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The TINA Manual Landmarking Tool

1. Landmark point number Landmark point name Stored x coordinate for the landmark point Stored y coordinate for the landmark point Stored z coordinate for the landmark point An arbitrary integer allowing the user to store additional information for the landmark point The point that this point is linked to when the Linklines option of the 3D Tv draw checklist is used Move downwards in the list of landmark points Choose the type of file to load or save Names a list of landmark point numbers and names and corresponding linking lines file if one exists Raw a TINA specific ASCII text format that contains all of the information stored in the landmark list TPS a standard format for morphological data NTSYS another standard format for morphological data TPS NTSYS files Study name TPS NTSYS files TPS and NTSYS files can hold multiple lists of points this field selects which one to load if there is more than one list in the file Absolute or relative pathname of the file from to which to load save landmark data Start a file browser to select the file to load or save Load data from the file specified in the Pathname field using the format specified in the Format field Save the current landmark point list to the file specified in the Pathname field using the format specified in the Format field Delete the current axis points Delete the current plane points D
2. 3D Tv draw 2D Tv draw 3D Cursor Position Resolution Bone threshold Starts the Volume Renderer Control dialog box which allows the user to set the various options used to produce the image in the 3D Tv see below Starts the Landmark Points dialog box which allows the user to load view and save lists of landmark points see below Starts the Keyboard Controls dialog box which allows the keyboard controls for interaction with the Tvs to be re defined The list of available Tvs in the Manual Landmarking tool selecting an item in this list will make it available for installation on a Tv tool see above x axis 2D Tv showing images of the z y plane through the 3D cursor y axis 2D Tv showing images of the x z plane through the 3D cursor z axis 2D Tv showing images of the x y plane through the 3D cursor 3D 3D Tv showing a volume rendering of the data loaded into the sequence tool Switch the volume renderer off on NULL switch the volume renderer off VR switch the volume renderer on Switch to control mouse interaction with the 3D Tv Zoom mouse interaction moves rotates and zooms the image Pick mouse interaction picks points on bone surface or displays intensity profiles Switch to control mouse interaction with the 2D Tvs Zoom mouse interaction moves or zooms the image Pick mouse interaction moves the 3D cursor cross hairs Select how landmark axis and plane points will be displayed in the 3D
3. Perceptual illusions and brain models Proc Roy Soc Lond B 171 1024 279 296 1968 3 P Lacroute and M Levoy The volpack volume rendering library http graphics stanford edu software volpack 4 P Lacroute and M Levoy Fast volume rendering using a shear warp factorization of the viewing transform In Proc SIGGRAPH 794 July 24 29 Orlando Florida pages 451 458 1994 5 N A Thacker and P A Bromiley Tina 5 0 user s guide http www tina vision net docs memos php 37
4. im Enter the replaced part of the filename from the first file into the Start field including any leading zeros 00 in this example and the relevant part of the filename from the last file into the End field 10 in this case During image loading the wildcard characters in the pathname will be replaced with the contents of the Start field and the number contained there will be incremented until it is equal to or greater than the End field loading a file each time If the numbers in the filenames increase by more than 1 between each file then the Stride field can be used to specify the increment For example entering im into the Image file field 00 into the Start field 10 into the End field and 2 into the Stride field will load the images im 00 im 02 im 04 im 06 im 08 and im 10 in that order Note that there are some restrictions on loading multiple files in this way The substitution only works for numbers can only be applied to one contiguous segment of the pathname and only works in ascending or descending order In addition all files must be in the same directory e If the sequence is too large to load into memory the Stride and Downsample fields can be used to down sample the data as it is loaded The Stride field down samples data in the inter slice direction by skipping over slices as the data is loaded For example if the Stride field is set to 2
5. R 0 4 G 0 4 B 0 4 Specular R 05 G 05 B 05 Shinyness RGB 1 0 Lighting Control Foreground colour Background colour E Options Scan Load Save Figure 6 The interface to the volume rendering engine New Feature in Manual Landmark Tool v1 2 The Text option in the 3D Tv draw check list of the Manual Landmark tool now displays text labels for any axis and plane points that have been marked Axis point labels A1 and A2 are displayed in yellow and plane point labels P1 P2 and P3 in cyan Since a single point might be used simultaneously as a landmark axis and plane point the labels are arranged around the point such that they should not overlap New Feature in Manual Landmark Tool v1 4 The Linklines option has been added to the 3D Tv draw check list In many cases the landmark point list will include pairs of points arranged symmetrically around the plane of bilateral symmetry e g points on the tips of the coronoid processes of the mandible on the left and right hand sides The user can optionally prepare a file listing the landmark point numbers of such pairs see Section 7 for details of the format and loading of this file If such a file has been prepared and loaded then when the Linklines option is selected in the 3D Tv draw check list white lines will be drawn between these pairs of points in the 3D Tv whenever both points have been manually identified This can
6. Scan button For AIFF RAD NEMA and PGM file types the sequence tool will automatically add the correct file name extension aiff rad ani and pgm respectively and so the filename should be entered without the extension However for Analyze or DICOM files the sequence tool will not automatically add an extension and so the correct extension must be entered into the filename field The file browser started using the scan button will automatically strip the extension from any selected file and so when loading DICOM files the extension must be manually re entered into the filename field e Select the format of the image file from the File choice list For file types e g Analyze where multiple slices of data are contained within a single file enter the number of slices in the file into the End field If you are unsure of the number of slices then enter a number that is too high the sequence tool will load data until it reaches the end of the file and then reset the End field to show the number of slices loaded For file types e g AIFF where each slice is contained in a separate file use the character as a wildcard For example if the directory contains 10 files named im 00 to im 10 enter the pathname of the first file into the Image file field either by typing or by using the file browser Then replace the part of the name that changes between files with the character so that it becomes
7. Tv Cursor display a red cross hair representing the 3D cursor LM display green cross hairs for all marked up landmark points Axis display yellow cross hairs for the axis points Plane display cyan cross hairs for the plane points Text display the number of each marked up landmark point Poly display a line representing the axis and a grid representing the plane Ball display 3D spheres instead of cross hairs for the landmark axis and plane points Linklines display white lines linking symmetrical pairs of points Select how the images in the 2D Tvs will be displayed Rotate display the 2D Tvs using the rotation from the 3D Tv Axis display yellow cross hairs for the axis points Plane display cyan cross hairs for the plane points Displays the coordinates of the 3D cursor X the x coordinate of the 3D cursor Y the y coordinate of the 3D cursor Z the z coordinate of the 3D cursor lt decrement the relevant coordinate of the 3D cursor by the number of pixels spec ified in the resolution choice gt increment the relevant coordinate of the 3D cursor by the number of pixels spec ified in the resolution choice The number of pixels by which to move the 3D cursor when the arrow keys are pressed Specify an intensity value that corresponds to bone surface 31 Current landmark Markup Jump lock Jump stored Axis lock Rotate to plane Rotate to axis Reflect cursor Sna
8. Tv graphics channel it must be associated with a Tv tool e Start a new Tv tool by pressing the New Tvtool button in the top level TINA tool A new Tv tool window will appear on the screen as shown in Fig 1 e Select the Tv you wish to display by selecting on its field in a Tv list Note that since multiple lists are available in various TINA sub tools this may be required even if it appears that the desired field is already selected e Press the install button in the new Tv tool The title of the Tv tool will change to the name of the Tv it is displaying Once a Tv has been installed on a Tv tool the Tv tool will display the graphics produced by that Tv auto matically updating whenever the graphics change without further user interaction Tv tools can be minimised or closed at any time without affecting algorithmic functionality Tv tools can also be freely reassigned by selecting another Tv and pressing the install button again Note that when a Tv is installed onto a Tv tool any other Tv tool displaying that Tv will be un installed the title of the Tv tool will change to reflect this Each Tv tool has the following menus and buttons e Size set the size of the Tv tool to various default values 256x256 512x512 and 768x768 Tv tools can also be freely resized by clicking and dragging the corner of the Tv tool window with the mouse e Mouse sets the mouse interaction with the image in the Tv tool e RO
9. loaded or not In order to mark up an axis or plane point e Move the 3D cursor to the desired point in the 3D image e Select the desired point in the Markup list of the Manual Landmark tool e g P1 1 is the first plane point e Press the Mark Point button in the Manual Landmark tool this will save the current coordinates of the 3D cursor to the point specified in the Markup list of the Manual Landmark tool 25 X Tv keyboard controls OX Select the text entry field for the key you wish to reassign then press the required key on the keyboard 2D Tvs Up Up Left Left Right Right Down Down 2D amp 3D Tvs Pick Shift_R Zoom Control_R Mark Return Figure 15 The keyboard controls dialog box In order to re use an existing landmark point as an axis or plane point e Scroll through the list of landmark points either in the landmark control dialog box or in the Manual Landmarking tool e Press the Jump to button in the Manual Landmarking tool this will move the 3D cursor to the coordinates of the current landmark point as specified in the landmark control dialog box and in the Manual Landmarking tool e Select the desired point in the Markup list of the Manual Landmark tool e g P1 1 is the first plane point e Press the Mark Point button in the Manual Landmark tool this will save the current coordinates of the 3D cursor to the point specif
10. shown in red such that the image shown in the x axis Tv is generated from a plane perpendicular to the x axis a the image shown in the y axis Tv is generated from a plane perpendicular to the y axis b and the image shown in the z axis Tv is generated from a plane perpendicular to the z axis c 5 1 Definition of Coordinates The coordinate system used in the TINA manual landmarking tool is derived from the original data and relates to the images displayed by the sequence tool as follows the z dimension is the inter slice dimension such that Z Zmin is the first slice and z Zmaz is the last slice Within each image the x dimension runs from left to right such that x min is the left hand edge of the image and x Zaz is the right hand edge and the y dimension runs from top to bottom such that y ymin is the top edge of the image and y ymaz is the bottom This definition is visible to the user in several places such as in the definitions of the 2D Tvs and in the landmark coordinates and is shown in Fig 4 When loading large medical image volumes it may be necessary to use the downsample and stride fields of the sequence tool depending on available memory In this case it should be noted that the 3D cursor position will always be displayed in the coordinates of the down sampled volume but all landmark positions displayed in the Landmark Points dialog box and save to file using that dialog will automatically be
11. side 23 Joining of squasmosal body to zygomatic process of squasmosal left side 24 Joining of squasmosal body to zygomatic process of squasmosal right side 25 Intersection of zygomatic process of maxilla with zygoma jugal superior surface left side 26 Intersection of zygomatic process of maxilla with zygoma jugal superior surface right side 27 Intersection of zygoma jugal with zygomatic process of temporal superior aspect left side 28 Intersection of zygoma jugal with zygomatic process of temporal superior aspect right side 29 Basion 30 Bregma intersection of frontal bones and parietal bones at midline 31 Intersection of parietal bones with anterior aspect of interparietal bone at midline 32 Intersection of interparietal bones with squamous portion of occipital bone at midline 33 Nasion Intersection of nasal bones coudal point 34 Nasale Intersection of nasal bones rostral point 35 Opisthion 36 Intradentale superior 37 Most posterior projection of the posterior nasal spine 38 Most superior point on the external auditory meatus right side 39 Anterior edge of the alveolar process where right first molar hits alveolus right side 40 Most anterior medial point on the right carotid canal right side 41 Most superior point on the external auditory meatus left side 42 Anterior edge of the alveolar process where right first molar hits the alveolus left side 43 Most anterior medial point on the left c
12. this effect Furthermore the lighting model used by the renderer does not take account of radiosity i e diffuse lighting 20 A Landmark Points JOG Up No Name NULL x 1 0 yi 1 0 z 1 0 Type 1 Link no 1 No 1 Name NULL M1 1 0 ye 1 0 2 1 0 Types 1 Link no 1 No 1 Name NULL x 10 y 10 Zz 1 0 Type 1 Link no 1 No 1 Name NULL L 10 ye 1 0 2 1 0 Type 1 Link no 4 No 1 Name NULL we 1 0 Pya 1 0 2 1 0 yoe 1 Link no 1 Down Format Names Raw TPS NTSYS TPS NTSYSID NOT SPECIFIED TPS NTSYS Field no 1 Pathname Scan Load Save Clear axis Clear plane Clear links Clear landmarks Figure 14 The landmark control dialog box reflected from multiple surfaces within the volume Instead it only takes account of direct rays of light from the light sources reflected off of one surface to the viewer This can cause a characteristic artefact in which rough bone surfaces appear to be speckled with small dark patches Correcting this with a more realistic lighting model would increase the processor time requirements to the point where the renderer could not run in interactive time However the effect can be minimised with careful choice of lighting parameters e g using a single light shining onto the front of a rodent skull seems to give a good result Finally the TINA Manual Landmarking tool was designed primarily for use on very large micro CT image volume of rodent s
13. user scrolls through the landmark list using the Up and Down buttons in the Manual Landmarking tool or in the Landmark Control dialog box to change the current landmark to a landmark for which coordinates have already been stored and then clicks the Jump stored button the 3D cursor will be moved to the stored coordinates for the current landmark If the Jump lock switch is set to On then this becomes the default behaviour when scrolling through the landmark list the 3D cursor will automatically be moved to the stored coordinates of the current landmark whenever such stored coordinates exist The Snap button provides a basic snap to grid style functionality When the 3D cursor is outside the bone clicking the snap button will move it to the nearest bone surface as defined by the bone threshold This function will have no effect if the 3D cursor is inside bone or already on a bone surface 8 1 Axis and Plane Points In addition to landmark points the TINA Manual Landmarking tool supports three plane points and two axis points these are not displayed in the landmark dialog box The plane points are used to specify the plane of bilateral symmetry The axis points are used to specify an arbitrary axis within the 3D image Both sets of points are used to implement various utility functions that make the manual landmarking process easier Axis and plane points can be specified regardless of whether a landmark list is
14. you about any it fails to find In particular if it cannot find the tina libs or tina tools libraries and headers then they can be passed to the configure command using the following flags with tina includes PATH with tina libraries PATH with tinatool includes PATH with tinatool libraries PATH e g configure with tina libraries usr local Tina6 tina tools lib If the tarballs were unpacked in usr local Tina6 then the correct locations are e g with tina includes usr local Tina6 tina libs 6 0rcbuild005 with tina libraries usr local Tina6 tina libs 6 0rcbuild005 lib with tinatool includes usr local Tina6 tina tools 6 0rcebuild005 with tinatool libraries usr local Tina6 tina tools 6 0rcbuild005 lib Finally type make to build the toolkit The TINA Manual Landmark toolkit needs to find the Volpack header and library On standard Linux systems these should be located in usr local include and usr local lib once Volpack has been installed The header file should be picked up automatically by the compiler and the library location should be automatically identified if usr local lib is listed in etc ld so conf and if ldconfig has been run or the machine rebooted since Volpack was installed If these files cannot be located the build will fail with error messages about functions with names starting with vp e g vpRenderRawVolume these are the functions provided by the Volpack library In that case the l
15. 0x Help Current TV 3D dump Bkgrnd white light grey dark grey black blue Line o 1 2 3 Color black blue white red Colormap Standard Greyscale Anaglyph False colour default colors 0 Default Font 6x10 endian Show cmap Show tv s cmap_lookup Push tv screen x dump tool 7O7 Movie init add one make seq show random ses tiff Rot x 0 0 Roty 0 5 Steps 10 Filename Timer 0 01 sec 100 Count 4 Dump Type Baw colour js bpp Figure 16 The view tool and dump tool can be reassigned to any key with the exception of a few keys reserved by the window manager such as the print screen key using the Keyboard Controls dialog box This dialog box is started by clicking the Keyboard Controls button at the top of the Manual Landmarking tool and is shown in Fig 15 In order to reassign a key left click with the mouse inside the field displaying the keyboard control you want to reassign and then press the key you want to specify The name of the key will appear in the entry field The same set of keys are used across all Tvs 10 The View Tool The View and Dump tools provide additional interaction with graphics displayed in Tv tools See the TINA User s Guide 5 for full instructions on how to use these tools Two functions of these tools are of particular interest when using the TINA Manual Landmarking tool the creatio
16. I select a region of interest within the image e Proj select the projection function for the Tv tool e install install the currently selected Tv onto the Tv tool e clone install a duplicate of the currently selected Tv onto the Tv tool allows multiple Tv tools to display the same Tv e init re initialise the image display to the default viewpoint removing any translation rotation or zooming of the image e repaint re display the image with the current translation rotation or zooming used if the image display should become corrupted for any reason See the TINA User s Guide 5 for full details Each Tv tool also displays two messages the name of the Tv installed onto the Tv tool displayed in the title bar and the current mouse functionality for the Tv tool displayed just below the button row The mouse functionality X Sequence Tool 0x DICOM re scale Help Tv sequence File AFF ANLZ RAD NEMA Pem Dicom Image type bin chr int ft m Stat 0 Stride 1 Downsample 1 Cur frame 0 End 0 Image File Scan Scales x 1 0 y 11 0 z 10 t 10 Load Save First lt gt End Jumpto Del Seq Del Ins Rep Push Stack gt Seq Figure 2 The Sequence Tool used for loading 3D medical image data lists the name of the function type followed by the functionality of the left middle and right mouse buttons e g zoom3D shift zoom rot indicates that
17. Set the foreground colour for pseudo colour rendering Set the background colour for pseudo colour and full colour rendering Specify a file from to which all the options of the renderer can be loaded saved Start a file browser for the options file Load renderer options from the file specified in the Options field Save renderer options to the file specified in the Options field 33 12 4 Lighting Control Dialog Box 1 6 On off x X Z r 8 b Reset to defaults Apply Switch the light on or off a maximum of six lights are supported The x component of the direction vector of the light 1 0 to 1 0 The y component of the direction vector of the light 1 0 to 1 0 The z component of the direction vector of the light 1 0 to 1 0 The red component of the colour of the light 0 0 to 1 0 The green component of the colour of the light 0 0 to 1 0 The blue component of the colour of the light 0 0 to 1 0 Reset all options to the default of a single white light shining down the z axis Implement any changes to the lighting options 34 12 5 Landmark Points Dialog Box Up Type Link no Down Format TPS NTSYS ID TPS NTSYS Field no Pathname Scan Load Save Clear axis Clear plane Clear landmarks Move upwards in the list of landmark points the next five rows of fields show the information stored for the landmark points the middle row of the five is the current landmark
18. Tina Memo No 2010 007 Technical Memo The TINA Manual Landmarking Tool P A Bromiley Last updated B 27 201 TINA WWW TINA VISION NET Imaging Science and Biomedical Engineering Division Medical School University of Manchester Stopford Building Oxford Road Manchester M13 9PT The TINA Manual Landmarking Tool P A Bromiley Imaging Science and Biomedical Engineering Division Medical School University of Manchester Manchester M13 9PT UK paul bromiley manchester ac uk 1 Introduction The TINA manual landmarking tool is designed to support the manual identification and specification of mor phological landmarks for subsequent analysis using techniques such as Procrustes analysis This user manual covers Section 2 installation of TINA the Volpack volume rendering library and the TINA Manual Landmarking toolkit on Linux systems Section 3 the TINA graphical subsystem Tv s and Tv tools Section 4 the TINA Sequence tool used for loading 3D medical data sets Section 5 the Manual Landmarking tool definition of coordinate systems and the Tv s available in the tool Section 6 the TINA interface to the Volpack volume rendering library used to produce the volume rendered images displayed in the 3D Tv of the Manual Landmarking tool Section 7 the Landmark Control dialog box used to load save and manipulate lists of landmark points Section 8 the use of the Manual Landmarking tool to mark up the p
19. VR Control dialog box Each line of the lighting control dialog box controls one of the lights The buttons on the far left specify whether the light is switched on or switched off The next three fields x y and z specify the normalised x y and z components of the direction of the light values between 1 0 and 1 0 are valid The final three components r g and b specify the colour of the light as normalised RGB components values between 0 0 and 1 0 are valid The default is to have a single white light shining down the z axis the Reset to defaults button resets all parameters to these default values Changes to the lighting parameters are not implemented until the Apply button at the bottom of the dialog box is pressed and even then have no effect unless the volume renderer is running If the Apply button is pressed with invalid parameters in the dialog box error messages will be printed to the text window of the top level tinaTool and any lights with invalid parameters will be disabled Finally the lighting control dialog features an emergency mode to ensure that even if all lights are disabled due to invalid parameters the default lighting will be applied so that a rendering is still produced Note that if coloured lights are specified with the renderer in greyscale mode then the rendering will show the intensity of the lighting but not the colour Switch to full colour mode to display the coloured lighting 6 2 Li
20. aTool window The view tool will start and will display the name of the currently selected Tv in the Current Tv field e Click the Dump button in the View tool This will start the Dump tool Enter a relative or absolute pathname relative pathnames are relative to the directory containing the tinaTool executable into the Filename field and select the colour depth using the Dump Type field B amp W will give a greyscale image Colour will give a full colour image and lbpp will give a black and white image which can be useful for saving graphs displayed in the Imcalc Graph Tv e Click on either the TIFF or EPS button to save the image from the currently selected Tv to file in TIFF or Encapsulated Postscript format 28 11 Using the Manual Landmarking Tool A complete set of steps required to specify a set of landmarks is as follows Prepare a landmark names file specifying the points that you intend to identify see Section 7 Start TINA start the Manual Landmarking tool Start the sequence tool assign a Tv tool to the sequence tool Tv optional see Section 3 and load a 3D medical image volume see Section 4 Start the volume renderer using the 3D Tv switch in the Manual Landmarking tool Start four new Tv tools and install them on the four Tvs of the Manual Landmarking tool Start the VR Control dialog box and the lighting control dialog box and man
21. al bones left side 4 Intersection of frontal process of maxilla with frontal and lacrimal bones right side 5 Frontal squasmosal intersection at temporal crest left side 6 Frontal squasmosal intersection at temporal crest right side 7 Center of alveolar ridge over maxillary incisor left side 8 Center of alveolar ridge over maxillary incisor right side 9 Lateral intersection of maxilla and palatine bone posterior to the third molar left side 10 Lateral intersection of maxilla and palatine bone posterior to the third molar right side 11 Anterior notch on frontal process lateral to infraorbital fissure left side 12 Anterior notch on frontal process lateral to infraorbital fissure right side 13 Most posterior point of the anterior palatine foramen left side 14 Most posterior point of the anterior palatine foramen right side 15 Anterior most point at intersection of premaxillae and nasal bones left side 16 Anterior most point at intersection of premaxillae and nasal bones right side 17 Most infero lateral point on premaxilla maxilla suture left side 18 Most infero lateral point on premaxilla maxilla suture right side 19 Intersection of parietal temporal and interparietal bones left side 20 Intersection of parietal temporal and interparietal bones right side 21 Most inferior aspect of posterior tip of medial pterygoid process left side 22 Most inferior aspect of posterior tip of medial pterygoid process right
22. arotid canal left side 44 Anterior nasal spine 45 Intersection of the right occipital condyle and the foramen magnum taken at the lateral most curvature right side 46 Intersection of the left occipital condyle and the foramen magnum taken at the lateral most curvature left side The file can be prepared in any text editor and on each line should contain a point number at the start of the line followed by one or more spaces or a tab character then the text description of the point If the user wishes to use the Linklines option in the 3D Tv see Section 5 2 2 in order to draw lines linking any pair of points that are arranged symmetrically about the plane of bilateral symmetry then a file listing these links must also be prepared Each line of the file contains two landmark point numbers corresponding to the landmark point numbers in the names file separated by a tab or one or more spaces Lines will then be drawn in the 3D Tv between the specified points whenever the Linklines option is selected in the 3D Tv draw check list and coordinates have been specified for both points The file must have the same filename as the landmark names file 22 and must have the extension llf e g if the names file is called points txt then the linking lines file must be called points llf It must also be placed in the same directory The linking lines file will then be automatically loaded or saved whenever the names
23. bottom of the Sequence tool The Push button copies the current slice to the top of the Imcalc stack see the TINA User s Guide where it can be processed or passed to other tools The Ins button takes the image from the top of the Imcalc stack and places it into the sequence after the current slice if no sequence is loaded then a new sequence will be created with the image as the first slice The Rep button takes the image from the top of the Imcalc stack and replaces the current slice of the sequence with it The Del seq button deletes the entire current sequence allowing it to be replaced with other images from the Imcalc stack The Stack gt Seq button will take all of the images currently held in the imcalc stack and use them to create a new sequence any current sequence is deleted in this process the images will be placed into the sequence in reverse order i e the image on the top of the stack will become the last image in the new sequence The sequence tool can also save data to file although not all file formats are supported this is to prevent the user from saving sequences where essential header data is not available or is no longer valid due to processing that has been applied to the images In order to load a tomographic image data set e Enter the pathname of the image file files into the Image file field of the tool either directly or using the file browser started by pressing the
24. ch set of landmarks in the file has a unique identifier the contents of the TPS NTSYS ID field will be used as the identifier However the software does not check whether this is unique in the file i e it is up to the user to do this NTSYS files can hold multiple lists of landmark points If landmark points are saved to a NTSYS file that already exists then the new set of landmark points will be appended to the existing file The contents of the TPS NTSYS ID field will be saved in the file as a comment The landmark point names will be saved to file as a list immediately preceeding the data matrix however NTSYS only supports labels of up to 16 characters and so the names will be abbreviated if necessary Users should be aware of this when preparing lists of landmark point names if they intend to use the NTSYS file format The landmark point coordinates will be saved to the data matrix of the NTSYS file as columns i e each column of the matrix represents a point e Click the Save button in the Landmark Control dialog box Landmark point information can also be loaded from any of these file formats The TPS Field No field allows the user to specify which record to load from a TPS file that contains more than one set of landmark points Since the software can only maintain one list of landmark points at a time a conflict may arise in situations where the user attempts to load a file when some landmark i
25. d Save buttons then load or save the options to or from the file New Feature in Manual Landmark Tool v1 2 Several example volume renderer options files are available in the extra_files sub directory of the max planck toolkit directory that is created when the Manual Landmarking Toolkit is extracted e tmlt_surface_style txt the options used in Fig 9 these provide a surface rendering style 3D image for many micro CT scans of rodent skulls e tmlt_pseudo _colour txt similar to the options used in Fig 9 but with pseudo colour rendering enabled and a light blue background allowing the User to easily see the opacity of the rendered image e tmlt_full_colour txt similar to the options used in Fig 9 but with multiple coloured lights enabled similar to the options used to produce the image on the front page of this document e tmlt_printing txt similar to the options used in Fig 9 but with pseudo colour rendering enabled with a white background and with all landmark points displayed as spheres rather than crosshairs these options are useful for producing images to be incorporated into publications 6 1 The Lighting Control Interface The volume rendering engine supports up to six fully configurable light sources Fig 12 shows the lighting control dialog box which allows the parameters of the lights to be specified by the user The dialog box is created by pressing the Lighting Control button in the
26. dering with options chosen to give a surface rendering style image showing the effects of coloured lighting this requirement Such algorithms rely on identifying a set of points on the bone surface within the volume tesselating these points to produce a representation of the surface and then only rendering this surface i e only rendering a small fraction of the data However this approach has a drawback in that it relies on a specific interpretation of the data i e some technique must be used to identify the surface prior to rendering If for example a simple threshold is used then this is equivalent to the assumption that all bone surfaces in the volume have a well defined grey level At any point where this assumption fails e g where the bone is thin and so obscured by partial voluming is of low density or is corrupted by image noise errors will be generated in the rendering e g pseudofenestrations holes in the rendered bone surface that do not exist in the original data The TINA Manual Landmarking tool uses a volume rendering algorithm in order to avoid such problems Volume rendering produces an image using the entire 3D volume each pixel in the rendered image represents a vector through the 3D volume and the renderer runs along these vectors converting the intensity and intensity gradient of every voxel in the 3D volume into opacity and reflectivity and combining these together to produce the intensity of the final pixel in the re
27. displayed in the Tv tool just above the image When zoom is selected the mouse can be used to manipulate the image Clicking and dragging with the left mouse button will move the image around in the Tv Clicking and dragging with the middle mouse button will zoom in or out Clicking and dragging with the right mouse button will select a rectangular region of interest and then zoom into that region when the mouse button is released During the moving or zooming operations the image will be replaced with a wire frame in order to increase speed When Pick is selected the mouse can be used to manipulate the 3D cursor via the 2D Tvs Only the left mouse button has functionality assigned to it in this mode Clicking on any point in the image will move the 3D cursor to that point clicking and dragging will move the 3D cursor interactively Only the coordinates displayed in the Tv will be altered e g the x axis Tv can be used to manipulate the y and z coordinates of the 3D cursor When marking up large numbers of points in multiple images it is desirable to keep the mouse pointer within the Tvs i e not to have to move it repeatedly back to the Manual Landmark tool window in order to click buttons there Therefore the Tvs also provide a set of keyboard shortcuts for commonly used functions e Up arrow key move the 3D cursor position upwards by one increment e Down arrow key move the 3D cursor position downwards by one increment e Left ar
28. elete the current landmark points list 35 12 6 Keyboard Controls Dialog Box Up Left Right Down Pick Zoom Mark Select a shortcut key to move the cursor upwards in the currently selected 2D Tv by the number of pixels specified in the Resolution choice list in the Manual Landmark tool Select a shortcut key to move the cursor left in the currently selected 2D Tv by the number of pixels specified in the Resolution choice list in the Manual Landmark tool Select a shortcut key to move the cursor right in the currently selected 2D Tv by the number of pixels specified in the Resolution choice list in the Manual Landmark tool Select a shortcut key to move the cursor downwards in the currently selected 2D Tv by the number of pixels specified in the Resolution choice list in the Manual Landmark tool Select a shortcut key that switches the mouse functions to Pick mode for all Tvs Select a shortcut key that switches the mouse functions to Zoom mode for all Tvs Select a shortcut key for the Mark Point button i e markup the point currently selected in the Markup choice of the Manual Landmark tool with the current co ordinates of the 3D cursor and then if Curr LM is selected move the current landmark to the next one in the landmark list 36 References 1 R A Drebin L Carpenter and P Hanrahan Volme rendering Computer Graphics 22 4 65 74 1988 2 R L Gregory
29. enderer full control of image colour this allows the use of coloured lights and material properties A user defined curve controlling the transformation from intensity in the original data to opacity in the rendered image spline produce a spline curve linking the control points linear produce a piecewise linear curve linking the control points reset reset the curve to a linear ramp apply implement the changes made to the curve A user defined curve controlling the transformation from intensity gradient in the original data to surface shading in the rendered image spline produce a spline curve linking the control points linear produce a piecewise linear curve linking the control points reset reset the curve to a linear ramp apply implement the changes made to the curve The thickness of the depth queing fog at the front of the image gt 0 The rate at which the depth queing fog becomes thicker with depth through the image gt 0 Switch depth queing on off depth queing acts like a fog in the rendered image so that more distant parts of the data are dimmer The reflection coefficients of surfaces for ambient light red green and blue 0 0 to 1 0 The reflection coefficients of surfaces for diffuse light red green and blue 0 0 to 1 0 The specular reflection coefficients of surfaces red green and blue 0 0 to 1 0 The shinyness of surfaces 1 0 to 100 0 Start the Lighting Control dialog box
30. ensity 11 0 Depth queing Off On Ambient R 01 G 01 B 01 Diffuse R 10 44 G 0 4 B 0 44 Specular R 0 5 G 0 5 B 05 Shinyness RGB 1 0 Lighting Control Foreground colour Background colour Options Scan Load Save Figure 8 Opacity only volume rendering 17 Figure 10 X VR Control a x Fastest Highest Render quality Fast High Pseudo colour Full Colour Render type Opacity Greyscale Scalar Classification n I spline linear reset apply Gradient Classification ae spline linear reset Pi apply DQ Front fac 1 0 DQ Density 1 0 Depth queing Off On Ambient R 01 G 0 1 B 0 1 Diffuse R 04 G 04 B 04 Specular R 05 G 05 B 05 Shinyness RGB 1 0 Lighting Control Foreground colour Background colour EE Options Scan Load Save X VR Control ox Render quality Fastest Fast High Highest Render type Scalar Classification oce a OS Opacity Greyscale Pseudo colour Full Colour 3 spline a linear h reset Fi apply Gradient Classification ee spline linear 3 reset a apply DQ Front fac 1 0 DQ Density 1 0 Depth queing Off On Ambient R 01 G 01 B 01 Diffuse R 10 44 G 0 4 B 0 44 Specular R 0 5 G 0 5 B 05 Shinyness RGB 1 0 Lighting Control Foreground colour Background colour Options Scan Load Save Pseudo colour volume rendering with
31. ent to whichever Tv the mouse pointer is inside In order to switch to focus follows pointer mode in Suse 10 3 e Click on the start button in the bottom left corner of the screen select Configure desktop Select the Desktop tab from the menu on the left Select the Window Behaviour tab from the menu on the left e Select the Policy drop down menu in the Focus box e Select Focus follows mouse from the drop down menu e Click the Apply button at the bottom of the window The window manager focus will now follow the mouse pointer These instructions are valid for openSuse 10 3 using the KDE desktop Other window managers may vary see the instructions for the window manager you are using if necessary The keyboard shortcuts can be reassigned to any set of keys with the exception of a few reserved by the window manager e g the print screen key using the keyboard controls dialog box see Section 9 11 Additional display functionality can be accessed via the 2D Draw check list in the Manual Landmarking tool If Axis is selected then any currently specified axis points will be displayed as small yellow cross hairs in the 2D Tvs Similarly Plane will display any currently specified plane points as small cyan cross hairs Note that these are projected onto the Tvs so that they are displayed even if they do not lie in the plane of the image Rotate takes any r
32. esolution 0 105 1 0 20 5 0 Bone threshold 1500 0 Current landmark Up Down Na 1 Name NULL Markup Curr LM Ax 1 Ax 2 PI 1 PI 2 JEL By Jump lock Off On Jump stored Axis lock Off On Rotate to plane Rotate to axis Reflect cursor Snap Mark point Figure 3 The Manual Landmarking Tool In order to save a tomographic image data set e Enter the pathname of the image file files into the Image file field of the tool e Select the format of the image file from the File choice list AIFF RAD ANLZ and PGM are supported NEMA and DICOM are not supported For file types e g AIFF where each slice is contained in a separate file use the character as a wildcard For example if the sequence contains 10 slices to be saved to files named im 00 to im 10 enter the pathname of the first file into the Image file field Then replace the part of the name that changes between files with the character so that it becomes im During image saving the wildcard characters in the pathname will be replaced with the slice numbers of the images in the sequence If the numbers in the filenames increase by more than 1 between each file then the Stride field can be used to specify the increment For example entering im into the Image file field and 2 into the Stride field will save the images im 00 im 02 im 04 etc Note that there are some restrictions on saving multiple file
33. ew tool by clicking the View button in the tinaTool window The view tool will start and will display the name of the currently selected Tv in the Current Tv field e Select the parameters of the movie Rot x the rotation to apply about the x axis of the image in radians Rot y the rotation to apply about the y axis of the image in radians Steps the number of frames in the movie Timer 0 01 sec the time delay between each frame during playback Count the number of times to loop through the movie e Click Make seq to prepare each frame of the movie and store it to the Tv e Click Show to play the movie in the Tv e Clicking Init will delete any previously stored movie allowing a new one to be prepared The Dump tool which is a sub tool of the view tool can save the image displayed in any TINA Tv tool as a TIFF or Encapsulated Postscript file TIFF files can be used to transfer images to Windows machines e g for incorporation into MS Word documents whilst EPS files can be used to incorporate images into documents prepared under Linux e g using Latex To save the image displayed in a Tv tool to a file e Select the Tv for which you wish to produce a movie by clicking on its entry in the Tv list of the tool it is associated with e g click on 3D in the Tv list of the Manual Landmarking tool e Start the View tool by clicking the View button in the tin
34. file is loaded or saved An example is shown below An example landmark point links file for mouse skulls corresponding to the names file above 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 38 41 39 42 40 43 45 46 Names files and other files containing landmark points are loaded and saved using the Landmark Control dialog box which also displays the currently loaded list of landmark points and provides some basic tools to manipulate it This dialog box is started by clicking on the Landmark List button at the top of the Manual Landmarking tool and is shown in Fig 14 In order to load a landmark names file e Prepare the names file in advance using any text editor e In the Landmark Control Dialog box enter the absolute or relative pathname of the landmark names file into the Pathname field either directly or by using the file browser started by clicking on the Scan button e Select the format of the file in this case Names from the Format choice list e Click the Load button in the Landmark Control dialog box Once a names file has been loaded the names and numbers of the landmarks can be viewed in the Landmark Control dialog box The top half of the dialog box shows five landmarks at a time displaying their number name any stored x y and z coordinates a type field see below and a link no field which specifie
35. g entering 2 means that each image will be down sampled by a factor of 2 on the x and y axes during loading The current image in the sequence i e the one displayed in the sequence tool Tv The number of the last image in the sequence The absolute or relative pathname of the file to load save Starts a file browser for the Image File field The dimensions of each voxel in the sequence Load data from the file specified in the the Image File field Save the current sequence to the file specified in the the Image File field Set the first image in the sequence as the current image Move backwards through the sequence i e decrement the current image Move forwards through the sequence i e increment the current image Set the last image in the sequence as the current image Set the image specified in the Cur frame field to be the current image Delete the current sequence from memory Delete the current frame from the sequence Take the image from the top of the Imcalc stack and insert it into the sequence after the current image Take the image from the top of the Imcalc stack and insert it into the sequence replacing the current image Copy the current image to the top of the Imcalc stack Take the entire Imcalc stack and produce a new sequence with it in reverse order 30 12 2 Manual Landmark Tool VR Control Landmark List Keyboard Controls Tv 3D Tv 3D Tv Mouse 2D Tv Mouse
36. ice is the most suitable during mouse interaction with the image displayed in the 3D Tv The volume renderer is also capable of producing several different types of image depending on the selection in the Render type choice list The Opacity choice will render an image showing only the opacity of each voxel i e with no surface shading so that the Gradient classification lighting and material parameters are all ignored This provides a transparent view of the data as shown in Fig 8 The Greyscale choice will render an image with both opacity and surface shading so that the Gradient Classification lighting and shading parameters are all applied However only the overall intensity of light from each voxel is displayed and so the resulting image is greyscale The Pseudo colour choice produces a greyscale image but then colours the result using the colour chosen with the Foreground colour button and sets the background to a uniform colour as specified with the Background colour button The Full colour choice gives the renderer complete control of image colour so that coloured lights and material properties can be used see below the Background colour field can also be used to change the colour of the background in this mode Pressing the Lighting Control button spawns the Lighting Control dialog box which provides the user with full control over the lighting parameters used by the vol
37. ied in the Markup list of the Manual Landmark tool In order to display axis or plane points within the 3D rendering select the desired options in the 3D Tv Draw check list in the Manual Landmarking tool Plane points are displayed in cyan and axis points in yellow As with landmark points and the 3D cursor the points are displayed as 3D cross hairs Any parts of a cross hair that lie behind a bone surface as specified by the Bone threshold field in the Manual Landmarking tool from the current viewpoint are displayed in a lower intensity whilst points that are not behind a bone surface are displayed in a higher intensity this provides 3D cues to the user making it easier to see how each point interacts with the bone surface However this functionality is disabled during rotation of the 3D rendered image in order to prevent slowdown during rotation all points are displayed in a medium intensity Plane points are used by the Reflect cursor button in the Manual Landmarking tool Once three plane points have been specified pressing this button will project the current 3D cursor position through the plane to an equidistant point on the other side and reset the 3D cursor to that point This can be useful when marking up symmetrical structures Axis points are used to limit the rotation of the volume rendered image in the 3D Tv Once both axis points have been specified press the Lock Rotation button in the Ma
38. ipulate the volume renderer options to produce a good volume rendering see Sections 6 and 6 1 for suggested settings Use the techniques described in Section 5 2 2 to specify a suitable bone threshold Load the landmark names file using the Landmark Control dialog box see Section 7 The current landmark will now be the first one in the list manipulate the rotation of the image in the 3D Tv with the 3D Tv mouse interaction in Zoom mode until you can see the corresponding point on the bone surface Switch the 3D Tv mouse interaction to Pick mode and then left click on the position of the landmark point in the 3D Tv the 3D cursor will be moved to that point Check the position of the 3D cursor in the 2D Tvs if necessary refine it using the arrow keys in the Manual Landmarking tool or by using mouse or keyboard interaction with the images in the 2D Tvs see Section 5 2 1 When you are happy with the position of the 3D cursor click the Mark point button in the Manual Landmarking tool or use the keyboard shortcut in the 2D or 3D Tvs see Sections 5 2 1 and 5 2 2 The coordinates of the 3D cursor will then be transferred to the current landmark and the current landmark will then be incremented i e the next landmark in the list will become the current landmark Proceed through the landmark list marking up each point in turn until the coordinates of all points have been specified Save the landmark list to file usi
39. is 2 3 Install Volpack The TINA Manual Landmarking toolkit requires the Volpack volume rendering library A version of this library can be found in http www tina vision net tarballs manual_landmark_toolkit Unzip and unpack the tarball this can be done in any directory although it is standard practice to put user installed software in usr local cd into the new Volpack directory created when the tarball was unpacked and use configure make make install as root to build the library On standard Linux systems the Volpack library and header file will be copied into standard locations usr local lib and usr local include respectively The compiler should automatically pick up the location of the header file and the location of the library will be automatically picked up if usr local lib is specified in etc ld so conf the system wide list of library locations If it is not then add usr local lib to the file Run ldconfig to refresh the list of libraries after the installation of Volpack or restart the machine 2 4 Install the Manual Landmarking Toolkit Download the manual landmarking toolkit max_planck_toolkit 1 0 tar gz from the TINA web site place it in a convenient directory e g home my_username tina_toolkits then unzip and unpack it A new sub directory will be created cd into this subdirectory and type configure The configure script will search for the external libraries needed to build the toolkit warning
40. kulls typically several GB in size In order to make proper use of the accelerated 3D graphics hardware found in most PCs the data to be rendered must be copied to the video card memory in order to avoid continual paging of data from system memory to video card memory across the system bus However the majority of current video cards lack sufficient memory to hold an entire micro CT rodent skull volume Therefore the volume renderer used in the Manual Landmarking tool does not use graphics hardware it runs on the CPU and from system memory 7 The Landmark Control Interface The TINA Manual Landmarking tool was developed to allow the generation of lists of landmark point positions for use in Procrustes analysis In this type of analysis it is essential that each list of landmark points contains the same set of physiological locations in the same order Therefore rather than allowing the free form generation of lists of points the Manual Landmarking tool requires the user to prepare a text file containing a list of point names and point numbers referred to as a names file which must be loaded into the tool before point locations can be specified An example is shown below 21 An example landmark point names file for mouse skulls 1 Most anterior point of the anterior palatine foramen left side 2 Most anterior point of the anterior palatine foramen right side 3 Intersection of frontal process of maxilla with frontal and lacrim
41. l packages are required see the documentation for the Linux distribution you are using for instructions on how to install them Installation of these packages should also result in installation of various other packages atk pango fontconfig pkgconfig required by both GTK 2 and TINA 2 2 Install the TINA libraries Download the latest tina libs and tina tools tarballs from http www tina vision net tarballs The TINA Manual Landmark toolkit version 1 3 requires rcbuild005 or greater As root create a directory called Tina6 in usr local Copy both tarballs into the new directory Then unzip both tarballs using e g gunzip tina libs 6 0rcbuild005 tar gz gunzip tina tools 6 0rcbuild005 tar gz and then unpack both using tar xvf tina libs 6 0rcbuild005 tar tar xvf tina tools 6 0rcbuild005 tar Build the tina libs libraries first cd into the tina libs xxx where xxx is the build number directory created when the tina libs tarball was unpacked and type configure make make install Build the tina tools libraries after the tina libs libraries cd into the tina tools xxx where xxx is the build number directory created when the tina tools tarball was unpacked and type configure make make install Note that the configure script in the tina tools directory provides some information about the required libraries in particular if you do not have the necessary GTK 2 libraries installed see step 1 it will warn you about th
42. mitations of the Volume Renderer In order for the Manual Landmarking tool to be usable mouse interaction with the 3D image must be fast enough that the image can be manipulated in interactive time i e the renderer must be able to produce several frames per second This places severe constraints on the amount of processing that can be performed during rendering Traditionally landmark identification software has used surface rendering algorithms in order to meet 16 yo VR Control O x Render quality Fastest Fast High Highest Render type Opacity Greyscale Pseudo colour Full Colour Scalar Classification spline linear reset apply X Gradient Classification Size Mouse ROI Proj spline install clone init repaint linear zoom3D rot zoom shift reset apply DQ Front fac 1 0 DQ Density 11 0 Depth queing Off On Ambient R 01 G 01 B 01 Diffuse R 10 44 G 0 4 B 0 4 Specular R 05 G 05 B 05 Shinyness RGB 1 0 Lighting Control Foreground colour Background colour E Options Scan Load Save Figure 7 The volume renderer using the default options XX VR Control ox Render quality Fastest Fast High Highest Render type Opacity Greyscale Pseudo colour Full Colour Scalar Classification spline linear reset apply X m Gradient Classification Size Mouse ROI Proj spline install clone init repaint linear zoom3D rot zoom shift reset apply DQ Front fac 1 0 DQ D
43. multiplied by the relevant down sampling factors so that they are in the coordinate system of the original data For example if the original image volume consists of 1000 slices each 1000x1000 voxels in size and this is down sampled by a factor of 2 on X 3 o x X Y Axis lolx Size Mouse ROI Proj Size Mouse ROI Proj install clone init repaint install clone init repaint zoom3D rot zoom shift imzoom shift scale roi X X Axis o x X Z Axis SE Size Mouse ROI Proj Size Mouse ROI Proj install clone init repaint install clone init repaint imzoom shift scale roi imzoom shift scale roi Figure 5 The four Tv s of the Manual Landmarking tool arranged so that the cross hairs for the three 2D Tv s are consistent across all three windows each axis when it is loaded i e the downsample and stride fields in the sequence tool are both set to 2 then the coordinates of the 3D cursor placed at the centre point of the volume will be 256 256 256 and this will be displayed in the X Y and Z fields of the Manual Landmark tool however if this point is marked up as a landmark point then the coordinates will automatically be multiplied by the down sampling factors to become 512 512 512 before they are displayed in the Landmark Points dialog box or saved to file This prevents the choice of down sampling factors from affecting any subsequent Procrustes analysis of the landmark point
44. n of movies from 3D images and the saving of images to files The View tool can be used to prepare a movie from any Tv displaying a 3D image e g the 3D Tv of the Manual Landmarking tool in which the image rotates in 3D around its central point Each frame of the movie is rendered in turn and stored as a 2D image within the Tv tool during playback these 2D images are displayed in the Tv as a slide show Therefore no rendering is performed during playback allowing the movie to play in a much shorter time than it took to render This can significantly increase the viewer s perception of 3D and so can be useful in seeing exactly where landmark points are located in the 3D image The user can specify the angles of rotation the number of frames in the movie the time delay between each frame during playback and the number of times the movie loops during playback Note that the rotation angles are specified in radians around the current x axis i e left right axis and y axis i e up down axis of the Tv i e they do not refer to the coordinate system used in the Manual Landmarking tool Once a movie has been created it is stored in the Tv tool until the user deletes it 27 To create a movie in a Tv tool displaying a 3D image e Select the Tv for which you wish to produce a movie by clicking on its entry in the Tv list of the tool it is associated with e g click on 3D in the Tv list of the Manual Landmarking tool e Start the Vi
45. ndered image The final rendered image thus provides a more complete view of the data than a surface rendering at the expense of significantly more processing 19 X Lighting Control 1 Off On x 0 0 y 0 0 N e g 2 Off On x 0 0 y 0 0 z 10 r 1 0 g 1 0 b 1 0 3 0fflOn x 0 0 y 10 0 z 1 0 a1 0 g 1 0 b 1 0 4 Off On x 0 0 y 10 0 z 1 0 r 1 0 g 1 0 b 1 0 5 Off On x 0 0 y 10 0 z 10 r 10 g 1 0 b 11 0 6 Off On x 0 0 y 10 0 z 1 0 r 1 0 g 1 0 b 11 0 Reset to defaults Apply Figure 12 The lighting control dialog box Viewing Rays Shear A A A Volume Slices project t warp 4 Image Plane a b Figure 13 Volume rendering a 3D data block from an arbitrary viewing direction results in arbitrary angles of intersection between the viewing rays and the slices of the 3D data a Shear warp volume rendering pre calculates an overall shear of the volume that makes the viewing rays parallel to one axis of the sheared volume b The sheared data is then projected along the parallel rays into a buffer which is finally warped onto the image plane to produce the rendered image This results in a much more favourable alignment of the data in memory vastly increasing rendering speed at the expense of a small reduction in the quality of the rendered image In order to pr
46. nformation has already been loaded In such situations the lengths of the two lists will be compared If they are the same then the software will assume that the points are in the same order and will load all of the information contained in the new file into the relevant fields of the current landmark list If the lengths are different then the software will either refuse to load the new file or will discard the current landmark list and replace it with the information from the file always choosing the option that discards the least data i e if the user attempts to load a names file after a TPS or Raw file has been loaded the software will refuse to load the file if the user attempts to load a TPS or Raw file after loading a names file then the names will be replaced with those from the file However the Landmark Control dialog box provides a Clear Landmarks button that allows the current landmark list to be cleared and also provides Clear Axis and Clear Plane buttons allow the user to discard any currently stored axis and plane points see Section 8 1 Note that Raw NTSYS and TPS files do not contain the information from the line linking lines file However the user can load this information by loading a names file with a corresponding linking lines file after loading a Raw NTSYS or TPS file as long as all files contain corresponding lists of landmark points 8 Manual Landmarking The aim of the manual landmarking tool i
47. ng the Landmark Control dialog box see Section 7 At this point the user can load another 3D image volume and repeat the process Note that the previous landmark list will still be in memory and so can be used as starting points if the data sets are similar enough or can be deleted using the Clear Landmarks button in the Landmark Control dialog box allowing the names list to be re loaded 29 12 Quick Reference 12 1 Sequence Tool DICOM re scale Tv sequence File Image Type Start Stride Downsample Cur frame End Image File Scan Scales x y z t Load Save First lt 2 End Jumpto Del Seq Del Ins Rep Push Stack gt Seq Selects the type of scaling tags in a DICOM image rarely used The Sequence tool Tv Selects the file format AIFF TINA s standard image file format ANLZ ANALYZE medical image format RAD RAD format NEMA Older pre DICOM format PGM Portable grey map DICOM DICOM format Displays the variable type of the images in the sequence and can also be used to cast the current sequence to a different type by selecting the desired type after loading the sequence bin binary chr short int integer flt floating point The number of the first image in the sequence The number of images to skip whilst loading the sequence e g entering 2 means that every other image will be loaded Down sampling factor used during image loading e
48. nt 3D cursor coordinates as the currently selected landmark These can be reassigned to any desired keys using the keyboard controls dialog box see Section 9 As well as displaying a volume rendered image of the data currently loaded into the sequence tool the 3D Tv can display any stored landmark axis or plane points The user can choose which points to display using the 3D Tv draw check list in the Manual Landmark tool The available choices are e Cursor display a red cross hair representing the 3D cursor switched on by default e LM display green cross hairs for all marked up landmark points e Axis display yellow cross hairs for any specified axis points e Plane display cyan cross hairs for any specified plane points e Text display the number of each marked up landmark point next to the point e Poly display a line representing the axis and a grid representing the plane e Ball display 3D spheres instead of cross hairs for the landmark axis and plane points e Linklines display white lines linking equivalent landmarks on the left and right sides of the sample 13 X VR Control BEE Render quality Fastest Fast High Highest Render type Opacity Greyscale Pseudo colour Full Colour Scalar Classification spline linear reset apply Gradient Classification spline linear reset apply DQ Front fac 1 0 DQ Density 1 0 Depth queing Off On Ambient R 01 G 01 B 01 Diffuse
49. nual Landmarking tool The volume rendered image will then only rotate around an axis parallel to that defined by the two axis points and passing through the centre of the volume This functionality can be useful in viewing the extremal extents of some structures The viewpoint of the 3D Tv can also be aligned using the Rotate to Axis and Rotate to Plane buttons in the Manual Landmarking tool Once three plane points have been selected clicking the Rotate to Plane button will rotate the volume such that the viewing direction after rotation is the normal to the plane using the smallest rotation angle possible Clicking the button a second time will flip the volume over to give the view from the other side of the plane Once all axis and plane points have been defined clicking the Rotate to Axis button will rotate the volume such that the projection of the axis onto the plane is aligned with the left right axis of the 3D Tv such that using both buttons in combination will completely align the volume Again the rotation applied is through the smallest angle possible and clicking the button a second time will flip the volume over to give the view from the opposite side 9 Keyboard Controls As described in Sections 5 2 1 and 5 2 2 a number of keyboard shortcuts are available in the 2D and 3D Tvs enabling commonly used functions to be applied without moving the mouse cursor away from the Tv tools These 26 xK View Tool
50. ocations of the Volpack library and header file can be specified manually to the configure command using the flags with volpack include PATH with volpack library PATH The executable file for the toolkit is located in the sre subdirectory alternatively typing make install will copy it to the bin subdirectory In either case cd to that directory and type tinaTool to run the toolkit Upon typing tinaTool the top level TINA tool will appear on the screen This provides access to various sub tools that in turn provide access to the algorithmic functionality The sub tools of most interest for manual landmarking are the manual landmarking tool itself the sequence tool used for loading medical image data and the Tv tools used to display graphics The text window at the bottom of the top level TINA tool is used to display information and error messages 3 Tv s and Tv Tools The TINA image display system is designed to provide the maximum range of configuration options to the user It consists of two components Tv s and Tv tools The majority of the TINA sub tools will have a choice list at the top of the sub tool window labelled Tv Each button in the list represents an available graphics channel however Tv s are not displayed by default in order to save space on the screen X Tv Tool1 ax Size Mouse ROI Proj install clone init repaint null Figure 1 A Tv Tool In order to display a
51. oduce volume rendered images in interactive time the TINA Manual Landmarking tool uses a fast volume rendering algorithm known as the shear warp algorithm The operation of this algorithm is illustrated in Fig 13 Projecting along vectors from some arbitrary viewpoint would involve complex geometrical calculations in order to find which voxels were intersected by which vectors Therefore the shear warp algorithm calculates an overall shearing of the volume that makes all of the vectors parallel to the nearest major axis of the volume The data is then projected into an intermediate image which is parallel to one face of the volume before being warped to produce the final rendered image This results in a much more favourable alignment of the data in memory vastly increasing rendering speed at the expense of a small reduction in image quality introduced by the warping Several additional limitations have been implemented in order to maintain rendering speed The renderer uses a parallel projection rather than a perspective projection i e assumes that all rays from the viewpoint through the data are parallel rather than diverging The drawback of this approach is that it can introduce an optical illusion known as the Necker Cube 2 in which particularly if the image has high transparency it can be difficult to tell which side of the volume is closest to the viewer Using renderer settings that minimise the translucency of bone surfaces will minimise
52. options chosen to give a surface rendering style image 18 X 3 Size Mouse ROI Proj install clone init repaint zoom3D rot zoom shift Figure 9 Greyscale volume rendering with options chosen to give a surface rendering style image X Size Mouse ROI Proj install clone init repaint zoom3D rot zoom shift X VR Control ox Render quality Fastest Fast High Highest Render type Opacity Greyscale Pseudo colour Full Colour Scalar Classification i spline a 2 linear reset Hea apply X m SA Gradient Classification Size Mouse ROI Proj 4 goin instali clone int repaint linear zoom3D rot zoom shift reset Gi apply DQ Front fac 1 0 DQ Density 1 0 Depth queing Off On Ambient R 0 1 G 01 B 01 Diffuse R 0 4 G 0 4 B 04 Specular R 05 G 05 B 05 Shinyness RGB 1 0 Lighting Control Foreground colour Background colour EE Options Scan Load Save a b X Lighting Control 0X 1 Off On x 0 0 y 0 0 z 10 r 0 6 g 103 b 103 2 Off On x 0 0 y 11 0 z 00 r 0 3 g 10 6 b 10 3 3 0OfflOn x 11 0 y 10 0 z 0 0 r 0 3 g 10 3 b 0 6 4 Off On x 0 0 y 10 0 z 1 0 r 1 0 g 1 0 b 1 0 5 Off On x 0 0 y 10 0 za 1 0 r 1 0 g 1 0 b 11 0 6 Off On x 0 0 y 10 0 z 10 r 110 g 11 0 b 11 0 Reset to defaults Apply c Figure 11 Full colour volume ren
53. ory usage the volume renderer is not activated by default and must be explicitly switched on by the user This is done using the 3D Tv choice list in the Manual Landmarking tool if NULL is selected then the volume renderer is switched off Selecting VR will switch on the volume renderer and prepare the sequence for rendering this may take several tens of seconds to complete In order to switch on the volume renderer e Select VR in the 3D Tv choice list in the Manual Landmarking tool e Select 3D in the Tv choice list of the Manual Landmarking tool start a new Tv tool and click Install in the Tv tool the title bar of the Tv tool will change to indicate that it is now displaying the 3D image stream e Click the VR Control button in the Manual Landmarking tool to start the volume rendering controls dialog box e Use the volume rendering controls see below to produce a satisfactory rendering Mouse interaction with the 3D Tv can be selected using the 3D Tv Mouse switch in the Manual Landmark tool In zoom mode mouse interaction controls the 3D image Clicking and dragging with the left mouse button will rotate the image Clicking and dragging with the middle mouse button will zoom in or out moving the mouse left and right or rotate the image within the image plane moving the mouse up or down Clicking and dragging with the right mouse button will move the image ar
54. ositions of landmarks specified in the landmark point list Section 9 the Keyboard Controls dialog box used to assign keyboard shortcuts to the Tv s of the Manual Landmarking tool Section 10 the TINA View tool which provides functions to save the images displayed in TINA Tv tools Section 11 and example landmarking session Section 12 quick reference guides explaining the functions of each button data entry field etc in the Sequence tool Manual Landmarking tool and Manual Landmarking tool dialog boxes This manual covers the Manual Landmark Tool v 1 4 which requires TINA 6 0 build number 005 or higher Some familiarity with the Linux OS is assumed e g how to start and use a shell tool Throughout this guide boxed sections contain detailed instructions on how to perform specific tasks with the Manual Landmarking software 2 Installation Installation of the TINA manual landmarking tool is done in three stages installation of the TINA libraries which provide the TINA machine vision functionality installation of the Volpack library which is used by the TINA manual landmarking tool to produce 3D volume rendered images of tomographic image data and installation of the TINA manual landmarking toolkit which provides the manual landmarking functionality and the user interface 2 1 Install GTK 2 The TINA libraries depend on the GTK 2 libraries which must be installed prior to installing TINA Both the gtk2 and gtk2 deve
55. otation that the user has applied to the image displayed in the 3D Tv and applies it to the images displayed in the 2D Tvs New Feature in Manual Landmark Tool v1 2 Manual Landmark Tool v1 1 1 and earlier The Rotate option affects only the displays in the Tvs i e the increment and decrement operations for the 3D cursor still apply to the original axes of the sequence not the rotated axes of the Tvs This is true for both the increment and decrement buttons i e the arrow buttons in the Manual Landmarking Tool window and the keyboard shortcuts in the 2D Tvs Manual Landmark Tool v1 2 and later When the Rotate option is selected the increment and decrement buttons i e the arrow buttons in the Manual Landmarking Tool window still move the position of the 3D cursor along the major axes of the original image volume However when the keyboard shortcuts are used in the 2D Tvs the cursor is moved along the rotated axes of the image displayed in the Tv not along the axes of the original volume This allows the User to define a preferred orientation using the axis or plane points rotate the volume to that orientation and then select extremal points on structures displayed in the 2D Tvs relative to the defined plane or axis 5 2 2 3D Image Display The 3D Tv displays a volume rendering of the data loaded into the sequence tool Since the preparation of this image involves a significant amount of processor time and mem
56. ound within the Tv When pick mode is selected mouse interaction within the 3D Tv controls the 3D cursor Left clicking within the 3D Tv will move the 3D cursor to the first bone surface under the mouse pointer i e the position of the mouse pointer specifies a vector through the data depending on the current rotation of the 3D image the software will run along this vector starting at the uppermost point from the current view direction until it reaches a bone surface The 3D cursor will then be moved to this point on the bone surface At the current time the bone surface is defined by a threshold which the user can set in the Bone threshold field of the Manual Landmarking tool It is anticipated that this will be replaced with something more quantitative in a future version of the software However the software also provides a profiling tool to aid the user in selecting a suitable threshold Right clicking with the mouse within the 3D Tv will produce a grey level profile along the vector under the mouse pointer and display it in the Imcalc Graph Tv 12 In order to select a bone threshold intensity e Start the volume renderer as described above Using the Zoom mouse mode rotate the image such that a point with a solid bone surface is clearly visible e Start the Imcalc tool from the top level tinaTool e Click Graph in the Tv choice list of the Imcalc tool start a new Tv tool and click Install in
57. p Mark point The current landmark in the landmark list Up move to the previous landmark in the list Down move to the next landmark in the list No the number of the current landmark Name a text description of the current landmark Choose which point to mark up when the Mark point button is pressed Curr LM the current landmark from the landmark list Ax 1 the first axis point Ax 2 the second axis point Pl 1 the first plane point Pl 2 the second plane point Pl 3 the third plane point If this switch is on then when the selection in the markup choice list is changed or when the choice of current landmark is changed if Curr LM is selected in the markup choice list the 3D cursor will automatically by moved to the stored coordinates for that point if any Move the 3D cursor to the coordinates of the point specified in the markup choice list if those coordinates have already been marked up Lock the rotation of the image in the 3D Tv so that rotation only occurs around an axis parallel to the axis defined by the two axis points and passing through the centre of the volume Rotate the image in the 3D Tv such that the view direction is normal to the plane pressing the button a second time will rotate the view by 180 degrees around the y axis to show the opposite side of the volume Rotate the image in the 3D Tv such that the projection of the axis defined by the two axis points onto the
58. plane defined by the three plane points is aligned with the left right axis of the Tv pressing the button a second time will rotate the view by 180 degrees around the y axis of the Tv to show the opposite side of the volume Project the cursor through the plane defined by the 3 plane points Move the 3D cursor to the nearest bone surface as defined by the bone threshold unless it is already inside bone Save the coordinates of the current 3D cursor position to the point specified in the markup choice list i e the current landmark or one of the axis or plane points A landmark list must be loaded before landmarks can be marked up 32 12 3 Volume Renderer Control Dialog Box Render quality Render type Scalar classification Gradient classification DQ Front Fac DQ Density Depth queing Off On Ambient R G B Diffuse R G B Specular R G B Shinyness RGB Lighting Control Foreground colour Background colour Options Scan Load Save Set the balance of speed vs rendering quality by ignoring low opacity voxels the recommended option is Fast Choose the type of rendering Opacity show an image of opacity transformed intensity only Greyscale show both opacity and surface shading transformed gradient Pseudo colour show a greyscale image in which the object is tinted with the Fore ground colour and the background is filled with the Background colour Full Colour give the r
59. plays the number and name of the current landmark and has copies of the Up and Down buttons However the current landmark is always kept consistent between these two windows so when scrolling through the landmark list using 23 the buttons in the Manual Landmarking tool the user will also see the list scroll in the Landmark Control dialog box The Landmark Control dialog box can also load and save a variety of other file formats as specified in the Format choice list Raw is a TINA specific ASCII text format that can contain all of the information from the landmark list TPS and NTSYS are standard formats for morphological data All of these formats are ASCII text files and so can be viewed or edited in any text editor In order to save a landmark list e In the Landmark Control Dialog box enter the absolute or relative pathname of the landmark file into the Pathname field either directly or by using the file browser started by clicking on the Scan button e Select the format of the file from the Format choice list Raw files can only hold one list of landmark points If a Raw file is overwritten then the previous version of the file will be replaced TPS files can hold multiple lists of landmark points If landmark points are saved to a TPS file that already exists then the new set of landmark points will be appended to the existing file The TPS format assumes that ea
60. provide a quick visual check of the landmarking process since the linking lines should all be approximately parallel if they are not then the user may have made an error e g skipped over a point during landmarking 6 The Volume Rendering Interface The TINA manual landmarking tool uses the Volpack volume rendering library 4 3 to produce 3D views of the data loaded into the sequence tool In general terms it is easier to see the general position of a morphological landmark when the data is displayed in 3D although for maximum accuracy it is important to refine the landmark position by checking the 2D views since these provide a more direct view of the data Pressing the VR Control button in the manual landmarking tool spawns a dialog box that provides access to various user controlled parameters of the volume rendering engine as shown in Fig 6 The most important of these are the graphs contained in the Scalar Classification and Gradient Classification fields Each of these takes the form of a small user controlled graph with four associated buttons The curve shown in the Scalar Classification graph controls the way in which intensity grey level in the original 3D image data loaded into the sequence tool and displayed on the x axis of the graph is converted into the opacity of the corresponding pixel in the volume 14 rendered image the y axis of the graph The shape of the curve is controlled by a se
61. reen and blue components can be set independently The specular field controls the intensity of specular reflections i e highlights and again the red green and blue components can be controlled independently The shininess field controls the overall shininess of surfaces for which there is only a single parameter Valid parameters for the ambient diffuse and specular rgb components are in the range 0 0 to 1 0 the shininess parameter should be in the range 1 0 to 100 0 The colouration of surfaces will only be visible when the renderer is in full colour mode in greyscale or pseudo colour modes the rendered image is produced using only the overall intensity of the reflected light i e the intensity of each of the red green and blue components combined Although the Volpack library provides the ability to assign different material properties to different tissues using the techniques described in 1 the current version of the Manual Landmarking tool assumes a single material type Changes to the material properties are not implemented in the rendered image until the next time it is regenerated the user can force the image to be rendered with the new parameters by clicking the Repaint button in the Tv tool displaying the 3D Tv It is important to note that none of the options in the VR Control or Lighting Control dialog boxes will affect the accuracy of landmark point placement except to the extent that they affect the user s ability to see
62. row key move the 3D cursor position left by one increment e Right arrow key move the 3D cursor position right by one increment e Right ctrl select zoom mode for mouse interactions in all Tvs e Right shift select pick mode for mouse interactions in all Tvs e Enter equivalent to clicking on the Mark point button in the manual landmark tool i e store the current 3D cursor coordinates as the currently selected landmark The size of the increment for cursor movement is selected using the Resolution choice list in the manual land marking tool by default it is set to one pixel Note that in order for the Tvs to receive the keyboard inputs the window manager focus must be on the Tv In many window managers the window that has the current focus is displayed with a coloured title bar all other windows have a grey title bar Most window managers provide two modes for focus selection click to focus in which the user must left click with the mouse inside a window in order to switch focus to that window and focus follows pointer in which the focus in on whichever window the mouse pointer is inside If click to focus is selected then the user will have to left click on a specific Tv tool in order to send subsequent keyboard instructions to it Therefore if significant use is made of keyboard shortcuts it may be easier to change the window manager focus policy to focus follows pointer so that keyboard instructions are s
63. s 5 2 Image Display The manual landmarking tool provides four Tvs see Section 3 Three of these provide 2D views of orthogonal slices through the volume centred on the 3D cursor The fourth provides a 3D volume rendering of the volume The Tvs can also display 3D cursor landmark axis and plane points Figure 5 shows the four Tvs in a recommended arrangement such that the axes are consistent across the three 2D Tvs 5 2 1 2D Image Display The three 2D Tvs display orthogonal slices through the sequence centred on the current 3D cursor position which is displayed in each Tv as a large red cross hair Whenever the 3D cursor is moved the images displayed in these Tvs will be updated to reflect this change The Tv s are named according to the axis that is perpendicular to the image displayed in the Tv see Section 5 1 as shown in 4 Therefore the x axis Tv displays an image in which the left right axis is the z axis of the sequence and the top bottom axis is the y axis of the sequence The y axis Tv displays an image in which the left right axis is the x axis of the sequence and the top bottom axis is the z axis 10 of the sequence The z axis Tv displays an image in which the left right axis is the x axis of the sequence and the top bottom axis is the y axis of the sequence Mouse interaction with the 2D Tvs can be selected using the 2D Tv Mouse switch in the Manual Landmark tool The functions assigned to each mouse button are
64. s in this way The substitution only works for numbers can only be applied to one contiguous segment of the pathname and only works in ascending or descending order e Press the Save button 5 The Manual Landmarking Tool The Manual Landmarking tool Fig 3 allows morphological landmarks to be identified within any 3D data set loaded into the sequence tool It provides multiple views of the data three 2D Tvs showing orthogonal slices through the sequence and a 3D Tv showing a volume rendering of the whole sequence The functionality of the manual landmarking tool is based around the concept of a 3D cursor a single point within the volume whose coordinates can be manipulated by the user in a number of ways The aim is to move the 3D cursor to the point the user wishes to mark and then to store the coordinates of the cursor in a list of landmark points When all landmark points have been specified in this way the list of points can be saved to a file for further processing e g Procrustes analysis Figure 4 The coordinate system used to refer to the data is shown in a the z direction is the inter slice direction the x direction is the left right axis of images seen in the sequence tool Tv and the y direction is the top bottom direction of images seen in the sequence tool Tv The images shown in the three 2D Tvs of the manual landmark tool are generated from orthogonal planes passing through the current 3D cursor position
65. s to allow the user to manually specify morphological landmarks in any 3D medical image volume that has been loaded into TINA via the sequence tool In order to do this the user must manipulate the position of the 3D cursor until it corresponds to the desired point and then store the coordinates of the 3D cursor When data is first loaded the 3D cursor if initialised at the centre of the volume Its position is displayed graphically in all Tvs as the red cross hair Its coordinates are also displayed numerically in the X Y and Z fields of the Manual Landmarking tool INTSYS read write has been implemented as of version 1 3 24 The position of the 3D cursor can be manipulated in a number of ways e Numerical values can be entered directly into the X Y and Z fields of the Manual Landmarking tool e The arrow keys after each of the X Y and Z fields in the Manual Landmarking tool allow the user to increment or decrement each coordinate of the 3D cursor the size of the increment can be chosen via the Resolution choice list in the Manual Landmarking tool e When the 2D Tv mouse interaction is in Pick mode the user can move the large red cross hair representing the 3D cursor by left clicking on a position in the Tv or by left clicking and dragging Alternatively the keyboard shortcuts can be used to shift the position of the 3D cursor see Section 5 2 1 e When the 3D Tv mouse interaction is in Pick mode the user can lef
66. s which if any other point the point is linked to when the Linklines option is used in the 8D Tv draw checklist The user is free to edit any of these fields manually The Manual Landmarking tool assigns a type of 1 to any point that has not yet been marked up and a type of 0 to any point that has been manually marked up The user is free to enter any integer into this field and so it can be used to hold additional information about the point e g if museum specimens are included in the sample group and parts of the bone surface are missing in some specimens then the user could assign type 5 to indicate landmark points that have been approximated because the bone surface is missing After loading a landmark names file one landmark in the list is always considered to be the current landmark During manual landmarking whenever a point is marked the coordinates of the 3D cursor will be transferred to the current landmark The current landmark is always the one displayed in the middle of the five rows of landmark information in the Landmark Control dialog box The user can specify the current landmark so that points can be marked up in any order by scrolling up and down through the landmark list using the Up and Down buttons in the Landmark Control dialog box In order to avoid having to keep the Landmark Control dialog box open during landmarking a subset of the dialog is also available in the Manual Landmarking tool which dis
67. t click on any position in the Tv the 3D cursor will then be moved to the upper most bone surface under the mouse cursor The bone surface is detected using a simple intensity threshold specified in the Bone Threshold field of the Manual Landmarking tool see Section 5 2 2 Once the 3D cursor is in the desired position its coordinates can be stored by clicking the Mark Point button in the Manual Landmarking tool The coordinates will be transferred to the point specified in the Markup choice list If Curr LM is selected then the coordinates will be transferred to the current landmark i e the landmark specified in the No and Name fields in the Manual Landmarking tool and also displayed in the middle of the five rows of landmark information in the Landmark Control dialog box A list of landmark names must already have been loaded in order to do this otherwise the software will issue a warning that no landmark list has been loaded After transferring the coordinates the software will also increment the current landmark i e move to the next one in the landmark list so that the user does not need to scroll through the landmark list during landmarking The other choices in the Markup list allow the user to specify axis and plane points see Section 8 1 The Jump lock switch and the Jump stored button allow the user to re use coordinates of landmarks that have previously been identified If the
68. t of points placed within the graph by left clicking with the mouse or moved by left clicking and dragging with the mouse cursor placed over an existing point The spline and linear buttons set the shape of the curve to be a spline or piecewise linear curve through the control points The reset button returns the shape of the curve to the default linear ramp After setting the curve to the desired shape the apply button must be pressed to pass the new curve to the volume renderer The effects of these parameters can be seen in Figs 7 8 9 10 and 11 in general the curves should both be set to sigmoid functions using steep sigmoids as shown in Fig 9 will produce a surface rendering style image The balance between rendering speed and image quality is controlled by the Render quality choice list These choices control an upper and lower threshold voxels with intensities below the lower threshold are ignored during rendering and voxels with intensities higher than the upper threshold are assigned 100 opacity so that no voxels behind them need to be rendered The Fastest choice sets these thresholds to their most extreme values so that many voxels are ignored the rendering is then faster at the expense of lower image quality The Highest choice disables the thresholds completely so that all voxels are rendered the rendering is then slow but produces the best image quality In general the Fast cho
69. the Tv tool to assign it to the Imcalc graph Tv e Select Pick mode for the 3D Tv mouse e Move the mouse pointer to a location within the 3D Tv that has a clearly visible bone surface e Right click with the mouse a grey level profile through the image volume along the vector under the mouse pointer will be displayed in the Imcalc Graph Tv The x axis of this graph represents depth through the 3D image with 0 being the back of the image and 1 being the front of the image from the current viewpoint The y axis represents the intensity grey level of the data along the profile e Identify the step change in the intensity profile that represents the transition from soft tissue to bone Several bone surfaces may be visible in the profile also be sure to clearly identify soft tissue from background e Calculate an intensity value half way between the mean intensity of bone and the mean intensity of soft tissue e Enter the calculated intensity value into the Bone threshold field of the Manual Landmarking tool As with the 2D Tvs see Section 5 2 1 the same comments about window manager focus apply to the 3D Tv several keyboard shortcuts are available in the 3D Tv e Right ctrl select zoom mode for mouse interactions in all Tvs e Right shift select pick mode for mouse interactions in all Tvs e Enter equivalent to clicking on the Mark point button in the manual landmark tool i e store the curre
70. the mouse has been set for 3D interaction with the image displayed in the Tv tool clicking and dragging with the left mouse button moves the image around in the Tv tool clicking and dragging with the middle mouse button zooms the image and clicking and dragging with the right mouse button rotates the image in 3D 4 Loading 3D Medical Image Data The Sequence Tool The TINA Manual Landmarking Tool is allows manual identification of anatomical landmarks in 3D medical image data it was designed for use with micro CT images of rodent skulls but can interact with any other tomographic medical image data e g MR images Tomographic medical image data is loaded into TINA using the sequence tool shown in Fig 2 The current sequence can be viewed by installing a Tv tool onto the Sequence Tv This displays the slice specified in the Curr frame field When a sequence is loaded the current slice is set to be the first slice in the sequence Pressing the gt button increments the current slice number i e moves forwards through the sequence Pressing the lt button decrements the current slice number i e moves backwards through the sequence The First and Last buttons set the current slice to be the first and last slice of the sequence respectively To view a specific slice enter the slice number into the Curr frame field and press the Jumpto button Individual image slices can be manipulated using the buttons on the
71. then every other slice will be loaded i e the sequence is down sampled by a factor of 2 in the inter slice direction No use is made of the discarded slices they are never loaded The Downsample field down samples data within each slice For example if the Downsample field is set to 2 then each image is down sampled by a factor of 2 along its x and y axes after it is loaded and the down sampled image is entered into the sequence Linear averaging is used during this process so that the discarded data is used to reduce image noise e Press the Load button Any previous image sequence will be deleted from memory and the file s specified in the Image file field will be loaded in order to produce a new sequence The Image type choice list will be updated to show the variable type of the images loaded into the sequence The Start and End fields will be updated to show the slice numbers found during loading The Scales fields will also be updated to show the size of each voxel if this information is contained in the image file headers A Manual Landmark Tool ay ba 6 VR Control Landmark List Keyboard Controls Automatch Ty y axis z axis 3D 3D Tv NULL VR 3D Tv Mouse Zoom Pick 2D Tv Mouse Zoom Pick 3D Tv draw Cursor LM Axis Plane Text Poly Ball Linklines 2D Ty draw Rotate Axis Plane 3D cursor position X 128 C lt gt Mi 128 C lt j gt Ea 128 C lt j gt R
72. ume renderer See the following section for more details The volume renderer also supports depth queing This function allows a user controlled fog to be applied to the volume rendering which grows thicker with depth through the image More distant objects therefore appear dimmer which helps to create a more three dimensional effect Depth queing can be switched off or on using the Depth queing buttons and is controlled by the two parameters Front fac the thickness of the fog at the front of the image and Density the rate at which the fog grows thicker with depth through the image according to fog thickness front factorie ore Both Front fac and Density must be positive numbers Changes to the these parameters are not implemented in the rendered image until the next time it is regenerated the user can force the image to be rendered with the new parameters by clicking the Repaint button in the Tv tool displaying the 3D Tv When the rendering type is set to greyscale pseudo colour or full colour the intensity gradient of the original 3D image data is used to shade the surface of each voxel Finer control over the reflectivity of the surfaces can be achieved using the material property parameters contained in the Ambient Diffuse Specular and Shiny ness fields The ambient and diffuse fields control how the surface reflects ambient and diffuse light respectively the red g
73. where the 15 landmark point should be placed When the user selects a point in the 3D image by placing the mouse cursor over that point and then left clicking with the Pick mode of the 83D Tv Mouse function selected the 3D cursor is moved to the first bone surface lying under the point specified by the mouse cursor However this is not done using the 3D renderer instead it is done by searching through the original 3D image data as contained in the sequence tool until a voxel with an intensity equal to or greater than the intensity specified in the Bone threshold field of the Manual Landmark tool is found None of the options contained in the VR Control dialog box is used in this process and so the user is free to reset them in order to produce the best possible rendering of the data without this process having any effect on subsequent analysis of the landmark points generated using the software Significant user experimentation with the options displayed in the VR Control dialog box may be required in order to produce the best possible 3D display of the data Therefore the software provides the ability to save load all of the currently selected volume rendering and lighting options to from a file The pathname of the file can be entered into the Options field at the bottom of the VR Control dialog box either by typing the pathname directly or by using the file browser started with the Scan button The Load an

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