Copyright 2018 Medical IP - Tutorial Medip v x 06/2018, Revision

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2 List of Contents 1. Introduction Overview Medical IP Overview Medip History From Image to Model File Explanation Medical Imaging Before You Start Download and Install Medip How to activate Medip software How to Use this Tutorial Navigation Main Toolbar Crop Open D View Segmentation Segmentation Screen Segmentation Button Window Property Shortcut Measurement Measurement Screen Measurement Button Window Property Shortcut Tutorial Explanation Segmentation Threshold and Region Growing DrawCut Mesh Explanation Tutorial Conclusion Contact Us

3 1. Introduction Medip (Medical Image Processing) is a Medical IP s software for processing medical images and creating 3D models. Medip uses 2D cross-sectional medical images such as from computed tomography (CT) and magnetic resonance imaging (MRI) to construct 3D models, which can then be directly linked to rapid prototyping, computer-aided design (CAD), surgical simulation and advanced engineering analysis. 2

4 2. Overview 2 1 Medical IP Overview Medical IP is an international company, best known for its activities in the field of medical imaging and prototyping. Started in 2015 as a spin off corporation from the Seoul National University Hospital, it began as a rapid prototyping service bureau. Since then, Medical IP has grown into the world s rapid prototype producer. The company also enjoys a worldwide reputation as provider of innovative software solutions, such 3D Printing Technology and Virtual-Augmented Reality for surgery simulation. For the medical and rapid prototyping industries, Medical IP offers complete software solution for 3D visualization. Medip is the medical image based processing tool for creating 3D models, and linking the models to rapid prototyping (RP). It allows user to import patients data, attempts segmentation, and prepare a 3D object (STL and OBJ) files for additive fabrication as well as performs easy mesh and geometry manipulation. This files further can be imported in any 3D printer in the world. Owning its intellectual rights on customized 3D printing technologies, Medical IP moreover provides patientspecific 3D fabricated organ service, called Anatdel. It supports surgeons, doctors and medical students to understand and simulate surgical planning that match to the operation in the operating room. In order to support better visualization of patient s organ, Medip enable users to visualize the volumetric 3D model into virtual reality visualization. It allows user to virtually simulate and slicing each organ and performing surgical simulation before operation. Therefore, Medical IP provides one stop solution for both real and augmented 3D visualization of medical images. 3

5 2 2 Medip History After the start of the company Medical IP in 2015, it didn t take too long for the company to see the analogy between RP and CT (or MRI) images. In RP, a 3D model is built slice per slice, whereas a CT scanner does the reverse, it breaks down a 3D model (the human body) into a stack of image slices. In 2015, Medical IP wrote software that linked the image information to RP models. Since then, Medip was born. 2-3 From Image to Model A sequence of medical images can be loaded into software, Medip, and this usually consists of image in the XY plane (axial images). Medip then calculates and create images in the XZ(coronal) and YZ (sagittal) direction. Based on this method, those sequence of medical images then reconstructed as 3D rendering. The key to converting 3D model into RP is a process called segmentation. From the 3D rendering, then user draws specific targeted organ which will be used for volume and surface rendering (masking), and this surface further can be exported in STL and OBJ format so it can be printed in the 3D printing machine. 2-4 File Explanation STL (Stereolithography File) STL or STereoLithography is a file format as a Standard Triangle Language. This file format is widely used for rapid prototyping. The other file is obj files which is a simple data-format that represents 3D geometry. These files describes only the surface of geometry of 3D object without any color, texture, etc. MIP (Medical IP Project File) MIP is a Medical IP Project File. With this file, all the setup and data during the MEDIP last session will be save. You can open this file with Medical IP s related software (MEDIP). 4

6 2-5 Medical Imaging Medical imaging is the technique and process of creating visual representations of the interior body for clinical analysis and medical intervention. It is a part of biological imaging and incorporate radiology which aim to reveal internal structures hidden by the skin, bones, as well as to diagnose and treat disease. It uses several modality medical images including CT, and MRI. And the process for visualizing the specific targeted organ uses some segmentation techniques, image enhancements, noise reduction, etc. Accurate segmentation is important in order to extract meaningful information from the images. 5

2-6 Before You Start 2-6-1 Download and Install Medip Make sure to

downloaded at www.medicalip.com/en/medip-en/ a.

7 2-6 Before You Start Download and Install Medip Make sure to install the Medip Software from Medip CD, or free version can be downloaded at a. Double click Medip setup file and click Next button. b. Accept User License Agreement and click Next button. 6

8 c. Choose installation folder, and click Next button. d. Accept User License Agreement and click Next button. e. Finish 7

9 2-6-2 How to activate Medip software a. Get the license code from Medical IP. b. Open your Medip software Go to "Info" at the main toolbar c. Insert activation key How to Use this Tutorial You will see the following conventions while following the step by step section in this tutorial:. Phrases in bold (example) represent tools, buttons and functions in Medip. Anything in double quotation marks ("example") signifies exactly what you will see in Medip (not functions) 8

10 3. Navigation 3-1 Main Toolbar Main toolbar is located on the left side of the program. Open Crop Open Save Save As Undo Redo Reset View Send File to Server Connect to Medical IP Info Tab list Cross Section Histogram Each button has the following function: Open / Crop Open / Save / Save As : Open / Save File Undo / Redo : Do the previous or next action Reset View : Reset screen setting Send File to Server : Send.mip file to MedicalIP Server Info : Software Information Cross Section : Open / Close Cross Section Window Histogram : Open / Close Histogram Window 9

11 3-2 Crop Open Press the Crop ( ) button on the toolbar and select and load the DICOM (*. dcm, *. *) file. The Cropping Window opens as follows: You can specify the area that will be cropped by dragging the white line in the Cropping View with the left mouse click. Image Cropping is very important for the PC with low specification because cropping the DCM file will decrease the memory and computational cost. 10

3-3 3D View The sequence of 2D image data from dicom can be reconstructed back to 3D. Clipping Plane allows you to cut the 3D reconstruction to see the inner body and also experience with VR.

12 3-3 3D View The sequence of 2D image data from dicom can be reconstructed back to 3D. Clipping Plane allows you to cut the 3D reconstruction to see the inner body and also experience with VR. Clipping Plane Clipping Plane is a tool that allows you to cut the 3D Volume at any angle. This tool is very useful when you want to look the inner part of the body. <Before Activated> <After Activated> *When the Clipping Plane is activated, it can be operated with Ctrl to keyboard to control the 3D model. 11

3-4 Segmentation 3-4-1 Segmentation Screen The Medip screen is broken up into four main views; 3D, axial, coronal, sagittal.

13 3-4 Segmentation Segmentation Screen The Medip screen is broken up into four main views; 3D, axial, coronal, sagittal. Users can think of axial as a top down view, coronal as a front view, and sagittal as a left view. The axial view comes from the imported stack of images. To obtain the coronal and sagittal views, Medip transposes the axial images into their respective positions. The 3D pane is where 3D models are visualized. Clicking on an image with the left mouse button automatically updates your location in all views. There are eight additional thumbnails on the right side, four thumbnails at the top represent four files upfront the current image position, and vice versa. To activate, click Cross Section ( ) in the toolbar. Each of the 2D views contains a slice number and coordinate at the top-left corner and slice sliding bar at the bottom. You can use PageUp and PageDown keyboard to move the slider. To make it a single viewer, you can click space keyboard 12

14 Each viewer has the direction of L, R, A, P, S, and I. These initials stand for: L (Left) : The left part of the object R (Right) : The right part of the object A (Anterior) : The front part of the object P (Posterior) : The back part of the object S (Superior) : The top part of the object I (Inferior) : The bottom part of the object 13

3-4-2 Segmentation Button There are some buttons for Segmentation in each 2D Viewer

Below is the description of each button; Polygon Selection Selection Region Selection

shape mask. As shown below, the red segmentation mask was drawn in a polygon plane b.

hover. Left-Click the starting point, hold and move the pointer.

15 3-4-2 Segmentation Button There are some buttons for Segmentation in each 2D Viewer (Axial/Coronal/Sagittal). Below is the description of each button; Polygon Selection Selection Region Selection Selection Pixel-wised Selection tion Eraser Test Annotation Full Screen Working Region Boundary Viewer a. Polygon Selection Polygon Selection is the basic segmentation tools for making polygon shape mask. As shown below, the red segmentation mask was drawn in a polygon plane b. Region Selection Region Selection creates a mask based on shape created from mouse hover. Left-Click the starting point, hold and move the pointer. Segmentation mask will be created inside the line. Another function of Region Selection is to remove the segmentation mask. Right-Click the starting point, hold and move the pointer. The segmentation inside the region mask will be removed. 14

to And this removing function also can be

16 c. Pixel-wised Selection Pixel-wised Selection creates a mask based on mouse pointer movement. Click the starting point, hold and move the pointer. Segmentation mask will be created according to pointer. And this removing function also can be used in 3D Viewer. Note that all the removed part is perpendicular to the current viewer projection. So, every mask behind the selected region will be deleted. d. Eraser Eraser is the basic tool to remove the segmentation mask. Left-click and hold the mouse to specific segmentation mask. 15

e. Text Annotation It is also possible to use the

17 e. Text Annotation It is also possible to use the function by right-clicking on the viewer as shown below: f. Working Region Working Region is the area which will be calculated. You can enable / disable it by clicking on the Working Region. While active, you can change the region by dragging the lines. g. Boundary Viewer Boundary Viewer is a feature of viewing the outline of the ROI mask. Click to enable/disable the Boundary Viewer 16

18 j. Full Screen Full Screen is for displaying a selected viewer as a full screen. 17

3-4-3 Window Property The properties panel has various tabs. a. 2D Visualization 2D visualization tab is for setting or processing the 2D image or viewer.

19 3-4-3 Window Property The properties panel has various tabs. a. 2D Visualization 2D visualization tab is for setting or processing the 2D image or viewer. Preset Preset is the predefined 2D image window width and window level. Select one of to change the image window width with the preset option. Window Width / Level Window Width / Level is the process to change the brightness of the 2D image corresponds to selected Houndsfield Unit. To operate this function, click and drag the slider or put the number in the text box. Auto Auto button is for the automated window width and window level. Reset Reset button is for reset the window width and window level to initial setting. Direction Indicator On/Off Displays the orientation of the image on the 2D screen. Slider Repositioning On/Off Press left click mouse to change the position of 3D Image. 18

b. 3D Visualization 3D visualization tab is for setting or processing the 3D image or viewer. Preset Preset is the predefined 3D image window width and window level.

Window Width / Level 3D Window Width / Level is the process to change the brightness of the 2D image corresponds to selected Houndsfield Unit.

20 b. 3D Visualization 3D visualization tab is for setting or processing the 3D image or viewer. Preset Preset is the predefined 3D image window width and window level. Select one of to change the image window width with the preset option. Window Width / Level 3D Window Width / Level is the process to change the brightness of the 2D image corresponds to selected Houndsfield Unit. To operate this function, click and drag the slider or put the number in the text box. You can change the 3D window width/level in the histogram graph. Click Histogram button, click and drag the brightness below the histogram graph. Drag Up-Down to adjust window level and drag Left- Right to adjust window width. 19

Shader & Quality Shader & Quality is for setting the 3D rendering quality. It has 3 option: Invisibility: The 3D rendering viewer will show 3D multiplanar.

21 Shader & Quality Shader & Quality is for setting the 3D rendering quality. It has 3 option: Invisibility: The 3D rendering viewer will show 3D multiplanar. The segmentation mask is not displayed, only the surface volume. Low: The 3D rendering viewer will show 3D Volume with low quality rendering. Middle: High definition 3D Volume rendering. 20

22 Mix Mode This function will visualize the intersection between Volume and Segmentation layer (Volume Layer) <Before Activated> <After Activated> * The displayed volume only the parts correspond to the Bone Layer. 21

23 Clipping Option You can slice the volume to see the inner parts of the 3D object. Exclude Volume/Layer This mode will slice the other parts except the volume and layer. Exclude Surface This mode will slice the other parts except the surface. Show clipped image This mode will show 2D Image viewer from free angle. <Before Activated> <After Activated> 22

24 Visible Surface This is for hiding the entire surface rendering. Backface Culling When activated, the surface is not displayed in the background in the visualization. <Before Activated> <After Activated> 23

Navigate the location that you want to see with VR in 2D view. c.

25 VR On It is for experiencing VR mode. The visualization coordinate is based on VR device so makes the VR simulation easier. Currently, only VIVE VR Device is officially supported, but it will work without the device. 1. Click VR button 2. Navigate the location that you want to see with VR in 2D view. c. Volume Image Processing Volume Image Processing is the feature to apply image processing to 3D volume data. X1 to X5 Current feature is for x1 to x5 scale of noise reduction. Reset Reset back to original data. 24

This function allows z-axis at each case has the same spacing with x and y axis. Also known as isotropic conversion.

26 d. Volume Processing "Volume Processing" is the function to process the volume data. Z-Isotropic Z-isotropic is a function to normalize the depth (z-axis) image spacing by an isotropic-b-spline algorithm. This function allows z-axis at each case has the same spacing with x and y axis. Also known as isotropic conversion. Z-Flip Z-Flip is a function to reverse the depth (z-axis) of the images. <Assume that you have the following files loaded> Click the Z-Flip button to flip the axis of the file image. Above is the result after z-flip. 25

e. ROI To manage the ROI layer. You can add, duplicate, or delete layers up to 30 layers. f.

background). Lambda It is the parameter to adjust the results of DrawCut.

Select the foreground (targeted) area with left-click-drag to the image.

27 e. ROI To manage the ROI layer. You can add, duplicate, or delete layers up to 30 layers. f. Draw Cut Draw Cut is a semi-automatic 3D segmentation tool based on two criteria (foreground and background). Lambda It is the parameter to adjust the results of DrawCut. Reset Reset the Lambda to default. DrawCut Activate DrawCut by click DrawCut button. Select the foreground (targeted) area with left-click-drag to the image. Select the background area with right-click-drag to the image. The blue line is the foreground area that will be segmented, and the red line is the background area that will not be segmented. 26

Apply By clicking Apply button, the algorithm will be executed according to spe Activate DrawCut by click DrawCut button. Select the foreground (targeted) area with left-click-drag to the image.

28 Apply By clicking Apply button, the algorithm will be executed according to spe Activate DrawCut by click DrawCut button. Select the foreground (targeted) area with left-click-drag to the image. Select the background area with right-click-drag to the image. The blue line is the foreground area that will be segmented, and the red line is the background area that will not be segmented. By clicking Apply button, the algorithm will be executed according to specified foreground and background area. g. Threshold This feature is for selecting only HU in the threshold. Type It is the specified HU range that commonly used for particular organ. Start / end Starting and ending point of the HU threshold. Within Selected Layer Compute the process at the scope of the ROI layer, not the whole image volume. 27

Show preview Show preview is for previewing the selected threshold region if the algorithm is executed. You can also specify the color via Preview Color.

29 Show preview Show preview is for previewing the selected threshold region if the algorithm is executed. You can also specify the color via Preview Color. Reset Reset button is to reset the start / end value to default value. Apply Execute the algorithm according to start/end threshold value. If the Working Area is specified, the algorithm will only calculate inside the working region. If Within Selected Layer is checked, the process will be executed only inside the layer region. Region Growing Region Growing is an algorithm for segmentation according to threshold. Mode Select whether to perform region growing based on threshold or based on existing layer. Reset Reset the Seed List Apply If it is in the threshold mode, the segmentation is based on the seed position and refers to the value in the threshold. If it is in the layer mode, it is based on seed position and perform the connectivity of the existing layers. Select Seed Select seed is to specify the Seed point for performing Region Growing. Click the Select Seed button and select the position of the targeted seed in the 2D View. Also can be done by right click in the 2D view. The selected seed is listed in the Seed List. 28

h. Annotation This is for managing the text annotation. The Annotation created in the 2D viewer will be listed in here. All annotation can be deleted and edited here. i. Path Animation Path Animation is the movement view starting from the selected view to end view (path view).

30 h. Annotation This is for managing the text annotation. The Annotation created in the 2D viewer will be listed in here. All annotation can be deleted and edited here. i. Path Animation Path Animation is the movement view starting from the selected view to end view (path view). Path Animation is the ability to move the View along given path. This function is designed to collaborate the viewer with VR mode. If VR Mode is active, then 3D View will move. If VR Mode is inactive, then 2D View will move. 29

Create point Select seed is to specify the Seed point for performing Region Growing. Click the Select Seed button and select the position of the targeted seed in the 2D View.

31 Create point Select seed is to specify the Seed point for performing Region Growing. Click the Select Seed button and select the position of the targeted seed in the 2D View. Also it can be done thru right click in the 2D view. The selected seed is listed in the Seed List. Create point button is to create the starting view point. * Multiple selections are available in all 2D views Play Press Play button to see the movement of viewer along the specified path. 30

j. 3D Export 3D Export tab is for setting the surface smoothness and for export it. Smooth Smooth slider is for smoothing the segmentation surface.

32 j. 3D Export 3D Export tab is for setting the surface smoothness and for export it. Smooth Smooth slider is for smoothing the segmentation surface. Preview Surface To check the result before exporting it, you can click Preview Surface, which created the surface from selected layer and visualize it in 3D View. Export as Provides the ability to export the selected surface to STL and OBJ and NII files. k. Summary "Summary tab display an overview of the loaded files. 31

33 i. Option "Option" tab is to adjust other detail settings. Gamma Apply a gamma value to all 2D / 3D screens. Reset Reset gamma value to default. Wheel / Slider Setting the wheel and slider action for all 2D Viewer Zoom/Depth This means when you scroll in the 2D Viewer, it will zoom the image, and when you scroll in the slider, it will move to next/previous slice. Depth/Zoom This means when you scroll in the 2D Viewer, it will change to next/previous slice, and when you scroll in the slider, it will zoom the image. Temporary Directory Change the storage path of temporary file. 32

34 3-4-4 Shortcut Open Save Save as Undo Redo Action Shortcut Info Ctrl + O Ctrl + S Ctrl + Shift + S Ctrl + Z Ctrl + Y Next Image Previous Image Full Screen Page Up Page Down Space Reset View Ctrl + 0 Window Width Up / Down Right-click + right / left drag ONLY 2D view Window Level Up / Down Zoom In / Out Move Image Add ROI Layer (New) Rename ROI Layer (Rename) Duplicate ROI Layer (Duplicate) Inverse ROI Layer (Inverse) Erosion Dilation Right-click + up / down drag Mouse Scroll up / down Slider move Mouse Scroll pressed Ctrl + Shift + N F2 Ctrl + J Ctrl + Shift + I Ctrl + E Ctrl + D ONLY 2D view In option Tab 33

35 3-5 Measurement Measurement provides several tools for analyzing dicom files Measurement Screen As same as the segmentation screen, measurement screen has four main views: 3D View, Axial, Coronal, and Sagittal View. 3D View Axial View Coronal View Sagittal View Measurement Button Below is the description of each button in the 2D Viewer of Measurement. Thickness Length Annotation Text Annotation Angle Annotation Arrow Annotation Line Profiling Region Profiling Polygon Profiling Full Screen 2 Axises Coordinating 34

Text Annotation Text Annotation is for labeling the image with text.

36 a. Length Annotation You can measure the length by click Length Annotation. The line represents the actual distance in mm. b. Text Annotation Text Annotation is for labeling the image with text. You can change the size and color of the annotation. c. Angle Annotation You can measure the angle by left click to Angle Annotation and select 3 points. After lines are created, you can move the lines and edit the color, etc. 35

d. Arrow Annotation Click Arrow Annotation button to

37 d. Arrow Annotation Click Arrow Annotation button to create an arrow. e. Line Profiling Line Profiling is the summary of distance, maximum, minimum, average HU value along the selected line. f. Region Profiling Region Profiling is the summary of Area (in mm 2 ), minimum, maximum and average HU inside the selected region. 36

2 Axises Coordinating In each 2D viewer, you will see 2 lines representing axis that can change the coordinate and view angle.

38 g. Polygon Profiling Polygon Profiling allows you to create custom shape and analyze the minimum, maximum, average HU, and the area of selected region. h. 2 Axises Coordinating In each 2D viewer, you will see 2 lines representing axis that can change the coordinate and view angle. In each viewer, you can rotate the line by left mouse click and hold the line. By turning this line, you can view the medical image from a custom angle rather than straight forward angle. You can change also the coordinate by click and drag the middle point. 37

image(s) depending on the thickness spacing.

39 i. Full Screen You can view the current viewer by press space on your keyboard or click the Full Screen button. j. Thickness For each 2D view, it will overlaps the medical image(s) (or mask) with the next or previous image(s) depending on the thickness spacing. If the thickness is set to 20mm, it will adjust the transparency of the data within total of 20 mm spacing (front and back) from current coordinate and display it on the screen. 38

Sagittal) of 2D multiplanar which will be activated.

40 k. 2D Multiplanar 2D Multiplanar is the 2D multiplanar view on 3D model. After you click 2D Multiplanar, there are 3 options (Coronal, Axial, and Sagittal) of 2D multiplanar which will be activated. If you change the slider in the 2D viewer, the activated multiplanar also will be changed. 39

Move the mouse cursor over the layer and right click to measure the Similarity Coefficient and Texture feature

41 3-5-3 Window Property a. ROI The ROI tab in the Measurement will show the layer from Segmentation s ROI. Click eye icon in front of each layer name to enable or disable the mask in 2D/3D View. Move the mouse cursor over the layer and right click to measure the Similarity Coefficient and Texture feature between two layers. Similarity Coefficient is the calculation of Dice Similarity Coefficient which the percentage of 2 layers are the same. 40

42 Texture Feature is the statistic information of selected layer such as the HU distribution, max, min, avg value, etc. b. Annotation This tab shows all the annotations you have put. 41

43 3-5-4 Shortcut Open Save Save As Undo Redo Action Shortcut Info Ctrl + O Ctrl + S Ctrl + Shift + S Ctrl + Z Ctrl + Y Next Image Previous Image Full Screen PgUp PgDown Space Reset View Ctrl + 0 Zoom In / Out Move Image Position Mouse Scroll up / down Slider move Mouse Scroll pressed Option Tab Setting 42

44 4. Tutorial 4-1 Explanation Segmentation is the main activity in Medip. Medip has several tools to segment, or section, region of interest and this process is an interactive process. So, we can use both use the manual tools (such as Pixel-wised Selection, Eraser, etc) and other functions in Segmentation Toolbar (such as Region Growing, etc) Suppose we want to use the Segmentation Toolbar, there is main function in ROI tab called Region Growing. Region Growing is an algorithm which creates a segmentation mask depending on the values of surrounding selected data-points. To use this function, click the Select Seed button first, then select the data point inside the image. Note that the calculation will be done inside the working region. If we don t set the working region then whole body will be calculated, therefore, setting the Working Region ( ) is really important. The checkbox Inside Region Proposal is the region growing applied to segmentation mask. However, if you do not check the inside region proposal, the region growing will calculate whole image. All of segmentation masks can be managed inside ROI LIST box. The mask that is selected in the ROI is considered the active mask. There are several functions like Duplicate, Merge, Inverse, Erosion, Dilation, etc for managing the segmentation mask. The 3D segmentation and rendering from Medip also can be exported into various files including STL, RAW, OBJ, etc. These files further can be imported and printed using 3D printer. 43

4-2 Segmentation 4-2-1 Threshold and Region Growing Threshold tab is the segmentation based on the HU threshold.

45 4-2 Segmentation Threshold and Region Growing Threshold tab is the segmentation based on the HU threshold. For example if you want to segment the Bone, change the type option to Bone, than the range will be automatically filled. If you check Show Preview you will see the preview result within that range. Once you have accepted the desired area, click Apply button in the Threshold tab. The result will be store in the selected ROI layer. 44

46 . We also can perform a segmentation using Region Growing inside the Threshold tab. To use it, first click Select Seed button and choose the point that want to be segmented (for example bone). Then Click Apply inside the Region Growing tab. 45

47 Above picture is the result of Bone segmentation using Region Growing. Region Growing is a segmentation method based on selected seed HU value, therefore if the bone has noise (which usually has different intensity) will not be segmented as bone. In most of the cases, when we apply threshold-based segmentation, there are some parts out of the bone regions are also segmented. For example like this case: 46

Once we can do to reduce inappropriate segmentation result is by checking the

The connectivity that we mention is the connectivity in between the segmentation layer.

Now we want to reduce the object at blue color (the one that not connected to the

48 Once we can do to reduce inappropriate segmentation result is by checking the connectivity. The connectivity that we mention is the connectivity in between the segmentation layer. Like in the picture below: The red object is not connected with the blue object. Now we want to reduce the object at blue color (the one that not connected to the specific organ). This is the step by step procedure for it: 1. Select the organ that we want to select. 2. Select Layer Option in the Region Growing tab. 3. Click Apply button. 47

49 Result after checking the connectivity: 48

4-2-2 DrawCut DrawCut requires two areas for segmentation: foreground layer for the area that we want to segment, and background layer for the area that we do not want to

Below is the step to do it: 1. Set the working region in all 2D

50 4-2-2 DrawCut DrawCut requires two areas for segmentation: foreground layer for the area that we want to segment, and background layer for the area that we do not want to segment. You can use left (foreground) or right (background) click button to specify the area. Another one is you can choose the foreground or background from ROI Layer. Below is the step to do it: 1. Set the working region in all 2D Viewer. 2. Assume that we want to segment a kidney, then create two layers in ROI Layer, the first one is for foreground, another one is for background. Use the segmentation tool like Region Selection and select the area that you want to segment (as foreground area) like the picture below. 49

51 3. Choose the second layer (cyan color), and use Region Selection to select the area that you do not want to segment (as background area). 4. Clik DrawCut button. 5. Right-click the first layer (foreground layer) and click To ForeSeed. After click this function, you will see that the color will change to blue (foreground). 50

52 6. Right-click the first layer (background layer) and click To BackSeed. After click this function, you will see that the color will change to blue (background) 7. Click Apply button to execute DrawCut. < Result of DrawCut> 51

53 5. Mesh 5-1 Explanation Mesh is the visualization and processing of 3D model (Mesh). You can extract the 3D model into STL or OBJ file. 5-2 Tutorial a. Preview Surface Preview Surface is to convert the ROI segmentation layer into 3D Mesh data (surface model). Assume that the segmentation is an intestine organ with green color like below. 52

54 1. Right click Instestine layer. 2. Click Preview Surface. < Result of Preview Surface> 53

3. If the surface is not smooth, you can use Smooth function in the Export tab.

Export Surface file 3D Export tab is the function to export the result of 3D Surface to STL,

55 3. If the surface is not smooth, you can use Smooth function in the Export tab. This function will make the surface become smoother. < Result of Preview Surface> b. Export Surface file 3D Export tab is the function to export the result of 3D Surface to STL, OBJ and NII file. This file further can be printed using 3D printing. c. Export to RAW file -Mask This function is to export the segmentation mask to.raw file. Below is the step to do it: 1. Right-click the segmentation layer that want to be exported. 2. Click Export as... > ROI Mask raw(.raw, current layer) 54

56 -HU This function is to export the HU value inside the segmentation layer to.raw file. Below is the step to do it: 1. Right-click the layer that HU value want to be extracted. 2. Click Export as... > HU raw (.raw, current layer) 55

With Medip software, performing medical imaging for segmentation, image enhancement, and 3D modeling is no

57 6. Conclusion Through the manual book, we have explored various functions of Medip from installation to how to use. Medip also can be used for different type of organs except for the mentioned above. With Medip software, performing medical imaging for segmentation, image enhancement, and 3D modeling is no longer difficult. We provide comprehensive tools for these tasks which aim to assist medical practices for easy and better visualization. 56

If you use this software for your research, please refer to Software (MEDIP, MEDICALIP, Seoul, Korea) with the version you used and if you would like more information

58 7. Contact Us CONGRATULATIONS! You now know how to utilize the tools in Medip to transform 2D data into 3D models. Thank you for using Medical IP s lab book for your learning experience. If you use this software for your research, please refer to Software (MEDIP, MEDICALIP, Seoul, Korea) with the version you used and if you would like more information about any of the Medical IP solutions, please contact us at: Republic of Korea , Cancer Research Institute, Seoul National University Hospital,101, Daehak-ro, Jongno-gu, Seoul (+82) USA 480 Jacobs Court, Palo Alto, CA 94306, United States (+1) contact@medicalip.com 57

Copyright 2017 Medical IP - Tutorial Medip v /2018, Revision

Copyright 2017 Medical IP - Tutorial Medip v.1.0.0.9 01/2018, Revision 1.0.0.2 List of Contents 1. Introduction......................................................... 2 2. Overview..............................................................