3D Anatomical Models

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Revision as of 00:16, 30 May 2012 by Hurtstotouchfire (talk | contribs) (adding people's datasets)
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Instructibles posted a great article on 3d printing brains and head models from MRI scans. We are playing with some ideas for similar projects we could do at noisebridge. Discussion of this project is on the neuro mailing list if you want to get involved.


In order to do this, we'll need some DICOMs (nifti is also ok). T1 MRIs of heads are great, but we could use other anatomical scans as well.

  • T1 MRI of my head, DICOM and nifti formats. Will get files sharable. -- Hurtstotouchfire 00:16, 30 May 2012 (UTC)
  • T1 MRI of Chris's head, DICOM format. Will ask him if we can share this publicly. --Hurtstotouchfire 00:16, 30 May 2012 (UTC)
  • Liz said she has T1 MR head DICOMs as well and might be up for sharing them. --Hurtstotouchfire 00:16, 30 May 2012 (UTC)

Image segmentation

The instructibles tutorial describes in step two how to "select only the brain" with tissue thresholding using InVesalius. The slightly more sophisticated approach would be to use 3d image segmentation algorithms like FSL's BET or the watershed algorithm (the videos are awesome), which is nicely implemented in BioImage Suite and less nicely implemented in Freesurfer.

The approach described in the Instructibles article is a crude implementation of the watershed algorithm, which is a very elegant image segmentation algorithm. I am personally still fond of FSL's BET algorithm, which is substantially less elegant, but has awesome errors.

3D Printing

What formats can we easily feed to a makerbot, laser-cutter, or CNC mill? -- Hurtstotouchfire 00:02, 30 May 2012 (UTC)

File Formats:

  • .obj - "The OBJ file format is a simple data-format that represents 3D geometry alone — namely, the position of each vertex, the UV position of each texture coordinate vertex, normals, and the faces that make each polygon defined as a list of vertices, and texture vertices. Vertices are stored in a counter-clockwise order by default, making explicit declaration of normals unnecessary."
  • .stl - "STL files describe only the surface geometry of a three dimensional object without any representation of color, texture or other common CAD model attributes... An STL file describes a raw unstructured triangulated surface by the unit normal and vertices (ordered by the right-hand rule) of the triangles using a three-dimensional Cartesian coordinate system."
  • .pyl - "The format was principally designed to store three dimensional data from 3D scanners. It supports a relatively simple description of a single object as a list of nominally flat polygons. A variety of properties can be stored including: color and transparency, surface normals, texture coordinates and data confidence values. The format permits one to have different properties for the front and back of a polygon."