Instructables
Overview
This instructable will show you how to create an edible chocolate brain from sliced data sourced from an MRI scan.

Our colleague at Inition, Andy Millns had his brain MRI scanned as part of a research project (he didn't say what into!) and we managed to sneak a copy (get your copy below!).

The main steps involved are:
- Converting sliced DICOM data into the STL file format (a 3D geometry format widely used for 3D printing)
- Editing that model to clean up
- 3D printing a solid model
- Producing a latex mould
- Finally casting the chocolate and eating (image of Andy eating his own brain above).

We've made the original DICOM files and the STL file available for download below under the Creative Commons Attribution License. If you like the project - we would be very happy if you voted for it in the Instructables 'Make it Real' challenge - the voting button is top right of this page.

 
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Step 1: DICOM Data Import

Picture of DICOM Data Import
First we need to convert the DICOM data from the MRI scan into 3D geometry.

We did this using InVesalius 3, an open source medical application (available for Windows and GNU Linux).

First, import your sliced DICOM image files into InVesalius. For highly detailed data you may need to limit the number of images that are used to generate the 3D model.

Invesalius Download Link; http://svn.softwarepublico.gov.br/trac/invesalius

Step 2: DICOM Data Model Export

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Once InVesalius has calculated the model, you can adjust the settings to select only the brain. We did this by filtering out everything but fat tissue then adjusting the levels to select as much of the brain as possible.

Don't worry if other parts are selected - these can be removed later.

Once you are happy with your selection, save out as an STL file.

Step 3: Cleaning Data using Meshlab

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To clean the data you will need MeshLab, another open source appliation, primarily used for post-processing scan data.

Download Meshlab here: http://meshlab.sourceforge.net/

In MeshLab you will be able to view and navigate your 3D model as well as select and delete unwanted data. Use the two selection tools and the selection options in the filter menu to do this.

Once you are happy with the data, perform a poisson reconstruction to reconstruct the surface of the model. This forms a waterproof mesh suitable for 3D printing. This tool can be found in the filter menu under remeshing, simplification and reconstruction.

The reconstructed mesh will appear as a separate model in the layer dialog. Select this mesh and save it out as an STL file.

Step 4: Cutting the Brain in Half

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The waterproof STL brain model then needs to be taken into a CAD software to be cut in half. We used 3DS Max, however, you will be able to do this in any similar software including Blender, another free application.

We cut the model in half using the boolean tool to subtract a plane or thin cube from the model. Select and save out the two files separately as STL.

3DS max has an STL check tool in its modifier panel. It is a good idea to run this before saving out your model as it ensures your model is suitable for 3D printing. If your CAD package doesn't have this feature you can download MiniMagics, yet another free piece of software that identifies errors in STL files.


Step 6: Post Processing 3D Print

This next stage is specific to ZPrinters that use powder-based materials. Other 3D printing processes will vary but the idea is to end up with a model with physical strength and smooth finish suitable for creating a mould.

ZPrinter Part Finishing

The printed was was finished by brushing and de-powdering (as we do with all ZPrinter parts).

We then sealed the outer surface using multiple layers of epsom salt spray to create a hardened outer crust.

Step 7: Latex Mould

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To make the latex mould we covered both halves of 3D printed brain in multiple layers of a food-safe latex. Make sure you wait for each layer to dry before adding the next. Depending on the model, anything from five to ten layers should be enough.

As soon as you are happy you have a thick enough layer of latex over your model, carefully peel it off. Wash out the inside.

Step 8: Melt Chocolate

Melt chocolate in a microwave or on top of a pot of boiling water. Pour the melted chocolate into the mould. It’s a good idea to use a brush or a teaspoon to push the chocolate right into the corners. Once the mould is full, put it in the fridge and leave it to cool for a few hours.

When you remove the chocolate from  the mould wear rubber gloves and run them under cold water first to avoid melting the chocolate.

Step 9: Eat!

Food for thought...

According to Andy, there's nothing quite like eating your own chocolate brain, but we'll have to take his word for that...

If you like the project, please vote for it in the 'Make It Real' challenge above. Thanks. We'd love to see any photos of your attempts (and chocolates most welcome).

Check out the video of the process below. If you're in the UK (or Australia) and interested in 3D printing, get in touch - www.inition.co.uk

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gwynonite24 days ago

Happy Halloween! Has anyone actually gotten this to work? I tried loading an MRI into the InVesalius software, but I can't understand how to make layers to save as .stl files. I limited to fat tissue but the 3D model viewer just came out empty. I'm sure if I can get it to work, it would be really cool...If we could just get what we have into an .stl file I can manipulate it in another program, but it's like it's saving blank .stl files because there is something wrong with the layers. Post any solutions here!

Hello,

I am desperately trying to extract the 3D surface of a
juvenile brain MRI in Invesalius. I have tried many other DICOM
converting softwares, but I like Invesalius the best and is the only one
uploading my DICOM properly. What steps exactly did you use to
isolate/segment the brain surface? I've looked everywhere and can't find
a guide for this purpose sepcifically.

Thank you very much for the feedback. Congrats again on a superb idea.

Best, Caitlin

sniffrumble5 months ago

That's pretty cool, though I have to agree about the "creepy factor". Even so. Here's a thought: how about making your significant other a chocolate heart, taken from an MRI image....

Mmm brains! Here's my zombie seals of approval

mschutze7 months ago

Hi! There is a simpler way to get the Brain STL file (ie no 3D editing or thresholding necessary). Just download and install FreeSurfer, it's an open source software suite for processing and analyzing (human) brain MRI images. With only one command it's possible to extract the cortical surface, which in turn can be easily converted to an STL file. I was able to import this file directly in the slicer software to generate the Gcode print file. Worked like a charm! Next step will be making chololate versions!

sheepbars7 months ago

That's pretty cool, though I have to agree about the "creepy factor". Even so. Here's a thought: how about making your significant other a chocolate heart, taken from an MRI image....

sheepbars7 months ago

That's pretty cool, though I have to agree about the "creepy factor". Even so. Here's a thought: how about making your significant other a chocolate heart, taken from an MRI image....

sheepbars7 months ago

That's pretty cool, though I have to agree about the "creepy factor". Even so. Here's a thought: how about making your significant other a chocolate heart, taken from an MRI image....

Lili Angelika7 months ago

Oh! my God! this is wonderful

That's pretty cool, though I have to agree about the "creepy factor". Even so. Here's a thought: how about making your significant other a chocolate heart, taken from an MRI image....

Zocharim9 months ago

Hey! I've been trying to open DICOM files in invesalius... But it just keeps "loading DICOM files"... I have no idea what to do :( I need to convert the data to stl, but i cant do that without the program not loading the data.

gazumpglue9 months ago

This is very awesome. I am trying to do this with my cancer that I had. I have the DICOM files and I am able to see my scan in 3d but I cant get the cancer to show up at all.

chimplost10 months ago

You should anonymize the DICOM files of the brain MRI. The full name, date of birth, scan location, etc. is all there. DICOM files are like JPEGs on steroids for medical imaging. http://en.wikipedia.org/wiki/DICOM

steveazhocar11 months ago
OK, the link to the DICOM only shows on the PDF.
dmalpica11 months ago
OK, the link to the DICOM only shows on the PDF.
Thats striking...
Claydiz1 year ago
This is very awesome. I am trying to do this with my cancer that I had. I have the DICOM files and I am able to see my scan in 3d but I cant get the cancer to show up at all.
wwoww this is unbelievable. My son has been telling me about the 3D printer for a year, now I understand the basics about it. Thanks! Wonder if you could do a baby's face from a sonogram and make her a doll from it? Imagine her very own doll that was actually a model of her own image!
this is so cool!
I am just a little confused. In step 4, you cut the brain in half but when removing the print, it looked together to me. Especially in step 6. just wondering how the two halves got back together.
ckrause32 years ago
This is wonderful! I have collected many brain MRI's and CT's over the years (Yes, I'm a doctor) and have attempted to turn the DICOMs into 3D models. I never knew about InVesalius; You have made me very happy!

Next, I'm going to try files from the Visible Human Project: http://www.nlm.nih.gov/research/visible/
Marstole2 years ago
Mmm brains! Here's my zombie seals of approval
gjpetch2 years ago
Good luck with the make it real challenge! This tutorial is just spectacular.
kdlan2 years ago
It would be helpful to have more details on this step, please. Especially since the manual for this program is only available in Portuguese!
I'd like to do this with my own brain but they don't have a printer with 2 cell resolution do they ??
This is a great job. I love the fact that you have hacked loads of really different layers of tech here. The 3d stuff is great, but also from a brain scan - genius! Mould-making, chocolate-making, eating one's own brain, hilarious.

Great stuff and lots of details - love it!
mowdish2 years ago
I have the image slices from my brain but not the origian data. I wonder if there is a good way to work backwards from those. If not I'll have to track down the psych student that was running the experiment. I assume that if I eat my own brain I will acquire all of the powers I had when the data was collected. Mmmmm, younger me.
Inition (author)  mowdish2 years ago
What format are they in? The MRI data we had was stored as image slices, but in the DICOM format.
mowdish Inition2 years ago
They are in the _film_ format, which is to say that they were printed out on film. I would have to scan the images to get a digital copy. Probably for the best. Younger me had a lot of crazy ideas.
drmri2 years ago
You should anonymize the DICOM files of the brain MRI. The full name, date of birth, scan location, etc. is all there. DICOM files are like JPEGs on steroids for medical imaging. http://en.wikipedia.org/wiki/DICOM
Inition (author)  drmri2 years ago
Thanks for pointing this our drmi, we've taken them down for now.
Fymles2 years ago
Yummy!

...it awake the chocolate craving zombie in me...
Ceiling cat2 years ago
Chocolate braaaaain! Make you turn your head the other way!
Glad I'm not the only one who thought of Tay Zonday when I saw this....

http://www.youtube.com/watch?v=MnH5WgKBRCw
I wondered if I was the only one. I would have been surprised if I was.
Excellent idea and use of a ZPrinter! :)
wooac2 years ago
Can you really tell if its your brain? Nice project lack of recognition bothers me.
Inition (author)  wooac2 years ago
To be honest, I wouldn't be able to distinguise my chocolate brain my anyone elses! Could you?

In terms of whether the chocolate brain resembles the MRI data, absolutely, although maybe we could do a better job of showing this in the images.
HAS TO BE ASKED ---Hope that's not life size Andy !!! HeHe
Inition (author)  Lectric Wizard2 years ago
Hi Lectric Wizard - yes, it explained the rattling sound I've heard all these years. ;)

Andy
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