Introduction: 3D Printing From MRI Data in 5 Steps

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Objective: Take MRI data (brain, heart, bone, etc.) and 3D print it.

Software Needed (free):

To learn how to master 3D Printing see more posts at:

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and as always thanks for visiting,

The 3D Printing Ninja

Step 1: Obtain the MRI Data

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You should be able to obtain a DICOM (.dcm) file from your doctor. If not you can find some free online such as NBIA.

Step 2: Restrict the View

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Now we need to open our DICOM file in a software program mentioned above and then limit the view to what we would like to print. In the image below what is highlighted in green is what will be printed.

Step 3: Export the Model

Once we have the model in view we need to convert it into an .stl file which can then be printed. To do this we need to make a surface construction first and then export the file. Follow the steps in the software. This may take a while and slow down your computer, there should be a loading bar to see the progress (probably in the bottom right corner).

Step 4: Fix the Model

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Most likely the model will have many non-manifold errors (holes, separate parts, etc.) This is the hardest step in the process and will require an understanding of non-manifolds. Perhaps the easiest method is to upload the model(.stl) into the netfabb cloud, although this may not work. If it doesn't then you will need to try other methods found in the following post. I would start with Meshlab. An easy way to see the errors is in Meshmixer as seen in the image below:

Also one method may not be enough, as multiple methods may be needed to fix the model.

If you do not do this step then your model may not 3d print properly.

Step 5: Prepare & Print

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You will need to choose a side for the supports to be printed on. This should probably be the side that you care the least about the appearance of. You may also need to orient, scale, split, add a raft, etc.

It should be noted that these models are often complex and can take days to print, so make sure you are not on a deadline to have it printed. Also note that it may take a couple of hours for this model to slice alone.


VaishnaviG3 (author)2016-08-15

There was a significant jump between step 3 and 4 so I didn't really follow how the 2d image becomes a 3D object. Would one have to trace over multiple MRI images? If so, how do we connect the different layers?

cpramuk (author)2015-05-05

Meshmixer has a pretty neat method for step 3. You can "Select visible" from many viewpoints, then "separate" that outer shell from the mess (brain matter) on the inside. Then, run a made solid on the outer shell. get to select visible, you have to start with a small selection on the object. Make sure to press shift when choosing "Select Visible" from each viewpoint.