{"id":21040,"date":"2015-06-03T14:09:51","date_gmt":"2015-06-03T14:09:51","guid":{"rendered":"http:\/\/www.shapeways.com\/blog\/?p=21040"},"modified":"2017-04-17T12:44:44","modified_gmt":"2017-04-17T16:44:44","slug":"how-to-make-a-3d-print-of-your-brain","status":"publish","type":"post","link":"https:\/\/www.shapeways.com\/blog\/how-to-make-a-3d-print-of-your-brain","title":{"rendered":"How To Make A 3D-Print Of Your Brain"},"content":{"rendered":"

A few weeks ago, I made a 3D model of my brain and sent it to Shapeways to get 3D printed. My little brain arrived a few days ago and I\u2019m blown away\u00a0by how good it turned out.\u00a0I don\u2019t want to be overly dramatic, but I think this is one of the coolest things I\u2019ve ever done. The whole process was relatively straight forward once I figured out the best program to use. I wrote a step-by-step tutorial of what I did below in case you want to print your brain too.<\/p>\n

And if you want a brain on your desk and you don\u2019t care whose it is, you can order a 3D model of my brain\u00a0here<\/a>.<\/p>\n

\"Screen<\/a><\/p>\n

 <\/p>\n

INSPIRATION<\/p>\n

I have a deep fascination\u00a0of\u00a0the human brain\u00a0and I\u2019ve wanted a 3D model of my brain for quite some time. I considered using a modeling software (like Blender) to create my own 3D brain model based on my MRI scans, but I quickly abandoned that idea when I imagined manually outlining the cortex one slice at a time.<\/p>\n

A few months\u00a0ago, one of my friends posted a link to\u00a0a company that sells custom brain models<\/a>\u00a0that range from $165.00 (for half scale models) to $342.00 (for full scale models). I\u00a0was tempted to order a model, but I finally decided that it was too expensive. I love brains, but not quite that much.<\/p>\n

Then, a few weeks ago, I came across\u00a0this blog post<\/a>\u00a0that included do-it-yourself instructions for creating a 3D model of your brain for 3D printing. The neuroscientist and cheapskate in me rejoiced. My computer was being serviced so I bookmarked the page and waited until I got my laptop back.<\/p>\n

When I finally sat down to follow the tutorial, I found that it left out some crucial steps and required a lot of manual editing. I spent a few hours looking at other tutorials, downloading software packages, and trying to create a halfway decent 3D model, but none of the models I created had anywhere near the level of detail I wanted.<\/p>\n

Finally, I found\u00a0this tutorial<\/a>\u00a0which describes how to create a 3D model using Freesurfer. I had been wanting to learn how to use Freesurfer for awhile, so it was a win\/win. The tutorial is pretty thorough, but it didn\u2019t explain the installation of Freesurfer, which ended up being somewhat complicated. In case you\u2019re like me and haven\u2019t used Freesurfer before, I added detailed information about how to download and install Freesurfer below. If you already\u00a0use Freesurfer, you are in luck! You are only a few steps away to creating your own 3D brain model (you can skip to the \u201cCreate the 3D brain model\u201d section).<\/p>\n

GET YOUR BRAIN SCANNED<\/p>\n

    \n
      \n
    1. First, you need to get a T1 anatomical scan of your brain with MRI. I understand that that\u2019s easier said than done, but there\u2019s no way around it.<\/li>\n
    2. Add all of your DICOM files from the T1 anatomical scan into one folder.\u00a0My folder is named \u201ct1_mprage_DICOM.\u201d<\/li>\n<\/ol>\n<\/ol>\n

      DOWNLOAD AND INSTALL FREESURFER
      \nIf you already have Freesurfer installed, skip to the next section.\u00a0<\/em><\/p>\n

        \n
          \n
        1. Download Freesurfer\u00a0here.<\/a> I downloaded the\u00a0freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg<\/a>\u00a0file.<\/li>\n
        2. If you don\u2019t already have XQuartz installed, you\u2019ll\u00a0have to download and install it in order to use Freesurfer. Download the latest release\u00a0here<\/a>.<\/li>\n
        3. Install Freesurfer by following the detailed instructions\u00a0here<\/a>. You should come to a screen that looks like this:<\/li>\n<\/ol>\n<\/ol>\n

           <\/p>\n

          \"Screen<\/a><\/p>\n

           <\/p>\n

          In order to get everything set up correctly, you have to modify two files (the first time I tried to install Freesurfer I didn\u2019t read this this page (oops), and I ran into trouble later on). Your computer may be set up differently, so these steps may not apply to you.<\/p>\n

          4.\u00a0Create a .cshrc file in your\u00a0root directory by typing the following commands into the terminal window:<\/div>\n
          <\/div>\n
          <\/div>\n
          \"Screen<\/a><\/div>\n
          <\/div>\n
          <\/div>\n
          A new text file\u00a0should pop up. \u00a0Copy the\u00a0first two commands from the READ ME section of the install window, paste the text in the new text file, and save. Your file should look like this:<\/span><\/div>\n
          <\/div>\n
          <\/div>\n
          \"Screen<\/a><\/div>\n
          <\/div>\n
          <\/div>\n
          <\/div>\n
          5. Modify your .profile file by typing the following commands in the terminal window (I already have a .profile file that is\u00a0named .bash_profile so I opened that file):<\/div>\n
          <\/div>\n
          <\/div>\n
          \"Screen<\/a><\/div>\n
          <\/div>\n
          <\/div>\n
          <\/div>\n
          Copy the second set of command lines from the install window and paste it at the bottom of the file that pops up. My file looks like this:<\/div>\n
          <\/div>\n
          <\/div>\n
          \"Screen<\/a><\/div>\n
          <\/div>\n
          <\/div>\n
          <\/div>\n
          6.\u00a0Get an installation key by filling out the form\u00a0here<\/a>. You will receive an email containing\u00a0information about your license. Copy the text in between the \u2013CUT HERE\u2013 lines and paste them into a new TextEdit file. Convert the file into a plain text file by clicking Format \u2013> Make plain text. Name the file \u2018license.txt\u2019 and save\u00a0it in the Freesurfer folder.<\/div>\n
          <\/div>\n
          \n

          CREATE THE 3D BRAIN\u00a0MODEL<\/p>\n

          1. In your terminal window, type the following command to set up Freesurfer:<\/p>\n

           <\/p>\n

          \"Screen<\/a><\/p>\n<\/div>\n

          <\/div>\n
          <\/div>\n
          2.\u00a0We will use the function called recon-all to create the 3D brain model. Detailed information about the recon function is available\u00a0here<\/a>.
          \nThe function uses the following format:<\/div>\n
          <\/div>\n
          <\/div>\n
          \"Screen<\/a><\/div>\n
          <\/div>\n
          <\/div>\n
          Replace the <DICOM file> part with the path to any one of your DICOM files (and not the folder that holds all the files). Replace <folder name> with the name you want to call the folder that will contain all of the output files. The folder will be added to the same directory that your DICOM folder is in. My function looked like this:<\/div>\n
          <\/div>\n
          <\/div>\n
          \"Screen<\/a><\/div>\n
          <\/div>\n
          <\/div>\n
          <\/div>\n
          Enter the command into terminal and press enter to start the analysis. The analysis takes a\u00a0long<\/em>\u00a0time. The reconstruction took 8 hours on my computer, but others estimate that it can take between 10 and 20 hours. Make sure that you turn off your computer\u2019s sleep mode so that it won\u2019t go to sleep while the analysis running.<\/div>\n
          <\/div>\n
          <\/div>\n
          3.\u00a0After the analysis is completed, all of the output files should be located in the folder you named. In the folder, you should have another folder called \u201csurf\u201d which contains the surface reconstructions. We need to transform these file formats into\u00a0\u00a0a format that is used in 3D printing. To do so, navigate to the surf folder in the terminal and enter the following commands:<\/div>\n
          <\/div>\n
          <\/div>\n
          \"Screen<\/a><\/div>\n
          <\/div>\n
          <\/div>\n
          \n

          3D PRINT YOUR MODEL<\/p>\n

          If you don\u2019t have access to a 3D printer, you can get your brain 3D printed by a 3D printing service. I used Shapeways so I\u2019ll show you how to order from them.<\/p>\n

            \n
          1. Go to the\u00a0Shapeways website<\/a>.<\/li>\n<\/ol>\n
            2.\u00a0Click \u201cDesign\u201d in the top navigation menu. Then click the blue \u201cupload\u201d button underneath the Shapeways logo.<\/div>\n
            <\/div>\n
            <\/div>\n

            3. Sign in to your account or create a new one and click \u201cUPLOAD\u201d again. A box should appear that looks like this:<\/p>\n

             <\/p>\n

            \"Screen<\/a><\/p>\n

             <\/p>\n

            4.\u00a0Click \u201cSelect file\u201d and load the \u201clh.pial.stl\u201d file that you just made. The model units are in millimeters so keep that radio button checked. Click \u201cUPLOAD.\u201d The model should take a few minutes to upload. Once the model finishes uploading, you should see a screen like this:<\/p>\n

             <\/p>\n

            \"Screen<\/a><\/p>\n

             <\/p>\n

            5.\u00a0If you scroll down, you can see the prices for creating a 3D printed model in different materials. A full size brain replica costs about $250.00 per hemisphere. If you want to scale your brain down (and save a lot of money), click the \u201cSCALE\u201d button and change the SCALE % from 100 to 50. This will create a 3D printed replica of you brain that is 1\/8 of the actual size.<\/p>\n

            6.\u00a0At this point, you can decide what material you want to use to print your brain. I went with the strong & flexible material in polished white.<\/p>\n

            7.\u00a0Click the \u201cView 3D tools\u201d link under the name of the material you want to use.<\/p>\n

             <\/p>\n

            \"Screen<\/a><\/p>\n

             <\/p>\n<\/div>\n

            8.\u00a0Shapeways 3D tools will analyze your model and identify potential problems with printing. For one of my models, I had a wall that was too thin. To fix thin walls, click on the \u201cWall Thickness\u201d menu item on the left of the page, then click the red button that says \u201cFIX THIN WALLS.\u201d Shapeways will automatically adjust your model for you.<\/div>\n
            <\/div>\n
            <\/div>\n
            <\/div>\n
            9.\u00a0Go back to the model editing page and add your desired model to your shopping cart. Now repeat these steps for your right hemisphere model. Check out when you\u2019re ready and your little brain will be on its way! I got my brain in less than two weeks.<\/div>\n
            <\/div>\n
            <\/div>\n
            <\/div>\n
            Here\u2019s what my model looks like in Shapeways:<\/div>\n
            <\/div>\n
            <\/div>\n
            <\/div>\n
            \"Screen<\/a><\/div>\n
            <\/div>\n
            <\/div>\n
            <\/div>\n
            And here are more images of my final 3D printed brain:<\/div>\n
            <\/div>\n
            <\/div>\n
            <\/div>\n
            \"Screen<\/a><\/div>\n
            <\/div>\n
            <\/div>\n
            <\/div>\n
            \"Screen<\/a><\/div>\n
            <\/div>\n
            <\/div>\n
            <\/div>\n
            <\/div>\n
            \"Screen<\/a><\/div>\n

            \u00a0<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"

            A few weeks ago, I made a 3D model of my brain and sent it to Shapeways to get 3D…<\/p>\n","protected":false},"author":79,"featured_media":21043,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[489],"tags":[552,607],"class_list":["post-21040","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-products-and-design","tag-3d-scan","tag-how-to"],"thumbnail":"https:\/\/www.shapeways.com\/blog\/wp-content\/uploads\/2015\/06\/Screen-Shot-2015-06-03-at-10.37.04-AM.png","yoast_head":"\nHow To Make A 3D-Print Of Your Brain - Shapeways Blog<\/title>\n<meta name=\"description\" content=\"A few weeks ago, I made a 3D model of my brain and sent it to Shapeways to get 3D printed. 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