3D PRINT YOUR BRAIN

By Keiland Cooper (November 2016 version)

Some Information on how I 3D printed my brain from structural MRI images (Not actual size)

Programs needed:

• Freesurfer -open source mri software
• MRIcron (needs NIFTI format) or matlabs version -easily convert images
• meshlab or autodesk -open source stl viewer and manipulator

My Notes

1. Convert the MRI images, freesurfer was weird with dicoms for some-reason
   1. test out different micron settings, this will depend on the type of scanner used
   2. I think i ended up going with SFL/SPM8, I need to read up more on this though
   3. (Something funny happened to me with dti vs normal imaging around this or the next step)
2. Process the images in freesurfer
   1. recon-all -s {your name here} -all -i {path to your newly converted file}
   2. this will process for awhile (no really, took like 16+ hours on my MBP)
   3. to convert pial to stl etc. mris_convert {path to freesurfer}/subjects/mybrain/surf/ rh.pial rh.stl
   4. use the same code with the lh.pial to lh.stl
3. Import the stl’s into meshlab or whatever software you choose
   1. Run a smoothing algorithm on it and maybe reconstruct if the file is unseemly large
4. Print the STL
   1. It’s easiest to print hemisphere by hemisphere, then glue

Helpful links

• MRI Imaging Info
• freesurfer (and this was the most helpful page)
• Some forums on freesurfer from harvard detailing the steps freesurfer is doing
• some file converter info from mathworks

Debugging

• I had to move the free surfer install to the documents folder due to permissions errors, sudo wouldn’t fix it...
• use the mail archives to fix errors
• make sure the tutorials work on your machine first, this could save a lot of time (trust me)
• recon-all is amazing and will automate pretty much everything, especially the scull stripping stage, and was fun to read about

TODO for the next time

• figure out how to print the cerebellum with free surfer (I don’t want the 3D me to be shaky)
• use mri_tessellate?
• figure out the problems with the DTI anatomy images
• print my DTI connectome
• Print specific brain regions
• Automate with python code