3D Anatomical Models

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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.

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."


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