OsiriX and Horos Course
by Dr. Alexandre Amato & Dr. Daniel Benitti
The complete OsiriX and Horos course, created by Dr. Alexandre Amato and Dr. Daniel Benitti, vascular surgeons certified by the OsiriX Foundation, mirrored here from the free YouTube channel. Forty-two short, hands-on lessons, from beginner to advanced: an introduction to the Mac for those coming from Windows, navigating and configuring OsiriX, the database and Smart Albums, 3D reconstructions (Volume and Surface Rendering, fly-through, and 3D printing), Curved MPR and centerline, precise vascular measurements, automatic segmentation of the aorta and airway, EVAR and C-arm planning, carotid stenosis and cerebral angiography, reports, key images, and setting up a PACS network. Free software (OsiriX Lite and Horos) and open content: watch whenever you like, at no cost and without signing up.
42 lessons6h 32minIntermediateFreeHealthcare Professionals
Course content
1. Introduction and Basics
OsiriX from Scratch: Navigation and ToolsIn this lesson we introduce OsiriX, covering the interface and the basic tools most used in daily practice and in endovascular planning.
You will see:
What OsiriX is and how it works with DICOM studies
Differences between versions (free 32-bit, paid 64-bit and OsiriX MD)
How to navigate the main screen (albums, study list, thumbnails and database)
How to open and compare datasets (e.g., arterial and venous phases) and use synchronization
Windowing adjustment (HU) with brightness/contrast and why "bone" helps in vascular imaging
Why measuring only on the axial view can be misleading and how to use 3D MPR for slices perpendicular to the vessel
Using MIP to measure extent (and why not to use it for diameter)
Basics of organization (Albums/Smart Albums) and toolbar customization44min
Introduction to the Mac for PhysiciansIn this lesson we give an introduction to the Mac (macOS) aimed at those who will use the computer in medical practice, especially with OsiriX and DICOM medical image analysis. If you are migrating from Windows to the Mac, here are the tips that avoid the most common confusions and greatly speed up your work.
1) Windows, Linux and Mac: a quick overview
Windows: the most popular; it has to run on thousands of different hardware configurations (drivers), which can increase incompatibilities.
Linux: widely used on servers and “appliances” (e.g., routers); there are dedicated PACS solutions (e.g., Conquest / dcm4chee).
Mac: hardware and software made by the same company → better integration and, in general, fewer crashes when using imaging applications.
I also mention that there are many DICOM viewers (not just OsiriX), and cite the site idoimaging.com as a list of viewers by operating system.
2) Mac keyboard: equivalents and important shortcuts
Ctrl (Windows) ↔ Command (Mac)
Alt (Windows) ↔ Option (Mac)
On the Mac, the Delete key works like Backspace on Windows
For “Delete” as on Windows: Function + Delete
In OsiriX, these keys speed things up a lot:
Shift + mouse: zoom
Option + mouse: brightness/contrast
Command + mouse: pan the image
Ctrl: extra information
3) Windows-style accents on the Mac
The Mac's default method uses combinations with Option (e.g., Option+E, Option+C, etc.).
If you want to type as on Windows:
Go to System Preferences → Language & Text / Keyboard → Input Sources
Select US International PC
(This is the option that sets accents to the pattern most people are used to on Windows.)
4) Screenshots to document measurements/planning
Command + Shift + 3: captures the entire screen
Command + Shift + 4: captures a selected area
Command + Shift + 4 + space bar: captures a window
Useful for saving images with OsiriX measurements to print or share.
5) Closing apps on the Mac (a classic mistake for those coming from Windows)
Clicking the red X only closes the window; the program may remain open.
To really close it:
Command + Q (Quit)
Many open apps can slow down the Mac due to memory consumption.
6) Finder, organization and quick preview
Finder = the Windows “Explorer”
The space bar opens a quick preview of the file (image, PDF, video, etc.) without opening the app
Color tags help with organization (and you can name them in the preferences)
Command + I shows file information (size, details)
7) Spotlight: one of the most useful tools
Access:
Magnifying glass in the top right corner or Command + space bar
It is used to:
open programs quickly (e.g., type “OsiriX”)
do calculations (e.g., 20% oversize → 4*1.2)
find files by name or by content (including e-mails, contacts, etc.)
8) How to install OsiriX
Two methods mentioned:
Website: osirix-viewer.com → Downloads → download and install
App Store: updates automatically, but does not allow plugins (legal restriction)
In the installer, just follow the package and complete the installation.
9) Screen sharing / communication
Options discussed:
Messages/iChat: screen sharing and webcam (video conferencing)
Skype: screen sharing (no remote control)
TeamViewer, LogMeIn, CrossLoop, YouGoo: alternatives for sharing and/or controlling remotely (some paid, some free to use)27min
Essential OsiriX SettingsIn this video I share practical tips for configuring OsiriX through Preferences, focusing on what really helps in day-to-day use. I go through the General (Basic) and Database menus, showing what is worth adjusting, what is better left at default, and which options save you headaches (especially with importing and organizing studies).
1) Accessing Preferences
Path: OsiriX → Preferences
You will see groups such as Basic, Display and Sharing. Here I focus on Basic and then on Database.
2) Basic → General: what I recommend
Padlock (admin lock): locks the preferences and prevents other people from changing settings (useful on a shared computer).
Sync preferences: this is advanced; useful if you have several OsiriX installations on several computers and want everything standardized by an administrator.
Display notifications: controls the notifications that appear on screen.
DICOM system: keep it on DCMTK (there is no practical reason to change it).
JPEG in DICOM: remember that JPEG is lossy compression. It is important to be able to open studies like this, but:
Never recompress files that already came compressed (so as not to degrade the quality further).
Plugin and version updates: you can leave it on, but, depending on your workflow, the frequent update messages can be annoying.
Allow editing of DICOM metadata: I suggest leaving it off, because there is usually no reason to edit patient/study data.
Languages: choose the languages OsiriX will allow.
3) Database: settings that affect your daily routine
Database location
Usually left at the default (Documents Database).
Only change it if you want to keep the database on another disk (for example, an external one).
Import DICOM only
The “Import DICOM File Format Only” option: I like to leave it off so I can import JPEG/TIF and other images when needed.
Validate files
Can be useful to check whether the files are well-formed DICOM.
Copy vs. link imported files (critical point)
“Always copy files to the database” or “always ask”:
My recommendation: pick one default and stick with it, because mixing “copy” and “link” can make you lose the source and break the link → the study may then fail to open.
4) Data format and display
Date/time format: set it to the Brazilian standard.
Font and age: show current age and/or age at the study date (in the video, I keep both).
5) Database Autocleaner (automatic cleanup)
Used to save space, especially on laptops:
Delete studies according to criteria (for example, when disk space is low).
Options related to deleting original/linked files (be careful here: this is precisely for controlling storage).
6) Reports
You can choose which editor will open the reports: Pages, Word, TextEdit, LibreOffice, etc.
7) CD/DVD: when inserting a disc
Useful settings:
Copy all content to the database
Eject the disc when copying is finished
Search for DICOM: instead of relying only on the “DICOMDIR”, it can be useful to have OsiriX search the disc for files, because many imaging labs in Brazil burn CDs that do not follow the standard.
Burn CD
Avoid “prefer JPEG”, because it loses quality.
You can include an extra folder (e.g., material from your practice), if it makes sense.
8) Protocols and Hotkeys
Protocols: I don't go into detail here.
Hotkeys: shows useful shortcuts to speed up your work.8min
Customize the ToolbarIn this lesson I show how to set up and customize the OsiriX toolbar, both in the Database window and in the Viewer window. The idea is to keep on screen only what you actually use, saving space (especially on laptops) and making your workflow faster.
1) Toolbar in the Database window
Each OsiriX window has its own toolbar (the icons at the top).
By right-clicking an empty area of the toolbar, you can:
Show icons only
Show text only
Show icon + text (usually the most comfortable on large screens)
Use small icons
Hide the toolbar
Tip from the video: on small screens (MacBook Air / notebooks), it may be worth using icon only or text only to gain space.
Customize Toolbar
Still right-clicking an empty area, choose Customize Toolbar.
A window opens where you can drag tools into/out of the toolbar.
Everything shown there can also be accessed through the menus, so you can remove items you don't use often.
Suggestions from the video: what you can remove in the Database
Query and Sender (if you don't use OsiriX on a network)
Burn (on newer Macs without a CD burner)
Anonymize (if you don't export anonymized studies)
Movie Export (if you don't export videos)
E-mail (avoids sending as ZIP + password, which is often blocked by providers such as Gmail)
Metadata (if you don't edit the study's metadata)
4D Viewer (only for those who work with the “fourth dimension”/time)
Report (only for those who write reports)
If you want to put something back, just drag it onto the toolbar again.
To restore the default: drag the “default” set of items (the entire bar shown in the customization window) and drop it onto the Toolbar.
2) Toolbar in the Viewer window
When you open a study, the Viewer window has another Toolbar, with different tools.
The options are the same:
Icon only / text only / icon + text
Hide
Small icons
Customize Toolbar to drag and drop items
Note from the video: on laptops, some tools may “disappear” into the corner for lack of space, so adjusting the Toolbar helps a lot.
Items mentioned as important in the Viewer (examples from the video)
Access to the database
Main viewing tools
Reconstructions (gear icon) — very important
2D filters
Synchronization
WL/WW (Window Level/Window Width) for windowing (Hounsfield, abdomen, airways, etc.)
Plugins and specialized tools
The Customize Toolbar list also shows plugins and calculations:
E.g.: ejection fraction (cardiology)
E.g.: volume calculation (plugin)
E.g.: 4D
E.g.: printing (if you often use OsiriX to print)
E.g.: Cobb angle (orthopedics)
Final tip from the video: it's always worth checking this list, because it changes with each OsiriX version, bringing new features and new plugins.8min
OsiriX Without Ads (LXIV)In this video I share a tip that, in practice, solves one of the biggest complaints about the free version of OsiriX: ads for the paid version and limitations (32-bit), including messages and restrictions when opening large studies.
OsiriX is open source, so the source code is available and other people can compile it and create parallel versions (forks). The OsiriX company releases only the 32-bit version for free, with limitations. To use 64-bit, in general you would need to buy the paid version or compile it yourself (which is not simple).
The tip: a 64-bit fork “without the hassles”
I show a fork compiled by Alex Bettarini, referred to in the video as OsiriX “LXIV” (based on OsiriX version 5.9). The idea is to have a 64-bit OsiriX, without the ads and without those limitations of the 32-bit version.
In the video I walk through the complete workflow:
1) Where to download
On the site indicated in the video (Downloads section)
File of about 42 MB, based on OsiriX 5.9 (with the note that 6.0 exists, but may have lost some features in this context)
2) Avoid overwriting your current OsiriX
After downloading, I drag the app to the Desktop
Since the app comes named “OsiriX”, I rename it (e.g., LXIV)
This way you can keep two OsiriX apps on the same Mac without conflict.
3) Allow it in macOS (Security & Privacy)
Since it is not from an “identified developer”, macOS blocks it
I go to System Preferences → Security & Privacy and choose “Open Anyway”
I type the password and the app opens normally
4) Practical test
The new OsiriX already finds the same database as the original OsiriX
I open a large study and show that it opens without the image-count limitation that appears in the 32-bit version6min
OsiriX Free vs PaidIn this lesson I show, in practice, the difference between the free OsiriX and the paid OsiriX, focusing on what causes the most confusion day to day: the limitation of 32-bit OsiriX for opening studies with many images (large datasets) and how that changes in the 64-bit version.
1) How to identify the free OsiriX (Free)
In the free OsiriX:
an OsiriX MD advertisement appears (at the bottom).
when opening About, I see that it is a 32-bit version.
when entering a study, a warning appears suggesting it is not for medical use.
The main problem with Free shows up when you try to open a very large study (e.g., thousands of slices).
2) The big difference: opening studies with many images
In the video example, when trying to open a large study (e.g., ~2,800 images), the free OsiriX warns that the 32-bit version cannot open the full dataset.
What OsiriX Free lets you do as a "workaround":
Option A) Open in parts (two images from the same dataset)
It suggests opening the study "separately" to get around the limitation — but you do not get the complete dataset all at once.
Option B) Limit the range of slices that will be opened
To get to the limitation window:
press Option and click 2D Viewer
Then you can:
choose the highest and lowest axial slice (open only a segment)
reduce until you reach a number that Free can open (in the video, at ~1,400 slices a warning already appears)
Option C) Increase the "interval"
interval 2 = opens every other image
this lets you open the whole study, but skipping slices (lower navigation resolution)
These are ways to "get past" the 32-bit limitation without stalling your workflow.
3) Paid OsiriX (64-bit): what changes
In the paid version:
in About, 64-bit appears
when opening the study, the warning that appears is that the version has not been certified for medical decision-making (you click I Agree)
the main gain is that it can open large datasets in full, without needing to reduce the number of images
In the video, I show a computer with 16 GB of RAM managing to open the entire study.
Important note from the video: if the computer has little RAM, the advantage of 64-bit may be smaller — because opening large datasets also depends on available memory.
4) Even on 64-bit, you can still limit to gain performance
Even in the paid version, you can still:
press Option and click 2D Viewer
limit the slice range so OsiriX works faster
But, unlike Free, it is not required in order to open the study.5min
2. Database
How to Create a New DatabaseIn this video I show how to create another database in OsiriX (Database Folder). This is very useful for:
Backup on an external hard drive
Storing studies when the laptop's disk is running low on space
Creating a separate database for old studies without “weighing down” the main database
In the example, I already have the default database (Documents Database) and I create a second database on an external drive.
1) Create a new database (Database Folder)
In OsiriX:
Go to File → New Database Folder
Choose the external disk (or another location)
Create the folder (you can name it whatever you like)
Confirm with Create
From then on, you have two database folders available in OsiriX.
2) Move studies between databases (drag and drop)
With both databases created:
You can drag a patient/study from the main database to the new database
In the video I move two studies to the external drive's database
When you open the new database, the studies are already there.
3) What the “OsiriX Data” folder is (and what NOT to do)
Inside the chosen location, OsiriX creates the structure called OsiriX Data, with the tree needed for the database to work.
Important:
Although it contains DICOM files, this is not a “regular DICOM folder”; it is a database
I do not recommend manually editing the files inside this folder, to avoid messing up the structure and losing studies
4) Can I put the database in Dropbox?
In theory it works, but with risks:
If you keep everything synchronized and never open OsiriX on two computers at the same time using this same database, it can work.
If you open it on two Macs simultaneously, OsiriX changes the database in real time and one does not “understand” the other's changes, which can corrupt the database and cause data loss.
That is why I do not recommend this solution as a routine.
5) How to open this database on another computer
If you created a database on an external hard drive and want to use it on another Mac:
Connect the drive
Go to File → Open Database Folder
Select that database's OsiriX Data folder
Click Open
This creates the “link” to that database on the other computer.
It works very well for sharing a portable database between several computers, as long as it is not at the same time.
6) Essential tip: keep the same OsiriX version
If you use the same database on different computers:
Keep all OsiriX installations on the same version
A newer OsiriX may change the database in a way that the other (older) one cannot follow, which may cause loss of information/studies.5min
Remove a DatabaseIn this video I show a very quick tip: how to remove a database (created on an external hard drive, for example) from the Sources/image source list in OsiriX.
Many people try:
Right-click → no option appears
Delete key / Fn+Delete → doesn't work
The right way is through the preferences:
How to delete the database from Sources
Open Preferences
Go to Database
Go into Locations
Locate the database (e.g., Untitled, which is the external database that was created)
Select it and press Delete (the hint “Press delete to remove” appears)
Done: the database disappears from Sources and the problem is solved.1min
Separate Merged Studies (Merge)In this video I answer a common question: sometimes two studies/datasets end up merged in OsiriX (for example, a text report + an image, or two different studies that “become one”). This can happen when you select two items (usually with Shift) and use Merge.
To undo this merge and separate them again, the simplest solution is:
Right-click the study/patient (where everything ended up together)
Select Reindex Files
OsiriX rebuilds the index and separates the files/datasets correctly again
In the example, after Reindex Files, the items that were merged appear separately again, solving the problem.2min
Advanced Smart Album (SQL)In this lesson I show how to create a Smart Album in OsiriX using advanced criteria (SQL). Beyond the simple filters, the SQL criterion lets you create a condition: if the function is true, the patient/study automatically appears in the Smart Album.
1) How to create the Smart Album
In the Database window
Under Albums, right-click
Select Create Smart Album
2) Why use an advanced (SQL) criterion
A very practical use is separating patients by age.
To do that, we need to access fields from the study metadata (data about the data). In the video, I show two DataSheets with all the available fields and locate Date of Birth, which will be our criterion.
3) Example from the video: “Age” Smart Album
I name the Smart Album “age”
I define a criterion using Date of Birth
Applied example: Date of Birth > 01/01/1980
OsiriX creates the Smart Album and returns the filtered patients (in the example, it found 5 patients)
4) Editing the Smart Album
To edit, just double-click the Smart Album
I adjust the date to widen the filter:
01/01/1960 (increases the number of patients)
I also show another example with a date after 19504min
Smart Album with SQLIn this lesson I explain how to create a Smart Album in OsiriX using advanced (SQL) criteria — a very useful feature when the simple filters aren't enough. The practical example in the video is organizing the database by separating patients by age, using the date of birth (Date of Birth) found in the study metadata.
How to create a Smart Album (step by step)
Go to the database window
Under Albums, right-click
Select Create Smart Album
Simple criteria vs. advanced criteria
Smart Albums can be created with simple criteria (the default options in the window).
For more useful filters (such as age), we use an advanced criterion based on SQL.
The logic is: create a function/condition and, if it is true, the study/patient appears in the Smart Album.
Where to find the fields to use in the criterion
In the video I show two DataSheets with the available information (study metadata).
In them, you can locate the Date of Birth field, which can be used as a criterion.
Example from the video: Smart Album by age (via Date of Birth)
I create a Smart Album called “age”
I set the criterion to filter patients whose date of birth is later than a chosen date (example: 01/01/1980)
OsiriX creates the Smart Album and returns the patients that match the filter (in the example, 5 patients)
Editing and refining the Smart Album
To edit: double-click the Smart Album
I change the date to broaden the filter:
Example: adjust it to 01/01/1960 (increases the number of patients)
I also create/use another example with a date after 1950
If you have any questions, I'm available to help.4min
Fix a CT Scan with Stacked PhasesI'm Dr. Alexandre Amato, and in this lesson I show a very common problem when we receive exams from labs that don't save in the standard format: a study that looks normal in the axial view but, in 3D MPR, triggers an irregular-slices warning and distortion — because the lab placed two datasets “one on top of the other” within the same series.
In the example, when scrolling through the aorta exam, it looks normal. However, when opened in 3D MPR, a warning appears saying the slices are irregular, varying from ~1 mm to almost 500 mm, which can cause measurement errors and distortions. The cause becomes clear: there is an arterial phase (more contrast-enhanced) and, right below it, another less enhanced phase (probably venous/delayed) stacked in the same dataset.
How to fix it (step by step, as shown in the video)
1) Exit 3D MPR and go back to the axial dataset
Close the 3D MPR window and return to the exam's axial series (in the example, “Angio Aorta”).
2) Make a backup before changing anything
Before deleting anything:
I export the exam to the Desktop (DICOM), so there is no risk of losing the original study.
The idea is to edit the files safely, keeping an intact copy.
3) Find the “cut line” between the phases
In the axial image preview, I look for the last image that still has contrast (arterial phase).
In the video, you can spot the turning point because:
contrast is still visible up to a certain slice
suddenly more inferior images appear (e.g., hip/femur)
and the next image “goes back” to a superior region (e.g., lung)
This clearly indicates that the series “restarted” and contains two blocks (two datasets).
4) Delete the part you want to discard
I select all images from the cut point downward (the duplicated/unwanted block).
I press Delete and confirm the deletion.
In the example:
the dataset had 700-something images
after cleanup, it was left with 398 images
5) Reopen in 3D MPR and check the warning
When reconstructing again, the irregularity drops considerably (in the video, it now varies from 1 mm to 2 mm).
Result: you now have a single dataset, suitable for evaluating the patient without the distortions caused by the duplication.
6) How to recover the original exam (if needed)
I re-import the backup I exported to the Desktop.
This way, OsiriX has all the original images again, keeping your copy intact.
In the video, I also mention that there is another option (such as renaming the exam), but the main focus is the simple and safe method: backup → locate the cut → delete the duplicated block → reconstruct → re-import if needed.7min
3. 3D Reconstruction
3D Reconstruction: Volume RenderingIn this video I give an introduction to three-dimensional reconstructions in OsiriX, focusing on 3D Volume Rendering. It is a big topic (we will go deeper later), but here I show the basics so you can start using 3D in your daily practice: Crop to speed things up, Presets, brightness/contrast adjustment and how to remove bones from the volume.
1) Types of 3D reconstruction in OsiriX
In the gear icon menu, there are several three-dimensional reconstructions, such as:
3D MIP (Maximum Intensity Projection)
3D Volume Rendering (topic of this video)
3D Surface Rendering
3D Endoscopy
In Volume Rendering, OsiriX uses voxels (three-dimensional points) with density to generate the image and apply colors/transparencies according to a scale.
2) Opening 3D Volume Rendering
I open 3D Volume Rendering
To make it faster, I choose Clip (in the video)
3) Crop: the first thing to do for better performance
Often the whole exam is “too big” for what you need.
I use Crop to create a “box” around the volume and reduce the area of interest:
I shrink the cube (green dots) until only what matters is left
Result: less memory, faster graphics-card performance and smoother navigation
Then I remove the Crop and proceed with the final 3D image
4) Presets and brightness/contrast adjustment
In 3D Preset, I try a few of the presets, but the practical suggestion for vascular is:
Go into Soft Tissue
On the second page, use the vascular-oriented presets
My favorite here is Standard, very similar to what many labs deliver
After that, I adjust brightness/contrast to highlight the structures I want to see (arteries, skin, etc.).
5) How to remove bones in 3D (two ways)
A) “Skull” tool (automatic bone removal)
I click the skull icon and select a bone (e.g., a vertebra)
OsiriX tries to remove the bone automatically
Advanced adjustment:
Option + skull icon to configure the bone removal threshold/range
Common problem shown in the video:
Since bone density can be close to contrast density, it sometimes removes contrast-enhanced arteries as well
If the result is poor, I use Edit → Undo and try other values (it is trial and error)
B) Scissors (my preference)
I use the scissors tool to manually cut out the structures I do not want
I select the area and press Delete to erase it
Practical tips:
You have to “sculpt” from several angles (rotate the 3D and repeat)
If you delete something by mistake: Tab restores what was removed in that region/selection
In the end, you can make the image much “cleaner”, showing mainly the aorta and the vessels of interest.11min
Volume vs Surface RenderingIn this video I explain, in a practical and direct way, the difference between the two main types of 3D reconstruction in OsiriX:
3D Volume Rendering
Based on voxels/pixels (density)
Lets you adjust color, transparency, brightness/contrast and quickly visualize different "layers" (bone, vessels, soft tissue)
Ideal for analysis and dynamic evaluation of the image
3D Surface Rendering
Converts the volume into a vector/mathematical representation (surface)
Keeps good definition when zooming in and is better suited for export and use in other 3D software (e.g., OBJ)
Useful when you need a 3D model for external manipulation (e.g., planning/3D)
I also draw an analogy with Photoshop (pixel) vs Illustrator (vector) to make the concept easier to understand.13min
3D Surface vs Volume RenderingIn this lesson I explain the difference between the two main types of 3D reconstruction in OsiriX: 3D Volume Rendering and 3D Surface Rendering. Although both generate 3D images, the working principle, the type of result and the intended use are quite different.
1) Concept: pixels/voxels (Volume) vs vector (Surface)
Volume Rendering (voxel-based)
The CT scan generates a volume made up of "little dots":
pixels (2D) and voxels (3D)
Each voxel has characteristics such as density.
In Volume Rendering, OsiriX uses these voxels and lets you apply:
color
opacity/transparency
density-based adjustments
Result: a very "malleable" 3D image for evaluation, where you can progressively reveal layers (skin, subcutaneous tissue, veins, muscles, bones, etc.) just by adjusting transparency/contrast.
Surface Rendering (vector / mathematical image)
In Surface Rendering, OsiriX "transforms" the volume into a vector representation (a mathematical description).
You define a density threshold: OsiriX creates a surface based on that cutoff.
The result tends to be excellent for:
exporting
using in 3D software
modeling / 3D printing
And an important characteristic shown in the video: when you zoom in, the surface does not depend on pixels like Volume Rendering does — it is drawn by mathematical lines/shapes.
2) Example in OsiriX: Volume Rendering
I use a simple lower-limb case just to demonstrate the principle.
I open 3D Volume Rendering
I crop to reduce the block
I show the impact of changing contrast/transparency:
less dense structures become transparent first
progressively revealing deeper layers
This is the great strength of Volume Rendering: exploring and evaluating the volume with quick adjustments.
3) Example in OsiriX: Surface Rendering
I open 3D Surface Rendering
I choose to use just one surface (more didactic)
I define a density cutoff point (threshold)
In the example, with this threshold it extracts the bones (the denser structures) well
Comment from the video: you can adjust the settings to get more "perfect" surfaces, depending on the goal.
4) Analogy with Photoshop and Illustrator (to understand the difference)
In the video I make a comparison:
Photoshop: image made of pixels
if you zoom in a lot, you start to see the "little squares/dots"
you can adjust brightness/contrast with great flexibility
Illustrator: vector image
you "trace" the image and it becomes mathematical lines/shapes
when you zoom in, you don't see pixels — you see mathematically defined curves/lines
This logic is similar to:
Volume Rendering ↔ "pixel/voxel" (more malleable for visualization)
Surface Rendering ↔ "vector" (better for exporting and working in external 3D software)
5) When to use each one (as in the video)
Volume Rendering
Best for evaluation and dynamic manipulation of the image:
adjusting contrast/opacity
quickly exploring different structures
Surface Rendering
Best when you need a "mathematical" 3D object for:
exporting
editing in 3D software
applications such as modeling (e.g., prosthesis / planning) and external manipulation
6) Exporting the Surface (OBJ) and opening it in 3D software
At the end I show:
Exporting the Surface in a common format (e.g., OBJ)
Opening that file in a (non-medical) 3D application to demonstrate that:
you can apply colors
edit
manipulate the mesh and create different effects/visualizations
The goal is to make the difference between the two 3D reconstruction modes in OsiriX clear.13min
Why Exporting Doesn't Save 3D EditingIn this lesson I explain a point that seems simple but causes a lot of confusion in OsiriX: how to save the “editing” (sculpting/cropping) work done on a 3D Volume Rendering so that you can keep editing it later.
The example is a CT angiography of a patient with a stent graft. I create a 3D Volume Rendering, apply a vascular preset and start “skeletonizing” the image by removing surrounding structures (bone and unwanted vessels) using the scissors and the Delete key. I also show that, if you make a wrong cut, you can cancel it with ESC.
The big point: “exporting” is not the same as “saving to keep editing”
In OsiriX there are several ways to export what you are seeing, but most of them do not preserve the ability to keep editing later.
What does NOT work for continued editing
If you are in 3D (Volume Rendering) and do:
File → Export to Movie
✅ good for lectures/presentations
❌ it becomes just a video rotating the scene
Export JPEG / Export TIFF
✅ produces an image of what is on screen
❌ you cannot go back and edit the cuts
Export to DICOM Files (from the 3D)
❌ here is a common trap: OsiriX may generate an animated series (like a “movie” in DICOM), meaning you get a rotation of the image but keep neither the tools nor the editing for further work
In the video, I show this: when I export directly from the 3D, the result opens as an object you can rotate, but you cannot keep cutting, because the tools (scissors, etc.) are no longer there.
The right way to save the “edited 3D” to continue later
What really stores your work (the cuts) is the original dataset (the axial slices) — because the cuts you make in the VR are also reflected as changes in the axial series.
How to do it (step by step)
Do your editing in the 3D Volume Rendering (scissors + Delete)
Go to Window and open/look at the axial image of the study
You will see that the cuts appeared in the axial slices
Now, in the axial series, do: File → Export → DICOM Files
Export the entire series (from start to end) and give it a name (in the video: “3d volume lapidado”, i.e., “edited 3D volume”)
Result
When you open this newly exported series (“3d volume lapidado”, the edited 3D volume), all the cuts are still there
Then you can:
Create a new Volume Rendering from this already-edited series
Apply the preset again (e.g., “standard”/vascular)
And keep editing (cut more bone, adjust details, zoom in, etc.)
Practical tips mentioned in the video
To edit better: look for different angles, including “unusual” angles that make it easier to remove structures.
For fine details: zoom in/magnify to reach more delicate areas.
In the end, you get a skeletonized aorta/stent graft with minimal bone interference, ready for high-quality viewing.11min
Fly-Through: 3D CameraIn this lesson I show how to do a fly-through in OsiriX, a 3D reconstruction in which you create a path (trajectory) and the camera travels along it, generating an excellent video for presentations.
The example is an interesting case of lower-limb leiomyosarcoma originating in the muscular layer of the vein (venous leiomyosarcoma). In the study there are multiple lesions along the path, and I want to guide the viewer through the main areas — including regions in the middle of the path and a relationship/continuity close to the posterior tibial artery.
1) Opening Fly-through and adjusting the view
I locate the Fly-through icon and open the tool
I select GPU mode (using the graphics card)
I adjust brightness and contrast to visualize:
a bit of the muscle
and the venous lesions with better definition
2) Creating the “steps” (camera points)
With the fly-through window open, I start creating the key images (keyframes):
I set the initial image as the first step
I rotate the volume a little and adjust the zoom to focus on the first lesion → I add the 2nd step
I create a 3rd step to highlight another lesion
At this point, I adjust brightness/contrast to improve the view
I move further down and rotate a bit to show the intermediate lesions → more steps
I create a final image, for a total of 6 images/points along the path
These points work as “landmarks” the camera will pass through in the video.
3) Generating the video (frames and spline)
Once the steps are defined:
I choose 300 frames
I enable Spline, so the camera makes a smoother transition (a more natural curve)
I click to compute the images
Preview (Play)
The Play button lets you see how the movement will look
Not necessarily in real time, because it is computing frame by frame
4) Exporting to video (QuickTime)
I choose to export to QuickTime
I select the best-quality option
I save the file and OsiriX exports the fly-through, navigating the 3D according to the steps created
5) Tip on smoothness: frames per second
In the video I explain:
For a sense of motion, we think of ~24 frames per second
300 frames gives roughly 10 seconds of smooth video (in principle)
If the result feels “slower” (with the impression of pauses), you can speed the video up a bit on playback to make it more natural6min
4. MPR and Centerline
Centerline (3D Curved MPR)In this lesson I give an introduction to the Centerline in OsiriX, using 3D Curved MPR to measure the length/extent of the iliac artery in a case of iliac aneurysm.
The goal is to show the basics: how to draw a manual centerline (more precise than the automatic one), how to check that it is really in the center of the vessel, and how to use the Stretched and Straightened modes to measure distance.
1) Opening 3D Curved MPR
I select the arterial dataset (more images and denser contrast)
I open it via: gear icon → 3D Curved MPR
3D Curved MPR uses:
3 windows from 3D MPR (axial, coronal, sagittal)
and a 4th window (Curved) where the path appears
I adjust the windowing for vascular using Bone
Tip from the video: it is better to understand 3D MPR well before 3D Curved, so you don't get confused with the planes.
2) Creating the manual Centerline (points in the center of the vessel)
I zoom in to work with a larger image
I press the space bar to get the axes out of the way
I select the centerline path tool
I click and place points in the center of the vessel along its course
After 3 points, the 4th window already starts reconstructing the Curved view
I keep going down and marking:
aorta → common iliac → external iliac (main path)
3) Identifying branches and checking position (green dot + MIP)
When hovering the mouse over the Curved window, a green dot in the other windows shows where you are in the vessel
I use MIP (Maximum Intensity Projection) to increase the slice thickness and see the anatomy better
This makes it clear where the internal iliac origin is and where the vessel continues into the external iliac
I also rotate the image to confirm by the anatomy
4) Stretched vs Straightened (and centerline correction)
Stretched: shows the curved vessel with the centerline, useful for correcting small imperfections
I rotate to check that the green line is always in the center of the vessel
Straightened: “straightens out” the vessel, making it easier to read and to measure in a straight line
5) Perpendicular slices (A, B, C) and what they mean
The A, B and C markers correspond to the three side windows
In Stretched mode, the slices can “cross” because of the curvature
In Straightened, everything is aligned and easier to position
These slices are always perpendicular to the green line (centerline)
6) Measuring the iliac length (extent)
In Straightened, I use the straight ruler
I measure from the chosen point (e.g., bifurcation) to the point in the internal/external iliac, depending on the goal
In the example:
the measurement along a “straighter” line was 5.18 cm
when the curvature is taken into account, the measurement can change (e.g., 5.7 cm)
Final message of the video:
Centerline is especially useful for measuring distance/length (extent)
The perpendicular slices can be used for diameter measurements11min
Overlay to Measure AnglesIn this video I answer a question about how to measure angles using image "overlay" in OsiriX, with a knee example (orthopedics). I test overlay methods (such as MIP and mean, adjusting the slice thickness), but explain why this can blur the image and make analysis harder.
The most practical and precise solution in OsiriX, in most cases, is not to rely on overlay — but rather to measure the angle across different slices, keeping the same ROI while navigating between images.
Overlay attempt (and limitations)
Enable overlay and use:
MIP (Maximum Intensity Projection): sums intensities over a greater thickness → can become very blurred
Mean: sometimes helps, but can still lose sharpness depending on the case
These methods overlay several images, which is not always ideal for measuring an angle precisely.
The method that solves it: persistent ROI across slices (Shift key)
Select the Angle tool (angle ruler)
Hold down the Shift key on the keyboard
While keeping Shift pressed, draw the angle
Now you can change the slice/image and continue the measurement (the ROI "persists")
Finish the angle on the desired slice — with more control and no need for "transparency"
This tip is useful not only for orthopedics, but also for many measurements in other areas (including vascular), whenever you need to "complete" a measurement using different slices.5min
Synchronization: Pre- vs Post-OperativeIn this lesson I show how to synchronize images in OsiriX to compare two studies side by side, such as a preoperative and a postoperative study (example: abdominal aortic/iliac aneurysm). The idea is to open both series (usually the arterial phase) and synchronize the slices using an anatomical reference point (such as the celiac trunk).
1) Method 1: open two datasets in the 2D Viewer (selection with Command)
In the database, expand the studies/datasets (small arrow/triangle next to them)
Select the preoperative arterial dataset
Hold Command and select the postoperative arterial dataset
Open them in the 2D Viewer so that two windows appear at the same time
At this point, they are not yet synchronized: moving one does not move the other.
To synchronize:
Find the same point in both studies (in the video, I use the celiac trunk)
With both studies at the same level, click the synchronization button (Sync)
Done: when you scroll through one study, the other follows automatically.
2) Method 2: open one study and then open the other (Window → Database)
Open the first study (double-click)
Go to Window → Database to return to the database
Open the second study (double-click) — it opens next to the first one
Repeat the same process:
Align by an anatomical landmark (e.g., celiac trunk)
Click Sync
3) Important note
When you open two datasets within the same study (e.g., non-contrast and arterial), they often come already synchronized automatically, because the CT scanner itself organizes the series as synchronized within the study.6min
Measurement Layers (Overlays)In this video I show a simple and very useful tip in OsiriX: besides the traditional rulers and measurements, you can build a publication-ready image using annotation layers (overlays).
The idea is to import/use PNG images with a transparent background (for example, an arrow) and position them over the axial slice. This way, you can:
insert arrows, icons or markers anywhere in the image,
adjust size and position freely,
choose images of any color/style,
and save/export the image with these annotations already in place, ready for a class, article or report.
Practical tip: PNG is better than JPEG for this purpose because it allows a transparent background, leaving the marker "floating" over the image without a white square behind it.2min
5. Measurements and Tools
How to Measure Vessels: Straight vs Curved RulerIn this lesson, I show in detail two essential measurement tools in OsiriX: the straight ruler and the curved ruler (Open Polygon) — widely used in daily practice, especially in vascular assessments in MPR.
Where to find the tools
In the toolbar, select the straight ruler.
Click the small down arrow to see other ruler options.
The curved ruler appears as Open Polygon.
Straight ruler: linear measurement and reliable diameter
Click and drag to make a linear measurement (in cm).
For reliable vascular measurements, ideally measure in a plane perpendicular to the vessel (not just the axial plane).
In the example (iliac artery aneurysm), the step-by-step is:
Adjust the slice in the planes (e.g., the purple plane) so it is transverse to the vessel in the different windows.
Confirm the “perfect circle” (a truly perpendicular slice).
Use bone windowing to better identify calcium and the lumen.
Hide the axes/pointers with the space bar and then measure with the straight ruler.
Curved ruler (Open Polygon): length measurement
Excellent for measuring length/extent along the course of the vessel.
I adjust the MIP to better visualize the iliac artery and the aneurysm, zoom in, and adjust brightness/contrast.
To create the curved ruler:
Keep clicking and placing points farther apart from each other to accommodate the curvature.
Click the last point to finish.
Fine-tuning:
You can click any point and reposition it to fit the anatomy.
Note: if you place points too close together, the software may “ignore” the curve, compromising the measurement. Prefer more widely spaced points, according to the anatomy.
How to delete rulers and points
Delete a ruler: select the ruler and press Delete.
Delete everything on screen: Command + Delete.
Remove a point from the curved ruler:
If it is the last point, press Delete.
To delete a point in the middle: click/hold the desired point and press Delete.7min
Measuring in Photos: Import and RecalibrateIn this lesson I show how to take measurements on photos (JPEG/BMP, etc.) inside OsiriX and how to recalibrate the scale so that measurements stop appearing in pixels and start appearing in centimeters — letting you measure distances, dimensions and even area (cm²).
1) Enable image import (not just DICOM)
By default, OsiriX is configured to import DICOM only.
To import photos:
Go to Preferences
Open the Database section
Uncheck the “Import DICOM File Format Only” option
OsiriX will then also accept image files.
2) Import the photo into the database
Go to File → Import Files
Select the photo and import it
In the video example, I import two photos and open the one that contains a ruler/scale.
3) Why it shows “pixels” and how to fix it
If you use the ruler on a photo with no DICOM scale, OsiriX shows the measurement in pixels (the “dots” of the image).
That doesn’t help when you need, for example, to calculate:
size in centimeters
dimensions of a lesion
area in cm²
4) Recalibrate: teach OsiriX what 1 cm is
The process is:
Select the straight ruler
Measure a known segment (in the video, 1 cm on the ruler printed in the photo itself)
In the example, OsiriX shows that 141 pixels = 1 cm
Double-click the measurement and choose Recalibrate
Set Distance in centimeters = 1 (equivalent to 10 mm)
From that moment on, all rulers return measurements in cm, not in pixels.
5) Measure distance and dimensions
After recalibrating:
the ruler now shows measurements such as 13 cm
you can measure a lesion/ulcer as 2 cm x 1.5 cm, for example
6) Measure area with the brush (cm²)
To calculate the area:
Select the brush tool
Adjust the thickness (in the video, I increase it to 20)
“Paint” the ulcer/lesion
OsiriX returns the exact area in cm² (in the example: 3.8 cm²)
7) When this is useful
This recalibration can be applied to any imported image (JPEG, BMP, etc.), especially when a lab delivers non-DICOM images.
You can use a known reference to calibrate:
a ruler in the photo itself
a body measurement (e.g., “nipple to nipple”)
a measurement you take on the patient and enter into OsiriX5min
Measure Ulcer Area from a PhotoIn this video I show, at the request of Professor Eliud, how to assess an ulcer from a photograph using OsiriX (the same logic applies to Horos). The idea is to turn a photo (JPEG) into a calibrated image so you can measure area in cm² and track the wound's progress over time.
1) Enable JPEG import in OsiriX
By default, OsiriX usually allows only DICOM. To import a photo:
Go to Preferences
Open Database
Uncheck: Import only DICOM files
⚠️ Note: “JPEG” appears in several places in the preferences (including settings related to DICOM compression). The correct setting is in Database, in the option to import only DICOM files.
2) Import the photo
Drag the photo into the database or use the import files option
Double-click to open the image
3) Calibrate: tell OsiriX what 1 cm corresponds to
Since the photo is not DICOM, OsiriX measures in pixels (e.g., 105 pixels).
To convert to centimeters:
Use the straight ruler (Length) and measure 1 cm on the photo's reference (a ruler)
Right-click the measurement
Select Recalibrate resolution
Enter that this distance corresponds to 1 cm
After that, all measurements come out in cm instead of pixels.
(If needed, you can zoom in to calibrate more precisely and recalibrate again.)
4) Measure the ulcer area (cm²)
You can measure area in several ways. In the video I show two:
A) Closed Polygon
Place points around the ulcer
On the last point, double-click to close
OsiriX returns the area (e.g., ~10 cm² in the example)
B) Brush
Adjust the brush size
“Paint” the ulcer area
Double-click to finish and get the area (e.g., ~9.7 cm² in the example)
5) What this is for
With the same technique, you can assess several photos over time and compare whether the wound is improving or getting worse.
6) Calibration references (besides a ruler)
If the photo has no ruler, you can calibrate using an object of known size, for example:
a coin (knowing its diameter)
a credit card (standard size)
⚠️ Be careful with syringes: the mL markings do not always correspond to centimeters — keep an identical syringe next to the wound to confirm the real measurement.8min
Surface Length PluginIn this quick lesson, we introduce the Surface Length plugin for OsiriX, a tool developed for measuring length along surfaces in 3D reconstructions. See an overview of the plugin and how it complements OsiriX's measurement tools in your workflow.
The plugin is free and available on the author's software site, software.amato.com.br.1min
Surface Length 3DGet to know the Surface Length 3D plugin for OsiriX, a tool developed to measure lengths along surfaces in 3D reconstructions. In this short lesson, I show how the plugin works in practice and how it complements OsiriX's native measurement tools.
The plugin is free and available on the author's software site, software.amato.com.br.3min
6. Segmentation
Automatic Aorta SegmentationIn this lesson I show how to do automatic segmentation of the aorta (and other structures) in OsiriX, to turn a “cluttered” dataset into a clean image, ready for really nice 3D reconstructions (Volume Rendering).
The logic of the method is:
Select a point with good contrast and create an ROI that grows in 3D (up and down through the series)
Edit the ROI (close holes and dilate) to improve the selection
Turn everything outside the ROI into negative density (like air), making the 3D easier
Generate the 3D Volume Rendering and finish by removing whatever is left (scissors + Delete)
1) Create the 3D segmentation of the aorta (Grow Region)
I set a vascular windowing
I zoom in on a point where the aorta is well opacified
I go to ROI → Grow Region 2D/3D Segmentation
I choose 3D Grow Region
Adjusting the range (HU)
OsiriX selects a range in HU above/below the clicked point
I test smaller and larger values to understand the effect
In the example, 150 works well to select the aorta and branches with slightly lower density
Then I compute the selection and check, navigating up/down, that the following were included:
celiac trunk
superior mesenteric
renal arteries
2) Refine the ROI: close holes and dilate
Since holes appear inside the selection:
ROI → Brush → Closing
I close holes of size ≤ 4 voxels
So it is not limited to the lumen:
ROI → Brush → Dilatation
I dilate by 2 voxels to include a bit beyond the contrast (adventitia)
3) Paint everything outside the ROI with negative density
ROI → Set Pixel Value
I select Outside ROIs
I apply a negative value (in the video: -2048; it could be -1024)
This way, everything outside the aorta becomes “air”, which makes the 3D much simpler to build.
(In the example it is a large study, with ~2600 images, so the computation may take a while.)
4) Generate the 3D and deal with a large study (Clip vs Resample)
I go to 3D Volume Rendering
Since the dataset is large, a behavior related to the dynamic range appears
I show that you can:
Resample (compress the variation)
or Clip (cut the extremes) — I choose Clip because it is faster
Result: a segmented aorta with clearly visible branches and a “clean” 3D image to work with.
5) Quick finishing: scissors + Delete
If there is still something left:
vertebrae/pelvis
heart (it can pick up contrast too)
I finish with:
scissors tool in the 3D view
select and press Delete
It is a quick post-processing step and the result is quite impressive.9min
Aorta Segmentation v2In this lesson I demonstrate an automatic workflow for segmenting the aorta (and vascular structures) in OsiriX, to turn a “cluttered” dataset (with bones, organs and other structures) into a clean image, ideal for really nice 3D reconstructions (Volume Rendering).
The idea is: select the contrast-filled aorta, expand that selection in 3D, fix the ROI (close holes and dilate) and then paint everything outside the ROI with negative density (like air). With that, the 3D becomes much easier to generate and to “sculpt”.
Method overview
Select the contrast-filled aorta using a 2D ROI
Expand to 3D (up and down through the series) with Grow Region 3D
Edit the ROI:
Closing to close holes
Dilatation to include a bit beyond the lumen (adventitia)
Set Pixel Value (Outside ROI) to put negative density outside the selection
Generate the 3D Volume Rendering and finish with quick cuts (scissors + Delete)
Step by step (as in the video)
1) Prepare the view
I'm on the axial image
I adjust a vascular windowing (brightness/contrast) to make the selection easier
2) Create the automatic segmentation with an ROI
I zoom in on a region where the aorta has good density (well opacified)
I go to ROI → Grow Region 2D/3D Segmentation
I choose 3D Grow Region (not the 2D one)
Adjusting the range (HU)
OsiriX selects based on a range (e.g., X HU units above and below the clicked point)
I demonstrate by testing smaller values (e.g., 30) and larger ones
In the example, 150 worked well to also capture branches with slightly lower density
Then I have OsiriX compute the 3D selection and I can navigate up/down checking:
celiac trunk
superior mesenteric
renal arteries
selected along with the aorta.
3) Fix ROI defects (holes) and refine the selection
Since “holes” appear inside the selection:
I go to ROI → Brush → Closing
I close holes of size ≤ 4 voxels
Then, so as not to stay only in the lumen:
I go to ROI → Brush → Dilatation
I dilate by 2 voxels (in the example) to “fatten” the selection a bit
4) Paint everything outside the ROI with negative density
Now comes the trick to “clean” the dataset:
In ROI → Set Pixel Value
I choose:
Outside ROIs
A negative value (e.g., -2048; -1024 would work too)
This way, everything outside the ROI becomes “air” (negative density), making the 3D easier
In the video I mention that the exam is large (about 2,600 images), so this calculation may take a while.
5) Generate the 3D and handle the “dynamic range” (large exam)
After processing, I remove/hide the ROI to view the “clean” result
I go to 3D Volume Rendering
Since the exam is very large, a situation comes up where the scope/dynamic range becomes excessive
I show two options:
Resample (compresses the variation)
Clip (cuts the extremes) — I choose Clip because it's faster for the computer
Result: a segmented aorta with clearly visible branches and a much more “workable” 3D.
Quick finishing (post-processing)
Even with automatic segmentation, some things may remain:
a bit of heart (due to contrast)
vertebrae / pelvis
Then I use:
Scissors in the 3D
select and press Delete
Making cuts from different angles, you can “sculpt” quickly and reach a very clean result.9min
Airway SegmentationIn this video I show how to segment the airway from an MRI scan using OsiriX. The principle is similar to aortic segmentation, but “inverted”: instead of looking for a highly contrasted region, we look for a region with no density (air).
Note: in MRI, the study often has few images (e.g., 32), which reduces the quality of the 3D. Even so, it is still possible to segment and obtain a useful model.
Step by step (video workflow)
1) Select the “air” with Grow Region
Open the study
Go to ROI → Grow Region
Click on an area of air and run Compute to select forward and backward
If the selection comes out too large, I delete it and adjust:
Delete All ROIs
Reduce the selection range to better capture the low-density area
In the video, I use values such as 20 and then 30 to improve the selection
Compute again
2) Fix the small “holes” (Closing)
After selecting the air, internal gaps usually appear:
ROI → Brush ROIs → Closing
Adjust the radius (in the video, I used 8 as a reference)
This closes the holes and improves the airway outline.
3) Paint what is outside the ROI (negative value)
To “clean up” the dataset:
Select the option to apply to the ROIs
Paint Outside ROIs with a negative value (it turns “black”, like air)
Result: what is not of interest is visually “removed”.
4) Give high density to what is inside the ROI (positive value)
Now I reinforce the airway as a solid structure:
Paint Inside ROI with a high positive value (in the video: 1000)
This makes the airway stand out clearly for the 3D.
5) Generate the 3D and remove the external air
Open 3D Volume Rendering
The 3D model appears (airway + external air)
Use the scissors to erase what is external to the patient (air outside the head)
Select → Delete
You can rotate the 3D to check what is being cut
Only the airway remains in 3D.
How to calculate the airway volume (ROI Volume)
Go back to the image window (sagittal/axial)
Delete All ROIs to view only the “densified” airway
Re-select with ROI → Grow Region → Compute (now it is fast because everything has uniform density)
Go to ROI → ROI Volume and calculate
In the example in the video, the calculated volume was 55 cm³.6min
Bone Removal (“Skull” Tool)In OsiriX 7.0 (64-bit), the bone removal tool (the “skull” tool) is still available and can be adjusted and customized in the toolbar:
Adjusting bone removal
Option + click on the skull tool opens its settings.
You can raise/lower the threshold (density) for removal:
“higher” values → tend to pick up only the denser structures
“lower” values → remove more (higher risk of “eating” contrast-enhanced vessels)
Using the tool
After adjusting, click the skull tool and apply it to the image to remove bone according to the chosen threshold.
Adding or removing the skull tool from the toolbar
Right-click an empty area of the toolbar → Customize Toolbar.
Drag the skull tool in to include it, or drag it out to remove it.
That way you keep the toolbar with only what you use day to day.1min
7. Vascular Surgery
Complete Endovascular PlanningIn this presentation, Dr. Daniel Benitti discusses the importance of planning in vascular surgery, especially in endovascular aortic procedures, and how OsiriX becomes a central tool for precise diameter and length measurements, reducing improvisation and avoiding sizing errors (insufficient or excessive oversizing, with risk of endoleak and other complications).
The video also includes a discussion of how the axial slice can be misleading when it is not perpendicular to the vessel, producing elliptical images and incorrect measurements. The approach is to control the axes with multiplanar reconstructions (3D MPR) to obtain the true cross-section (the “perfect circle”) and, to measure length, to use the MIP technique (increasing the slice thickness) after aligning the vessel axis.
Main topics covered
Why axial measurements can be wrong when the vessel is cut obliquely
Relationship between incorrect measurement and oversizing error (undersizing vs. oversizing)
3D MPR: creating the “vessel plane” (without relying on fixed axial/coronal/sagittal views)
Aortic length: limitations of measuring “in a straight line” and why MIP helps in practice
Discussion of Centerline and differences between measurements and intraoperative reality
Importance of reducing contrast and radiation through detailed prior planning
Demonstration/concept of identifying the artery of Adamkiewicz in OsiriX for thoracic planning
Practical experience reported: use of small contrast volumes and a planning-guided procedure workflow
Present and future of OsiriX: improvements in 3D Curved MPR, virtual angioscopy, the possibility of digital subtraction from CT angiography, and examples of motion control (Kinect) discussed in the presentation
Questions and answers: application to the venous system (e.g., Nutcracker/Cockett), limitations in fistulas, the role of planning in secondary procedures, why the Mac platform, FDA-approved versions, OsiriX Pro, TeraRecon, and comments on not replacing planning with physical examination47min
EVAR PlanningIn this lesson from the Vascular Surgery module, we present an overview of EVAR planning (endovascular treatment of aortic aneurysm) using OsiriX/Horos. See how the DICOM viewer can assist in evaluating the CT angiography for endovascular planning.5min
C-Arm PlanningIn this lesson I demonstrate how to use OsiriX to plan the C-arm angles for the intraoperative setting, using the preoperative CT scan. The goal is to find the best angle to open up structures such as the iliac bifurcation (internal vs external iliac) and, when necessary, also adjust the angle to visualize the renal arteries.
1) Tool used: 3D Volume Rendering
To calculate angles, I use 3D Volume Rendering.
I adjust the volume (crop/resolution) to use less memory when necessary.
The initial image corresponds to the anteroposterior (AP) view, like the standard angiography view on the C-arm, with the typical overlaps (e.g., internal iliac over the external iliac).
2) Finding the best angle for the iliac arteries
I rotate the volume until the bifurcation “opens up” and the internal iliac is clearly separated from the external iliac.
In the video example:
Right iliac bifurcation: best visualization at about +38° (range ~35–40°)
Left iliac bifurcation: best visualization at about −43°
Key point: OsiriX shows the angle in the lower corner (values in degrees).
Pay attention to the equipment's reference: on the C-arm, the AP position is usually 0°. In OsiriX, it is important to understand this so you don't confuse it with other references (e.g., reset view).
3) Additional adjustment (obliquity + cranial/caudal)
Besides the right/left oblique, sometimes you need to tilt the C-arm cranially/caudally to better “separate” the structures. In the example, I show a case in which:
the oblique is around −50°
and the superior/inferior angle is around −36°
4) Standardizing the terms with SI and LR (as OsiriX displays them)
To avoid confusion between teams and hospitals, I standardize the terms the way OsiriX presents them:
Standard AP position: SI = 0° (superior/inferior, craniocaudal) and LR = 0° (left/right, oblique)
Cranial oblique: SI greater than 0°
Caudal oblique: SI less than 0°
Right oblique: LR less than 0°
Left oblique: LR greater than 0°
In other words: you position the volume in OsiriX the way you want to see it on the C-arm, note the SI and LR values, and take those values into the operating room.9min
Carotid Stenosis on CT AngiographyIn this lesson I demonstrate how to evaluate the carotid arteries on CT angiography using OsiriX, from the overview in 3D Volume Rendering to measuring the stenosis on the proper slice, comparing the NASCET and ECST methods. The main case shows an occlusion of the right internal carotid artery and a stenosis of the left internal carotid artery, with well-developed compensatory vertebral arteries. At the end, I show a second case with a glomus tumor to illustrate how 3D helps in diagnosis and planning.
1) 3D overview (before measuring)
I scroll through the axial images to identify the aortic arch and the supra-aortic trunks
I open 3D Volume Rendering and apply a vascular preset (e.g., Soft Tissue / Standard)
In 3D it is already evident:
Occlusion of the right internal carotid artery
Stenosis of the left internal carotid artery
Compensatory vertebral artery (with a larger caliber to supply the circulation)
I also demonstrate the use of Crop to isolate the intracranial circulation and better visualize the vessels.
2) Confirming the occlusion (MPR)
On the right side, in MPR:
I rotate the axes and show that no internal carotid artery appears at any angle at the expected point of the bifurcation
Practical confirmation of occlusion.
3) Finding the ideal slice of the stenosis (contralateral side)
To measure the stenosis correctly:
I zoom in
I scroll up/down to the bifurcation
I rotate to get the best view of the plaque (calcium + contrast-enhanced lumen)
I adjust brightness/contrast to differentiate:
contrast
calcium
vessel wall (estimated)
4) Two ways to measure: NASCET and ECST (with a numerical example)
I show the two classic methods:
NASCET
Uses the diameter distal to the lesion (“normal” internal carotid artery beyond the plaque)
Compares it with the diameter at the point of stenosis
ECST
Uses the estimated diameter of the bulb/vessel at the site of the lesion
Compares it with the diameter at the point of stenosis
In the video example:
Distal diameter (NASCET): 5 mm
Estimated diameter at the site (ECST): 8 mm
Diameter at the point of stenosis: ~1–1.2 mm (I show the measurements on screen)
Applying the formulas:
NASCET ≈ 76%
ECST ≈ 85%
Important: there is a relevant difference between the methods, because the “reference diameter” is different.
5) Warning: do not use MIP to measure carotid stenosis
I reinforce a warning:
MIP may make the image look nice, but it can underestimate the stenosis if there is a thin “thread” of contrast passing beside the plaque, or overlapping structures that misrepresent the true lumen.
To measure stenosis, avoid MIP.
6) Practical uses for planning (open and endovascular)
With 3D and the correct slice, you can:
Estimate the height of the lesion relative to the mandible (access planning for open surgery)
Assess whether the carotid is straight enough to accommodate a filter (endovascular)
“Clean up” the field with the scissors to better see the supra-aortic arch and anticipate how easy catheterization will be
7) Additional case: glomus tumor
I show a second case where:
3D reveals a large glomus tumor
On the axial view, the tumor appears to involve the internal and external carotid arteries (characteristic of a difficult surgical case)
I also briefly explain the choice between Resample and Clip when the software warns about dynamic range/gray levels:
Resample: “compresses” values to fit the scale (heavier)
Clip: cuts off the extremes (faster)16min
3D Cerebral AngiographyIn this video I show how to perform a cerebral angiography in OsiriX from a study with a well-opacified arterial phase. The case is a female patient with subclavian steal syndrome (visible in the reconstruction), but the focus of the lesson is visualizing the intracranial vessels and identifying a saccular aneurysm.
1) Choose the best dataset
I select the arterial-phase dataset with the largest number of images (in the example: 477)
Scrolling through the slices, I confirm that the cerebral vessels are well opacified
2) Open 3D Volume Rendering
I go into 3D Volume Rendering
I start with the three-dimensional reconstruction and adjust the viewing angle
3) “Clean up” the 3D to focus on what matters (Crop)
To work faster and use less memory:
I go into Crop and adjust the box (green dots)
I cut away everything that is not of interest (sides, bottom and areas with no information)
I make a cut to remove part of the skull so I can see “inside the head”
This makes the computer lighter and faster when manipulating the 3D.
4) Improve quality and performance: CPU vs GPU
To improve the 3D image:
I switch the engine to GPU (Graphics Card)
The GPU offloads processing to the graphics card, which is more efficient for 3D calculations, making the reconstruction smoother and, in many cases, of better quality than on the CPU.
5) Evaluate the intracranial vessels and find the aneurysm
With the crop done:
I zoom in
I adjust the angle
I evaluate the circle of Willis (in this case, it is not complete)
I identify a saccular aneurysm in the M2 segment
I can use the ruler to measure, if needed
6) Alternative to Crop: “trepanation” with the scissors
Instead of Crop, you can also:
Use the scissors to remove part of the skull cap (“trepanation” in 3D)
This lets you see the aneurysm through the opening
Caution: you need to be careful not to cut vessels you want to analyze.
In the video I demonstrate both approaches (Crop and scissors) to reach the same goal: clearly seeing the intracranial vessels and the aneurysm in 3D.8min
8. Image and Export
Digital Subtraction Angiography (DSA)In this lesson I show how to perform digital subtraction angiography (DSA) in OsiriX when the angiogram was saved to DICOM as a “raw” (unsubtracted) image, even if it already appeared subtracted on the machine.
1) Converting the raw angiogram into digital subtraction
Open the study in the 2D Viewer
Select Subtract
Done: OsiriX generates the digitally subtracted image.
In the video I demonstrate this with two examples:
an angiographic study saved without subtraction
a fibroid embolization, where subtraction greatly improves visualization
2) Creating a static image with the sum of the images
Another useful technique is to add up all the images to obtain a single “consolidated” image of the contrast.
The key point is choosing the correct projection:
MinIP (Minimum Intensity Projection): ideal when the contrast appears darker/inverted — this way the contrast-filled structures accumulate in the sum.
MIP (Maximum Intensity Projection): in this case it can “erase”/degrade the contrast, because it favors the highest values.
Result: you end up with a static image with the sum of the digital subtraction frames.3min
Export 3D Model for PrintingIn this step-by-step tutorial I show how to turn a study (DICOM) into a 3D model that can be exported for 3D printing, using OsiriX.
Open the study and generate the 3D reconstruction (Volume Rendering)
Open the skull dataset.
Adjust the preset to highlight bone (e.g., Bone/Standard) until the skull is clearly visible.
“Clean up” the volume (remove tissues that are not of interest)
Use the Scissors tool to erase soft tissue and unwanted structures.
Optional: use the automatic bone removal tool, but here the method is manual.
Adjust/trim artifacts (e.g., spicules from the prosthesis) to reduce imperfections.
Confirm that the cut affected the dataset
Exit the 3D window and check that the axial slices now have those regions removed (this ensures the “sculpted dataset” is ready).
Generate the vector model (3D Surface Rendering)
Open 3D Surface Rendering.
For printing, use 1 surface (single surface) and set a threshold suitable for bone.
Generate the surface model of the skull.
Export to printing/editing formats
Export as:
STL (most common for 3D printers)
OBJ (very useful for editing/alternative workflows)
Important note: STL almost always needs processing before printing (closing holes, removing noise, fixing the mesh, etc.).
Open in 3D editing software
Import the STL/OBJ into an editor (e.g., Meshmixer, Blender, 3D Builder, etc.).
From there you can:
Fix artifacts and “spicules”
Close holes
Smooth the mesh
Reduce the polygon count
Prepare for slicing (slicer)5min
Convert DICOM to VTIIn this tutorial I show how to run Linux inside a Mac via a virtual machine (preferably Parallels Desktop, but VirtualBox also works) to convert a DICOM dataset exported from OsiriX into a .vti file (VTK ImageData), useful for example in SimVascular.
Step-by-step workflow:
Create the virtual machine and install Ubuntu
In Parallels: “+” button → choose Ubuntu → download (~2 GB) → install.
(Alternative: VirtualBox with an Ubuntu ISO)
Install the required libraries/tools in Ubuntu
Open the Terminal and run:
sudo apt-get update
Install the GDCM tool that performs the conversion:
sudo apt-get install libvtkgdcmtools
Export the study from OsiriX as DICOM
In OsiriX: export the study (ideally anonymized) to a folder (on the Desktop, for example).
Copy the DICOM folder into Ubuntu
In Parallels, install Parallels Tools (if needed) and restart Ubuntu.
Drag the exported folder (with the .dcm files) to the Ubuntu Desktop.
Convert the DICOM folder to .VTI
In the Terminal, run:
gdcm2vtk dicom_folder output.vti
Typical example (dragging the folder and setting the destination):
gdcm2vtk ~/Desktop/Exam ~/Desktop/exam.vti
Watch out for the “folder inside a folder” problem
If the command fails, it is usually because you pointed to the “wrong” folder (an outer folder that contains another folder where the .dcm files are).
The solution is to point to the folder that directly contains the DICOM files.
Result
Instead of hundreds/thousands of DICOM files, you will have a single exam.vti file, usually smaller (because redundancies are removed), ready for use in VTK/SimVascular software.10min
Burn and AnonymizeIn this lesson from the former OsiriX/Horos Course, Dr. Alexandre Amato shows two functions that seem simple but make all the difference in daily practice: Burn (burning a CD/DVD or generating a DMG) and Anonymize (removing patient data before sharing or exporting).
You will see, in practice:
How to use Burn to burn media with the patient's study
How to anonymize automatically when burning and reduce file size with JPEG compression
The difference between burning a CD/DVD and generating a DMG file
Options to include viewers (e.g., ISIS, cross-platform) and auxiliary exports (HTML/QuickTime)
How to copy reports, encrypt as a password-protected ZIP and include an extra folder (materials, videos, brochure)
How to use File → Anonymize and choose which fields to remove (Replace and Export)
Privacy note: when sharing studies, anonymize properly and follow the rules and policies of your institution.4min
9. Reports and Network
How to Create Reports in OsiriXIn this lesson I explain how to create reports in OsiriX using the program's native system. It is a simple process: you choose which text editor OsiriX will use (Pages, Word, TextEdit, LibreOffice, etc.), create the report through the Report icon, and can customize the templates to match your identity (logo, layout, default text).
1) Choose the text editor for reports
In OsiriX:
Go to Preferences
Open Database
In the Reports section, select which program will be used to edit reports
In the video example, the options installed on the Mac are:
Pages (Apple)
LibreOffice (free)
TextEdit (macOS default)
Microsoft Word (Mac)
You can use any of them — OsiriX will simply open the template in the chosen editor.
2) Create a report using the “Report” icon
Open any study
In the top toolbar, click the Report icon
If the icon is not showing:
Right-click the toolbar → Customize Toolbar
Drag the Report icon back onto the toolbar
When you click Report, OsiriX opens a report based on a template. In the video, a sample text (default template) appears, which can be completely replaced.
3) Customize the template in Pages (Pages Templates)
When the selected editor is Pages:
Open the Finder
Go to Documents → OsiriX Data → Pages Templates
Open the template and edit it as you like (e.g., insert a logo, header, layout, fields)
After saving the template:
The next reports opened in new studies already use the updated template (a study that already had a report open keeps the old template).
4) Customize the template in TextEdit (Report Template)
In the TextEdit example:
Change the editor in Preferences → Database → Reports to TextEdit
Generate a Report in any study (to see the template)
To edit the template:
Documents → OsiriX Data → Report Template
Modify the text however you like and save
When you open a new Report in another study:
It already comes with the updated template.
5) The report stays attached to the study
In the video workflow:
You edit and save the report in the editor (e.g., TextEdit)
When you close it and return to OsiriX, the report is attached to the study
You can see in OsiriX that the report exists and check the “Report” column (showing when the report was created)6min
Cmd-K: Key Images for ReportsIn this video I show how to print from OsiriX in a practical way, using features that avoid printing the entire series (hundreds of images). The idea is to select only the important slices as Key Images and print them to PDF, and I also show how to print a 3D reconstruction.
1) Creating Key Images (Cmd-K)
In the study (e.g., aneurysm/tortuous aorta), I select a few relevant slices and mark them as Key Images:
Origin of the left renal artery → Cmd-K
Origin of the right renal artery → Cmd-K
Bifurcation → Cmd-K
OsiriX highlights the Key Images with a yellow frame.
2) Print menu and useful options
I go to File → Print and adjust:
How many images per page
Title/header (e.g., clinic, patient, study)
What to print:
Entire series (e.g., 262 images → can turn into dozens of pages)
Skip images (e.g., print 1 out of every 10)
Range (print from slice X to slice Y)
Current image (only the one on screen)
Key Images (my preferred option)
In the example, printing the Key Images produces a single page with the 3 selected images — excellent for documentation and reports (e.g., Doppler ultrasound).
3) Printing a 3D reconstruction
If I have a nice 3D image (Volume Rendering), I can:
A) Print directly
Print the 3D view → one image per page (in the PDF)
B) Export the 3D as DICOM (frames) and print by selecting images
Export → DICOM
I export, for example, 10 images (frames)
These images appear in the study as a "ready-made" series (not editable)
I can pick a few, mark them as Key Images and print only the selected ones
Result: an organized, much leaner printout, without wasting pages on irrelevant slices.6min
DICOM Intranet: PACS ServerIn this lesson I explain how to set up a basic network (intranet) using OsiriX as a PACS/DICOM server, with no external access and without depending on the internet. The goal is a simple clinic/office workflow: the ultrasound machines automatically send DICOM studies to a Mac running OsiriX (the server), and every computer on the internal network can access (view) and send studies to that server, centralizing storage.
Network concept (intranet)
OsiriX works as an image server (PACS): it stores, sends and receives studies in DICOM format.
Typical workflow:
Exam performed on the ultrasound machine
Automatic DICOM transfer to the server (Mac + OsiriX)
Other computers on the network access the studies on the server
External studies (e.g., a received CT scan) can also be sent to the server and stored there
Practical office example (from the video)
2 network-enabled ultrasound machines:
Siemens X300
SonoSite M-Turbo
Important tip: when buying an ultrasound machine, negotiate the DICOM client (software).
Avoid workarounds such as video capture, which does not generate DICOM.
1) Basic network planning
Understand the local network IP range:
Examples mentioned: 192.168.0.x, 192.168.1.x (the case in the video) and Apple routers defaulting to 10.0.0.x.
The router is usually .1 (e.g., 192.168.1.1).
2) Dedicated server (Mac)
Recommendation: a dedicated Mac mini as the server (low power consumption, small footprint).
Preferably keep the server free from other uses.
Network connection: a cable (Ethernet) is more reliable and faster than Wi-Fi.
3) Set a fixed IP on the server (avoid DHCP)
Do not use DHCP, to prevent the IP from changing after a power outage, router reset/replacement, etc.
In the video example:
Network: 192.168.1.x
Server: 192.168.1.10
Router: 192.168.1.1
Subnet mask according to the local network
4) Configure OsiriX as a Listener (DICOM receiver)
In OsiriX Preferences:
Enable the Listener (receive DICOM images while OsiriX is open)
Set the parameters:
AETitle: the node name on the PACS network (in the video: “amato”)
Port: 1112 in the video (you need to know IP + port)
IP: the server's own fixed IP (e.g., 192.168.1.10)
Enable:
OsiriX database sharing
Publish the DICOM node via Bonjour
This way, other OsiriX installations on the network detect the server automatically, with no extra configuration
Optional:
Server Mode (when the Mac is dedicated) to save resources and keep the server “light”.
5) Configure the ultrasound machines (DICOM)
Each manufacturer has its own screen, but the essential data are:
Alias / device name
Device AETitle
OsiriX server IP
Port (e.g., 1112)
Communication test: ping/verify (in the Siemens example, it connected immediately)
Settings shown in the video:
Siemens: OsiriX server with AETitle “amato”, IP 192.168.1.10, port 1112; use of DICOM auto-store (save automatically, even while the exam is being performed).
SonoSite: fixed IP on the device (e.g., 192.168.1.8, DHCP off), sending set up to the OsiriX server; option to send at the end of the exam (for the portable unit) and archiving in the “archiver”.
6) Remote access to the server (for remote administration)
Since the server sits “in a corner”, the video shows enabling on the Mac:
Sharing → Remote Management to access the server from another Mac.
7) Keep OsiriX running 24/7
The server only exists while OsiriX is open.
Add OsiriX to Login Items
Use Lingon 3 to keep OsiriX always running:
Create a “job” to automatically reopen OsiriX if it closes/is quit
In the video: Lingon 3 costs US$ 5
Enable automatic user login on the Mac after a restart (e.g., power outage)
8) How the server appears on the other computers
In OsiriX on the client computer, the server appears automatically (via Bonjour).
In the example:
One node shows the server's studies (database access)
Another node appears to receive transfers (drag a study from the client to send it to the server)25min