
Ask HN: How can I 3D print my skeleton for research? - i_am_good
Hello HN,<p>I would like to 3D print my skeleton to observe bone structure&#x2F;features.<p>1. What kind of medical scanning would be appropriate for this case? Where can I get such a scan and pay (out of pocket) for it? Are there any dangers, and if serious, is it worth the fun of replicating your own skeleton?<p>2. What kind of medical scanning hardware would best suit my need? Does it support exporting imaging data for later 3D printing?<p>3. What&#x27;s the best 3D printer (or printing service company) and material to print the imaging data from the scanning?<p>Thanks for your assistance!
======
tlb
Simply remove your skeleton from its packaging and place it in a 3D scanner.

Seriously, where it gets tricky is that there is a lot of stuff (cartilage) in
the gray area between bone and flesh. It shows up dimly in CT scans or other
X-ray based imaging. If you omit all of it, the skeleton will seem disjointed.
If you include all of it, it'll seem fused together.

BTW, you can buy actual human skeletons for around $5k.
[https://www.boneroom.com/store/c46/Human_Skeletons.html](https://www.boneroom.com/store/c46/Human_Skeletons.html)

~~~
i_am_good
Thanks for the insight!

Although there are readily available skeletons for purchase, I want to print
my own skeleton for "profiling and debugging" purposes :)

~~~
crooked-v
You could buy a skeleton, scan and print a copy, and then sell the skeleton to
someone else.

Of course, if you do that you could get an accurate anatomical model (like
those ones that show up in high school bio classrooms) for $200-$400 instead.

~~~
toomuchtodo
I wonder if there's a market in medical education for precise models of
different body parts with one-click ordering from model->3D
production->shipping to your education facility. This is distinct from the
efforts of facilities who are using 3D manufacturing to create patient models
on site for surgery planning.

~~~
roywiggins
Why 3D print if it's just going to be for education, not individualized
patient models?

~~~
toomuchtodo
Ya know, I suppose in an ideal world you drive down the cost of on site
manufacturing so you could spit out any model you wanted in the classroom.
Want a healthy kidney? Boom, done. Want an organ that has a specific issue for
a particular ailment being studied? Out it comes.

------
PlaceboGazebo
I've 3D printed my brain - I'm a biomedical engineer, and for a while was
working for a research institute in France. While there, I had many friends
and acquaintances who were doctors or surgeons performing their own research
work. I had made noises in the past that I really wanted to print my brain
sometime, so one of them referred me to an observational study in the area
using fMRI to observe the brain performing visuo-spatial tasks. I went through
the study, got paid €50 (score!) and asked for the morphological data in DICOM
format, which they happily handed over. The DICOM is essentially a whole bunch
of separate images, one for each slice the MRI takes, along with the metadata
that helps piece it together. The reconstruction of a 3D model from slice data
is usually called segmentation. I'm not overly familiar with the process, but
I'm sure someone here can chime in with various segmentation methods. In my
case I asked a technical medicine intern to do it for me. Interns can be
useful, after all. AFAIK the output is usually a mesh, like an .obj or .stl
file, which is thankfully pretty compatible with 3D printing.

To answer your specific points - I would go for MRI over CT - CTs tend to have
high radiation doses, especially if you plan to do a full-body scan. I can't
recommend it. MRIs are much less harmful. There are private clinics where you
can pay for a full body "preventive" MRI - this will set you back a nice sum,
>€1000 in the Netherlands, IIRC. Segmenting the resulting DICOM file is
difficult. It will require a fair bit of work. Look into ITK / VTK / 3Dslicer.
You will absolutely have to clean up and probably remesh any resulting
stl/obj, I recommend using meshlab for that. From there, 3D printing can be
done with any personal printer that has a large enough volume to not take
forever. Using an external service, e.g. shapeways will be very expensive. If
you don't have your own printer, you should probably look into an inexpensive
FDM printer, I personally use an original prusa i3 Mk2.5.

All in all, it will be a very expensive journey if you're not already in the
field and have connections. Maybe try to connect with local universities to
find observational studies.

edit because I realised I sound very negative. I actually think you have a
really cool idea. Please do go ahead if you have the time and money, and for
the love of all that is holy, blog it for posterity!

~~~
hughes
I did the same - participated in an MRI study & asked for a copy of the scan
data. They gave it to me on a CD which I promptly lost while moving.

Back up your brains people!

~~~
PlaceboGazebo
Mine lives on my Google drive, so no worries there!

------
amjaeger
If you get an mri or ct scan you can use this package to segment the bones and
the convert the image slices to 3D geometry.
[https://www.gibboncode.org/](https://www.gibboncode.org/) It’s open source,
but uses matlab which is not free if you are not at a university. It will also
take a while...

~~~
cr0sh
Could you substitute in octave for matlab? Or does it use something in matlab
that is not available in octave?

~~~
amjaeger
Octave looks really cool, I am not familiar with it. Like I said, gibbon is
open source, so you could attempt to port it. I didn't write gibbon, so I have
no idea what the dependencies are like. But I imagine it would not be trivial.

------
gaze
MRI may work... I think there's a skeletal MRI. That will be extremely
expensive. CT scan probably would work, but I don't think they'll let you dose
yourself with that many X-Rays for fun. Most of these scanners give you voxel
data, which you can then threshold some way and generate a water-tight surface
which can be turned into an STL and 3D printed

The best 3D printer probably uses a stereolithography process. They give the
highest detail at the expense of some mechanical properties. An objet might
work well, too.

~~~
schoen
> I don't think they'll let you dose yourself with that many X-Rays for fun.

There are companies that will let you get a "baseline" CT scan so that you can
compare it with a future scan to see if something has changed. I don't think
many doctors recommend this for the general public (because of the high
radiation dose), but it does seem to be an available service and not
prohibited by the FDA or something.

A CT scan comes with a strikingly high radiation dose, much greater than most
people are likely to receive in any other circumstance.
[https://xkcd.com/radiation/](https://xkcd.com/radiation/)

~~~
roywiggins
The FDA barely prevents people injecting themselves with snakeoil stem cell
treatments...

"Baseline" CT smells like an expensive solution looking for a problem to sell
to hypochondriacs. A hefty dose of ionizing radiation for no clear medical
benefit gets a thumb down from me.

MRIs are nearly perfectly safe though.

~~~
schoen
Yeah, I have the same feeling about the baseline CT service and I'm sorry I
wasn't more forthright about it above.

------
toomuchtodo
Consider building off of the work of this artist who did the same.

[https://www.cnet.com/news/artist-3d-prints-his-own-
skeleton/](https://www.cnet.com/news/artist-3d-prints-his-own-skeleton/)

[https://casparberger.nl/skeleton/](https://casparberger.nl/skeleton/)

~~~
i_am_good
That's amazing! I will look into their methodologies more. Thanks!

~~~
toomuchtodo
You are very welcome! If it's not too much trouble, consider
blogging/documenting your work as it progresses. A rising tide lifts all
boats.

------
hprotagonist
CT scanners usually speak DICOM. You'll have to make a 3D model from those
dicom stacks with, e.g., AMIRA[0], then fiddle the facets with Maya or
similar, and then you should be able to export to STL from there.

[0][https://www.thermofisher.com/us/en/home/industrial/electron-...](https://www.thermofisher.com/us/en/home/industrial/electron-
microscopy/electron-microscopy-instruments-workflow-
solutions/3d-visualization-analysis-software/amira-life-sciences-
biomedical.html)

------
MR4D
I mean this as a joke, but only sortof....

For my response to #3, an interesting thought would be to have a metal 3D
printer (or at least access to one).

Not long ago, Bugatti made a 3D printed brake caliper out of titanium that was
stronger and lighter than their own highly engineered caliper. [0]

Upgrading your skeleton to titanium might not be adamantium, but it sure would
be cool if you ever needed the spare parts!

Finally, lest you think I was totally out there, SLM Solutions (who printed
the caliper for Bugatti), actually has a medical division! [1]

[0] - [https://www.tctmagazine.com/3d-printing-news/bugatti-slm-
sol...](https://www.tctmagazine.com/3d-printing-news/bugatti-slm-solutions-
metal-3d-printing/)

[1] - [https://www.slm-solutions.com/industries/medical-and-
dental/](https://www.slm-solutions.com/industries/medical-and-dental/)

~~~
i_am_good
This is really cool. I did not know it was possible to print metallic
structures like this. Thanks for sharing!

~~~
MR4D
If you liked that, you'll love the video of it being speed & heat tested [0].
I watched it after turning up the sound and putting it on a big TV screen -
it's gorgeous!

[0] - [https://www.autoblog.com/2018/12/21/bugatti-3d-printed-
titan...](https://www.autoblog.com/2018/12/21/bugatti-3d-printed-titanium-
brake-caliper-testing-video/)

------
brianzelip
Here's a useful video to see "CT scan segmentation" via DICOM files first
hand. [0] The video shows a guy segmenting out the mandible from some CT data
(and mentions where to find other, open, CT data).

itk-snap, the imaging software used in the video, is open source. [1]

[0]
[https://www.youtube.com/watch?v=P44m3MZuv5A](https://www.youtube.com/watch?v=P44m3MZuv5A)

[1]
[http://www.itksnap.org/pmwiki/pmwiki.php](http://www.itksnap.org/pmwiki/pmwiki.php)

------
skwb
I would first start our by using CT since soft tissue subtraction is a very
easy task. This is because soft tissue has a certain density compared to bone
(houndsfield unit [1].) You would maybe need to smooth for a good 3D print,
but it's probably an easy starting place. Hell, a quick numpy script could
easily do this. I would also poke at radiological scanning softwear (I use
Radiant).

As far as data sources, I think you can probably find some open source CT
scans to do this [2, 3]. There are PLENTY of chest and abdominal open source
CT scans that exist. You may need to "mix and match" some body parts, but it
wouldn't be too hard as long as you're using same gendered scans with similar
height and anatomical features. Sort of the way they 'interpolate' for
dinosaur bones.

Is this for a research project?

Good luck!

[1].
[https://en.wikipedia.org/wiki/Hounsfield_scale](https://en.wikipedia.org/wiki/Hounsfield_scale)
[2].
[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3043884/](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3043884/)
[3]. [https://www.radrounds.com/profiles/blogs/list-of-open-
access...](https://www.radrounds.com/profiles/blogs/list-of-open-access-
medical-imaging-datasets)

------
gthtjtkt
You want to spend $10,000+ to "debug" your skeleton, and you're currently
stuck on the easiest part of that entire process?

I think a new hobby is probably the best option here...

~~~
i_am_good
I appreciate your candid critique. I did not know the cost nor the steps
involved in doing this. Also, by "debugging" I meant to find discrepancies or
signs of abnormalities (if any) by having a model skeleton on hand.

------
downrightmike
You could also print your brain:
[https://www.sculpteo.com/blog/2017/11/08/how-to-3d-print-
you...](https://www.sculpteo.com/blog/2017/11/08/how-to-3d-print-your-own-
brain-using-mri-or-ct-scans-free-software/)

------
inetsee
The least expensive option I can think of:

1: Get a 3d model of a skeleton. (One that you can edit in a free 3D modeling
application like Blender, etc.)

2: Get a tape measure and a cooperative friend/significant other and measure
as many of the skeletal dimensions you can without removing that pesky outer
wrapping.

3: Edit the 3D model to match your measurements.

4: Print!

------
nickthegreek
A decent and cheap 3d printer with a large build volume would be the Creality
CR-10s. You could print it using PETG filament.

~~~
i_am_good
Thanks! I will check it out.

------
Frost1x
I've done quite a bit of 3D modeling using medical imaging working with
various MDs for exploratory research projects.

For contrast, you'll want a CT because MRI typically isn't great for bone
features but that inherently has radiation exposure which I doubt you'll have
an MD sign off on if you're perfectly healthy. I don't recommend this
personally but...

Ignoring that, most all radiology/medical imaging, especially anything CT
based, uses DICOM as a standard data format. Many applications can read this
data (everything from Photoshop, Matlab/Octave to libraries for languages if
you want to go that far) but I highly recommend using 3D Slicer for your data
processing: [https://www.slicer.org/](https://www.slicer.org/)

It's a fantastic piece of software often used in medical research for
computational analysis work. It will allow you to import the DICOM data, read
the metadata correctly to adjust/apply transformations on the data, and
position the image frames in space correctly. From those frame stacks, you'll
be able to do all sorts of things from volumetric viewing (computing
interframe voxels), applying pre-mapped imaging specific color maps to the
data, 3D volumetric rendering (with stereo support), and slicing/clipping
which will all be useful.

There are lots of tutorials and even videos online for extracting 3D surface
meshes from the 3D image data using Slicer. Some automatic thresholding will
be useful to speed the process but you'll find for ball-and-socket joints,
you'll have tediously define these regions on the 2D images frame by frame.
From my experience the spine is the absolute worst based on the way the 3D
geometries interlock. Assuming you have a high enough spatial resolution CT or
series of independent CT scans, you'll likely need to step through the entire
spinal column frame-by0frame to produce quality surface meshes. This process
took me a good 4-8 hours just to do 4 lumbar vertebrae on a patient manually
(constantly checking 3D geometry references to see if what I was doing was
correct).

Once you're done with all of that, you'll then need to export all of these
individual surface meshes (I'm guessing you'll want them independently
segmented to play with/assemble, plus it'll likely be needed for 3D printing),
you may need to down-sample/simplify the surface meshes and smooth them for
printing. This can be done with a number of 3D modeling tools like Blender but
I recommend Meshlab personally. There are a lot of approaches for this, google
is your friend.

STL (or other surface mesh formats, say OBJ) will of course lose the DICOM
metadata and scaling may become an issue depending on how Slicer exports the
data and any additional post-processing you may do, so keep that in mind
before printing that scaling may not be 1:1.

I used a cheap online printing service for my vertebrae project and scaled one
of the lower lumbar vertebrae to about 1/7th actual scale for printing and
that cost me about $30. A full scale lumbar vertebrae from the same service
cost nearly $200 (this was about 6 years ago, no clue what prices are now).
There may be better options.

You may also need to keep in mind 3D printing limitations during the entire
process. Some 3D printers have maximum bounding box sizes (those arms only
move so far) so your model can only be so big which may require you to break
it into smaller parts and connect back together (glue? IDK, I've never done
this). You can also shop around for services that can 3D print larger
structures (I'm sure there's plenty) or do it yourself with some hacked out
DIY 3D printer.

Most of the projects I worked on did this type of work because physically
modeling bone in the real world with correct materials is quite difficult due
to a lot of factors (I only 3D printed a scaled down vertebrae from one
project as a keepsake for the work I did). Bones, for example, have a lot of
smaller internal microstructures you may need to account for which was a
critical concern since we were attempting to model bone fractures on a
specific patient's vertebrae for a proposed experimental procedure and new
process from a neurosurgeon. If you're interested in that sort of modeling, I
found voxel based physical modeling techniques that work better than the
finite element method/finite element analysis the group mechanical engineers
suggested (he was comfortable with FEA/FEM).

The mechanical engineers working with us initially wanted to get cadavers in
their lab do various physical stress tests on bone, but that was ruled out
early on since we pointed out structural properties of decaying bodies were
likely not representative of living bone/cellular structures (besides the
"hey, dead bodies/limbs in our lab" fact)--plus, hey, computational science
and modeling is cool ;)

~~~
hostcontroller
Thank you so much for your insightful comment, I was looking for a tool like
3D Slicer when I got my brain scanned last year.

I managed to spin a few gifs [1] out of the data but got stuck in the 3D-part.

Looking forward to finally trying it out! :)

[1]([https://www.reddit.com/r/interestingasfuck/comments/80vkr6/m...](https://www.reddit.com/r/interestingasfuck/comments/80vkr6/mri_scan_of_the_human_brain_from_different_angles/))

~~~
Frost1x
3D Slicer provides a wealth of training tutorials though sometimes there are
slight UI variations between versions that aren't covered that you need to
interpret for:
[https://www.slicer.org/wiki/Documentation/Nightly/Training](https://www.slicer.org/wiki/Documentation/Nightly/Training)

Here are some of the generic renderings for the spinal modeling project I
described, if you're interested (renderings created with Avizo--an expensive
commercial application--instead of 3D slicer for specific use case reasons for
the sake time savings):
[https://www.youtube.com/watch?v=dkDVeyLLmFM&list=PLZMGw4TBzq...](https://www.youtube.com/watch?v=dkDVeyLLmFM&list=PLZMGw4TBzqlv1S57K4FviLhIqZs0n4vWT)

------
somada141
So CT would be the best way to get a clearer picture of your own skeleton as
high-density structures like bones stand out much better (Hounsfield units and
all that). Then you'd have to segment the skeletal system and do a surface-
extraction. I have a decent writeup on how to do that with Python and VTK
under [1].

MRI might cut it, and unlike CT its not as radioactive, but typically in MR
the contrast between soft tissue and bones isn't as pronounced so segmentation
becomes trickier. I wrote a post on segmenting my own brain from a head MR I
had done and as you can see from the pics the bones don't stand out [2].
Honestly, I dunno how easy it'll be to convince a doctor to write you a
referral for a full-body CT scan given the potential health hazards.

Then comes the tricky part, no imaging modality or segmentation is perfect and
you'll end up with a noisy dataset that won't play well in 3D printing. Prior
to the surface extraction you'd have to post-process your segmentation to
clean little islands of tissue, possibly even manually, and close holes in the
segmented structures. A lot of that can be done automatically but you'll
likely have to do some by hand. Medical image processing frameworks like ITK
(and SimpleITK in Python) are your friends.

What I've found works very well (large part of my PhD was on medical imaging)
is multi-modal imaging where you perform a segmentation on two datasets, e.g.,
MR and CT, registered to one another so you can best disambiguate between soft
tissue and bone [3].

You'd then have to extract the surfaces into something like STL and post-
process it in some software like MeshLab [4] to create a smooth mesh which
you'll extract in a clean STL. That you can print but that's when you'll have
to deal with the quirks of 3D printing. Depending on the filament you use
overhangs are gonna become and issue (something about molten plastic and
gravity I presume) so you may have to split your model into separate pieces
that can be 3D printed (I think the skull will be particularly tricky) and
then eg glue them together.

Before you go down that rabbit hole I propose you try and print a 'clean'
skull that has already been segmented. I found [5] to be a fantastic resource
of anatomical part models! Have a look at [6] on how to configure the
interface to get the skull bones.

Good luck!

[1] [https://pyscience.wordpress.com/2014/09/11/surface-
extractio...](https://pyscience.wordpress.com/2014/09/11/surface-extraction-
creating-a-mesh-from-pixel-data-using-python-and-vtk/) [2]
[https://pyscience.wordpress.com/2014/10/19/image-
segmentatio...](https://pyscience.wordpress.com/2014/10/19/image-segmentation-
with-python-and-simpleitk/) [3]
[https://pyscience.wordpress.com/2014/11/02/multi-modal-
image...](https://pyscience.wordpress.com/2014/11/02/multi-modal-image-
segmentation-with-python-simpleitk/) [4]
[http://www.meshlab.net/](http://www.meshlab.net/) [5]
[http://lifesciencedb.jp/bp3d/](http://lifesciencedb.jp/bp3d/) [6]
[https://imgur.com/a/uGqDA5Y](https://imgur.com/a/uGqDA5Y)

~~~
i_am_good
Thank you for the detailed response! [2] was an interesting read for someone
new to medical imaging.

As you mentioned, it seems like it will be hard to get a referral for a full-
body CT scan as a healthy person. The costs of scans also look pretty steep to
quench a curiosity thirst :/

Nevertheless, I appreciate you sharing this knowledge and will try to print a
segmented skull to understand the process better.

------
zubairq
Wow this would be a great thing to try to fix body faults

~~~
magic_beans
How, exactly?

~~~
mirimir
Not OP, but perhaps minor skeletal deformities. Or serious injuries. For
example:

> By using a combination of 3D printing and adult stem cells, Dr. John Szivek
> hopes this will help injured combat veterans, cancer patients, and victims
> of serious injuries.

> "We developed the idea that maybe we could put in a scaffold that
> regenerates bone very quickly by adding stem cells from the patient, their
> own stem cells and by adding some calcium particles and using a pattern that
> would cause the bone to grow really quickly," he says.

> The 3D plastic bone shaped frames called scaffolds are locked in place with
> two screws and a rod that can all be easily removed when bone forms over the
> scaffold.

> "After about six months your body tends to give up producing new bone and
> starts producing scar tissue so if we can cause healing to occur really
> quickly we can save the patient from having that problem," Szivek explains.

[https://www.wthr.com/article/rebuilding-
bones-3d-printing](https://www.wthr.com/article/rebuilding-bones-3d-printing)

