Basic segmentation from CT: proximal femur

Transcription

1 Chapter 7 Basic segmentation from CT: proxima femur This tutoria wi demonstrate how to import DICOM data from a CT scan of a dry cadaveric femur and appy different fiters and segmentation toos. 7.1 What you wi earn Image Processing Meshing DICOM import FE mesh generation Resamping and cropping Image segmentation Using different fiters Assigning materia properties based on greyscae vaues Creating custom node sets using regions of interest (ROI) 7.2 The data The data fies for this tutoria can be found in the ProximaFemur foder within C:\Program Fies\Simpeware\Data\ - these fies incude a the DICOM images. 7.3 Importing and preparing the image data in Scanning Importing DICOM data To import a DICOM fie: 1. Start ScanIP. 2. Import the DICOM fies Fie"Import"DICOM images (or from the Wecome screen Import DICOM). 52

2 3. Seect the foder ProximaFemur, and cick Seect foder. 4. In the Import DICOM fies diaog (Figure 7.1), cick OK, and the Crop and resampe diaog wi appear. Figure 7.1: Import DICOM fies diaog 5. In the Crop and resampe diaog (Figure 7.2), review the import options for modifying the data. For this data eave a the defauts and cick OK to finaise the image import steps. Figure 7.2: Crop and resampe diaog 53

3 Note The Crop and resampe diaog can be used to optimise how the image data is imported in ScanIP. Crop: can reduce the voume of interest Pixe skip: basic form of downsamping the image to reduce the image resoution Window and eve: the pixe depth (8, 12, 16 and 32bit) is preserved during the import. Reducing the pixe depth by using the Window and Leve option can aso reduce the memory usage Typicay it is recommended to import the image data without modifying any of these parameters uness the images are too arge to import in to memory Navigating and visuaising the data in the 2D views Once the DICOM data has been imported, ScanIP wi ook ike Figure 7.3. The Document workspace tab contains the 2D and 3D views. In this section we wi expore some of the basics of navigating the images in the 2Dview. The next section (7.3.3) wi ook at the initia way of visuaising the data in the 3D view. 54

4 Figure 7.3: ScanIP after importing the DICOM images 1. Firsty to maximise the XZ sice view (top right as shown in Figure 7.3), either: a. Cick on the Expand 2D sice button, e.g., or b. Doube eft mouse cick on the 2Dimage pane 2. To navigate to sice 333, either: a. Type 333 in the sice number spin contro, or b. Use the mouse whee (oreft and right keyboard keys) toscro through, or c. Use the mouse to drag the sice position sider. 3. To zoom in to see the head of the femur in more detai, either: a. Cick and hod the midde mouse button whist moving the mouse up and down to zoom in and out respectivey. b. Use the + and - keyboard keys tozoominand out respectivey 4. Once zoomed in, you can pan the image by cick and hoding down the midde mouse button withthe Shift keyboard key aso pressed. Move the mouse to pan the image up, down, eft and right. By using these contros, try to get a resut simiar to Figure 7.4. Figure 7.4: Expanding the XZ sice view and navigating to sice 333 In Figure 7.4, you wi aso see some sice abes L, R, S, I, A and P which indicate the orientation of the data. Sice abe Stands for Description L Left Depicts the eft-hand side of the body R Right Depicts the right-hand side of the body 55

5 S Superior Depicts the direction towards the head I Inferior Depicts the direction towards the feet A Anterior Depicts the direction towards the front of the body P Posterior Depicts the direction towards the rear of the body Tabe 1-1 Anatomica directiona terms used in the sice abes for DICOM images Note The medica 2D sice abes for anatomica directions wi ony be dispayed after importing DICOM data and if the information is stored in the DICOM tags. For a other image imports, the sice abes wi dispay +/- X, Y and Z to indicate the image directions. The 2Dsice view abes canbe disabed at any time inthe ScanIP Preferences: Fie"Preferences, then untick the option Dispay orientation abes. 5. To return to the three 2D views and 3D view dispay, either: a. Cick on the Expand the 2D sice button again, or b. Doube eft-cick on the 2D image to minimise Visuaising the image data in the 3D view You wi aso notice that a 3D voume rendering of the data is automaticay dispayed in the 3Dview (Figure 7.3), aowing the background scan data to be previewed more intuitivey prior to segmentation. By defaut ScanIP wi automaticay render background data sets of up to 200 MB. This defaut can be edited within the Voume rendering settings of the ScanIP Preferences diaog (Fie"Preferences). The background voume rendering settings can aso be changed to suit the needs of the user. To open the Background voume rendering diaog, use the option in the 3D view toobar as shown in Figure 7.5. The diaog wi open as shown in Figure 7.6. Figure 7.5: Opening the background voume rendering settings 56

6 Figure 7.6: Background voume rendering diaog In the Background voume rendering diaog, presets may be chosen for a number of materias. The voume rendering parameters may aso be changed manuay and custom presets can be saved. The key parameters in the voume rendering settings are: Presets: provides a range of popuar voume rendering presets. Opacity: aows the opacity of the greyscae data to be adjusted. Left cick to generate a new point in the histogram ine, midde cick to deete a point. Coour: doube cick on the point to change coour, and move these points to change coour transitions. Auto set: provides a good set of opacity and coour functions based on the range of vaues present in the image. To improve the background voume rendering settings for this data: 1. In the Opacity mapping, eft cick on the Contro point at [Greyscae -1024, Opacity 0%] to seect it. The contro point wi now be highighted by a pink ring as shown in Figure

7 2. In the Greyscae vaue, type a new vaue of This wi mean a greyscae vaues of ess than -750 wi have an opacity of 0% (e.g. transparent), thus removing the background noise. 3. Cick Cose. The background voume rendering of the femur wi now ook ike Figure 7.8 Figure 7.7: Seecting a contro point in the opacitymapping Figure 7.8: The improved background voume rendering of the proxima femur For the proxima femur, it is aso suggested to view the data with the 3D view background ight turned off to increase the contrast, as shown in Figure

8 Figure 7.9: Background voume rendering of the proxima femur visuaised with the background ight turned off To togge the 3D view background ight on/off: 1. Maximise the 3D view by cicking View"View ayout"3d ony, or by doube cicking in the 3Dview, or by cicking on the Expand view button. 2. Cick View" 3D dispay" Background ight to turn off the 3Dview background ight. To begin the segmentation of the data: 1. Return to the defaut view ayout by cicking View"View ayout"three 2D, 3D. 2. Turn off the voume rendering by cicking Background voume render in the 3D view toobar. 3. Set the background back to its defaut (bright) setting by cicking View" 3D dispay" Background ight. Note It is aso worth noting that both surface rendering (e.g. a mesh) and the voume rendering can be viewed simutaneousy Preparing the image data It is often recommended to down-sampe your data to a resoution at which sma features are retained whie the overa size of the image is reduced. This wi usuay make the segmentation stepeasierdue 59

9 to ower memory requirements, reduced amount of pixes to process in the case of manua segmentation, and can aso reduce the number of eements in the fina FE mesh. In this exampe we assume that a mesh consisting of 0.7 mm base eements is the highest density that wi be required from the mode. Resamping can therefore be performed by assigning a new voxe size (i.e. spacing) of 0.7 x 0.7 x 0.7 mm. To resampe the image: 1. Open the Resampe diaog by cickingimage processing" Transforms" Resampe. 2. In the Resampe diaog appy the settings shown in Figure 7.10 a. Set the Units to Pixe spacing (mm) with vaues of 0.7 x 0.7 x 0.7. b. Choose Linear as the Background Image Interpoation method. At this stage the Mask interpoation method options are not reevant. c. Cick OK. Figure7.10: Resampe diaog Note To set the spacing vaues, you can aso simpy set the first one to 0.7 mm and then cick on Cubic resamping. This wi make the vaues in Y and Z match the X vaue. Again, for memory usage purposes, it is recommended that you crop your image in order to keep the necessary objects within the imits of your voume. 60

10 To crop your data: 1. Open the Crop diaog (Figure 7.11) by cickingimage processing"transforms"crop. 2. An easy way to determine how much you shoud crop is to start with the XY view and side throughthe sices tofind out how many sices actuay containthe object. Inthis case, the bone extends from sice 1 to sice 287 approximatey. This tes you how much you can crop in Z. Note It is not necessary to crop too cose to the object, in fact it is actuay preferabe to eave some space around the object uness it is a genuine cut. The reason behind this being that the mesher wi not smooth surfaces where they touch the border of the voume and wi eave them fat. 3. Repeat this for YZ view and ZX view, to find how much data can be cropped in X and Y. 4. Enter the vaues in the Crop diaog. In this case you can appy the foowing vaues using the siders or by typing in the vaues (as aso shown in Figure 7.11): a. X b. Y c. Z d. Cick OK Note In order to set more precise vaues, it is possibe to first move the sider with the mouse and then use the arrow keys on the keyboard to change the vaue. The actua position of the crop is indicated by purpe ines in the 2D sice views (Figure 7.11). Make sure that the whoe mode is within these purpe ines or boxes. After cropping, the number of pixes in the mode wi be 138x95x287. Due to the restrictions of the Student icence for ScanIP, a mode can ony be exported if it is smaer than 100x100x100 or 1,000,000 voxes. Therefore, the mode must be resamped again to meet this requirement. Open the resampe window and change the pixe spacing to 1.1x1.1x1.1. Then continue with the tutoria. Figure 7.11: Crop diaog (eft) and the crop preview in the 2D sice view(right) Now that your data is prepared, you can save your fie and begin segmenting. To save your project: 1. Open the Save as diaog Fie"Save as. 2. Save the project using the name ProximaFemur.sip. 61

11 7.4 Image processing in ScanIP Segmenting regions of interest and appying different fiters Start your segmentation by appying a Threshod to set a range of greyscae vaues to be added to the segmentation mask. To use the threshod segmentation: 1. Cick Image processing"segmentation"threshod. 2. In the Threshod pane appy the foowing settings (Figure 7.12): a. Seect Lower vaue as -590 and Upper vaue as b. Set Caibration as None. c. In the Mask operation section, seect Create new mask. d. Perform on A sices. e. Cick Appy. Figure 7.12: Threshod pane 3. Cick View" 2D sice views" Transparent masks to see the underying data through your segmentation. 62

12 Note If you tick Enabe in the Interactive threshod section and set the Mask operation to Repace with mask with Perform on A sices, then by moving the upper and ower siders you can interactivey see how the imits change the mask in the active 2D sice view. Notice how the inside of the bone features fine structures/trabecuae (e.g. sice 0 in XY). In most cases, you may prefer to either remove them or merge them with the rest of the bone in order to simpify the surface. The ow density nature of the bone in this trabecuar region can be refected in the fina FE mode by assigning materia properties based on signa strength. A Morphoogica cose fiter wi merge fine structures and add connectivity to the mask whie eaving most of the surface unchanged. This effectivey simpifies the shape of the object and therefore eads to a simper mesh. To appy a morphoogica cose on mask 1: 1. Cick Image processing"morphoogica"cose. 2. In the Morphoogica - Cose pane (Figure 7.13) a. Seect Appy on active mask. b. Tick Cubic vaues to appy the same radius in X, Y and Z. Type 2 in the X radius (pixes) box to create a Structuring eement (ba) of 2 x 2 x 2 in size. c. Cick Appy to appy the fiter. Figure 7.13: Morphoogica - Cose pane Note When appying this fiter on a mask, make sure that the mask currenty active/seected in the Dataset browser is the one you want to appy the fiter to. 63

13 What we woud ike to achieve is the remova of sma hoes whie preserving the marrow as a cavity within the femur. The Cavity fi fiter wi automaticay fi the cavities that are competey cosed. To appy a cavity fi fiter on the mask: 1. Cick Image processing"additiona"cavity fi. 2. Cick Appy. Figure 7.14 shows the change in the mask from appying the Morphoogica cose and Cavity fi fiters. Figure 7.14: After threshod (eft), after morphoogica cose (midde), and after cavityfi fiter (right) Smoothing and removing artefacts from the data Smoothing agorithms in ScanIP take into account partia voume effects. This means that the masks keep the greyscae information of the background to generate more accurate and faithfu surfaces. However as the mesh smoothing agorithms are feature preserving, they wi not remove surface artefacts on the mask from sources ike image noise. Therefore a smoothing image fiter needs to be appied on the mask to remove these. Figure 7.15 shows a screenshot before and after appying the Recursive Gaussian smoothing fiter. Usuay a vaue of 1 to 3 pixes in the given direction gives a good smoothing to start with. To appy the Recursive Gaussian fiter with binarisation: 1. Cick Image processing"smoothing"recursive Gaussian. 2. In the Recursive Gaussian pane: a. Seect Appy on active mask. Make sure Mask 1 is seected and is the active mask b. Tick Binarise in the Mask smoothing operations. c. Type in the vaues of 2.0 in the Gaussian sigma parameters for X, Y and Z. d. Appy the fiter. 64

14 Figure 7.15: Difference before (eft), and after (right) appying the recursive Gaussian fiter Note The Binarisation fiter can aso be appied separatey. On the Image processing tab, in the Additiona group, cick the arrow next to Advanced fiters, and then seect the Binarisation fiter. You wi notice that the femur has a hoow cana e.g. shown in the right hand image in Figure This is as a resut of the bone marrow touching the image boundaries which eaves it as an open cavity. As the bone marrow has significanty different materia properties to the bone, we can now create a new mask to define this region. To create a mask (Mask 2) for the interior of the bone: Cick Image processing" Segmentation" Food fi to open the Food fi pane: a. Seect Appy from active mask. b. In the Mode section, seect 3D. c. In the Mask operation section, seect Create new mask. d. Perform on A sices. To appy the Food fi, eft cick on the marrow (e.g. 89, 37, 127 in sice 127 in XY) as shown in Figure Figure 7.16: Foodfi pane and picking a seedpoint in the XY sice

15 You have now competed the segmentation. To tidy up your mode give appropriate names to the objects created. To rename and change the coours of the masks: 1. Rename Mask 1 to Femur. (Right cick on the mask name and seect Rename...). 2. Rename Mask 2 to Femur_Cavity. 3. Change the coourof the Femur mask by right cickingon the mask name: Change coour"bone. 4. Change the coourof the Femur_Cavity mask by right cickingon the mask name: Change coour"fat. Save your project again either by using the menu Fie" Save or by cicking on the Save button in the Quick access toobar. You have now created a project (a.sip fie) of the proxima femur (ProximaFemur.sip). If you woud ike to earn how to interactivey position a CAD impant into the femur, foow (Chapter 8 Import and positioning of CAD impant: proxima femur ). Aternativey you can continue to the next section to earn how to create an FE mesh of the segmented proxima femur. 7.5 Meshing in ScanIP (with +FE modue) Creating a mode for meshing The next section wi demonstrate how tocreate voume meshes of different sizes and how to assign materia properties. To create a new mode: 1. In the Dataset browser, right cick on Modes and seect Create a new FE mode. 2. Use a mutipe seection to highight both masks: i.e. use the [Shift] or [Ctr] keys and eft mouse cick to seect Femur_Cavity and Femur. 3. Drag both masks into Mode 1 (FE, active). The Dataset browser wi now ook ike Figure

16 Figure 7.17: Dataset browser after creating a new FE mode To configure the mode: 1. Right cick on Mode 1 (FE, active) in the Dataset browser and go to Mode configuration... Aternativey you can doube-cick on Mode 1 (FE, active) or use the [Ctr] + [M] key combination. 2. In the Mode configuration diaog eave FE as your Mode type and Abaqus voume (soid/shes) as your Export type. 3. Inthe Genera tabreview and eave the defaut settings. 4. Inthe Voume meshing tabreview and eave the defaut settings: The Compound coarseness sider contro for the +FE Free meshing aows you to easiy contro the mesh density. A vaue of 0 provides a consistent eement edge ength based on the voxe size. Moving to the eft (e.g. negative numbers) coarsens the mesh whereas moving to the right (e.g. positive numbers) wi densify the mesh. The meshing does not defeature your segmented masks so wi aways preserve sma features by automaticay controing the mesh size in these areas. The sider contros a combination of the advanced options incuding target minimum edge ength, maximum edge ength and eement change rate. 5. In the Materias tab, assign different materia properties to each part: a. Seect the Femur mask by cicking on the Femur tab. b. For the Femur mask we wi assign materia properties based on the image intensity. A higher greyscae vaue wi mean a greater materia moduus is assigned to the eement representing that voume. Materia properties are created by setting up mapping functions from greyscae to mass density, then from mass density to Young s moduus and Poisson s ratio. c. Set the Materia type to Greyscae based. A set of defaut vaues are automaticay shown. These vaues correspond to the pubished data by Rho et a 1 for a proxima femur 1 J. Y. Rho, M. C. Hobatho, R. B. Ashman, Reations of mechanica properties to density and CT numbers in human bone. Med. Eng. Phys, 17(5): ,

17 oaded in the superior-inferior direction. In addition, the constants have been modified to produce consistent units for the base units [mm/tonnes/secs]. d. Increase the Number of steps, i.e. the number of materias generated within the chosen mapped range, to 10. This sets the number of materias to be created within the mapped range. The materia configurationshoud now ook simiartofigure 7.18 Note Figure 7.18: Greyscae materia properties forfemur As you can see in Figure 7.18 there is a warning at the bottom of the Mode configuration diaog saying: Invaid materia properties vaues detected on this page. This indicates that the mapping function is creating negative materia properties at the ower vaues in the greyscae range. To avoid this we need to move the ower boundary of the mapping to create a minimum set of vaues. e. Use the mouse to drag the red vertica bar on the graph (initiay at GS) to the right unti the warning disappears For exampe you can set the ower bar to a greyscae of 0 by typing the vaue in the Start greyscae vaue. The materia set up shoud now ook ike in Figure As you can see the potted vaues beow 0 are set as constant using the owest mapped vaue. The maximum vaue is set by the maximum greyscae vaue in the mask (but can aso be controed by setting the End vaue for the upper bar). 68

18 Figure 7.19: Greyscae materia setupafter removing negative densities f. Once you have competed the setupof yourmateria mapping functions, you may save this materia definition to fie, by usingthe Save materia definition as... button. This aows you to use the same materia definition on other modes or even send the definition to a coeague. A previousy saved materia definition can be oaded by using the Load materia from ibrary button. g. For the Femur_Cavity mask (in the Femur_Cavity tab), set the Materia type to Pacehoder. This creates an empty materia property definition for the geometry which can be changed in the FE pre-processor. 6. In the Node sets tab we wi first create a custom node set using a region of interest (ROI), and then two node sets where the Femur and Femur_Cavity touch the Zmin Boundary. Node sets are usefu for setting up boundary conditions in the FE pre-processor: a. Cick on Add/manage seection voumes (ROI). The Mode Configuration diaog wi cose temporariy and the Mesh seection regions of interest pane wi open. b. Maximise the 3D view and ensure a Fast preview of the mode is visibe. c. Cick on the Eipsoid ROI button. d. In the 3D view, eft cick on the femora head, hod down and move, then reease to create the eipsoid. The ROI shoud ook simiar to Figure The region can be modified by using the arrows (to transate), ribbons (to rotate) and the orange circe (to resize). Aternativey type in the vaues as shown in Figure 7.21 after expanding the Position/Dimensions section. 69

19 Figure 7.20: Creating a custom node set using a region of interest (ROI) Figure 7.21: Exampe vaues for the region of interest (ROI) e. Once you are happy with your ROI cick Done in the Mesh seection regions of interest pane which wi bring you back to the Mode configuration diaog. f. In the From ist seect Femur, then seect [ROI] Eipsoid1 from the To ist. g. Cick Add node set. 70

20 h. Repeat the process for Femur to Boundary_Zmin. i. Repeat the process for Femur_Cavity to Boundary_Zmin. The Node sets tab shoud now ook ike Figure Figure 7.22: Node sets forthe femurmode 7. In the Contacts tab we wi use the aready created eipsoid ROI to define a surface set. Surface sets can be usefu for appying pressure oads for exampe. Aso some sovers require surface sets rather than node sets to appy boundary conditions. a. In the From ist seect Femur, then seect [ROI] Eipsoid1 from the To ist. b. Cick Add surface. The surface set is added to the Summary section. c. Cick Cose tosave a the settings and eave the Mode configuration diaog Generating the mesh To mesh your mode: 1. To mesh your mode, go to the FE mode tab and cick on Fu mode as shown in Figure The voume mesh wi be competed in approximatey 1 minute depending on the speed of your processors. Figure 7.23: Fumode commandin the FEmode tab 2. To view the mesh statistics, go to the Log workspace tab. This can be aternativey accessed by cicking Home"Tooboxes"Log Figure The mesh statistics wi be dispayed as shown in 71

21 Figure 7.24: Log tab with the mesh statistics Next we can visuaise the mesh in the 3Dview using different visuaisation options. To inspect interior eements: 1. Cick View"3D cipping"enabe to activate the cip box and inspect the interior eements (Figure 7.25). 2. The position and ange of the box panes can be changed by cicking and dragging on the spherica handes. 3. Reset the cip box by cicking View"3D cipping"reset. 72

22 4. Togge the cip box visibiity by cicking View"3D cipping"show box To show 2D sices in the 3D view: Figure 7.25: Cip box around the femur 1. The sices can be turned on in the View tab, in the 3D dispay group, by seecting Sice panes setup. In the Sice panes setup too seect Show Sice panes in the 3D view Figure 7.26: Showing the 2D sices in the 3D view: Defaut position of sices (1 in each orientation) (eft), and a sice views in XY pane (right) 2. The position of the sices can be changed by moving the Current sice siders in the 2D sice views. 73

23 3. The orientation of the sices can be changed by changing the View orientation buttons in the 2D sice views. 4. The transparency can be changed in the Sice panes setup pane, by changing the Opacity setting. To togge the visibiity of masks: 1. Cick View" 3D dispay" Visibiity options pane. to open the Visuaisation options 2. To make the Femur mask transparent, right cick on its name in the ist and change the Opacity setting to 0.2. The visibiity of a mask can aso be changed by right cicking anywhere on that mask within the 3D view and changing the Opacity. To visuaise contacts, sets and greyscae materia properties: 1. To visuaise the contacts that were set up in the Mode configuration diaog, seect Contact surfaces from the Surface entities drop-down ist in the Visuaisation options pane. 2. To visuaise the node sets, seect Nodes from the Surface entities drop-down ist. 3. To improve their visibiity, the mesh edges may be togged off by cicking View" 3D dispay" Soid 4., or by using the [S] key on the keyboard. Different exampes of visuaisation options are shown in Figure-. Figure 7.27: Exampes of Visuaisation options of the voume mesh: mesh - edges (eft), contact surfaces - edges (midde), and node sets - soid (right) 5. To visuaise the greyscae materia properties as shown in Figure 7.28, seect Mass density from the Active mask s materia properties shown drop-down ist in the Visuaisation options pane. You may need to reset the mask opacities to 1.0 if you have made changes. Aso make sure the Femur mask is set as active to aow the greyscae based materia properties to be seen. 74

24 Figure 7.28: Exampe of visuaisation options of the voume mesh: materia properties, mass density Saving and exporting the mesh If you are happy with your mesh simpy cick FE mode" Genera" Export mesh. To save you ScanIP project fie either by cicking on the Save button toobar or by foowing the path Fie" Save. 75 and save your in the Quick access