My Foot

From my previous work which dealt solely with lower limbs I was able to get some good CT scans of my feet under partial weight bearing conditions.  Segmenting the bones of the foot was a significant part of my work there.  Foot bones were also the first anatomical part I printed once I started working on my own 3D printers.  While printing bones was interesting it was not all that novel in the grand scheme of things.

Talus with red infill - Inferior View

Talus with red infill – inferior view

Talus with red infill Superior

Talus with red infill – superior view


Calcaneus – sagittal view



For quite some time I had wanted to print a whole foot with the bones printed inside the foot in a different color.  This task eluded me for a while as the size of my foot (10.5 US) and the need for a reliable triple extruder setup was not immediately forthcoming.  The three extruders are to account for the need that one of them is for the solvable support material while the other two take care of the bone color and the soft tissue color.  Now for the finished result after a long print it definitely looks like a foot, in fact is looks very similar to my foot.  While completely rigid it wouldn’t fit into one of my shoes; but it does fit perfectly into a TeeVa I had.

Right Foot Real and Printed

Right Foot Real and Printed

Feet in TeeVas

Feet in TeeVas










Now in an ideal world the ‘soft tissue’ (Skin, fat, tendons, facia, ligaments, muscle, etc) would show up as clear allowing for clear visualization of the bones in their respective areas within the foot.  In reality printing with with the FDM process results in opaque parts at best.  While the soft tissue material was natural PLA and is fairly clear on its own; because the volume is not solid and homogenious light is refracted as it goes through it and only the bones close to the ‘skin’ show through.

Right Foot

Right Foot

Just to prove that the bones are really there I have included a partial print that was stopped early due to a bad section of filament.  The red bone is clearly visible within.  This partial print was also a good test to try a post production step using Smooth-Ons XTC-3D to see if it helped improve transparency.  While the surface is certainly more shiny I can’t see a difference in the transparency.

Right Foot Partial

Right Foot Partial

PLA is only one material though, there are plenty of others that have greater potential for improved transparency.

Printing a Brain

When it comes to complicated 3D models, 3D printing is sometimes the only way to go.  For anatomical models there are few organs more geometrically complicated than the brain.  A recent client had a high quality model of his brain that he created while working on his PhD in medical imaging (focused primarily on modeling the brain from MRI scans).  Every persons brain is different as they fold upon themselves like a pile of over-sized spaghetti noodles.

Brain Transverse Slice

Both hemispheres shown together at a mid transverse slice to show the inner complexity

Traditional methods such as using a CNC mill or lathe couldn’t hope to create the shape with the complicated internal geometry.  Even with the very sophisticated 5 or 6 axis mills that can tilt both the spindle and the table.  Additive manufacturing conversely can do this by building the shape up layer by layer.  Our printers are in the category known as Fused Deposition Modeling (FDM) which function like a highly controlled hot glue gun.  One challenge with most printers including FDM is how to handle overhanging features.  This is typically accommodated by using support material.  After printing the support material is removed leaving the desired part.  For simple parts the material can be removed by hand by essentially breaking it and pulling it off and out.  For the brain though the inner passages can’t be entirely accessed by tools.  This requires the use of solublee support material.

Soluble support material is printed on each layer along with the primary material. To be able to use do this a printer needs at least two print heads that can be switched to alternate during printing.  This printer feature has been and is still being developed in the 3D printing community.  There are various technical approaches to do this as adding multiple print heads adds complexity the printer.  Medical Models has our own version incorporating features from other designs in the comunity.

The first print done was the right hemisphere using ABS (Acrylonitrile Butadiene Styrene) and HIPS (High Impact PolyStyrene) as the support material.  ABS adheres well to HIPS which dissolves in Limonene which is a strong solvent made from oranges.  The results came out fairly well until the removal of the support material.  ABS has a well known limitation for 3D printing where it tends to contract and warp; especially with certain geometries.  While off the printer the brain looked good.  While soaking in limonene for an extended period of time the internal stresses released causing the brain to crack along some of its layers.  HIPS was also found to not completely dissolve and instead only soften making complete removal challenging and time consuming.








For the next print the left hemisphere was printed in PLA (PolyLactic Acid) and PVA (PolyVinyl Alcohol). PLA is a bio-polomer that has very minimal warp compared to ABS and PVA is water soluble support material.  After a long print and a good soak in water the left hemisphere came out much better than the right one. The support material inside could be mostly removed by spraying with high pressure water for the areas that did not completely dissolve during the soak.










Clinical Scan Data

CT and MRI scans are used extensively to diagnose patient health. From the MRI of a shoulder to look for ligament damage (which I have had done after a few skiing accidents) to the CT of a hip or neck to examine bone alignment or bone health. The scans give crucial information about the insides of the body without requiring exploratory surgery.

Unfortunately, when it comes to re-creating anatomical structures many of these scans will have good in plane resolution but horrible out of plane resolution (slice spacing). For example the best MRI of my shoulder has a high quality 0.3125mm/pixel in plane resolution with a slice spacing of 4mm!

From the perspective of the physician this is fine, slices at different locations allow for a detailed look at the anatomy at different areas. From the perspective of creating a 3D model this will result in very chunky shapes when segmented and surfaced. Smoothing can only go so far.

So if the machines can output sub-millimeter resolution why not give us that data?

The Cost
The answer is time. For a CT scan to give nice out of plane sub mm voxel sizes the scan will take longer which means longer exposure to radiation which is to be avoided. For an MRI there isn’t danger from ionizing radiation but a MRI scan takes longer and since MRI’s in particular are costly and time is money the scans will be done with larger slice spacing. The other issue with long MRI scans is that if a patient moves during the scan the data will for the most part be useless. This isn’t a big problem for a 2 minute scan but for a longer scan like 20 minutes can you really hold still for that amount of time? Fixturing a patient can help but can only go so far.

A recent client was looking to use scan data of heads to create accurate skull bone flaps. The patients already had MRI’s and CT scans to work with so why not try to use them. Well the best CT scan had 0.5mm in plane and 2.5mm out of plane voxel dimensions.

Segmenting the bone from the CT scan worked fairly well yet the low out of plane resolution gave significant artifacts at the superior end of the head despite significant smoothing.

In an ideal world we would just get a nice CT of each patient with sub millimeter voxel sizing (slice spacing) but that adds cost and in this case modification to the researchers IRB application. The best MRI had 0.98mm in plane and 1mm out of plane voxel size.

Segmenting bone from MRI data is less than ideal but can give decent results.

With more time spent segmenting and adjusting the smoothing parameters the holes could be filled but in general there is little contrast between bone and soft tissue in MRI. Since bone (inner bone surface in particular) was of interest the CT scan was really the best option.

So after a few meetings my client requested looking at ways of improving the results while working with the preliminary data that we had. Could results be improved by combining data sets together in hopes of ‘filling in’ the data. Adding scan data together is not trivial it requires registering the scans together then adding up the intensities at each voxel. 3DSlicer was used to accomplish this.

After these extra steps it is debatable whether the results were significantly improved. My client was able to go back to the radiologist and look for possible ways to get better data. As it turns out the CT scan was done at higher quality but saved in a lower quality. Getting another dataset saved at greater density resulted in an in plane resolution of 0.39mm and an out of plane resolution of 0.6mm. This gave four times the out of plane resolution and 25% more in plane resolution; the data was now plenty adequate for a good 3D model.

Why the scan data was saved in a resolution lower than the actual scan is likely because most doctors are used to traditional methods of looking at data as a montage of images. While this may seem odd to take a 3D volume of data and not look at it in 3D, it is indeed simpler and faster to see it in a ‘flat’ way. After working with scan data from an engineers perspective for many years it is easy to forget that doctors don’t have the desire, time, experience, or software to see the scan data in all its 3D glory.