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

Transcription

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

2 List of Contents 1. Introduction Overview Medical IP Overview Medip History From Image to Model STL File Explanation Medical Imaging Before You Start Download and Install Medip How to activate Medip software How to Use this Tutorial Navigation Explanation Main Viewer Main Toolbar Icon List Segmentation Toolbar All Shortcuts Step by Step Tutorial Zooming and Panning Segmentation Toolbar Import Segmentation Explanation Step by Step Tutorial Region Growing ROI List Box Visualization Explanation Step by Step Tutorial Conlusion 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) files for additive fabrication as well as performs easy mesh and geometry manipulation. This STL file further can be imported in any 3D printer in the world. Owning its intellectual rights on customized 3D printing technologies, Medical IP moreover provides patient-specific 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. MAVR (Medical Augmented and Virtual Reality software) on the other hand is an extension of Medip which enable users to visualize the volumetric 3D model into virtual and augmented reality visualization. It support all of NifTI-1 files (.nii), which widely used for medical imaging. It allows user to virtually simulate and slicing each organ and performing surgical simulation before operation. As one of the Medical IP one stop solution, MAVR completes overall visualization both real and augmented world. 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 format so it can be printed in the 3D printing machine. 2-4 File Explanation STL or STereoLithography is a file format as a Standard Triangle Language. This file format is widely used for rapid prototyping, 3D printing and computeraided manufacturing (CAD) because of its simple file structure to match any contour desired. It describes only the surface of geometry of 3D object without any color, texture, etc. 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. 4

6 2-6 Before You Start Make sure to install the Medip Software from Medip CD, or free version can be downloaded at Download and Install Medip a. Double click Medip setup file and click Next button. b. Accept User License Agreement and click Next button. 5

7 c. Choose installation folder, and click Next button. d. Accept User License Agreement and click Next button. e. Finish 6

8 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) 7

9 3. Navigation Tools to learn : Navigation, Segmentation Toolbar, Rendering Toolbar 3-1 Explanation To process data in Medip, a set of stacked 2D cross-sectional images is first imported. These 2D images commonly in the DICOM (.dcm) format, come from medical scanning equipment. Once the stacked images are imported, they can be viewed and edited using the various tools available in Medip. The quality of the 3D images that Medip can create directly correlates to the slice thickness and pixel size of the 2D images Main viewer 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. 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 8

10 3-1-2 Main Toolbar The main toolbar contains 7 button menus (load, save, undo, redo, upload, and info), as default position, it set at the top left corner, but users can move the menu by holding and dragging the to any position. Load Save Save As Undo Redo Upload Info Icon List At each axial, sagittal and coronal viewer, there is an icon list which commonly used for segmentation tools. The description of each icon has been presented below. 9

11 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. Click the starting point, hold and move the pointer. Segmentation mask will be created inside the line. c. Pixel-wised Selection Region Selection create a mask based on mouse pointer movement. Click the starting point, hold and move the pointer. Segmentation mask will be created according to pointer. 10

12 d. Eraser Eraser is the basic tool to remove the segmentation mask. Left-click and hold the mouse to specific segmentation mask. e. Draw cut DrawCut is the segmentation tool based on the 2 criterions. The proposed segmentation area (drawn in blue line, left-click), and proposed background area (drawn in red line, right-click). DrawCut automates segmentation based on these two selections. f. Annotation Annotation is the practice of adding note underlining structures of medical image. Right-click on the viewer and select Text annotation list. 11

13 g. Region Proposal Region Proposal can be seen as working region. Everything inside working region will be calculated, and vice versa. Setting the working region can be done easily by moving the white line in all image viewer. h. Boundary Viewer Boundary Viewer is the tool for viewing the border of segmentation mask. 12

14 3-1-4 Segmentation Toolbar The Segmentation toolbar on the right panel is the tools for image processing. It contains tabs that correspond to each of the different task. For example, under the Enhancement tab, you will see the adjustment of window width level and image enhancement. And ROI is for arranging the segmentation mask All Shortcuts Load Save Save As Undo Redo Next Image Previous Image Action Shortcut Info Show 1 Image Viewer Window Width Up Window Width Down Window Level Up Window Level Down Zoom In Zoom Out Move Object Ctrl+O Ctrl+S Ctrl+Shift+S Ctrl+Z Ctrl+Y PgUp PgDown Space Right-click + right drag Right-click + left drag Right-click + up drag Right-click + down drag Scroll up Scroll down Scroll pressed In the image viewer In the image viewer In the image viewer In the image viewer In the image viewer 13

15 3-2 Step by Step Tutorial Zooming and Panning Zoom allows you to view a close-up of a selected region. Panning modes image up, down, left or right 1. Scroll up to zoom in 2. Scroll down to zoom out 3. Click and drag Scroll button to move image Segmentation Toolbar a. Window Width Level The gray values of CT images are expressed according to the Houndsfield unit, which has 4096 values. To map this scale onto the 256 gray values of your computer, Medip has a feature called windowing. Windowing is a tool to adjust the image contrast. Click and Drag Width slider to adjust the window width Click and Drag Level slider to adjust the window level Input number in the width and level text box and press OK to adjust manually. 14

16 b. Image Enhancement Image Enhancement is a tool to make the targeted organ in the current image more smooth and clear. Click any x times button to select the enhancement scale Click Original image button to go back to original image. Volume Rendering allows you to quickly visualize 2D data as a 3D object without having to take the time to segment and create a model. It is only visualization tool, but gives a nice impression of what your model will look like. Adjust window width and window level slider Adjust Smooth slider to make the surface smoother. Click Update to execute smoothing. Click Update Layer to render segmentation volume. You can choose activating volume opacity, layer transparency, or surface visibility. 15

17 4. Import a. Import Dicom File CT and MRI images are written in a dicom (.dcm) format. Dicom file contains sequential slices of inner organs picture, from top to the bottom of patient s body. To reconstruct and performing medical image analysis, Medip needs to load all of those images. Here, we will show how to accomplish this task. There are two ways to do import the file: < way A > 1. Drag and Drop dicom files to Medip software. < way B> 1. Click Load 2. Click one of dicom file (make sure all.dcm files in the same directory). Medip will automatically, read all.dcm files. 3. Open 16

18 5. Segmentation Tools to learn: Region Proposal, Region Growing, basic editing tools 5-1 Explanation Segmentation is the main activity in Medip. Medip has several tools to segment, or section, region of interest. Before doing the segmentation, we have to set the Region Proposal ( ). It can be seen as segmentation working area. By setting the region proposal, everything inside the region will be processed, and vice versa. This tool also can be used for slicing the 3D rendering view. In the Segmentation Toolbar, inside ROI tab, there is Region Growing function. Region Growing is a mask created based on how surrounding pixels compare to a selected datapoints, grey value, automatically determining from the window level slider. This tool proves very useful for segmenting such as blood vessels and nerves. To further segment various of an image, Medip has a selection of editing tools. Pixel-wised Selection can be helpful for manual segmentation. Region Selection, Polygon Selection, and Eraser provide the tools needed to draw and erase the mask. To perform the transformation from 2D to 3D, we only need to click update the 3D rendering. All of segmentation masks can be arranged 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. Depending on the type of file output needed, Medip has various exporting options including exporting the STL format. This file further can be imported and printed using 3D printer. Scenario : Your boss has asked you to review some scans and put together a presentation displaying a patient s anatomy. You will use Medip to highlight the colon and bone structure, and create a 3D model to fully display the patient s anatomy. The procedures outlined below will show you how to accomplish these tasks. 3-2 Step by Step Tutorial 17

19 5-2-1 Region Growing Region Growing allows you to grow a mask, starting from a selected datapoint(seed) to each slice of the images. 1. Go to Segmentation panel ROI Click Select Seed button 2. Click any colon seed in the image. 3. Click Seed Apply or Range Apply (Info. You can click Seed Apply or Range Apply again after change the level of range.) < The difference between Seed Apply and Range Apply > Seed Apply is only classifying the pixel near to seed (datapoint). However, Range Apply is the function to classify the all pixel within the level range in entire images. If you have large dicom file, seed apply is commonly used ROI List Box Result of Seed Apply Result of Range Apply 18

20 5-2-1 ROI List Box Medip provides several functions for maintaining the segmentation masks. All functions listed below are shown when right clicked button triggered inside the ROI LIST box. New Layer New layer button allows you to create new segmentation layer. There are 2 ways to insert new layer. < Way A > 1. Just click New Layer Button ( ). < Way B > 1. Right-click inside ROI LIST Box 2. Select New 19

21 Rename Layer Rename button allows you to rename the segmentation layer. There are 3 ways to rename segmentation layer. < way A > 1. Double click at the layer which will be renamed. 2. Type new name of the layer. 3. Press enter or click anywhere of ROI List window < way B > 1. Left click at the layer which will be renamed. 2. Press F2 key. 3. Type new name of the layer. 4. Press enter or click anywhere of ROI List window < way C > 1. Right click at the layer which will be renamed 2. Select Rename 3. Type new name of the layer. 4. Press enter or click anywhere of ROI List window 20

22 Duplicate Layer Duplicate button allows you to duplicate the segmentation layer. There are 2 ways to duplicate segmentation layer. < way A > 1. Left click at the layer which will be duplicated. 2. Click Duplicate Button( ). < way B > 1. Right click at the layer which will be duplicated. 2. Select Duplicate 21

23 Delete Layer Delete button allows you to delete the segmentation layer. There are 2 ways to delete segmentation layer. < way A > 1. Left click at the layer which will be deleted. 2. Click Delete Button( ) < way B > 1. Right click at the layer which will be deleted 2. Select Delete 22

24 Inverse Selection Inverse button will select the inverse area of selected segmentation mask. 1. Right click at the layer which will be inversed 2. Select Inverse < Result of Inverse> 23

25 Removing Overlap Mask First = First Second button will remove the overlap segmentation layer between two layers. The first is the upper layer than the second one. Assumption: We have 2 segmentation layers, left picture below is fat layer ( first ), and right picture is colon layer ( second ). Now we want to remove the overalapped segmentation layer of fat layer ( first ). The procedures below will show us how to complete this task. 1. Select Fat and Full Colon Layers. Make sure that the fat layer is above the colon layer. 2. Right click and select First = First Second. 24

26 < Result of First = First - Second > a. Both layers b. Fat layer c. Colon layer 25

27 Merging Layers Merge button allows you to merge between two (or more) segmentation layers Assumption: We want to merge the bone segmentation layers as shown below. These are the step for merging these two layer: < way A > 1. Select Bone and Bone Inside layers. 2. Press Ctrl+E in your keyboard. < way B > 1. Select Bone and Bone Inside layers. 2. Right click and select Merge 26

28 < Result of Merge Layers > 27

29 Reducing Area Segmentation Erosion button allows you to reduce the segmentation area. Assumption: We have Full Colon segmentation layer and want to reduce it 1. Right click at the Full Colon layer which will be reduced. 2. Right-click and select Erosion < Result of Erosion (three times)> 28

30 Enlarging Area Segmentation Dilation button allows you to enlarge the segmentation area. Assumption: We have Full Colon segmentation layer and want to enlarge it. 1. Right click at the Full Colon layer which will be enlarged. 2. Right-click and select Dilation < Result of Dilation (three times)> 29

31 Advance DrawCut Tools Medip provides two function for advance DrawCut useness. They are To ForeSeed and To BackSeed. As we mention in the previous section, we need 2 parameters for using DrawCut, which are proposed and unproposed layers. To Foreseed is function for select the proposed layer, and To BackSeed is a function for select the unproposed layer. Instead of drawing in the image viewer, we assume that specific layer is proposed or unproposed layer. Assumption: We want to do blood vessels segmentation of liver organ 1. Perform Seed Apply to liver blood vessel in the foreseed Layer 2. Create New Layer, rename it as backseed layer 3. Perform Seed Apply to liver organ 30

32 4. Create new layer and rename as result layer. 5. Click DrawCut 6. Right Click foreseed layer and click To Foreseed Now you can see that foreseed layer becomes blue, which means it is our proposed seed. 7. Right Click backseed layer and click To BackSeed 31

33 Now you can see that our backseed layer changed to red, which means it is our unproposed seed. 8. Click OK < Result of Advance Segmentation > Compare to normal Seed Apply 32

34 6. Visualization 6-1 Explanation Tools to learn: Surface Reconstruction, Export to STL File, Export to RAW File After finishing all organ segmentation, we can visualize it into 3D Model and exporting it into STL file. This file furthermore can be printed using 3D printer machine. In this section we will render 3D reconstruction and export it to STL File and RAW File. 6-2 Step by Step Tutorial Reconstructing Surface Reconstructing Surface allows you to render the 3D surface of segmented organ. 1. Right click at the Full Colon layer which will be reconstructed 2. Right-click and select Reconstructing Surface < Result of Reconstructing Surface> 33

35 Surface Smoothing Surface Smoothing allows you to smooth the surface of reconstructed 3D model. Assumption: We have performed surface reconstruction before. 1. Adjust the Smooth in 3D Rendering Toolbar. 2. Right-click and select Reconstructing Surface. < Result of Reconstructing Surface> 34

36 Export to STL File Export to STL File allows you to export 3D reconstruction to STL file. There are two ways to export the reconstruction, and we will show both methods. Assumption: We have performed surface reconstruction before. < way A > 1. Right Click ROI LIST 2. Click Export Stl File 3. Save < way B > 1. From 3D Rendering Toolbar, click Export to STL File. 2. Save 35

37 Export to RAW File Export to RAW File allows you to export 3D reconstruction to RAW file. Assumption: We have performed surface reconstruction before. 1. Right Click ROI LIST, click Export Raw File 2. Save 36

38 7. 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, such as lung, liver, and heart as we have shown below. 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. 37

39 8. 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 would like more information about any of the Medical IP solutions, please contact us at: Please have a look at our other services MAVR ANATDEL Medical Augmented and Virtual Reality Patient-specific Anatomical Model 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 38