copyright 2017 medical ip - tutorial medip v.1.0.0.9 01 ... ip... · medical images and creating 3d...

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List of Contents 1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

2. Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

2-1 Medical IP Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

2-2 Medip History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

2-3 From Image to Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 2-4 STL File Explanation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

2-5 Medical Imaging. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

2-6 Before You Start. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

2-6-1 Download and Install Medip. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

2-6-2 How to activate Medip software. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

2-6-3 How to Use this Tutorial. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

3. Navigation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

3-1 Explanation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

3-1-1 Main Viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

3-1-2 Main Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

3-1-3 Icon List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

3-1-4 Segmentation Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

3-1-5 All Shortcuts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

3-2 Step by Step Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

3-2-1 Zooming and Panning. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

3-2-1 Segmentation Toolbar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

4. Import . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

5. Segmentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

5-1 Explanation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

5-2 Step by Step Tutorial. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

5-2-1 Region Growing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

5-2-2 ROI List Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

6. Visualization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

6-1 Explanation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

6-2 Step by Step Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

7. Conlusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

8. Contact Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

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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.

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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.

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2–2 Medip History

2-3 From Image to

Model

2 - 4 File Explanation

2 - 5 Medical Imaging

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.

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.

STL or STereoLithography is a file format as a Standard Triangle Language.

This file format is widely used for rapid prototyping, 3D printing and computer-

aided 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.

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.

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2 - 6 Before You Start

2-6-1 Download and Install

Medip

Make sure to install the Medip Software from Medip CD, or free version can be

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

a. Double click Medip setup file and click “Next” button.

b. Accept User License Agreement and click “Next” button.

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c. Choose installation folder, and click “Next” button.

d. Accept User License Agreement and click “Next” button.

e. Finish

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2-6-2 How to activate Medip

software

2-6-3 How to Use this

Tutorial

a. Get the license code from Medical IP.

b. Open your Medip software → Go to "Info" at the main toolbar

c. Insert activation key

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)

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3. Navigation

3 - 1 Explanation

3-1-1 Main viewer

Tools to learn : Navigation, Segmentation Toolbar, Rendering Toolbar

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.

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

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3-1-2 Main Toolbar

3-1-3 Icon List

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.

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.

Load

Save

Save As

Undo

Redo

Upload

Info

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a. Polygon Selection

b. Region Selection

c. Pixel-wised 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

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.

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.

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d. Eraser

e. Draw cut

f. Annotation

Eraser is the basic tool to remove the segmentation mask. Left-click and hold

the mouse to specific segmentation mask.

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.

Annotation is the practice of adding note underlining structures of medical

image. Right-click on the viewer and select “Text annotation list”.

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g. Region Proposal

h. Boundary Viewer

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.

Boundary Viewer is the tool for viewing the border of segmentation mask.

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3-1-4 Segmentation Toolbar

3-1-5 All Shortcuts

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.

Action Shortcut Info

Load Ctrl+O

Save Ctrl+S

Save As Ctrl+Shift+S

Undo Ctrl+Z

Redo Ctrl+Y

Next Image PgUp

Previous Image PgDown

Show 1 Image Viewer Space In the image viewer

Window Width Up Right-click + right drag In the image viewer

Window Width Down Right-click + left drag In the image viewer

Window Level Up Right-click + up drag In the image viewer

Window Level Down Right-click + down drag In the image viewer

Zoom In Scroll up

Zoom Out Scroll down

Move Object Scroll pressed

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3-2 Step by Step

Tutorial

3-2-1 Zooming and Panning

3-2-1 Segmentation Toolbar

a. Window Width Level

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.

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.

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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.

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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

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5. Segmentation

5-1 Explanation

3-2 Step by Step

Tutorial

Tools to learn: Region Proposal, Region Growing, basic editing tools

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.

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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.

5-2-2 ROI List Box

Result of Seed Apply Result of Range Apply

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5-2-1 ROI List Box

New Layer

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 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

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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.



< way C >

1. Right click at the layer which will be renamed

2. Select Rename



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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

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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

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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>

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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.

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< Result of First = First - Second >

a. Both layers

b. Fat layer

c. Colon layer

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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

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< Result of Merge Layers >

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Reducing Segmentation

Area

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)>

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Enlarging Segmentation

Area

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)>

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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

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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

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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

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6. Visualization

6-1 Explanation

6-2 Step by Step

Tutorial

Reconstructing Surface

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.

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>

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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>

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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.


< 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

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Export to RAW File

Export to RAW File allows you to export 3D reconstruction to RAW file.


1. Right Click “ROI LIST”, click Export Raw File

2. Save

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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.

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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

Republic of Korea

807-809, Cancer Research Institute,

Seoul National University Hospital,101,

Daehak-ro, Jongno-gu, Seoul

(+82) 2 3668 7958

USA

480 Jacobs Court, Palo Alto,

CA 94306, United States

(+1) 646 532 7994

www.medicalip.com

[email protected]

MAVR ANATDEL

Medical Augmented and Virtual Reality Patient-specific Anatomical Model

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