file 1 5 5 Menu Bar 4s Able Software 3D DOCTOR 3dhead_prj File Edit View Image 3D Rendering Window Help The menu bar provides the access to 3D DOCTOR s processing commands Each type of display window
274. posite image Input images can be 8 bit or 16 bit grayscale images or color images of different sizes Image stretching will be automatically applied if the images have different dimensions The resulting image is a 24 bit RGB color image When the Color Fusion commai See Figure Enter the file names for the Back Image and the Blue Source Ima need to combine only 2 images components If an image is to be check the Negate box next to tl given output file name If image created using the given name wit Use the File Open command to d 5 9 3 Focus Fusion comn This command is used to creat Color Fusion Dialog Color Fusion Dialog x m Input Source Images Negate Background Browse 7 r Red Browse CApetientwPETWPETimegedem Vv Green Browse Blue Browse Output Image Browse C patient Fusion CTPETImage til X Red Source Browse m Green Source Browse m Blue Source Browse m Output Image Browse Cancel different focal planes The resul PEE the focused portion in the resulting image to include all focused details After the command is started the Depth Focus Image Fusion dialog box appears See Figure 158 IMAGE MENU COMMANDS Depth Focus Image Fusion X Source Images D images3d focusfusion soill tif D images3d focusfusi
275. r apply log scale or square root scale functions to the image histogram to give stronger contrast to a certain range of pixel values In addition you can display images with or without pixel interpolation Section 4 12 Image Contrast e 3D Image Segmentation to Generate Object Boundaries Before you create a surface or volume rendering for a 3D image use one of the segmentation commandis to extract object boundaries Multiple objects are supported so you can visualize single objects or a combination of many objects in 3D 24 OVERVIEW AND TUTORIAL e 3D Surface Rendering to Create 3D Surface Models From boundary data 3D surface models are created using the surface rendering functions The display settings such as color and transparency can be adjusted interactively within the 3D SURFACE WINDOW using the View Object command You can export the models to formats such as DXF IGES STL VRML and 3DS 3D volume and surface area can be calculated from the surface rendered models e 3D Volume Rendering The ray tracing based volume rendering provides several display modes opaque or transparent voxels in color or grayscale e Boundary Data Editing and Processing You can define or update object boundaries using the Boundary Editor Boundaries can be processed using functions under the Edit Boundary Process submenu such as smooth split object delete by length delete by image planes and other functions Chapter 6 Boundary Process Commands
276. r the rendering 1 1 creates a 3D image the same size as the original This size will have the best display resolution but will take a longer time to render 1 2 is half the dimension of the original image and 1 4 is a quarter of the original size Direct 3D volume rendering algorithms project the original 3D voxels to a 2D viewing plane at an angle and create a display of the 3D volume image Unlike 3D Rendering Surface Rendering Volume Rendering involves all voxels within the object not just the voxels on the surface to create the 3D view Volume data can be saved using the File Save Volume command to VOL XYZ and other formats 192 3D RENDERING COMMANDS 7 6 3 Multiple Color Rendering Volume Rendering submenu This command creates a 3D volume rendering using a user defined color map The rendering includes voxels within defined object boundaries if present or a region of interest or the entire volume if no boundaries or regions of interest ROI are present The volume rendering uses ray tracing based algorithms to create a 3D display of the 3D image If your image is a grayscale image the contrast of the volume rendered image is related to the contrast set for the original image display You can use the View Image Contrast command to adjust the display contrast before doing volume rendering Object boundaries will be used by volume rendering when available Use either the 3D Rendering Interactive Segment command or the 3D Re
277. r zoom out When in the Zoom In mode use the ARROW keys PAGE UP and PAGE DOWN keys to scroll in the IMAGE PLANE WINDOW When a 3D image is displayed you can use F5 to go to the previous image plane and F6 to go to the next image plane For the 3D SURFACE WINDOW and the VOLUME VIEW WINDOW use the ARROW keys to rotate the 3D display 33 OVERVIEW AND TUTORIAL 1 5 9 Draw A Selection Rectangle and Measure Distance In 3D DOCTOR there are many places you need to draw a selection rectangle to indicate the image region of interest The rectangle is used by zoom in zoom out image crop and some editing functions To get a selection rectangle in the selection mode Arrow Cursor hold the left mouse button and the SHIFT key to drag a selection rectangle in the IMAGE PLANE WINDOW When the cursor is not an arrow the selection is not directly available because it is currently in an editing session such as the Boundary Editor or the Control Point Editor To get a selection rectangle during an editing session you need to hold the SHIFT key down and hold the left mouse button at the same time to drag a selection rectangle in the IMAGE PLANE WINDOW The current editing session will not be interrupted To measure length or distance hold down the CONTROL key press the left mouse button and drag to draw a line The length of the line is displayed in real time in the Status Bar at the bottom of the IMAGE PLANE WINDOW 34 OVERVIEW
278. rendering from contours with or without an image Step 1 Use the File New Workspace command to open a blank window Step 2 Use the File Boundary and Point Import Boundary command to open the boundary data file for display in the blank window The boundary data must be stored in a format supported by 3D DOCTOR The native boundary data format bnd used by 3D DOCTOR is an ASCII file For each closed boundary the first number is the Z value followed by point pairs of X and Y values X Y along the boundary The last point is the same as the first point to indicate that it is a closed boundary The word END follows the last point of the boundary The next boundary starts the same way After the END of the last boundary the word END is used one more time to indicate the end of the file The following example shows what the syntax looks like 53 OVERVIEW AND TUTORIAL Zl XILYII X12 Y12 XIN YIN XILYII END Z2 X21 X21 X22 Y22 X2M Y2M X21 Y21 END ZK XKLYKI XK2 YK2 XKO YKO XKI END END Step 3 If you need to adjust the size of the workspace use the Edit Resize Workspace command Changing the workspace size will not affect the size of the boundary lines only their relative location in the window Step 4 If you need to edit your boundary data use the Edit Boundary Editor command Step 5 Use the 3D Rendering Simple or Complex Surface Rendering command to create a 3D display of your data
279. rent image volume with a scaling factor The new image is saved to an image file that can be displayed using the File Open command When the Image Resize Volume command is selected the Resize Image Volume dialog box appears Resize Image Volume x Resize Parameters When the Down Sample P option is selected the Down Sample mem image size is reduced by Scaling Factor Z EN C Up Sample eme the XY scaling factor while the number of Current Size Size planes is scaled by Z scaling factor The size x Columns 128 X Columns g will be increased by the i Y Rows 128 Y Rows 64 scaling factors in all 3 directions when the Up Z Planes 5 Z Planes 5 Sample option is selected Save Image As This command is often newimage ti used together with the Image Deconvolution command to restore images acquired at a low resolution You can first up sample the image and then deconvolve the image using one of the deconvolution commands 149 IMAGE MENU COMMANDS 5 6 Image Alignment Commands 5 6 1 Auto Alignment command Image Menu When an object moves during the imaging process or images are taken at different times image slices may not be aligned properly This can affect the accuracy of image analysis The Image Auto Alignment command uses a maximum likelihood algorithm to align image slices accurately across the stack
280. ries for a sub volume to create quick volume rendering The following are the steps to create the 3D cube type boundaries 1 If you plan to use one of the defined objects to hold the cube boundaries you can set it as Current in the Object management dialog box Otherwise the currently displayed object will be used to receive the new cube boundaries 2 Go into the single IMAGE PLANE WINDOW and hold down the left mouse button to draw a selection rectangle This user defined selection rectangle will be the boundary for all image slices 179 BOUNDARY PROCESS COMMANDS 3 When the selection rectangle is _ defined select the 3D_ Cube Boundary Dialog i Rendering Cube Boundary command to turn the rectangle image planes for depth into real object boundaries for x The current selection rectangle will be used for the cube Define all image slices When the m Image Planes Cube Boundary command is From Pins D To Plane 126 selected the Cube Boundary IG abs Dialog box appears See Figure The color of the current object will be used for Cancel all the new boundaries If no selection rectangle is given the boundaries will be created for the entire image The cube boundaries can be used together with other boundaries to create 3D renderings of different shapes 6 7 Hollow Object command Boundary Process submenu This command creates hollow object boundaries donut shape from the CURRENT object Th
281. rlay Boundary Ends command toggles on and off the display of end point markers for boundary lines This option is for display only and it will not affect any data or processing The View Overlay Boundary Ends menu item is checked when line end point markers are displayed The menu item is grayed out if no boundary data is available in the current session 4 13 5 Points command Overlay submenu The View Overlay Points command toggles on and off the display of points If no points exist the option is disabled This option is for display only and it will not affect any data or processing The View Overlay Points menu item is checked when points are displayed The menu item is grayed out if no points exist 4 13 6 Control Points command Overlay submenu The View Overlay Control Points command toggles on and off the display of control point markers for all user selected control points This option is for display only and it will not affect any data or processing The View Overlay Control Points menu item is checked when control point markers are displayed The menu item is grayed out if no control point exists 4 13 7 Annotations command Overlay submenu The View Overlay Annotations command toggles on and off the display of annotations This option is for display only and it will not affect any data or 133 VIEW MENU COMMANDS processing Annotations can be created or changed using the Edit Annotation Editor comm
282. rocess will start and be recorded to the AVI file If you need to adjust the speed of the animation use the View Animate Animate Pace function to change the elapse time between frames Click the Stop button to stop the recording The AVI file records the animation until the Stop button is pressed Select Finish to exit You can use an AVI file viewer to play the movie by opening the created AVI file Note When using the Full Frames Uncompressed encoding to create an animation you may get a movie AVI file that s quite large There are several things you can do to reduce the file size Before you start the animation reduce the window size The smaller the window the less storage it takes Use a compression based encoding For example using the Microsoft Video 1 encoding can reduce the size significantly But be careful not to choose one that s not installed on your machine 210 SURFACE WINDOW COMMANDS 8 14 Surface Info command Tools Menu This command shows the number of face triangles and nodes for all currently rendered objects When the Tools Surface Info command is selected a 3D DOCTOR dialog box appears with the surface information See Figure The number of triangles and nodes can be reduced using the Tools Smooth Surface command 3D Surface Information brain 22874 Triangles 11372 Nodes head 18700 Triangles 9297 Nodes 8 15 3D Volume Calculation and Measurement Commands 8
283. roject As commands Save submenu Use this command to save a 3D DOCTOR project file A project file will include all the data layers excluding the original image file you have created using the 3D DOCTOR processing functions Project files can be opened using the File Open command and have the extension prj A 3D DOCTOR project file is in binary format and is only used internally by 3D DOCTOR A project file includes boundary data object attributes image file paths not the pixels control points and annotations if available Each time you save the project file a backup file for the previous version is created with a different file extension pbk but with the same file name and saved in the same folder If for some reason you want to go back to the previous version you can rename or move the current project file to a different folder change the extension of the backup file to prj and then open it 2 8 New Workspace command File Menu This command can be accessed from the IMAGE PLANE WINDOW only The File New Workspace command opens up a blank window where new boundary and point data files can be imported for editing without using an image 70 FILE MENU COMMANDS 2 9 Boundary and Point File Menu This command can be accessed from the IMAGE PLANE WINDOW only The File Boundary and Point menu provides options for importing and exporting boundary and point files In 3D DOCTOR boundary data is used together with th
284. rs to allow the entering of the 3D point data file name Select the data file and click OK to read the data in A 3D sparse data set must be stored in an ASCII file without any header Each data line contains four items ZI VALUEI X2 Y2 Z2 VALUE2 Xn Yn Zn VALUEn Where X Y and Z are the location of a point in 3D space and VALUE is the intensity or value of the point The VALUE field is not used when bringing points into surface models The delimiter between items is a single space and other characters should not be used The data items can be either integer or floating point Empty data lines are not allowed in the file Once the 3D points are read in successfully contour lines are created based on the sparse points The points are also displayed as points in 3D DOCTOR You can modify the contours using the Edit Boundary Editor and then create a 3D rendering using one of the surface rendering commands 2 10 4 Points To Image command Sparse Points Import submenu Use this command to convert a data set of 3D sparse points to a 3D image for processing and analysis 3D sparse points can be obtained from 3D scanners or other instruments Select the File Sparse Points Import Points To Image command A file Open dialog box appears to allow the entering of the 3D point data file name Select the data file and click OK to read the data in and specify an output image file name to save the created image A 3D sparse data
285. rs to allow you to select the font to be used for the annotation text With the Annotation Editor you can e Add new annotations Delete existing annotations Modify the text of an existing annotation Set Object Convert to Boundaries 3 12 1 Add Text command Annotation Editor submenu This command switches to the Add Text editing mode The Add Text editing mode allows you to add new annotations in the image The cursor will change to a Cross Cursor during this editing session Point the cursor at the upper left corner where you want to place an annotation Press and hold down the left mouse button and move the cursor to the lower right corner Once you reach the correct size for the annotation release the left mouse button An editing window will appear to allow you to enter the text Click anywhere outside the editing window to confirm The added annotation will be displayed in the IMAGE PLANE WINDOW Repeat this process to add more annotations or text labels Use the Delete option to delete an existing annotation You can switch to another editing session by selecting a different option from the Annotation Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Annotation Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 12 2 Delete command Annotation Editor submenu This command switches to the
286. ruction uses either a Filtered Back Projection or an lterative reconstruction algorithm The back projection method generates a smoother image than the iterative method while the iterative method maintains high frequency signal better than the back projection method If you choose the iterative reconstruction the Number of Iterations needs to be defined The more iterations requested the longer it takes to reconstruct the 3D image images to be used for reconstruction must be in the same dimension and have the same bit depth The images must be taken by rotating the object or the imaging device in the horizontal direction such as to the left or right If the images are stored in separate files you need to use the File New Stack command to create a stack list for all the image files Then you can open it as a single multi plane image and use the Reconstruction command to create a new image 164 IMAGE MENU COMMANDS 5 15 Conversion Commands Image Menu 24 bit RGB gt Palette 24 bit RGB gt GrayScale 8 bit Palette gt RGB 6 bit Palette gt Grayscale G bit Palette gt Bidevel 16 bit GrayScale gt 8 bit 5 15 1 24 bit RGB Palette command Conversion submenu This command is used to convert a 24 bit true color to an 8 bit palette image This command changes the image from a three band RGB color image to a single band palette image The color information is kept using a color palette If the image has only a single
287. s new upgrades and bug fixes to this mailing list We strongly suggest that you register in order to get the latest information about the availability of new upgrades and new features added to the software To register please send an email to 3d 9 ablesw com with your contact information Your contact information will only be used for product support purposes If you need any assistance or have any questions please send email to support ablesw com 27 OVERVIEW AND TUTORIAL 1 5 User Interface 3D DOCTOR software has a similar user interface as other Windows programs It includes several types of windows to display a 2D image plane IMAGE PLANE WINDOW 2D image panes organized as a montage MONTAGE WINDOW 3D volume images VOLUME VIEW WINDOW 3D surface images 3D SURFACE WINDOW and 1D curves in a PLOT WINDOW 3D DOCTOR uses menu bars tool buttons floating pop up menus a mouse and keyboard commands to interact between the user and the software The on line help provides information on commands and options implemented in 3D DOCTOR The menu options can be selected with either a mouse or with keyboard shortcuts Please refer to Windows documentation about using Windows tools dialog boxes menus icons etc In the following sections we will discuss various user interface items supported by 3D DOCTOR 1 5 1 IMAGE PLANE WINDOW and MONTAGE WINDOW A 3D image consists of a number of 2D image planes or slices When a 3D image is
288. s Bar describes the action to be executed by the selected menu item or by the pressed toolbar button It also highlights the Ioobar keyboard latch state num lock caps lock scroll lock cae v Status Bar 122 VIEW MENU COMMANDS A check mark appears next to the menu item when the Status Bar is displayed Status Bar For Help press F1 Right mouse button for quick options 217 04 131 57 54 00 The Status Bar is displayed at the bottom of the image window To display or hide the Status Bar use the View Toolbars Status Bar command The current image coordinates are displayed in the Status Bar The left area of the Status Bar describes actions of menu items as you navigate through menu commands This area similarly shows messages that describe the actions of toolbar buttons as you depress them before releasing them If after viewing the description of the toolbar button command you wish not to execute the command then release the mouse button while the pointer is off the toolbar button The middle area displays the current cursor location within the image When View Calibrated Coord command is selected the calibrated coordinates are displayed in this area The right areas of the Status Bar indicate which of the following keys are latched down Indicator Description CAP The Caps Lock key is latched down NUM The Num Lock key is latched down SCRL The Scroll Lock key is latched down 4 4 Montage View Commands Vie
289. s of reference information Once you open Help you can click the Contents button whenever you want to return to the opening screen 12 2 About command Help menu Use this command to display the copyright notice and version number of your copy of 3D DOCTOR for Windows 12 3 Context Help command 2 Use the Context Help command to obtain help on some portion of 3D DOCTOR for Windows When you choose the Toolbars Context Help button the mouse pointer will change to an arrow and question mark Then click somewhere in the 3D HELP MENU COMMANDS DOCTOR for Windows window such as another Toolbar button The Help topic will be shown for the item you clicked Shortcut Keys SHIFT F1 257 SOFTWARE LICENSE AGREEMENT Software License Agreement Able Software Corp 3D DOCTOR for Windows Please read this license carefully before use You are purchasing a license to use the 3D DOCTOR for Windows Software The Software is owned by and remains the property of Able Software Corp is protected by international copyrights and is transferred to the original purchaser and any subsequent owner of the Software media for their use only on the license terms set below Opening the packaging and or using 3D DOCTOR for Windows Software indicates your acceptance of these terms If you do not agree to all of the terms and conditions or if after use you are dissatisfied with your 3D DOCTOR for Windows Software return the software
290. sect with the rectangle are assigned with the current plane value You can switch to a different editing session by selecting another option from the Boundary Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Boundary Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 7 9 3 Set Object command Boundary Editor submenu Use this command to get into the Set Object mode Once in the Set Object editing mode use the mouse to point at a boundary line and click the left mouse button to set it as the current object Objects are used to create groups for boundary lines depending on the types defined You can use the Edit Object Settings command to define and edit object parameters and select an object as the current object You can switch to a different editing session by selecting another option from the Boundary Editor submenu or from the floating pop up menu brought up by pressing the right mouse button 109 EDIT MENU COMMANDS You can terminate the Boundary Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 7 9 4 Show Info command Boundary Editor submenu Use this command to show information related to a line Parameters include Object Length of the line Area if the line is closed Center and the Mean and the Variance of
291. shold value or use the scroll bars to adjust the threshold You can segment each plane individually using the same or different thresholds If the current thresholds are suitable for the rest of the image planes you can use the Segment button to segment all image planes that have not been segmented If the Use Connectivity box is checked then a connectivity rule is applied to segment only those object boundaries that are interconnected between image slices When Use Connectivity option is used the defined regions of interest ROI applies only to the current image plane and other planes are segmented based on the connectivity rule If an image plane has boundary data for the current object then it will not be processed If the image pixel value calibration is available through a DICOM file or calibration parameters have been entered using the Edit Calibrations command the check box Use Calibrated Value will be enabled This allows you to show either the raw pixel value or the calibrated pixel value when adjusting the threshold If you need to restore previously used thresholds click the Previous Threshold button Click the Finish button to leave the interactive segmentation function The boundary lines can be edited using the Edit Boundary Editor options Use the File Boundary and Point Export Boundary command to save boundary data to a file 185 3D RENDERING COMMANDS 7 4 Segment Object Commands 3D Renderin
292. st be open before you start the following steps Section 3 1 Calibration command Step 1 Select the Edit Calibrations command The Image Calibration Parameters dialog box shown below appears 44 OVERVIEW AND TUTORIAL Image Calibration Parameters X Y 2 Voxel Resolution Pixel Rescale X voxel width o5 Slope Y voxel height o5 Intercept Z slice thickness QN Unit hu rawvalue Unit cm mm m Slope RawPixel Calculate XY OK Cancel L il Step 2 If your image already has calibration parameters for example DICOM image files the provided values will be displayed in the fields Otherwise default values are used The X and Y values for voxel resolution is the size of one pixel in a slice For example a CT image has a pixel size of 1 5mm You can enter 1 5 for both X and Y fields and the unit as mm The slice thickness is the physical thickness of one slice plus the gap distance between 2 neighbor slices in the same measurement unit as the XY sizes You can also think of slice thickness as the distance between the centers of 2 neighbor slices in the 3D space If your image is scanned from a film or from other sources the XYZ parameters can be calculated from the physical size of the imaged volume or the field of view FOV and the image size For example a 3D image covers a 3D volume with the physical width of 200mm a height of 400mm and a depth of 100mm The Image Inf
293. such as a raw image data file with or without a header at the beginning or an uncompressed file in a vendor s proprietary format the file can be read into 3D DOCTOR by creating a header file This header file tells the software the configuration of the image data stored in the file The following steps Non Standard Image Data Files To Be Imported describe how to create D images3d vhuman c_vm1012 fre Grief D images3d vhuman c_vm1013 fre image headers for D images3d vhuman c_vm1014 fre D images3d vhuman c_vm1015 fre multiple files D images3d vhuman c_vm1016 fre D images3d vhuman c_vm101 7 fre D images3d vhuman c_vm1018 fre D images3d vhuman c_vm1019 fre Step 1 Select the D images3d vhuman c_vm1020 fre D images3d vhuman c_vm1021 fre File Raw Image File D images3d vhuman c_vrn1022 fre D images3d vhuman c_vm1023 fre Import Multiple Files D imanesar vhumanie svm1f24 fre zi command A Create ListFileNeme mei Endien Multiple Headers Image Configuration dialog box See Figure r Photometric Display of Columns X 512 of Rows Y 512 appears to enter all of C Min is White the required image data of Slices Z 1 Bits Per Pixel 8 16 16 Minis Black configuration C RGB Color Number of Bytes To Skip Before Image Data enter 3416 parameters 1 if not sure Step 2 All parameters must be entered correctly in order for the software to read the im
294. t command is selected the 3D Object Setting dialog box appears See Figure object is visible when the Display attribute is When the Wireframe attribute is a 3D surface model will appear as a wire frame model You can also select this as a separate 3D Object Setting Color Texture Shape Apply Move Up Move Down Delete command under the View menu Click the left mouse button in each field to change the attributes as well as the name of an object The opacity value ranges between 0 and 1 0 means total transparent while 1 means total opaque When multiple objects are present and some objects are inside other objects the inner objects should be moved to the beginning of the object list so they are displayed before the outer objects and visible To move an object up the list select the object from the list first and then click the Move Up button To move an object down the list select the object from the list first and then click the Move Down button The Color button allows you to change the color properties of an object while the Shape button lets you to change the orientation location and scale the dimension of an object The Texture button allows you to load a small texture image to be applied to the entire model surface By changing the color properties of certain objects when rendering multiple objects together you can create
295. t Image Dimension degrees but you can use other Columns width 2304 values if needed Rows Height fi 800 Cancel Click the OK button to Angle Between create the two files and use Image degree them for stereo display di 222 VOLUME WINDOW COMMANDS 9 2 Opacity command View menu This command is used to change the opacity curves used in the Smooth Volume Rendering There are 2 curves used for the rendering Density and Gradient Each curve defines the corresponding opacity of the density gradient values When the opacity value is close to 1 for a density range a voxel within this range will appear to be opaque It will be visible if voxels in front of it are transparent but it will block anything behind it When the opacity value is close to 0 then the voxel within the range will be totally transparent so everything behind it will be invisible To change the curve first click the left mouse on the curve to show the points Click the left mouse on the curve again to add a point Hold down the left mouse to move a point up and down Click the right mouse on a point to delete Click Apply to update the rendering Opacity Map for Volume Rendering x Density Gradient Click on the curve to start editing Left click to add a point Right click to delete Opacity 0 total transparent 1 opaque 0 99 _ 0 0 25 551
296. tates counterclockwise around the X axis while the Y and Z are similar for the Y axis and the Z axis respectively e Move By The increments for location shifting along the X Y and Z axis at each frame e Scale The increments for the scaling factors along the X Y and Z axis at each frame e Steps This defines the number of steps to be used in a loop for the above movement parameters For example if Rotate has 10 steps and the X increment is 5 then the object will be rotated 10 times each time the angle is the current angle plus 5 degrees The next parameter controls how the loop continues to the next loop e Loop Control Two options can be used Return to Starting Point and Reverse Direction When the Return to Starting Point option is used the object will 208 SURFACE WINDOW COMMANDS jump back to its initial position and shape when each loop ends When the Reverse Direction option is used the increment will become decrement at the end of each loop and the object will move back in the reverse direction The viewing angle controls the change of the three angles by using the three increments The viewing angle controls the global display You can use the Test button to preview the animation 8 13 4 Object Animation command This command allows you Xx to create an animation sequence to hide or show OBJECT Opaque OBJECT ACTION selected objects during the brain T i Opaque animation E
297. ten notice is provided to Able Software Upon such transfer Licensee must transfer or destroy all copies of the Software 5 Except as expressly provided in this License Licensee may not modify reverse engineer decompile disassemble distribute sub license sell rent lease give or in any other way transfer by any means or in any medium including telecommunications the Software Licensee will use its best efforts and take all reasonable steps to protect the Software from unauthorized use copying or dissemination and will maintain all proprietary notices intact LIMITED WARRANTY Able Software warrants the Software media to be free of defects in workmanship for a period of ninety days from purchase During this period Able Software will replace at no cost any such media returned to Able Software postage prepaid This service is Able Software s sole liability under this warranty DISCLAIMER LICENSE FEES FOR THE SOFTWARE DO NOT INCLUDE ANY CONSIDERATION FOR ASSUMPTION OF RISK BY ABLE SOFTWARE AND ABLE SOFTWARE DISCLAIMS ANY AND ALL LIABILITY FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR OPERATION OR INABILITY TO USE THE SOFTWARE EVEN IF ANY OF THESE PARTIES HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES FURTHERMORE LICENSEE INDEMNIFIES AND AGREES TO HOLD ABLE SOFTWARE HARMLESS FROM SUCH CLAIMS THE ENTIRE RISK AS TO THE RESULTS AND PERFORMANCE OF THE SOFTWARE IS ASSUMED BY THE LICENSEE THE WARRANTIES EXPR
298. tessa toss toss tassa 221 9 1 VOLUME FILE COMMANDS eee ee enne eene tn setas etas to seta states sess eo setae ease seta seta sesso 222 9 1 1 OPEN VOLUME COMMAND FILE enne entere nnne 222 9 1 2 SAVE VOLUME COMMAND FILE MENU 222 9 1 3 SAVE STEREO PAIR COMMAND FILE MENU 222 enne enne enne enne 222 9 2 OPACITY COMMAND VIEW MENU eee eee eee eese 223 9 3 COLOR COMMAND VIEW MENU ecce esee eee etes sete sten 224 9 4 VIEWING ANGLE COMMANDS VIEW 224 9 5 SLICE SELECTION COMMANDS VIEW 224 9 5 1 SLICE RANGE COMMAND VIEW 224 9 5 2 HIDE AND SHOW SLICES COMMANDS VIEW 224 9 5 3 ALL SLICES COMMAND VIEW MENU ener nennen ne 224 CHAPTER 10 3DBASIC MENU 5 setas 225 10 1 CREATE COMMAND 3DBASIC 4 e eere ee eee enses stone tn aeta setas e ta seta stesse 226 12 TABLE OF CONTENTS 10 2 RUN COMMAND 3DBASIC MENU e eee e eene eese en oeste tnos seen tee seen ases seen ee seen esee ena 226 10 3 3DBASIC SCRIPTING LANGUAGE eee e eee
299. th image slices stored in separate files You can also select some slices by drawing a selection rectangle in the montage view window Range of Slices m New Location then move the selected slices EISE b TEN within the montage window to P the correct location Last fe a 5 3 4 Delete Slices command Reslice submenu This command is used to remove a range of image slices from the image stack This command works only with image slices stored in separate files Delete Image Slices from the Stack x You can also select some slices by Range of Slices drawing a selection rectangle in the E montage view window then press First the Delete key to remove them m E from the stack list Cancel it 141 IMAGE MENU COMMANDS 5 3 5 Add Slices command Reslice submenu This command is used to add more image slices to the image stack This command works only with image slices stored in separate files Click the Add button to select image files to be added Define the location where the new image slices are to be inserted Select the OK button to add the slices to the stack The current image will reload and display with the new slices added Add Image Slices x Image Slices To Be Added 9 85 20031126 120518 1 0001 0001 000137 Add 9 85 20031126 120518 1 0001 0001 000138 dem 9 85 20031126 120518 1 0001 0001 000139 9 85 20031126 120518 1 0001 0001 000140 Delete
300. the floating pop up menu brought up by pressing the right mouse button 113 EDIT MENU COMMANDS You can terminate the Point Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 10 3 Delete Point command Point Editor submenu Use this command to delete a point from the current object The cursor will change to a Delete Cursor Point the cursor at a point and click the left mouse button to remove it The system will always remove the closest point to the location clicked When deleting a point try to be as close as possible to the point to be removed You can switch to a different editing session by selecting another option from the Point Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Point Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 10 4 Set Plane Value command Point Editor submenu Use this command to set the current plane value to be used to label a point A Define Plane Value dialog box will appear to allow you to SetPlane Values f enter a number The value can be either positive or negative After the value is set you can start m Automatically by o labeling points by switching to the Assign Plane dc m mode If the Automatically Increase By option K is selected then the current default plane
301. tinuously at a short time interval when this command is started Selecting this command again will stop the animation process 4 10 2 Animation Pace command Animate submenu Animation Pace Control x Selecting the View Animate Animation Pace command will bring up the Animation Pace Control dialog box See Figure 40 milliseconds This dialog box allows you to control the amount of time in milliseconds between frames during the animation process Cancel 127 VIEW MENU COMMANDS 4 10 3 Create Movie command The View Animate Create Movie command captures screen actions into an AVI movie file When you select this command the Create AVI Movie dialog box will appear See Figure First enter an AVI filename using the Browse button and adjust the Frames Per Second The frame rate defines how many frames per second will be generated for the movie Because it takes time to generate each frame image it s recommended to reduce the size of your image window so the movie file will have a smoother transition from frame to frame Click the Start button to start Create Movie Save Movie To Frames Per Second fis gt Status Start Ready to record Stop Finish recording The animation process will start and be recorded to the AVI file If you need to adjust the speed of the animation then use the View Animate Animate
302. tions More iteration will increase the computation time but may improve the classification quality Use the Save Window button to save the current display window to a bitmap file This saves only the current image plane display Use the Save Image button to saved the entire classified image all image planes to a file The new image file can be displayed using the File Open command 5 13 2 Negate command Process submenu The Image Process Negate command is used to reverse the image pixel intensity values For example if the image is a 1 bit bi level image pixels with a value of 1 will become 0 and pixels with a value of 0 will become 1 after the Negate operation This command is only needed when an image is scanned with reversed polarity If your image is a multi plane image the new image will be saved to a file and can be displayed using the File Open command 5 13 3 Remove Background command Processing submenu The Image Processing Remove Background command is used to remove or clean up a grayscale image background This command works only with grayscale images If an image is in color you can convert it to a grayscale image first and then use this command If your image is a multi plane image the new image will be saved to a file and can be displayed using the File Open command 162 IMAGE MENU COMMANDS 5 13 4 Sobel Edge command Process submenu The Image Process Sobel Edge command creates an edge en
303. to rotate the object Use the middle mouse wheel or the UP DOWN key to adjust the cutting plane location You can then use the Split Object command to cut off the part in front of the cutting plane The split object is a new object and the original object is hidden You can use the View Object command to change the display properties or delete an object Specular Like diffuse light specular light is directional but it is reflected sharply and in a particular direction A highly specular light tends to cause a bright spot on the surface it shines upon which is called the specular highlight Transparency When an Object Shape Properties x object contains other smaller objects you will need to set its Rotate in degrees p Move By Scale transparency property to x X X 1 00381 ON in order to see other objects inside this object X fo Y i 1 0031 If you need to change the i iei size orientation location of an object first ER select the object from the list and then click the Reset CENE Shape button to bring up the Object Shape ObjectName bone 201 SURFACE WINDOW COMMANDS Properties dialog box see Figure for changing the shape properties Once you have entered the parameters click Apply to display the object in the new orientation location and scale Rotate You can define three angles to rotate the object from the current orientation The angl
304. truction algorithm and saves the reconstructed image to a new image file Syntax RECONITER imagevar filename 5 0 2 RECONITER imagevar filename angle numiterations where IMAGE3D imagevar STRING filename FLOAT angle INTEGER numiterations 252 3DBASIC COMMANDS Example IMAGE3D imagel image2 FLOAT angle INTEGER num angle 5 0 num 2 OPENIMAGE imagel c 3ddoctor head3d tif RECONITER imagel c3ddoctorviewimage tif angle num OPENIMAGE image2 c 3ddoctor newimage tif SHOWIMAGE imagel SHOWIMAGE image2 END 253 Window menu commands The Window menu offers the following commands which enable you to arrange multiple views of multiple documents in the application window Creates a new window that views the same document Arranges windows in an overlapped fashion Arranges windows in non overlapped tiles ge Icons Arranges icons of closed windows Window 1 2 Goes to specified window 11 1 New command Window menu Use this command to open a new window with the same contents as the active window You can open multiple document windows to display different parts or views of a document at the same time If you change the contents in one window all other windows containing the same document reflect those changes When you open a new window it becomes the active window and is displayed on top of all other open windows 11 2 Cascade command Window menu Use this command to arrange multip
305. types for example the Interactive Segment command is used with grayscale 8 bit or 16 bit images only Windows Bitmap files save most image types 1 bit monochrome 4 bit grayscale 8 bit grayscale 8 bit color as palette type images 3D DOCTOR automatically converts 1 bit and 4 bit images to black and white image types For 8 bit grayscale images which are saved as palette color image type you should convert the image type from 8 bit palette color to 8 bit grayscale before doing any processing Use the Image Information command to check the image type Project prj volume vol and surface suf files are proprietary binary files used by 3D DOCTOR Shortcuts Toolbar Keys CTRL O directly brings up the Open dialog box 61 FILE MENU COMMANDS 2 2 1 File Open dialog box The File Open dialog box will appear when certain commands are selected It allows you to specify which file to open Ce o Look in Images3D e E3 hubble Samples 3dbrain prj 7 Align IPS Stanford a 3dbrain SL 1 demoCD Microscopy Stephane an Dentrac navy suny 3dhead prj 1 dicomimages New Folder Terratech se 3DKNEE F Film paultec CJ Transcan se 3dknee pri 1 Fusion Recon Vrat 3dknee SL Ryder vm spine sr Nr2 bmp Files of type Project pri TIFF Files tif Dicom Files dem dic Surface Files suf Volume Files vol Image Stack L
306. undary ellipse 100 Boundary export 185 boundary inflate 178 boundary manual creating 52 boundary merge 106 Boundary merge overlapped 175 boundary move 103 boundary move node 101 boundary move section 102 boundary new 99 boundary non simple 176 Boundary rectangle 100 boundary replicated 177 boundary report 175 Boundary ROI 87 Boundary ROI format 72 boundary rotate 103 boundary simplify 176 Boundary simplify 176 B spline contours 218 B Spline smoothing 218 C Calculate Volume 211 calibation estimate 45 calibrated coord 135 calibration 44 72 135 Calibration 80 Calibration calculate 81 Calibration enter 185 calibration slice thickness 21 Calibration slope intercept 81 Calibration use 185 calibration voxel size 21 Cascade 254 circle boundary 100 Classification 162 classify 162 Close 68 close a line 106 INDEX close boundaries 178 Close Line 106 CLOSEIMAGE 241 color clustering 162 color for boundary lines 82 Color fusion 158 color image 162 Color separation 166 color volume rendering 193 combine image 158 command line option 57 225 Commands for Surface Window 195 Commands for Volume Window 221 Complex Surface rendering Full Rendering 188 Context Help 256 contour 21 contour display 206 contour file 218 contour file format 198 Contour Report 218 contour color 219 contour smoothing 218 contours 21
307. w Menu If an image has multiple planes then this command is automatically called to create a MONTAGE WINDOW of all of the image planes When an image has a large number of image planes it may take some time to create the MONTAGE WINDOW A 3D image with multiple image planes can be displayed in several ways in 3D DOCTOR e An image plane window with a montage window by default You can use the View Montage View command to switch to this configuration e An image plane window a montage window the side profile view window and the top profile view window You can use the View All Views command to switch to this display e An image plane window only You can use the View Image View command to start this display 123 VIEW MENU COMMANDS 4 4 1 Montage View command View Menu This is the default montage view mode for displaying image slices The plane ID is displayed inside the image pane The MONTAGE WINDOW helps you to navigate and jump to a certain image plane quickly and easily The MONTAGE WINDOW displays the image slices at a lower resolution than the IMAGE PLANE WINDOW The MONTAGE WINDOW is connected to the normal IMAGE PLANE WINDOW If a MONTAGE WINDOW is closed you can use the View Montage View command to create one If you want to save the montage image data to a file use the File Save Save Image As command If you want to save the contents displayed in the MONTAGE WINDOW then use the File Save Save Window co
308. w Value to be mapped A lookup table can be used to map the pixel values The lookup table file is a text file where each line has two numbers The first number is the original pixel value and the second number is the desired value or the new value to be mapped to The lookup table file looks like this 163 IMAGE MENU COMMANDS 10 200 11 200 12 200 13 201 14 201 If your image is a multi plane image the new image will be saved to a file and can be displayed using the File Open command 5 14 Reconstruction command Image Menu The Image Reconstruction command is used to reconstruct xl a parallel cross section 3D image Output Image File from a group of images taken at Browse P images3d Recon CT ctrecontt regular angle intervals For example if you take an X ray Angle Increment m Reconstruction Method image of an object at 10 degree This angle must be in the C Filtered Back Projection n horizontal direction angle intervals by moving to the Iterative left or right of the object you 5 625 Degree Number of Iterations will have a total of 17 images to cover the total 180 degree range Cancel You then use the Image Reconstruction command to recreate the parallel cross section image and use the new image for 3D modeling and analysis When the Reconstruction command is started the Image Reconstruction dialog box appears See Figure The reconst
309. x error needs to be corrected The Run button will execute the program Use Open button to open an existing 3DBasic program for editing Use Save to save the program to a file 10 2 Run command 3DBasic Menu This command executes a 3DBasic script program stored in a file 3DBasic is a Basic like scripting language implemented to allow programming with 3D DOCTOR s advanced image processing functions to perform sophisticated tasks in batch mode A 3DBasic program can be created using a text editor such as Windows NotePad or use 3D DOCTOR s 3DBasic Create command 226 3D BASIC COMMANDS 10 3 3DBasic Scripting Language 3DBasic is a Basic like scripting language implemented to allow programming with 3D DOCTOR s advanced image processing functions to perform sophisticated tasks in batch mode A 3DBasic program can be created using a text editor such as Windows NotePad or use 3D DOCTOR s 3DBasic Create command Use 3DBasic Run to run an existing 3DBasic program directly For more details about each command please see the Online help 3DBasic supports most of the standard Basic commands including ASSIGNMENT 2 PRINT INPUT IF THEN FOR NEXT TO GOTO GOSUB RETURN END and REM In addition 3DBasic provides a new set of commands to provide enhanced functionality for programming and image processing The new commands include LOGFILE OPENIMAGE SHOWIMAGE CLOSEIMAGE SAVEPROJE
310. xf EL f sp C Show Source Image Only Vy E C Show Source Image Only l C Show Target Image Orly Show Target Image Ony a intak oxy gt 0 Show Bah Imager oww gt Save Regetered Image To Save Regetered Image To sowe Scucelmage E umag Aapse Ahead V Bem Cone Soucelmage Cancel If you want to adjust the orientation and scale of your current image you can use it as the target image and repeat the above steps For example you can reslice the image using this command 154 IMAGE MENU COMMANDS 5 8 2 Registration with Control Points Image Menu The Image Registration command is used to register the current image based on the defined control points Use the Edit Control Points Open Control Points to select a control point set for image registration This command can be used only when a control point set exists or is loaded in the current image window This command geometrically transforms or registers a 3D stack image source image against another 3D image target image using user defined control points The command will create a new image from the source image that has the same orientation scale and dimension as the target image so they can fused or compared When an image is acquired with some geometric distortion it can be geometrically corrected to its original shape when proper control points can be identified When the Imag
311. xt boundaries should be placed within a real object boundary on the top or bottom image slice so the label will be visible on the model 3 12 7 Project Notes command Edit menu This command is used to enter notes about the current project The notes are saved in the project file 3 13 Text to Boundaries Command Edit Menu This command converts all annotation text to object boundaries so they can be used in surface rendering process to create text labels on a model 119 EDIT MENU COMMANDS 3 14 Shortcut Keys command Edit menu Customize Shortcut Keys x Commands Current Keys 3D Rendering Auto Segment Ctrl eA OK 3D Rendering Cube Boundary 3D Rendering Interactive Segment Cancel 3D Rendering Segment Object Draw Training Area 3D Rendering Segment Object Segment All 3D Rendering Segment Object Segment Plane 3D Rendering Surface Rendering Convex Surface 3D Rendering Surface Rendering Fast Complex Surface 3D Rendering Surface Rendering Full Complex Surface 3D Renderina Surface Renderina Simple Surface 2 gun Currently assigned to Select New Shortcut Key Reset All Use this command to define and customize shortcut keys to access 3D DOCTOR commands First select a command from the Commands window Move the cursor to the Select New Shortcut Key box and type the desired key combination on your keyboard to assign For example if you want to use Ctrl A for the Auto
312. y on the keyboard to close the polygon and the current image plane is segmented automatically The object boundary in the current image plane is displayed in the IMAGE PLANE WINDOW If you want to continue the segmentation process to another plane use the Previous Plane or Next Plane options from the 3D Rendering Segment Object submenu or from the floating pop up menu brought up by clicking the right mouse button Hit any key or select the Segment Current option from the Segment Object submenu or from the floating pop up menu to segment with the same training area You can draw a new training area by clicking the left mouse button in the image and drawing a new polygon The existing training area will automatically be removed when a new training area is defined If the defined ROI region of interest and the training area are general enough for the entire volume image you can select the Segment All command from the Segment Object submenu or from the floating pop up menu brought up by clicking the right mouse button This command will apply the signatures generated from the training area to all image planes that have not been segmented 186 3D RENDERING COMMANDS If you want to remove the boundary lines from the current plane and restart the process use the Remove Boundaries command If the training area is not properly defined to produce a reasonable segmentation you can delete all boundary lines using the Delete All Boundaries command
313. y pressing the right mouse button You can terminate the Boundary Editor by selecting the Done option from the floating pop up menu brought up by pressing the right mouse button 3 7 4 Boundary Copying Commands 3 7 4 1 Copy Boundary command Boundary Editor submenu Use this command to copy one or more boundaries to memory and then paste them to a new image plane or in the current image plane The cursor changes to a Copy Cursor when the Boundary Editor is in the Copy Boundary editing mode To copy a single boundary point the cursor at the boundary Click the left mouse button to copy it to memory You can then use the F5 or F6 key to switch to the image plane where you want to place the boundaries and use the Paste Ctrl V command to paste Duplicate lines may cause abnormal effects in 3D rendering so be careful when pasting boundaries To copy a group of boundaries hold down the SHIFT key and the left mouse button to draw a selection rectangle surrounding the boundaries to be copied Select the Copy Boundary command from the floating popup menu by clicking the right mouse button or use the short cut key Ctrl C Use the Move Boundary option to move the boundary to its new location You can switch to a different editing session by selecting another option from the Boundary Editor submenu or from the floating pop up menu brought up by pressing the right mouse button You can terminate the Boundary Editor by selectin

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