As it turns out, the reason they give you the CD after you take an MRI or CT scan is not to show other doctors, but to print your own (or your girlfriend’s) body parts.

After reading a few great blog posts about selecting areas of interest from these scans and making a printable version of them, I managed to create a printable STL file of my girlfriends’ skull. These posts were good, but either I couldn’t read the DICOM data into the software they used or the latest version of the software was different. In the end I used 3dSlicer and Autodesk Meshmixer to create the model.

You can get 3dSlicer here. Start it up and load the DICOM data from the CD.

LOAD DICOM DATA > Import > Choose directory with all the scan files > Choose to copy files to local directory rather than just link them > Select patient > Load

Now that all the data is loaded, go to All Modules > View Controllers

Here you can choose the Axial Sagittal and Coronal (X, Y and Z, maybe not in that order) slices.

Once you’ve done that, the slices have to be centered in the three viewing windows. To do that you first have to click on all three eyes to set the visibility to on, for each view. Then, each view has a small crosshair shaped icon (upper left of each black view window) which you have to click to center the slices in their respective windows. You have to do this for each view.

Once all slices are loaded a label map can be created. A label, apparently is an area which you can select in all the slices (or something similar). We’ll use this to separate the area that we need to print.

Choose the Editor module from the Modules menu. The Master Volume is the direction or view that will be converted to a 3d model. Some work better than others, in my case the axial view had a better resolution (smaller distance between individual slices). The merge volume is the volume that will be referenced later on when creating the model. Make note of this name. Next, click on the icon with a gradient pictured. This is the Threshold effect. Basically you set some limits with the range slider and you look at the three windows to see which areas are glowing. These areas will make up our 3d model. After setting the threshold limits, take a look at what number the label has. The idea is that you can use different colors to highlight different areas at the same time and each will be a different label and have a different number. Make note of this number. Now click Apply.

Next, the model is created after the label map. Go to the Model Maker module. Here set the Parameter set to Create new command line module. Input Volume will be the name I previously mentioned to note and in Models choose Create new Model hierarchy. Choose a Model Name. Now, under Model Maker Parameters in the Labels field, fill in the number of the label previously noted. The filter type I used was Laplacian. You can also play around with the smoothing and other sliders. Now click Apply.

In order to save the model click on the save button in the upper left corner and choose only the model you just created with the Model Name, name and from the dropdown menu choose filetype: stl and the path where you wish the file to be saved.

Now open the model in Meshmixer. I first used the Inspector from Analysis to repair any mesh problems, with the Smooth fill option.

From Edit > Separate Shells is used to separate unconnected parts of the model. The object browser opens and you can delete the other shell parts and keep the one that’s needed.

To smooth the ridges left between the CT slices, I used the BubbleSmooth brush from the Sculpt menu and smoothed all areas that were rough.

I also cut the skull in half to print it more easily with the plane cut tool from the Edit menu.

Here is what the model looked like before exporting:

Now export the model as an Stl file and get printing!

I used supports for the lower half printed upside down and no supports for the upper half. 0.2mm layer height and 30% infill. After printing, the parts were acetone welded together and filed down imperfections. The seam is still visible for now.