Osirix Imaging - Articles, Tutorials & Resources for Medical Illustrators

In OsiriX, a fly through is a movie sequence. You have the control of selecting specific key frames from a 3D reconstruction by moving, rotating and zooming in and out of the 3D volume render, surface render, MIP or endoscopy. OsiriX will interpolate or “tween” the key frames to create a smooth movie sequence.

1. Download a study from the DICOM sample image sets . For this tutorial, I used MANIX, a CT scan of the head.

image via http://pubimage.hcuge.ch:8080/

2. Copy the study to your desktop. Open the folder to unzip it.

3. To import the study into OsiriX, click the unzipped folder from your desktop and drag to the Local DICOM database window. You can also click the Import button.

4. There are four series in this study.
unnamed
SANS I.V.
ANGIO CT
AVEC I.V.

To open the series, select ANGIO CT from the Local DICOM database window and press enter. Or select ANGIO CT and click on the 2D Viewer button.

5. The study opens in the 2D-3D Viewer. Click on the 2D/3D viewer button pull down and select 3D volume rendering.

6. If you want to cut out any areas of the 3D volume rendering, select the scissors tool and click points on areas to be removed and press the delete key. If you are not happy with your scissors selection, simply select another tool and click on an area outside the image. Or if you cut too much of the image, select Edit –> Undo.

7. Selecting the area and pressing the delete key will cut out the selected area. Selecting the area and pressing the enter key will cut out everything outside the area.

8. Rotate the 3D volume render and continue to cut out areas until you are satisfied with it.

9. To edit the colors of the image, click on CLUT and select 16-bit CLUT (color look up table) editor.

10. The 16-bit CLUT editor will display a histogram of the image. A tutorial on the 16-bit CLUT editor can be found here .

11. I added another curve by clicking on the + button to the left of the histogram. I also lowered the opacity for the white points and moved the graphs by selecting the small black squares in the center of the graphs.

12. If you want to recreate this 16-bit CLUT, here are the values and alphas for my two graphs. Right click the graph to save as a preset.

graph 1

(black) value: -802, alpha: 0.000

(red) value: -612, alpha: 0.099

(yellow) value: -285, alpha: 0.026

(white) value: -158, alpha: 0.001

graph 2

(black) value: 14, alpha: 0.000

(red) value: 204, alpha: 0.002

(yellow) value: 406, alpha: 0.059

(white) value: 557, alpha: 0.002

13. Click on the Fly Thru icon.

14. Adjust the 3D rendering by using the Contrast Adjustment, Move and Pan, Zoom and Magnify, Rotate, and Manipulate 3D Object tools.

Click on the + button to add a key frame. Click on the - button to delete a key frame. Click and drag key frames to change the order. You can save the steps of the fly through as an XML file by clicking on the export button. So the next time you work with this series, you can reuse the steps by importing the XML file in the fly through.

15. You can also use the crop tool to move in and out of the 3D volume rendering in the fly through. After clicking on the crop tool, select a green sphere from the crop box and it will turn red. Click and drag the sphere up, down, left or right. The crop tool is not permanent so you can un-crop the 3D volume rendering at any time. After you are finished cropping, click on the crop tool icon again to get rid of the crop box or it will show up in the fly through.

16. Click on the Movie settings and enter the number of frames. Increasing the number of frames results in a smoother sequence and larger file size. Check loop if you want it to reverse the sequence in the second half of the movie. Choose the spline method for smooth transitions between key frames. The linear method will be similar to a slide show and it will not interpolate between the key frames. Click compute and play. At this point, you can edit the sequence by going back to the steps, adding or deleting key frames and moving the key frames around. Once you are happy with the sequence, click save to export the QuickTime file.