Oct 3, 2015 | By Tess

If you’ve ever wanted to hold a model of your own brain in your hand or display it on a mantle you are now in luck. An Instructables user going by the fitting moniker of 3d_printed_brain has recently posted the steps for creating your own 3D printed brain, and it doesn’t seem to require too big of a brain to execute!

In order to start the process of additively manufacturing your very own brain model you only need four key resources: the raw data from an MRI scan of your brain, the computer program FreeSurfer, MeshLab, and of course, access to a 3D printer, whether it be your own or through a 3D printing hub.

The Instructables user who has posted the instructions explains that he had searched extensively for a 3D printed brain tutorial and found that the only ones available lacked many of the details he has opted to include. Thus, 3d_printed_brain has made an exhaustive step-by-step guide to making a 3D printed brain with very little room for error.

In order to begin the process, you must first undergo an MRI scan of your brain from which you can obtain the raw data. If, like most of us, you do not have an MRI scanner handy, you can always look into participating in an MRI study at a local university. 3d_printed_brain recommends specifically asking for the raw data from the MRI operator as sometimes the scans are given in PNG files, which cannot be processed. The raw files should either be in NIFTI or DICOM formats. If your files happen to be in DICOM format (.dcm), they can easily be converted to NIFTI (.nii) using the dcm2nii tool by MRIcron.

Once you have obtained the raw data of your brain’s image the next step is to extract the brain tissue through FreeSurfer, an open source software used specifically for processing and analyzing MRI brain images. In order to do this 3d_printed_brain suggests prepping the software for the easiest drag and drop usage. To do so, follow these steps:

- Open the VirtualBox and start the FreeSurfer image

- Select Device and Insert Guest Addition CD image

- Double click "autorun.sh" and insert pseudo password "freesurfer"

- Restart the virtual machine (upper right corner "fsuser" -> restart)

For the actual brain extraction process, you first need to drag the NIFTI file (3d_printed_brain has named his brainscan.nii.gz) to the Virtual Machine’s desktop. Next, open the terminal and type the following:

recon-all -s mybrain -all -i /home/fsuser/Desktop/brainscan.nii.gz

Then press enter, where brainscan.nii.gz is the name of your NIFTI file. Once these steps are completed you need only wait for the process to finish, which could take from several hours to a couple days depending on the size and capability of the host computer.

The next step is to convert the brain image files to .stl, prepping it to be 3D printed. Currently, your brain should be in .pial format, in order to convert it to .stl you need simply go through a tool offered by FreeSurfer and then find the files rh.stl and lh.stl (right hemisphere and left hemisphere, respectively) and drag them to your Windows system. The files are now converted.

Next, if you don’t already have MeshLab installed or any other modelling software, it can easily be downloaded for free from sourceforge. This next step entails merging both brain hemisphere meshes into one image. 3d_printed_brain notes that MeshLab does not have an “undo” option in its interface and suggests being wary of the changes you make.

From this point your brain is more or less ready to be printed, however if you notice your mesh only has two vertices it may be too complex for a standard 3D printer. Have no fear, however, the mesh can be easily simplified to accommodate all 3D printers.

If you’ve correctly followed all those steps on Instructables your brain should be ready to 3D print, whether on your own desktop 3D printer, or through a 3D Hub. Thanks to 3d_printed_brain’s comprehensive guide to making a 3D printed brain, we are sure to never again hear the Scarecrow’s lament, “If I only had a brain.”


Posted in 3D Printing Applications





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ChrisRorden wrote at 3/26/2018 6:02:58 AM:

Sinead, assuming you have Matlab and SPM installed, you can use this script to convert a NIfTI image into STL: https://github.com/rordenlab/spmScripts/blob/master/nii_nii2stl.m A nice feature is it makes your brain hollow, which is much less expensive than printing a solid object.

Sinead wrote at 12/12/2017 10:56:19 AM:

Hi TEss, I wonder can you help me convert my NIFTI to stl? I would really appreciate it. My number is 07821577952 thanks

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