This document provides a guide to using the medical imaging software OsiriX. It discusses how to open and view DICOM images, perform multi-planar reconstruction, volume rendering, image fusion, and other functions. Key points covered include how to customize windows and toolbars, use navigational shortcuts, perform measurements and create regions of interest, synchronize views, and adjust rendering settings such as shading and color lookup tables. The guide provides an overview of the software's main viewing and post-processing capabilities in 3 sentences or less.

1. OsiriX guide 2022
Maki Sugimoto MD PhD
OsiriX Ambasador

2. I n t r o d u c t i o n f r o m O s i r i X Te a m
Introduction

3. https://www.osirix-viewer.com/about/ambassadors/

4. https://www.osirix-viewer.com/osirix/overview/

5. In the main window, select the patient/study you want,
then open the images by clicking on 2D-3D viewer.
Viewing and Saving the DICOM Header of DICOM Images

6. Displaying a study
①
②
④
③
From the DatabaseWindow:
① Double-Click in the list (Return key)
② Double-Click on the thumbnail
③ Double-Click in the Preview pane
④ 2D-3DViewer icon

7. Merge Series
• Select series + right click and “Open Merged Selection”
shift +
• Open an entire study (all series) :

8. Split Series
• Open a subset of a series:
option
al
+
Image No.
1.
2. Select series +

9. Open a patient
fi
le and select multiple series thumbnails
Opening multiple series simultaneously
1. ‘Shift’ -Click for a
continuous selection
2. ‘Command⌘’ -Click for a
noncontinuous selection
3.‘Drug-Drop’ for a
continuous selection
then press Return key or 2D-3DViewer icon
• Use the thumbnails bar (same patient): Cmd-Click to create a new window
• Go back to the Database window: Cmd-D to display the Database window

10. OsiriX Format Menu
Customize Toolbar
This selection brings up the following window, which lets you rearrange the way
your toolbar looks.
drag and drop tool icons
onto the toolbar

11. Font
This selection brings up the following window, which
lets you choose different font characteristics.
Modify the tool bar of the viewer window

12. It is sometimes useful to modify the Graphic User Interface (GUI).
All windows are customizable.You can modify the tools displayed in the toolbar.
Select “Customize Toolbar” from the “2DViewer” or “3DViewer” menus.
Customizing OsiriX windows
drag and drop tool icons
onto the toolbar

13. You can directly click in the toolbar by holding the ‘ctrl’ key.
Or you can also directly click in the toolbar by the right mouse button.
The “Customize” window will appear.
Customizing OsiriX windows
or
control
+

14. Customizing OsiriX windows
You can move any icons in the toolbar
by holding Command + “drag-and-drop”.
command ⌘ +

15. Navigational shortcuts
★window level adjustment (Option+Click)
★translation(command+Click)
★zoom(Shift+Click)
★rotation (Cntl+Click)
★series browsing
The following functions are helpful in the rapid
and ef
fi
cient interpretation of images.
These icons in the toolbar represent these basic
functions;
To save time, you can also use one of the
following keyboard and/or mouse combinations:
+

16. Navigational shortcuts
The following functions are helpful in the rapid
and ef
fi
cient interpretation of images.
The following small icons in the toolbar represent
these basic functions;
★measurements
Length
Angle
★ROI (regions of interest)

17. Orthogonal Re-slice
The Orientation icons in the toolbar represent orthogonal reslices
You can do the same function in the toolbar:
Plugins - Image Filters - Orthogonal Reslice

18. Select the “Image Tiling” from the “2DViewer” menu.This function will tile all opened
windows and you will be able to see all opened series at the same time.
Viewing multiple images simultaneously
1
2
1 2 3 4

19. Thumbnails bar
• Red : current displayed series
• Yellow : series displayed in another window
• Green : the fused series with the displayed series

20. Synchronization between windows
• Propagate Settings:
• WL WW
• Origin X-Y (Pan)
• Scale (Zoom)
• Rotation
• Sync Series:
• Image position (Z direction)

21. • Propagate Settings
• Sync Series
Synchronization between windows

22. Studies Synchronization for comparison

23. Quickly identify the displayed series
control

24. Magnetic Windows
Magnetic Windows
option
alt
Still Windows

25. 3D Point
double-click

26. Lens : focal 4x zoom
shift

27. Shortcuts

28. 2-D thick slabs
There are actually 3 modes:
Mean: all slices are added and the mean is computed.
MIP (Max Intensity): maximum intensities of all pixels are extracted and displayed.
MinIP (Min Intensity): minimum intensities of all pixels are extracted and displayed.
You can view the thick slab information in the lower left hand corner of the window:
Thick slab mode is controlled in the tool bar
Total thickness is 27.0 mm.
Example
Set no. of total thickness
Images 1 to 9 are displayed.

29. Using 2-D thick slabs

30. Draw ROIs on all images

31. Draw multi ROIs on all images
shift
+ click

32. Delete ROIs
delete
delete
+
command ⌘

33. ROIs as Key Images
Expor
Send
Print

34. 4D

35. 4-D viewer
You can load multiple series of a study that is acquired dynamically.
For example, multiphase reconstructed series from a cardiac CT can be loaded for a
CINE mode review.
Simply select available series and then click “4D viewer”.All series will be loaded into
the same window.
fast
slow
Select multiple series and then
click on the “4D viewer” icon.

36. 4D Navigator
Navigator
You can navigate and review in a ‘dynamic’ fashion by
using the “Navigator” function from the toolbar.
Navigator

37. 4D Navigator
‘time’
dimension
Navigator
slice
dimension
scan 1st
2nd
3rd
4th
5th
6th
7th
8th
Navigator

38. + Scroll
option
alt
navigate in the ‘time’ dimension
4D Navigator
Scroll
Navigator
Navigator

39. 4D beating heart
4DVolume rendering
Export as a Quicktime movie

40. Fusion

41. CT PET
PET-CT
Images obtained during the same imaging
session will be automatically aligned.
The stack synchronization
(under the 2DViewer menu)
can be useful in linking the two
series.
Fusion images

42. Fusion images
Open an image sequence in the 2DViewer, and open the same sequence for a second
time, so that the image sequence is displayed in two separate windows.
Turn off synchronization by selecting 2DViewer Stack Syncronize Off.
Drag the icon of one window and drop it onto the image in the second window
to call up the fusion functions.
The window icon is located
at the left of the window name.
CT PET

43. Fusion images
When initiating the drag of the window icon for fusion, you have to click on the icon and
then wait a second or so before starting the drag.
Otherwise the entire window will be dragged.
Drag and drop
CT PET

44. You can manually align such image series to create fusion images,
using the Move and zoom tools.
When fusing two images from series with different numbers of slices,
it is necessary to
fi
rst turn off stack synchronization (under the 2DViewer menu).
Fusion images
And click the Image Fusion button PET-CT

45. You can control the fusion intensity with the “Fusion Percentage” slider.
20%
70%
fusion percentage
Fusion Percentage
Note that if you close one of the two series, the fusion will be stopped.
If you make a modi
fi
cation on the
fi
rst series (CLUT, zoom,rotation, ...),
these modi
fi
cations will be applied to the second one.

46. Automatically Fuse Defuse
command ⌘
shift
F
+
+

47. Merge two series with different orientation

48. Manual Registration
You can manually align such image series to create fusion images,
using the Move and zoom tools.

49. Point based image fusion
1. Select the pairs
of 3 reference points
2. Rename each points
with the same name

50. 3. Drag drop the icon
4. Point-baced Registration
Drag and drop

51. Image fusion for 2D and 3D
MPR
Volume rendering
Orthogonal MPR
3D MIP

52. Manual 3D positioning

53. Annotations
tab
None
Graphics Only Full (Patient Name)

54. Annotations
You can choose different font characteristics in the following window.

55. Annotations

56. reconstruction
MPR
Multi-planar
( ver. 3.5- )
( ver. -3.3 )

57. Multi-planar reconstruction (MPR)
2D/3D MPR
2D Curved-MPR
2D Orthogonal MPR

58. This 2D MPRViewer allows generating a MPR slice in any position and orientation through the
3D volume.This mode shows three viewing ports.
In the picture above, the two on the left are labeled A and B.The third, on the right, is labeled C.
2D MPR
A
B
C
( ver. -3.3 )

59. A
B
C
The primary purpose of the A and B view ports is to specify the plane that will be
shown in the C view port. The A and B are partially obscured by lines used specify
the plane to be seen in C.
The C is designed for diagnostic viewing and the other two view ports are primarily
to specify what is to be shown in C. (These lines cannot be hidden.)
Diagnostic viewing
2D MPR
Primarily viewing
Primarily viewing
( ver. -3.3 )

60. The view ports are not all equal, which may be different from what users of
other MPR interfaces are expecting.
•A shows a blue line which corresponds to the orientation of C,
and contains a red line that corresponds to B.
•B shows only a blue line that also corresponds to C.
•C has no lines.
A
B
2D MPR
C
( ver. -3.3 )

61. The specifying A will show the original images in the plane that they were originally
acquired, most commonly the axial plane. You can scroll through these images to choose
the one that you want to work off. The specifying B shows planes that are orthogonal to A.
If A is axial, B will show sagittal, and C will be showing coronal reconstruction ( blue line).
2D MPR
A
B
C
( ver. -3.3 )

62. To see a clean sagittal image, you want to grab the blue line in A and swing it 90
degrees. At this point, the C will show a sagittal image.
You cannot grab the red line to do this rotation. (Only the blue line can be
grabbed. )
You can move the intersection of the two lines by grabbing within the red circle
(center the point of rotation).
A
B
C
2D MPR ( ver. -3.3 )

63. 3D MPR ( ver. 3.5-)

64. 3D MPR ( ver. 3.5-)

65. 3D MPR ( ver. 3.5-)

66. 3D MPR ( ver. 3.5-)
3D MPR MIP

67. 3D MPR ( ver. 3.5-)
3D MPRVolume Rendering

68. 3D MPR ( ver. 3.5-)
ON OFF
Available for
each window

69. Sync Centering
Sync ON Sync OFF
3D MPR ( ver. 3.5-)
move object move axis

70. 3D MPR ( ver. 3.5-)
Axis OFF
Available for
each window

71. 3D MPR ( ver. 3.5-)
Mouse position
OFF
Available for
each window

72. Curved MPR
Virtual cholangio-pancreatography

73. • activate “Spline Rendering for ROI” in
Preference
Curved MPR

74. Creating a curved-MPR
1) Open a series from the database
window.
Use the slider bar and move to axial
image you want to make your curved-
MPR
2) Select the Open Polygon (F12) or the
Pencil (F14) ROI tool from the ROI menu
bar
3) Place your the 1st point as a start,
with holding shift.
shift
1st point

75. 3) Place your curve on all slices with clicking and scrolling continuously,
these should align to the curve cut you want
Keep holding shift before end
Set thin ROI for more precision
Don’t click if previous point is highlighted (pink)
or it will stop editing the ROI
clicking scrolling

76. 5) A box will appear asking you if
you want to produce a thick slab
and at what thickness, you can
also choose to produce a cross
sectional series at this time.
6) Another window will appear
with your curved MPR cut.
4) Select the 2-D Curved MPR
option from the 2D-3D menu.
Virtual cholangio-pancreatography

77. This mode shows three orthogonal planes.
Green lines on each window show the location of the other two orthogonal
planes.
2D Orthogonal MPR

78. You can move the green indicator lines freely in any of the view ports.
Zooming and windowing will affect all the ports simultaneously.
A scroll wheel will work in any of the windows to move back and forth through the stack.
If you are content to be viewing only the orthogonal planes, this mode is easier and more
informative than the 2D MPR.

79. It is important to realize that hitting the space bar allows toggling through three states.The
fi
rst state shows only the green lines, the second state adds intersecting hairlines to show
the common point of the three view ports and the third state hides all the lines.
Add intersecting hairlines to show the common point
hide all the lines
only the green lines
+ + +
+

80. Zooming, windowing, moving and paging
will affect by short cuts
or press short cuts keys with left click.
3D MIP in 3D Panel

81. 3-D reconstructions

82. 3-D reconstructions
OsiriX supports four 3D reconstruction
modules:
1)Maximum Intensity Projection (MIP)
2)Volume Rendering
3) Surface Rendering
4)Virtual Endoscopy

83. Maximum Intensity Projection (MIP)
This reconstruction uses a ‘ray-tracing’ technique to identify
which pixel has the maximum intensity on each ray.
This technique is useful for contrast MRIs or CTs, and bone CTs.

84. 3DVolume Rendering

85. Volume Rendering
Use a ‘ray-tracing’ technique to apply a transparency/opacity to each pixel depending on their
position and their intensity.
Nice images of soft tissues for MRI and CT.
Most used 3D technique and will produce the nicest images in many situations.
• Requires a lot of memory :
8 GB recommend
• 64-bit OsiriX recommend

86. View Size inVolume Rendering
You can enlarge it during rendering

87. Background color
You can change background color

88. Manipulation
Contrast/Intensity Pan
Rotate
Zoom

89. Manipulation
Tag reference points
Angle of view
Manipulate 3D object
Measurement tool

90. • Reduce the dataset - orthogonal
• Increase rendering speed
Sculpting
Cropping Cube

91. : right click
command ⌘
Crop all dimension simultaneously
turn to green
Rotate object during cropping:
Pan cube
:
drag outside of the cube
and slide
Cropping Cube

92. Cropping Cube
Tips! :Table removal

93. Bone removal - CT only
click
click
click
alt
option
The default values for bone removal are set between
250 and 2000 Houns
fi
eld values for CT images.
• Value : 1125
• Interval: 1750
You can change the values
by clicking
+

94. Scissors
delete
return
tab
free-hand sculpting 3D object
You can save and load the selected status

95. Undo Sculpting
• At anytime, you can cancel the last sculpting step, by using the Undo function !
! command ⌘
Z
delete

96. Shading
You can edit the shading
• Ambient Coefficent
• Diffuse Coefficent
• Specular Coefficent
• Specular power
High shading Low shading
and also save as a property name.

97. Smoothing with Filters
Basic Smooth Basic Smooth x2

98. 16 bit CLUT Editor

99. 16 bit CLUT Editor
add curve
remove curve
save CLUT
curves
point
Volume rendering techniques assign arti
fi
cial colors to the
different tissue densities that are in the original images.
Assigning the proper blend of colors that are in the range
of red and yellow will provide colors that mimic the real
aspect of bones and
fl
esh.

100. 16 bit CLUT Editor
pixel value
pixel
count
(alpha)
Patient histogram
density [HU]
opacit
y
Assigned color curve
transparent
opaque
alpha: 1.000
alpha: 0.001
Airway
Skin
Muscle
Organ
Contrast vessel
Bone
1st
curve
2nd
curve
Tips!
➀
➁

101. 16 bit CLUT Editor
pixel value
pixel
count
(alpha)
Patient histogram
density [HU]
opacit
y
Assigned color curve
transparent
opaque
add curve
remove curve
save CLUT
curve
point
alpha: 1.000
alpha: 0.001
alpha: 1.000
alpha: 0.001
(include all points)

102. Pixel range
16 bit CLUT Editor
using Point
Opacity
Pixel range
Opacity
drug on drop

103. Change Color
double click
copy color paste
double click on
select color
16 bit CLUT Editor
using Point

104. Shift the range (value)
16 bit CLUT Editor
using Curve

105. alt
option
Extend the range
+ drug drop
(right and left)
Shorten the range
16 bit CLUT Editor
using Curve

106. 16 bit CLUT Editor
using Curve
Change all color Copy curve
select color
copy curve paste

107. 16 bit CLUT Examples
Transplant skin
and airway
Skin
Muscle
Organ
Contrast vessel
Bone
Airway
Skin
Muscle
Organ
Contrast vessel
Bone
Tips!
➀
➁
➀ ➁ ➀ ➁
➀ ➁ ➀ ➁ ➀ ➁

108. There are many presets for colors, opacity,
fi
lters and etc.
Presets
Basic Bone CT Soft tissue CT Soft tissue CT

109. Presets
Add Current WL/WW
Set WL/WW Manually
shift
Remove Preset WL/WW
+
click Preset

110. 3D Surface Rendering

111. Surface rendering

112. Surface rendering

113. Surface rendering
Single Surface
Skin Bone

114. Dual Surface
Surface rendering
Colon Bone Bronchus Heart

115. 3D ROI in Surface Rendering

116. Virtual Endoscopy

117. Virtual Endoscopy
Required free space
air/CO2 insuf
fl
ation
At
fi
rst, click in the lumen

118. Virtual Endoscopy
Pre-setting
Window Level: -300
Window Width: 700

119. Virtual Endoscopy
Shading
Ambient Coef
fi
cient: 0.12
Diffuse Coef
fi
cient: 0.62
Specular Coef
fi
cient: 0.73
Specular Power: 50.0

120. Virtual Endoscopy
Pink pinhead allows you to adjust
the position and direction of the scope
by moving the pinhead or the green cursor.

121. Virtual Endoscopy
For MPR For virtual endoscopy
position
direction
of endoscope
scope rotation

122. Virtual Endoscopy
Tagging
The points will be displayed in all views 2D/3D.

123. Virtual Endoscopy
Level of detail

124. Virtual Endoscopy
1.Add key frame OsiriX will interpolate between key frames and
generate a smooth sequence of images in a movie
fi
le.

125. Virtual Endoscopy
Virtual Endoscopy
2. Interpolation
Set total no.
of frames
preview(if need)

126. Virtual Endoscopy
Virtual Endoscopy
3. Export
Virtual Endoscopy
Virtual Endoscopy
including MPR

127. Virtual Endoscopy
Virtual Endoscopy
4. Movie setting

128. Virtual Endoscopy
Virtual Endoscopy
5. Save movie
Virtual Endoscopy
Virtual Endoscopy
including MPR

129. Virtual Endoscopy
Virtual Endoscopy
Automatic detection
of centerline

130. Virtual Endoscopy
Virtual Endoscopy

131. 4DVolume rendering
Beating heart exported as a Quicktime movie

132. ROI
Region of Interest

133. If the current image does not contain the appropriate pixel size,
the ROI data can be calibrated by manually setting the pixel size.
Once a ROI is outlined, it is possible to set the pixels inside or
outside the ROI to a certain value.
If you want to erase all data outside a region of interest on a CT
image for example you have to set the pixels to lowest possible
value (black) of -1000 Hounds
fi
eld value for example.
ROI Segmentation

134. Segmentation Tools
clicking
Don’t click if previous point is
highlighted (pink) or it will stop
editing the ROI (because too
close)

135. Segmentation Tools
You can change the name, thickness and opacity of the ROI line.

136. Repulsor tool
This allows to re-shape irregular regions of interest
by pushing the contour with a circle shape repulsor.
The diameter of the circle is bigger if you start far from the contour
and smaller if you start closer.

137. 3D ROI
• Set of 2D ROIs
all with the same name
• Set default ROI name
• Rename ROIs
• Posibility to compute/visualize the volume

138. Manual Segmentation
You don’t need to draw a ROI on each slice.
OsiriX will interpolate the missing slices in
the volume computation.

139. Generate Missing ROIs
More slices will give a
more precise result.

140. ComputedVolume
Quantitative Informations
Volume of lt liver: 935.2 cm3

141. Display Options
Wireframe
Surface Color

142. 3D ROI +Volume Rendering

143. 3D ROI + Surface Rendering

144. Region Growing
Region Growing technique allows to initiate an automatic
image segmentation starting from a given “seed” point and
expanding to include all the pixels that are within a given
range of density values.

145. Region Growing
If the current image does not contain the appropriate pixel
size, calibrated by manually setting the pixel size.

146. Region Growing
1. Select 2D/3D Growing Region
2. Select Algorithm
3. Click starting point in the current image
4. Check the Value in the left upper corner
(or parameters window)
5. Set Threshold
Brush ROI

147. 3D Region Growing

148. A surface area generated by the brush ROI tool or the automatic edge detection tool
can be modi
fi
ed by applying morphological
fi
lters
such as erosion, contraction, closing and opening.
Morphological
fi
lter
closing
opening
Copyright © 2008 Maki Sugimoto

149. Region Growing
Inside pixel=1000
Volume Rendering
Polygon
The result is either a
polygon region of interest or
a brush ROI of a surface
area on each image.
You can generate a new series with changing
pixels of the inside or outside.

150. Region Growing
If the current image does not contain
the appropriate pixel size, calibrated by
manually setting the pixel size.
Once a ROI is outlined it is possible to
set the pixels inside or outside the ROI
to a certain value. Inside pixel=1000
Outside pixel= -1000
If you want to erase all data outside a
ROI on a CT image for example you
have to set the pixels to lowest possible
value (black) of -1000 Hounds
fi
eld value
for example.

151. Region Growing
Virtual colonography

152. Exporting
DICOM images

153. Exporting DICOM images
The Export menu item has a submenu to allow speci
fi
cation of the particular image
format (TIFF, JPEG etc.).
To export a single image, you can either select Export from the File menu or
press ‘(Command⌘-C’ to copy it to the clipboard.
Using the default preferences, OsiriX will export the image as it appears on the screen --
same size, zoom, rotation, window level, etc.
You can
fi
nd the exact size of the image on the upper left corner of the window:
The exported image resolution will be 1266 x 709

154. The same principle applies for images sequence.
Select Export to Quicktime from the Export submenu or click on the Quicktime button
from the toolbar.With Quicktime export, you have the possibility to export the image fusion
dimension of the 4D viewer dimension, if these modes are activated:
Select which ‘dimension’ you want to export

155. Exporting DICOM images
You can export your DICOM images as TIFF, JPEG, RAW or DICOM images or as a Quicktime
sequence.
This allows you to capture selected images in a format that will allow you to bring them into,
for example, iPhoto, iTunes, iMovie, Keynote, or PowerPoint presentations or import them into
a Microsoft Word document.
iPhoto Keynote Word

156. OsiriX Web page
http://www.osirix-viewer.com/