Introduction: How to Convert Medical Scan Data Into a 3D Printable Model (also, Dinosaurs!)

Picture of How to Convert Medical Scan Data Into a 3D Printable Model (also, Dinosaurs!)

In this instructable I'll walk you through how to turn data from CT or MRI scans into a 3D printable model. While I will use a dinosaur skull as an example, you can use any data in DICOM format to do the same thing.

Step 1: Get the Software

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I'll be using a software package called Osirix, which is designed for medical imaging. Download and install the free version from here. It is available for Mac only, if you are using a PC check out a similar package called Invesalius, developed by the Brazilian government and made available for free.

We'll also be using Meshlab and Netfabb Studio Basic (the download link is hidden on the right of the page), so go ahead and download those too while you're at it. It's all free.

Step 2: Get the Scan Data

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Most (all?) medical scanners will produce files in a format called DICOM. This usually takes the form of a folder filled with a bunch of files with a .dcm extension. 

For the purposes of this example, I'm using the Euoplocephalus skull from the Witmer lab at Ohio University. Download it here and unzip the .zip file.

Step 3: Get the Scan Data Into Osirix

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Launch Osirix. In the top left corner of the screen is an Import button. Click that, and browse to the folder that has your DICOM data.

Tip: when the FOLDER name is selected in the dialog, press the Open button, and Osirix will load all the files contained in the folder.

Another tip: It will ask you whether to Copy or Link the files - use Copy, that way Osirix will copy the files to its own database, and you can delete the downloaded .zip file and the copies of the DICOM data. 

Step 4: Open the Scan Data in a 3D View

Picture of Open the Scan Data in a 3D View

Once your files are imported, select your data set in the top panel, and then double-click the thumbnail image down below. It will open in a 2D view - you can use the the scroller along the top to go through all the various "slices".

You will get a warning message about the software not being medically certified, proceed anyway, the patient in this case has been dead for 65 million years.

To open it in a 3D view, look in the top toolbar for a button with a gear labelled 2D/3D. It is a drop-down menu, you want 3D Surface Rendering. Accept the defaults, and wait a bit, you'll get a 3D view of your skull. You can move it around by dragging on the view cube.

Step 5: Export Scan As 3D Model

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In the top toolbar, there is a button with a gear, labelled "Export 3D-SR". That leads to a menu with different export format options, you will probably want OBJ or STL formats. Go ahead and export your model, and save it somewhere where you can find it.

Step 6: Clean Up the Model

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Quit Osirix and open Meshlab.

Load up your STL or OBJ file that you have exported in the previous step.

You'll notice that there are some loose bits floating around, and that the texture of the model seems to reflect the resolution of the scan (noticeable as a kind of stair-stepping effect).

To clean up the loose bits, turn the model so that the loose parts don't overlap any part of the skull, and use the rectangular selection tool to select them, then delete them using the filter menu.

To smooth it, go to the Filters menu, and go to the Smooth sub-menu. Choose the Laplacian Smooth filter. When you open it, change the parameter for Smoothing Steps from 3 to 1. (Otherwise it will be too smooth and "blobby"). Apply it. You should notice a dramatic improvement in surface texture.

Go to the File menu and Export the Mesh. You can export as STL or OBJ, though generally OBJ files seem to be more robust when used in other tools. Add a suffix to the file name to differentiate it from the file you exported from Osirix - I generally add "-smooth" to the filename.

Step 7: Prepare for Printing

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In order to more easily print the resulting skull, I want to slice it into two pieces. (If you have a fancy printer that uses support material, you can probably skip this step.)

Start up Netfabb Studio Basic, and import your cleaned up STL (or OBJ) by going to the Project menu and choosing Open.

Use the View menu to rotate the part until you can see it in the most useful orientation for making the cut. In this case, I want to cut it into a front and back piece, so I am seeing the skull from below. Using the XYZ sliders on the right, choose where you want the cut to go. Select the Cut and Execute Cut buttons as appropriate. Make sure the Triangulate Cuts checkbox is marked, so that it will fill in the cut surfaces.

The model is now cut into two parts. Select each part in turn, and using the Part menu, export each as an STL.

Step 8: Print It!

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Load the two halves of your model into Makerware (or whatever print utility you are using), and get ready to print!

Top tip: Make sure that you do not allow Makerware to automatically scale your parts - wait for them both to be loaded, select both, and scale them at the same time. Otherwise the two halves won't match!

Depending on your model, you may or may not need to enable support material. Your call.

Once printed, glue the halves together, take a picture of it, and enjoy!


jeromeb13 (author)2015-12-26

hello ,

i m a laparoscopic surgeon . that is for sure that 3 D printing could help us before the surgery and also to train our resident in what we call lap trainer . but we need to print other things than just the shape of the organ . does anyone want to work with me to be able to print also artery-veins inside and find a way to make it more real for the training and more usefull than just shape for surgery .

SkirmishersS (author)jeromeb132016-04-17

I am a cross sectional radiographer in the UK. I have successfully created a skull model from an x-ray phantom. I have built my own 3d delta printer and I am involved in developing a new delta printer. I am very keen to get in to bio fabrication. I am very interested in finding medical applications for 3d printing, and working with others interested in this new field. I use GE and Philips MRI scanners at work and GE CT scanner. We also have a vascular fluro room. Please contact me if I can be of any help. I also have a physics degree and programming skills.

Several people have written to me asking for CT and MRI datasets. I can not provide you with such data sets for legal and ethical reasons.

There are CT scan data sets online

You might also be able to get human data sets from here but it's probably going to be expensive.

Note animal CT scans have no such restrictions.

HimanshuR36 (author)SkirmishersS2017-03-12

Please send me on

HimanshuR36 (author)SkirmishersS2017-03-12

I want ct scan data for PHD Research

ManarshhjotS (author)jeromeb132016-05-31


I recently handled a case in which I modeled the walls of heart for visualizing the shape of the hole and also the aortic arch for a patient. I would like to work on other projects. Please feel free to drop a mail at

ManarshhjotS (author)jeromeb132016-04-23

Hello Jerome,

I have a masters degree in CAD/CAM Engineering and I would be very interested in working with you. Please feel free to drop a mail at

DaveW126 (author)ManarshhjotS2016-05-31

I am also interested in this project. We are the leader in tangible user interface for stereoscopic objects. Please contact me at

Thank you,

Dave Woods

Founder 3Di LLC

DaveW126 (author)jeromeb132016-05-31

I am creating 3D stereoscopic software which would enable touch interaction. Please visit my website at

I am looking for people in the medical field to help bridge my tangible user interface3 with the medical field.

Please contact me so we can see if a collaboration would be mutually beneficial.

Thank you,

David P. Woods

Founder 3Di


OliverG27 (author)jeromeb132016-05-01

Hello jeromeb13
I had cancer in my intestine, and had it removed , he part of my intestine removed . And 3D printed and using stemcells to grow new intestine, Dr gave me 3 months to live back in nov 2015 now fit

OliverG27 (author)jeromeb132016-05-01

Hello hero men 13

adamtimm1 (author)jeromeb132016-01-15

Jerome, that is exactly what I am attempting to arrive at. I am a respiratory therapist and recognize the medical uses of 3D printing. Please feel free to contact me at I am still getting the hang of this printer but I have a huge print volume bed and can easily get a set of lungs or heart etc. I was planning in a few months to start marketing to surgeons and other specialists. Currently, I am practicing using ABS filament but I have access to nylons of several types which can give you some textural feel and one that can make clothing or shoes. I would like to talk with you.

wanderingronin7 made it! (author)2017-03-31

There is another similar instructable on how to create bone and muscle 3D printable models using a free and automated online service. The conversion process is quick and requires no specialized knowledge of medical imaging or CAD software. Thought this might be of interest to readers here.

nrainey (author)2017-01-31

hello all,

does anyone have methodology, platform, ect. for non irradiating medical imaging i.e. 3D ultrasound DICOM to 3D printable format?

BahaA6 (author)nrainey2017-02-06

We are planning this for MakePrintable, you will basically be able to upload the file and get a 3D printable version in a couple of minutes and a couple of clicks. would love to connect with you so that I can understand more how we can streamline the process for medical uses.

ohoilett (author)2016-11-21

This is pretty cool.

ChristopherE18 (author)2016-11-01

Check out for DICOM to STL file conversions or contact

wanderingronin7 (author)2016-10-04

Embodi3D has an online service that automatically converts CT scans to 3D printable bone models for free. It is super easy and available at the link below. Attached are pics of some of the models I made. Each took less than 10 minutes.

nissim.hadar (author)2016-08-19

If any one is interested - I am the VP of Technology for a company doing 3D visualization of DICOM imagery, that is used today for planning and supporting brain surgery.

Our website is My mail is

ImpresionM (author)2016-07-15

In i3D we don't handle the design of the model directly but we do offer a 3D printing service with different materials and technologies. We guarantee up to 16 micras in precision of the 3D print.
If anyone would like to know more about us, this is our webpage.

we are located in Calle Kepler 117 int. 103 col. Anzures Mexico City. 11590.
and we ship anywhere.

Hope you hear from you! :)

poia69 (author)2016-04-19

There is a DICOM to STL conversion service at

It charges 10 USD

CarrieS30 (author)2016-02-05

Hello! Thank you so much for this tutorial. I'm having a bit of a religious experience seeing forms I am so familiar with in the physical reality rendered in 3d from computing software. I'm sure most people have the opposite experience. THIS IS AMAZING!!! Does anyone know where I may be able to find a female dicom file?

armfielding (author)2016-01-27

Hi All,

May i ask what type of PC specs you guys are using? I am able to export the stl from invesalis 3D and open it in meshlabs. However when i try to rectangle select some of the surfaces meshlab stops responding. I am using a Lenovo laptop Nvidia 2GB GDDR5 Graphics card, 8GB RAM with an Intel i7 4720HQ CPU @ 2.60GHZ. Do i need more power than this?

maltesea (author)2015-11-22

Osirix question: I can import my images and see them, but there seem to be sets of images. I tried to do the surface rendering with the larger sets, but nothing would come of it. If I did other renderings it seemed to bring up something, but clearly not what I was looking for (brain). Thoughts?

adamtimm1 (author)maltesea2016-01-19

For myself I am still learning. I have put up a manual for InVesalius which may give you a clue to using Osirix. Programmers do not like reinventing the wheel so the two might be analogous.

I suspect your software prints a "default" which if you do not tell it differently it will just print. Have you selected a series of specific cleaned up images then tried to print? I.E. go down to brain level and clean up the images then select that. Alternatively save the images in a file called "brain" then print them. Really I am only guessing with Osirix. I'm a PC user who has taught Apple useage. On the other hand I have been using computers for 35 years and my approximation is usually a good one. Good luck! :-)

adamtimm1 (author)maltesea2016-01-15

CTs and MRIs are often composed of hundreds of images. I have worked in hospitals doing clinical rotations and have some ability to read what I see. It's the compilation of those hundreds of images that make it possible to get a good 3D "all around" image. They are done a layer at a time sometimes in millimeters per layer, and it is necessary to have a good background in anatomy to know what you are looking at. With Invasalius you can move through each layer but if you don't know what a pituitary gland looks like you'll miss it. If you can find a "Visible Brain" or Visible Skull or Visible man or woman at a hobby store it will give you a better feel for what you are looking at. If that seems like a childish idea it really isn't. Also check out an anatomy book, specifically Tortora and Anagnostacos Anatomy and Phsiology. The pics are wonderful. There may be a better book but that is the one that got me through A&P.

maltesea (author)adamtimm12016-01-15

Yes, I do know how to differentiate most of what I'm looking at in the images, but I can't technically get things to go from scans into a 3D model that I can export. If I can get close, it usually includes the skull - I haven't found a way to get these separated.

alcurb (author)2014-06-24

This is super cool.

Where can you obtain the DICOM images online? I've looked for them, but no success. Seems that they are located beyond the prying eyes of the google search engine.

adamtimm1 (author)alcurb2016-01-15

The easiest way is to ask your friends if they have CT's or MRIs. HIPPA won't allow that kind of information into the hands of "just anyone." If you are old like me you have a lot to work with. <:-(

Danny Tas (author)alcurb2014-07-22

@ alcurb the actual Osirix site has some

jose.f.jimenez.395 (author)2015-04-09

hi. Are you tried to use .3dh or .mvl files (3d ultrasound files) to make a 3d model?

Hey, have you had any luck converting from .3dh/.mvl? Having the same problem here

Check out your import export files. There is a long list of import as or import as... and I have often overlooked the file extension I can import with. I have asked my doctors and radiologists specifically for Dicom files. I have 7 herniated disks, scoliosis, and spinal stenosis along with a torn rotator cuff and a pituitary tumor. I have a lot of files to work with. Dental files are CT files and save as a specific form of Dicom but it is convertable from Invasalius to STL. When you import the file just import the entire folder that it is in. Then save the entire file as an STL. I hope I haven't given you an insulting statement of the obvious. More I hope this is useful.

GoodLegProject (author)2015-09-10

Invesalius download links for PC no longer appear to be working. Anyone have any luck?

adamtimm1 (author)GoodLegProject2015-11-01

No problem downloading InVasalius. It's working on my Win 10 pc and in fact I translated the manual from Portuguese into English and sent a PDF copy back to Paulo. They use a word processor called Latex. I suppose when you use it things get a little sticky. I also sent them a Word Doc of the manual for those of us who like to mess with the pictures etc. Sorry I could not get screen shots in English but I figured that those of us who are using it are geeky enough that we already recognize the screens.

ObjectForm (author)adamtimm12016-01-15

Hey AdminTimm1, are you able to send over an english manual translation? So far we have been hands on with the software and done very well, but a manual always helps ;) Many thanks!

adamtimm1 (author)ObjectForm2016-01-15

Scott, I tried to email you but your email came back from the postmaster as invalid. I can send you or share Invasalius with anyone who wants it as it is open source and I sent an English copy in PDF form to the original author in Brazil. I did find a few errors in my translation but the former translation was much worse because the good guy that translated it was from India and did not have a Latin Language background. People who speak Portuguese will deny that Portuguese is at all like Spanish but it's pretty close. The syntax however was impossible and meanings of words very general. I did not translate the GUIs or the windows because most of us who are old users get what the windows are saying anyway. Please feel free to contact me directly at I am teaching myself FreeCad so I can clean up STLs myself.

ObjectForm (author)2016-01-15

For those of you whom are wanting to share information about the use of Invesalius (the PC version) then please do get in touch thanks

ObjectForm (author)2016-01-15

Hi ObjectForm here ( We run a paid for service taking CT Scans, converting them to STL formatted files and 3D printing them. The Tech is young and there is often a lot of work required on the STL file to clean up in preparation for 3d print, but it is a service we would like to offer at a reduced rate for test business/surgeons cases. Please get in touch via our website (and click on contact).

Look forward to hearing from those innovators ;)

ChristopherE18 (author)2015-12-30

Jeromeb13, Please contact me concerning your request to 3D print artery-veins. You can check out an example of the work I do at: We often print AAA, LVs, skull models, etc. for training and surgical planning.

Take care, Chris Ebeling (

EmmaW12 (author)2015-09-01

Will the PC software work with a inv. file? Meaning Invivo, based on what i have read a scan can either be in Dicom or Invivo, but i do not have the software to change my Invivo file to Dicom, so do you know if the Invivo file will work?

bill_brown (author)2015-08-21

Downloading Osirix does not work. Nothing happens when I clicked on the 64 bit download link.

gpvillamil (author)bill_brown2015-08-22

Works for me. Bear in mind the 64 bit version is the paid version. You can do everything I describe in the Instructable using the free 32 bit version.

guslacerda (author)2015-04-25

BillC4: have you had any luck? I'm having the exact same problem.

BillC4 (author)2015-02-21

Alas, the gear does not appear in the recent versions of free osirix. Perhaps this is now a feature of the paid version. I used to be able to do this, but all the 3d stuff appears to be disabled now. Alas, this stops the whole process.

mrevlje (author)2015-01-15

Tnx, gpvillamil for this instructions. It works. I am just printing a bone extracted from a full body CT scan. However, it would be more challenging to be able to print an organ. In Osirix MD I can render organs only via volume renderring, but than I do not see any .stl, .obj, etc. export option. How would you approach this ... Tnx in advance.

noel.henke (author)2014-11-02

what should the pixel resolution be at?

noel.henke (author)2014-10-25

I downloaded the free version of OsiriX and I can't view my scan as a 3-D file. All of those options are grayed out. Is there another way or am I just not highlighting something the right way?

gpvillamil (author)noel.henke2014-10-29

In the database window, double click the series you want to view. That will open a more detailed viewer. The 3D options should then be enabled in the menu, and there is also a 3D viewer button in the toolbar. It's labelled 2D/3D and looks like a gear.

kateme (author)2014-07-31

Thank you! Really nice job, congrats.

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