연구의 선진화와 생산성 향상에
필요한 최적의 소프트웨어와 컨설팅을
공급하도록 노력하겠습니다.

 3D-Doctor에 관해 자주 질문되는 내용을 정리하였습니다.

3D-Doctor에 관한 기본적인 질문들

1. 3D-DOCTOR 란?

2. 다른 3D 모델링 및 가시화 제품들과의 차이는 무엇인가요?

3. 3D-DOCTOR가 어떻게 작동하는지 보여 줄 수 있나요?

4. 2D Slices로 부터 3D 렌더링을 만드는 과정을 간단히 설명해 주세요.

5. What display settings should I use to run 3D-DOCTOR?

6. Can I use the demo version for my work?

7. What platforms (Operating Systems) does 3D-DOCTOR run on?

8. Does 3D-DOCTOR run on a Unix system?

9. Does 3D-DOCTOR run on a Linux system?

10. Does 3D-DOCTOR run on a Macintosh system?

11. What's a reasonable set up for my PC to run 3D-DOCTOR?

12. What's the ideal hardware set up to run 3D-DOCTOR?

3D Formats, Handling, and Reslicing

13. What image formats does 3D-DOCTOR support?

14. What 3D formats does 3D-DOCTOR support for export?

15. What types of images can be used in 3D-DOCTOR?

16. Is there any limit on image size?

17. How do I define slice thickness?

18. How do I bring my images into 3D-DOCTOR? What can be done if the images are on film?

19. Can I process color images using 3D-DOCTOR?

20. How do I put a stack of 2D image slices into a volume?

21. Can I reslice my 3D image along another axis?

22. How do I reslice a 3D CT/MRI image at an arbitrary angle?

23. How to convert SLC format files into STL format in 3D-DOCTOR software?

24. What is deconvolution?

25. What is a point spread function (PSF)?

3D Image Segmentation & Editing Tools

26. How do I define an ROI (region of interest) for segmentation?

27. What does segmentation do?

28. How do I split/cut objects for 3D rendering?

29. Can I generate object boundaries manually?

30. How do I use color image classification and segmentation?

 3D Surface Modeling, Rendering & Animation

31. What is 3D surface rendering?

32. How do I create a 3D surface model from my images?

33. How do I adjust the scale (X, Y, Z) of my 3D rendering?

34. How do I create a 3D surface model using contour data from other programs?

35. How do I split/cut objects for 3D rendering?

36. How do I combine and compare multiple 3D models?

37. How do I display image slices together with 3D models?

38. How do I control the animation of objects separately?

 3D Volume Rendering

39. What is 3D volume rendering?

40. How do I split/cut objects for 3D rendering?

 Measurement, Report, Quantitative Analysis, and Presentation

41. How do I get images created by 3D-DOCTOR into my presentation program, for example, PowerPoint?

42. What types of measurements can be done by 3D-DOCTOR?

43. Can I calculate the 3D volume of my 3D surface model?

44. How do I calculate the surface area of a 3D surface model?

45. How do I create object report for density measurement?

46. How do I get object size analysis report?

47. How do I calculate the histogram of 3D objects?

48. How do I get 3D measurements on an object, for example, along the airway?

49. How do I create a movie or animation using 3D-DOCTOR?

3D Image Registration, Fusion and Comparison

50. Can I register two 3D images for fusion or comparison?

51. How do I create an image mosaic using 3D-DOCTOR?

52. How do I compare a pair of CT/MRI images using 3D-DOCTOR?

53. How do I create a 24-bit RGB color image from a grayscale image?

54. How do I combine image slices to create a fusion?

 Image Slice Alignment & Reslicing

55. Can I automatically align the slices in a 3D image?

56. How do I manually align image slices?

57. How do I reslice an image with uneven spacing between slices?

 3DBasic Scripting Tool

58. Is there a scripting tool in 3D-DOCTOR for customized programs?

59. Can I run 3DBasic script outside of 3D-DOCTOR?

 

 

 

3D-Doctor에 관한 기본적인 질문들

 1. 3D-DOCTOR란?

3D-DOCTOR는 Abble Software사가 개발한 탁월한 3D 영상 처리 소프트웨어로, 3D 영상 분할, 3D Surface 모델링, 렌더링, 볼륨 렌더링, 3D 영상 철, Deconvolution, Registration, Automatic Alignment, Measurements 및 이외에 다양한 기능을 제공합니다.

 

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2. 다른 3D 모델링 및 가시화 제품들과의 차이점은 무엇인가요?

3D-DOCTOR는 3D-Doctor만이 갖는 벡터(Vector) 기반의 기술을 이용하여 CT, MRI 및 현미경 영상 등과 같은 영상들로 부터 보다 좋은 품질의 3D 모델을 생생합니다. 아래 열거한 리스트들은 다른 소프트웨어 패키지와 다른 주요한 기능 몇가지들을 소개합니다. :

?

벡터 기반의 독특한 기술로 보다 뛰어난 3D 모델을 만들고 편집이 용이함.

?

Surface 모델은 보다 적은 수의 삼각망을 활용하면서도 모든 자세한 정보를 유지함으로써 고품질의 프로토 타입 어플리케이션을 빠르게 생성.

?

탁월한 메모리 관리 기술로 처리할 Slice수에 제한 받지 않음. - 256MB의 PC에서 2,000 Slices 이상을 처리할 수 있음.

?

단 하나의 명령으로 볼륨을 계산하고 정량적 분석을 할 수 있음.

?

DICOM은 물론 TIFF, JPEG, PNG, GIF, BMP, Interfies 등과 같은 여러 영상 포맷 그리고 각 장비 업체의 자체 원시 포맷 등도 지원.

?

그레이스케일과 칼라 영상(칼라 분류 및 분리) 모두 처리 가능.

?

CT, MRI, PET, Microscopy, 산업용 CT, 스캔한 필름 영상, Boundary Slice,Slice 데이터, 및 XYZ 포인트 데이터.

?

고품질 영상 처리 기능 : image registration for multi-modality application, image fusion, image resizing, image reslicing, 외 다수

?

3DBasic Script을 이용하여 자주 사용하는 단계들을 자동화하기 위한 여러분 자신만의 프로그래밍을 할 수 있음.

?

3D 출력 형식: STL, VRML, DXF, 3D Studio, IGES, Wavefront OBJ 외 다수.

?

소프트웨어 신뢰성 : 버그가 발견될 때 마다 즉각적인 수정으로 인해 현재 알려진 버그가 없음.

?

기능 대비 합리적인 가격.

?

모든 기능을 편리한 하나의 패키지에 통합하여 별도의 값비싼 추가 모듈을 구입할 필요가 없음.

?

철저하고 빠른 고객 서비스. 전화 혹은 이메일을 통해 빠른 기술 지원

 

 

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  3. 3D-DOCTOR가 어떻게 작동하는지 보여 줄 수 있나요?

3D-Doctor를 어떻게 사용하는지 쉽게 이해 하도록 비디오 자료를 제공하고 있습니다. 자료실(Data Room)에 가셔서 회원 가입 후 다운 받으실 수 있습니다. 압푹을 풀고 Window Media Player를 이용하여 보실 수 있습니다.

 

 

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  4. 2D 영상 Slices로 부터 3D 렌더링을 만드는 과정을 간단히 설명해 주세요.

아래 설명된 단계를 따라 해 보시면 여러분의 2D 영상 Slices로 부터 3D 렌더링을 만들 수 있습니다 :

 

1. File/New Stack 명령으로 처리하고자하는 모든 Slice들을 Stack List에 추가 한 후 읽으십시오. 이미 list 파일에 추가했거나 하나의 영상을 읽을 경우 File/Open 명령을 사용하십시오.

 

2. 기능 키 - F2(확대 - Zoom in), F3(축소 - zoom out),  F5(이전 Slice 보기), F6(다음 Slice 보기)

Animation tool bar - 영상 Slice를 처음부터 마지막 영상까지 순차적으로 보여줌

View/Image Contrast - Display Contrast를 조정. 이외에 다양한 기능

 

3. Edit/Calibrations - 영상의 공간/분광(spatial/spectral) 해상도 입력.

 

4. Edit/Object Settings -  to add new object groups for holding the boundary

data.

 

5. 3D Rendering/Auto Segment을 실행하여 빠른 자동 영상 분할(Segmentation)을 위해 오브젝트의 수를 입력하십시오. 또는 3D Rendering/Interactive Segment이나 Edit/Boundary Editor을 이용하여 오브젝트 경계선들을 자동 혹은 수동으로 그릴 수 있습니다.

 

6. 3D Rendering/Surface Rendering 명령을 이용하여 3D Surface 모델을 생성합니다. 3D 모델이 디스플레이되었을 때, View/Object을 이용하여 투명도(Transparency)와 칼라 속성을 바꿀 수 있고, 추가 분석을 위한 여러 기능들이 제공합니다.

 

7. 3D Rendering/Volume Rendering을 이용하여 3D 가시화를 위한 3D 볼륨 렌더링을 생성합니다.

 

8. 여러분의 영상에 대한 정량적 분석을 위해 Edit/Object ReportBoundary Report 명령을 수행하십시오.

 

 

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  5. What display settings should I use to run 3D-DOCTOR?

Set your display to either 16-bit or 24-bit color. 3D-DOCTOR is optimized for these settings.

  6. Can I use the demo version for my work?

Yes, you can use 3D-DOCTOR's demo version to create 3D rendering and publish your results and images. In return, we ask you to mention 3D-DOCTOR wherever appropriate and give us some feedback and comments about the software and your work. We'd love to hear from you..

 

Please keep in mind that the demo version is not a full version, and many high end image processing and export functions are not available in the demo.

 

 

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  7. What platforms (Operating Systems) does 3D-DOCTOR run on?

3D-DOCTOR runs on PC running Windows, including Windows 9x, Windows ME, Windows NT/2000/XP, or newer versions of Windows.

 

 

8. Does 3D-DOCTOR run on a Unix system?

 

Not directly. However, it could work on a Unix machine if a Windows binary emulator is installed.

 

 

9. Does 3D-DOCTOR run on a Linux system?

 

The current version does not run directly on a Linux system. There are Windows binary emulators available but we have not tested them for compatibility. We are looking into the possibility of creating a Linux version for a future release.

 

 

10. Does 3D-DOCTOR run on a Macintosh system?

 

 No.

 

 

11. What's a reasonable set up for my PC to run 3D-DOCTOR?

 

3D-DOCTOR can pretty much run on any PC in use today. The only requirement is setting up your display to high color (16-bit or higher).

 

 

12. What's the ideal hardware set up to run 3D-DOCTOR?

 

To get the best performance, you can do the following if you have the available budget:

 

? add more RAM (128MB or more recommended for processing large size volume images and renderings)

? faster CPU

? faster video display board with built-in OpenGL support

? faster and larger hard disk drive

 

 

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3D Formats, Handling, and Reslicing

 

 13. What image formats does 3D-DOCTOR support?

3D-DOCTOR supports a variety of image formats in both 2D and 3D.  These formats include DICOM, TIFF, JPEG, BMP, Interfile, GIF, PNG and RAW.  Other non-standard image formats are also supported, but only with known dimensions (number of columns, rows and planes), bit depth per pixel, little endian or big endian, and the size of file header.

 

 14. What 3D formats does 3D-DOCTOR support for export?

3D surface models created using the surface rendering commands can be saved as AutoCAD DXF, IGES, STL, 3D Studio 3DS, VRML, Wavefront OBJ, raw triangles, and 3D-DOCTOR's own binary format.

 

Object boundary contours can be saved as AutoCAD DXF, IBL (for Pro/Scan), ASCII boundary (BND), and XYZ formats.

 

Download sample files created by 3D-DOCTOR from the pelvis CT image in DXF, STL, VRML, OBJ, 3DS and IGES format to check the compatibility with other programs you use. The files are zipped for faster downloading. Click the right mouse button and use Save Target As to get the file:

 

 ◆ DXF Format (AutoCAD DXF)

 ◆ IGES Format

 ◆ VRML Format

 ◆ STL Format

 ◆ 3DS Format (3D Studio)

 ◆ OBJ Format (Wavefront OBJ)

 ◆ 3D-DCOTOR's 3D .SUF Format

 

3D volume rendering can be saved as VOL and XYZ formats.

 

 

15. What types of images can be used in 3D-DOCTOR?

 

3D-DOCTOR can process a wide variety of images, including CT (computed tomography), MRI (magnetic resonance imaging), microscopy, industrial CT, seismic wave data, scientific volume data, 3D contours, and 3D cloud points. Images can be obtained from medical imaging devices or scanned from films or other image sources. 3D-DOCTOR supports TWAIN-compatible imaging devices and functions for cropping medical film images.

 

3D-DOCTOR supports grayscale images in 4, 8, 12 and 16 bits, 1-bit black/white images, and 8 and 24 bit color images.

 

 

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16. Is there any limit on image size?

 

3D-DOCTOR can handle very large 3D volume images thanks to the efficient memory management implementation. 3D-DOCTOR does not load an entire 3D volume into memory for processing, instead it only keeps what's needed in memory to get the best performance. 3D-DOCTOR is designed to handle image sizes way above what today's scanners can produce.

 

It is always recommended to add more memory (RAM) to reduce disk swapping and improve performance. 256MB RAM should be a reasonable point for most 3D medical images.

 

 

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17. How do I define slice thickness?

 

Use the Edit/Calibration command and enter the thickness and unit. The thickness is actually the slice thickness plus the distance/gap between slices.

 

 

18. How do I bring my images into 3D-DOCTOR? What can be done if the images are on film?

 

Images are brought into 3D-DOCTOR by file. You can read an image file directly from a server where the image is stored when direct network access is available. If direct access is not available, you can copy the image file to a removable storage media (ZIP disk, CD, or tape) and then move the data file to the system where 3D-DOCTOR is installed. Read the image file into 3D-DOCTOR and start from there.

 

If your image is on multiple films where each film has a matrix of slices, then simply scan the films using a regular image scanner with a transparency kit or a film scanner. Bring the scanned images into 3D-DOCTOR and then use the template based Crop Film command to separate the slices for 3D visualization with just a few simple mouse clicks.

 

 

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19. Can I process color images using 3D-DOCTOR?

 

Yes, 3D-DOCTOR supports both 24-bit and 8-bit color images. The 3D Rendering/Segment Object function lets you segment both color and grayscale images to get object boundaries. You can also use the Image/Processing/Color Classification function to group the colors and then extract boundaries using the segmentation function. Color images can also be used in 3D Volume Rendering.

 

You can convert color images to grayscale using the Image/Conversion function.

 

 

20. How do I put a stack of 2D image slices into a volume?

 

The following are the steps needed to create a stack list which can be used as if it is a single image file.

 

Step 1. Select File/New Stack. The New Stack definition dialog box will appear.

 

Step 2. Use the "Add Files" button to add files to the stack list. A file open dialog box is used to browse and get file names.

 

The file open dialog box supports multiple file name selections so you can add several files in one group. Make sure the order of the files added correspond to the order the image planes are acquired. The "Delete" button allows you to delete a file from the current list. Select a file from the list first and then press the "Delete" button.

 

If you need to preview an image file added in the list, select the file name in the list and then press the "Preview" button. The image will be displayed in the preview window. If the image can not be previewed, then you may have a problem with the file or the file format used. You may have to use 3D-DOCTOR's File/Raw Image File Import function to configure the file first.

 

Step 3. Once the files are added to the list, you can save the list to an image list file. You can also open an existing list of files for editing by pressing the “Open List” button.

 

Step 4. Click OK to open the 3D image list you just created. In the future, you can use the File/Open command to open the list file directly. All files stored in the list will be treated as an image plane within the 3D image.

 21. Can I reslice my 3D image along another axis?

  Yes. See the 3D-DOCTOR tutorial for step by step instructions.

 

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 22. How do I reslice a 3D CT/MRI image at an arbitrary angle?

 

This is can be done quite easily.  Resliced volume images make 3D measurement of certain objects more accurate. It works as if you are allowed to rotate your CT or MRI scanner around the patient for the perfect imaging position, but a lot easier.

 

Open your image and then select the Image/Reslice/Reslice Volume command. Enter the 3D angle you want to use and click "Start" to create the resliced image in a few seconds.

 

 

23. How to convert SLC format files into STL format in 3D-DOCTOR software?

 

SLC file is a stack of slices of a model. SLC format is used by many software packages, including JewelCAD, 3D Systems and others.

 

Use the following steps to convert the SLC file to STL file for rapid prototyping applications:

 

Step 1. Start 3D-DOCTOR.

Step 2. File/New Workspace to get a blank window

Step 3. File/Boundary/Import Boundary to open the SLC file

Step 4. Use Edit/Calibration to adjust the values. Change them to 1 if you like.

Step 5. 3D Rendering/Surface Rendering/Simple Surface to create a 3D Model

Step 6. File/Export Model to save to a STL file.

 

 

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24. What is deconvolution?

 

Image deconvolution is used to remove or reduce degradations caused in the imaging process. These include the blurring introduced by optical systems and by image motion, as well as noise due to electronic and photometric sources. 3D-DOCTOR provides two types of deconvolution to restore degraded 3D images, one is a Fast Nearest Neighbor deconvolution and the other is an iterative Maximum Entropy deconvolution method.

 

 

25. What is a point spread function (PSF)?

 

A point spread function is the impulse response function of an imaging system, which makes image restoration possible by deconvolution.

 

A PSF of an imaging system can be obtained by imaging a point light source or it can be estimated theoretically. 3D-DOCTOR has a function to create a synthetic PSF when one is not available.

 

 

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 3D Image Segmentation & Editing Tools

 

 26. How do I define an ROI (region of interest) for segmentation?

A properly defined ROI can normally enhance the performance of the segmentation functions.  

 

The following steps describe how to define one or more ROI:

 

Step 1. Select Edit/Region Of Interest/ROI Tool On/Off to toggle the drawing tool on. The default drawing option is polygon, however, you can select the rectangle or circle method using the right mouse button.

 

Step 2. Click the left mouse button within the image window to draw polygons.  Press the spacebar key to close and finish the polygon.

 

Step 3. Repeat Step 2 to draw more ROIs.

 

Step 4. When you are finished,  press the right mouse button to bring up the pop-up menu options and select "Done" to leave the ROI editing mode.

 

Once the ROIs are defined, you are now ready to start the segmentation process.

 

 

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 27. What does segmentation do?

Image segmentation traces object boundaries that are necessary for creating 3D surface models and volume rendering. You can experiment with the different segmentation methods to find the best one for your image.

 

The Auto Segment command works well for images with distinguishable texture, color and contrast between objects. It is very simple to use and you only need to enter a number for how many objects you'd like 3D-DOCTOR to detect. That's all you need to do to generate object boundaries and create a quick 3D view of your image.

 

The Interactive Segmentation method is best for objects with uniform intensity level. The Segment Object which uses texture defined by training area can be used to handle complex objects. For all segmentation methods, a region of interest (ROI) should be defined for more accurate boundary extraction.

 

 

 28. How do I split/cut objects for 3D rendering?

With 3D-DOCTOR, an object defined by object boundaries can be cut or split into smaller objects.

 

The following are the steps required for cutting or splitting objects:

 

Step 1. Activate the image plane window where the object boundary is displayed. Select the 3D Rendering/Split Object command. The cursor will change to a cross. Move the cursor to the starting location of the cutting line and click the left mouse button. Now you'll see a rubber band line which connects the cursor to the starting location. Move the cursor to the ending location and click the left mouse to define the line. A dialog box appears to let you select the range of image slices to be cut. Select the option "Only keep object on the right" to keep the split object on the right side of the cutting line or uncheck it to keep objects on both side.

 

Step 2. Once the new object boundaries are cut, use Edit/Object Settings to turn off objects that are not to be used for 3D rendering. Now select a 3D rendering (surface or volume) command to create the 3D rendering of the split objects.

 

 

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 29. Can I generate object boundaries manually?

   예, 가능합니다. Tutorial을 참고 하십시오.

 

 

 30. How do I use color image classification and segmentation?

You can create a color image from 2 or 3 grayscale images (both 8-bit or 16-bit) using the Image/Image Fusion/Color Fusion function. Each grayscale image is used as one color component, therefore, 3 images will make the red, green, and blue components to form a RGB image. Some users have created color images by combining CT and MRI images. You can use Image/Registration to register the images if they are in different orientation or scale.

 

 

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3D Surface Modeling, Rendering & Animation

 

 31. What is 3D surface rendering?

 

3D-DOCTOR's, 3D surface rendering commands create 3D surface models from object boundary lines or contours. The 3D surface model consists of triangle faces. Multiple objects can be combined together using 3D surface rendering.

 

There are 2 surface rendering commands in 3D-DOCTOR: Simple Surface Rendering and Complex Surface Rendering. They both create 3D surface model but use different algorithms and are suitable for different objects.

 

The simple surface rendering uses a proprietary algorithm to create smooth and simpler surface models. This method is fast and the models are better suited for rapid prototyping and volume calculation applications.

 

The complex surface rendering uses a triangulation algorithm.  This method is slow but robust, and is better for rendering objects with complicated branches and topologies.

 

With 3D-DOCTOR, you can select the proper rendering method for an object and mix multiple objects created using different rendering methods for 3D display.

 

 

  32. How do I create a 3D surface model from my images?

아래 절차들은 영상 자료로부터 3D Surface 모델을 만드는 과정에 대한 설명입니다. Tutorial을 보시면 좀더 자세한 내용을 보실 수 있습니다.

 

Step 1. Open the 3D image using the File/Open Image command.

 

Step 2. Segment the image using one of the segmentation commands to generate boundaries for an object.

 

Step 3. Edit the boundary lines using the Edit/Boundary Editor, if necessary. Use the File/Boundary/Export Boundary command to save the boundary data to a file. If you need to render only part of an object, you can use the 3D Rendering/Split Object command to split the object along an arbitrary axis.

 

Step 4. Now you can create a 3D surface rendering using the 3D Rendering/Surface Rendering commands. You can also create a volume rendering using the 3D Rendering/Volume Rendering command.

 

 

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 33. How do I adjust the scale (X, Y, Z) of my 3D rendering?

When you create a 3D rendering with only a few slices, the 3D rendering may appear as a very thin object because, by default, 3D-DOCTOR assumes the slice thickness (or distance between slices) is the same as the pixel size in the XY plane (column and row).

 

This can be adjusted easily by using the Edit/Calibrations command. At the dialog box, enter the values for X, Y, and Z. The X and Y are the size of a pixel within a slice. The Z value is the slice thickness plus the distance or gap between slices. If you need to increase the slice thickness, enter a larger value for Z so its scale will be adjusted automatically in the 3D rendering.

 

If you know the size in all dimensions and the physical unit, you can enter them in the Image Calibration Parameters dialog box, and the correct scaling will be applied when making measurements and calculating 3D volume and surface area.

 

 

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 34. How do I create a 3D surface model using contour data from other programs?

The following steps explain the process of creating a 3D surface model from object boundary or contour data. More details can be found in the 3D-DOCTOR tutorial:

 

Step 1. Use File/New Workspace to open a blank window.

 

Step 2. Use File/Boundary/Import Boundary to open the boundary data file for display in the blank window. The boundary data must be stored in a format supported by 3D-DOCTOR. The boundary file format (*.BND) is an ASCII file.  A very simple example is shown below:

 

Z1

X11,Y11

X12,Y12

...

X1N,Y1N

X11,Y11

END

Z2

X21,X21

X22,Y22

...

X2M,Y2M

X21,Y21

END

...

ZK

XK1,YK1

XK2,YK2

...

XKO,YKO

XK1, YK1

END

END

 

 

The Z value is the slice number for a contour. It must be an integer and its neighbor contour should be either Z-1 or Z+1 in order to create proper 3D rendering.

 

Step 3. If you need to adjust the size of the workspace, use the Edit/Resize Workspace command. Changing the workspace size will not affect the size of boundary lines, only the relative location in the window.

 

Step 4. If you need to edit your boundary data, use the Edit/Boundary Editor On command.

 

Step 5. Use the 3D Rendering/Surface Rendering command to create a 3D surface model.

 

 

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 35. How do I split/cut objects for 3D rendering?

With 3D-DOCTOR, an object defined by object boundaries can be cut or split into smaller objects.

 

The following are the steps required for cutting or splitting objects:

 

Step 1. Activate the image plane window where the object boundary is displayed. Select the 3D Rendering/Split Object command. The cursor will change to a cross. Move the cursor to the starting location of the cutting line and click the left mouse button. Now you'll see a rubber band line which connects the cursor to the starting location. Move the cursor to the ending location and click the left mouse to define the line. A dialog box appears to let you select the range of image slices to be cut. Select the option "Only keep object on the right" to keep the split object on the right side of the cutting line or uncheck it to keep objects on both side.

 

Step 2. Once the new object boundaries are cut, use Edit/Object Settings to turn off objects that are not to be used for 3D rendering. Now select a 3D rendering (surface or volume) command to create the 3D rendering of the split objects.

 

 

 

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 36. How do I combine and compare multiple 3D models?

Multiple 3D surface models can be combined and displayed together using 3D-DOCTOR for 3D simulation and analysis. The following explains how it can be done:

 

Step 1. Use the File/Open Model command to display the base model or skip this step if you already have a surface window.

 

Step 2. Use the File/Add/Merge Model command to add another model into the current display window. Repeat this step to add more models.

 

Step 3. Use the View/Object command to adjust the display (the Material button) and shape properties (the Shape button). You can rotate, move and resize an object in 3D space to align with other objects.

 

 37. How do I display image slices together with 3D models?

 

3D-DOCTOR can easily displays the image slices together with your 3D models. If you have a surface model display window open, use the View/Image Planes command to turn on the image plane display. You can use the View/Image Settings command to change the transparent and opaque properties and individual plane display status.

 

This is an example of knee bone model displayed together with the original MRI image:

 

 

 

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   38. How do I control the animation of objects separately?

The View/Animation Control command allows you to define and control the animation sequence and movement for each object.

 

To define the movement of an object in the animation, first select the object from the Object List and then enter the following parameters:

 

 ◆ Rotate (in degrees): The X, Y, and Z are the increments in degree that changes the three angles that control the rotation of the object at each frame. The X is for the angle that rotates counterclockwise around the X-axis while Y and Z are similar for the Y and Z-axis respectively.  

 ◆ Move By: The increments for location shifting along the X, Y and Z-axis at each frame.  

 ◆ Scale: The increments for the scaling factors along the X, Y and Z-axis at each frame .

 ◆ Steps: This defines the number of steps to be used in a loop for the above movement parameters. For example, if Rotate has 10 steps and the X increment is 5, then the object will be rotated 10 times, each time the angle is the current angle plus 5 degrees. The next parameter controls how the loop continues to the next loop .

 ◆ Loop Control: Two options can be used: “Return to Starting Point” and “Reverse Direction”. When the “Return to Starting Point” is used, the object will jump back to its initial position and shape when each loop ends.  When “Reverse Direction” is used, the increment will become decrement at the end of each loop and the object will move back in reversed direction .

 

The viewing angle controls the change of the three angles by using the three increments. The viewing angle controls the global display.

 

You can use the “Test” button to preview the animation. Click here to see an example. (The animation is courtesy of G. Martins, Confocal Microscope and 3-D Imaging Facility,  SUNY at Buffalo.)

 

 

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 3D Volume Rendering

 

 39. What is 3D volume rendering?

While surface rendering creates 3D models with surface polygons and triangles, 3D volume rendering creates a 3D display from the voxels directly. Object boundaries are used to include or exclude image volume in the rendering process. The volume rendering displays voxel intensity in 3D space. With the 3D Rendering/Split Object command, you can cut object into smaller pieces and then use volume rendering to show the volume. The process of creating volume rendering is similar to surface rendering.

 

  40. How do I split/cut objects for 3D rendering?

With 3D-DOCTOR, an object defined by object boundaries can be cut or split into smaller objects.

 

The following are the steps required for cutting or splitting objects:

 

Step 1. Activate the image plane window where the object boundary is displayed. Select the 3D Rendering/Split Object command. The cursor will change to a cross. Move the cursor to the starting location of the cutting line and click the left mouse button. Now you'll see a rubber band line which connects the cursor to the starting location. Move the cursor to the ending location and click the left mouse to define the line. A dialog box appears to let you select the range of image slices to be cut. Select the option "Only keep object on the right" to keep the split object on the right side of the cutting line or uncheck it to keep objects on both side.

 

Step 2. Once the new object boundaries are cut, use Edit/Object Settings to turn off objects that are not to be used for 3D rendering. Now select a 3D rendering (surface or volume) command to create the 3D rendering of the split objects.

 

 

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  Measurement, Report, Quantitative Analysis, and Presentation

 

 41. How do I get images created by 3D-DOCTOR into my presentation program, for example, PowerPoint?

Use 3D-DOCTOR's File/Save/Save Window command, which saves the current display window to a Windows bitmap (BMP) file. You can then open the bitmap file from your presentation program.

 

The Save Window command saves only the bitmap displayed in the window, use other file formats to save the data, for example, the project (*.prj).

 

You should set your display to 16-bit or 24-bit color if you plan to use the File/Save/Save Window command.

 

 

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 42. What types of measurements can be done by 3D-DOCTOR?

3D-DOCTOR can make a variety of image measurements, including distance, area, surface area, volume, profile, and image region histogram.

 

3D-DOCTOR lets you measure angles using the Angle Measurement tool.

 

3D volumes of  3D surface models can be calculated easily.  When the surface model window is displayed, use the Process/Calculate Volumes command.

 

 43. Can I calculate the 3D volume of my 3D surface model?

Yes, the volume of  a 3D surface model can be calculated easily using the Process/Calculate Volume command within the surface model window. This command computes both volume and surface area. To adjust the scale and unit for volume calculation, the scaling parameters should be entered using the Edit/Calibration command before rendering is done.

 

If you have your 3D model saved in a format supported by 3D-DOCTOR, such as DXF, STL, raw triangle, etc., you can use File/Open Model to read the 3D model into 3D-DOCTOR and then calculate the volume.

 

 

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  44. How do I calculate the surface area of a 3D surface model?

The surface area of a 3D surface model can be calculated easily using the Process/Calculate Volume command within the surface model window. This command computes both volume and surface area. To adjust the scale and unit for volume calculation, the scaling parameters should be entered using the Edit/Calibration command before rendering is done.

 

If you have your 3D model saved in a format supported by 3D-DOCTOR, such as DXF, STL, raw triangle, etc., you can use File/Open Model to read the 3D model into 3D-DOCTOR and then calculate the volume.

 

   45. How do I create object report for density measurement?

Once you have defined object boundaries for a 3D image, select Edit/Object Report command to calculate the pixel density measurements from the 3D image. The measurements include number of pixels, min and max pixel density, and mean and variance.

 

If you have entered calibration parameters for image pixel density, the calibrated value will be used in the calculation.

 

If your image is color image, then the calculation will be done for all color channels. You can use the results for color analysis.

 

The data can be used in a spread sheet program for plotting or pasted directly into your report or paper.

 

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  46. How do I get object size analysis report?

With 3D-DOCTOR, you can generate boundaries or contours for multiple objects, or import boundaries from other programs. The boundaries can then be used to create a statistical report for the size, area, count, and other parameters of all objects using the Edit/Boundary Report command for quantitative analysis.

 

The data can be used in a spread sheet program for plotting or pasted directly into your report or paper.

 

  47. How do I calculate the histogram of 3D objects?

Once you have defined boundaries for the objects in a 3D image, select Edit/Object Histogram command to calculate the histogram from the 3D image.

 

If you have entered calibration parameters for image pixel density, the calibrated value will also be included in the histogram output.

 

If your image is color image, then the histograms for all color channels will be calculated. You can use the histogram data for color analysis.

 

The data can be used in a spread sheet program for plotting or pasted directly into your report or paper.

 

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  48. How do I get 3D measurements on an object, for example, along the airway?

3D measurements such as area and perimeter at a location on a 3D object, for example, along the airway, can be made using the Surface Contours command. The following process is suggested and please refer to the 3D-DOCTOR User's Manual for details on the functions:

 

Step 1. Create one or more 3D models to be measured from your CT or MRI image using the Surface Rendering command.

 

Step 2. Select Process/Surface Contours command to generate surface contours.  A contour is calculated as the intersection between the 3D object and a defined cutting plane. Move the cutting plane to each location you need to make the measurement and use the Get Contours button to acquire contours. Repeat this process until you have contours for all locations where measurements are needed. Click the Finish button to exit from the surface contour process.

 

Step 3. Select Contour Report command to get measurements for all the acquired contours. This command calculates the area, length and center location of all existing surface contours and displays in a report.

 

 

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  49. How do I create a movie or animation using 3D-DOCTOR?

You can use 3D-DOCTOR to create a movie for your 3D rendering. Click here to see an example.

 

Once you have your 3D rendering (either surface or volume rendering) created and displayed in 3D-DOCTOR, you can start the View/Animate/Create Movie command. Define the AVI file where you want to save the movie. Press Start Recording and then go back to 3D-DOCTOR to get actions you want to put in the movie file. When you are done, click Stop to finish. The movie is saved in the AVI file. Make sure you have enough hard disk space as the movie file can get quite big.

 

You can also use a screen capture program to record 3D-DOCTOR screen actions into an AVI file.

 

Or you can use the File/Save/Save Window command to save each rotation to a .BMP file and then use an animation program to put the frames together for a movie.

 

 

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 3D Image Registration, Fusion and Comparison

 

 50. Can I register two 3D images for fusion or comparison?

예, 가능합니다. Tutorial 페이지에서 13번 Automatic Alignment of Image Slices을 참고 하시기 바랍니다.

 

 51. How do I create an image mosaic using 3D-DOCTOR?

Creating an image mosaic is easy with the Image/Mosaic command. This command can be used to merge image slices from a 3D volume image or a 2D image to create an image mosaic.

 

The following are the steps:

 

Step 1.  Prepare your images: If the images to be combined are not the same type, for example, 8-bit grayscale and 16-bit grayscale, you need to use the image conversion commands to convert them to the same image type.

 

Step 2.  Start the Image/Mosaic command. When the Image Mosaic dialog box appears, define the mosaic matrix and the names of the image files to be used for the mosaic. Click the "Create" button and the generated mosaic image will be displayed. Save the image to a file or continue for additional processing.

 

 

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  52. How do I compare a pair of CT/MRI images using 3D-DOCTOR?

3D-DOCTOR provides many different ways to compare 2 or more 3D images (CT, MRI, or microscopy), including image registration, image color fusion, image fusion by arithmetic combination, 3D model combination, and object boundary combination.

 

The following explains each type of comparison and their benefits:

 

 

 

Image Registration: If 2 or more images are in a different orientation and size, you can define 4 or more control points in 3D-DOCTOR and register them against a base image. When images are properly registered, you can compare them using image fusion and other functions.

 

 

Image Color Fusion: For 2 or 3 images, use Image/Color Fusion to create a RGB true color image, where each image is used as a color component in the final RGB color image. Differences between images will be shown clearly in the color space as the combined colors.

 

 

Image Fusion Using Arithmetic Algorithms: This function combines two 3D images to create a new fusion image using one of the following operators: Add, Subtract, And, Or, Transparency, Max, Min, and others.

 

 

 

Combine Object Boundaries: Object boundaries from another image can be easily imported to compare to the current image to show the difference in terms of size, area, and location.  They can also be used together in 3D rendering.

 

 

Combine 3D Models: 3D models created from multiple images can be displayed together to show differences in terms of size, location, and material characteristics.

 

 

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 53. How do I create a 24-bit RGB color image from a grayscale image?

You can create a color image from 2 or 3 grayscale images (both 8-bit or 16-bit) using the Image/Image Fusion/Color Fusion function. Each grayscale image is used as one color component, therefore, 3 images will make the red, green, and blue components to form a RGB image. Some users have created color images by combining CT and MRI images. You can use Image/Registration to register the images if they are in different orientation or scale.

 

 54. How do I combine image slices to create a fusion?

The Image Fusion/Plane Fusion command combines all image planes or slices from a currently displayed image stack into a single slice image. The Image Plane Fusion dialog box appears. The slices can be fused using one of the following methods:

 

Minimum: This method checks all pixels at each pixel location of all image planes and keeps the smallest value for the final fusion image.

 

Average: This method adds up all pixels at each pixel location of all image planes and calculates the average value for the final fusion image.

 

Maximum: This method checks all pixels at each pixel location of all image planes and keeps the biggest value for the final fusion image.

 

Once the fusion image is successfully created, use the File/Save/Save Image As command to save it to a file.

 

 

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  Image Slice Alignment & Reslicing

 

 55. Can I automatically align the slices in a 3D image?

예, 가능합니다. Tutorial 페이지에서 13번 Automatic Alignment of Image Slices을 참고 하시기 바랍니다.

 

 56. How do I manually align image slices?

When image slices are not properly aligned, you can use existing markers within the image to help the alignment. The commands under Alignment are used to define alignment markers and align image slices with the corresponding markers. When only one marker is defined for each image slice, only linear shifting is effected. When two markers are available, a linear transform is applied to the image to correct any rotation and stretching indicated by the markers. When 3 or more markers are defined, a least-square linear or bi-linear transform is applied to correct any geometric distortion to align the image slices.

The following steps explain how to use the commands to align the slices of a multi-plane image:

(1)

 

Open the image using the File/Open command. You should see 2 windows, the single plane display window and the montage window.

(2)

 

 

 

 

Select Image/Alignment/Define Markers to start adding new markers. Move the cursor to a location within the single plane image window, and click the left mouse button to define a marker. The marker is displayed as a blue cross with its numeric ID. Click the right mouse button to choose other marker editing options, such as Move Marker and Delete Marker. Click the left mouse at a new location to add a new marker.

(3)

 

 

 

 

 

 

You need to define markers for all image planes that have corresponding markers and need to be aligned. Corresponding markers must have an identical ID number. You can define 1 or more markers for each plane that needs to be aligned and the markers should not be too close to each other within the same image plane. Use F5 and F6 function keys to move to the previous and next plane to define markers. You can use the Copy to All Planes option to duplicate the markers from the current plane to all other planes and then use the Move Markers option to adjust their position.

(4)

 

 

 

 

Once you have identified the markers for all image planes, click the right mouse button to bring up the image alignment menu, and select the Align Image command. You will be asked to enter the filename that is going to be used to store the new aligned image. Click OK to start the alignment process. When it finishes, use File/Open to open the aligned image file for display and processing.

(5)

 

 

The markers are kept during the image alignment process. Use the Image/Alignment/Delete All option to delete the markers when they are no longer needed.

 If there is a strong correlation between image slices, you can use Image/Auto Alignment to perform an automatic alignment of slices.

 

 

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  57. How do I reslice an image with uneven spacing between slices?

When your 3D image has uneven slice thickness or variable spacing between slices, it needs to be corrected to have accurate 3D rendering and quantitative analysis. 3D-DOCTOR's Reslice (Image Menu) command allows you to enter the uneven slice thickness and spacing values between all slices and creates a new image with even slice thickness and spacing between slices using an optimal interpolation algorithm.

 

The following are the steps needed to reslice an image:

 

Step 1. Open the image that has uneven spacing using the File/Open command. If the slices are in separate files and you have not put them into a stack, use File/New Stack to do so and then open it.

 

Step 2. Select the Image/Reslice/Reslice command. The Image Reslice dialog box appears that lists the slice thickness values between all slices. Edit the slice thickness values if necessary to reflect the exact uneven spacing between slices. The New Thickness is the desired slice thickness and spacing between all slices for the new image. A smaller value will add more slices while a bigger value reduces the number of slices in the resliced image.

 

Step 3. Enter a new image file name for the output image and click OK to start. Once the process is finished, you can close the current image and use File/Open to open the new image for 3D analysis and rendering.

 

 

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   3DBasic Scripting Tool

 

 58. Is there a scripting tool in 3D-DOCTOR for customized programs?

Yes, 3D-DOCTOR provides 3DBasic, a Basic-like scripting for writing customized programs. 3DBasic uses Basic syntax and no strong programming background is needed.

 

3D-DOCTOR's online help and tutorial include many 3DBasic examples for doing different tasks.

 

 59. Can I run 3DBasic script outside of 3D-DOCTOR?

Yes. 3DBasic can be used as a batch script in the command line form. 3DBasic can also be run within 3D-DOCTOR together with the displays. 3DBasic interpreter is implemented as part of 3D-DOCTOR.

 

 

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