Editing 3D Anatomical Models

Instructibles posted [http://www.instructables.com/id/Edible-Chocolate-Brain-from-MRI-Scan/ 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 [https://www.noisebridge.net/mailman/listinfo/neuro neuro mailing list] if you want to get involved.

==Datasets==
In order to do this, we'll need some DICOMs ([http://nifti.nimh.nih.gov/ 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. -- [[User:Hurtstotouchfire|Hurtstotouchfire]] 00:16, 30 May 2012 (UTC)
*T1 MRI of Chris's head, DICOM format. Will ask him if we can share this publicly. --[[User:Hurtstotouchfire|Hurtstotouchfire]] 00:16, 30 May 2012 (UTC)
*Liz said she has T1 MR head DICOMs as well and might be up for sharing them. --[[User:Hurtstotouchfire|Hurtstotouchfire]] 00:16, 30 May 2012 (UTC)

==Image segmentation==
The instructibles tutorial describes in [http://www.instructables.com/id/Edible-Chocolate-Brain-from-MRI-Scan/step2/DICOM-Data-Model-Export/ 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 [http://www.fmrib.ox.ac.uk/fsl/bet2/index.html FSL's BET] or [http://groups.csail.mit.edu/vision/medical-vision/SkullStripping/SkullStripping.html the watershed algorithm] (the videos are awesome), which is nicely implemented in [http://neuro.debian.net/pkgs/bioimagesuite.html#pkg-bioimagesuite BioImage Suite] and less nicely implemented in [http://neuro.debian.net/pkgs/freesurfer.html#pkg-freesurfer 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 [https://picasaweb.google.com/lh/photo/uzKNkaBtZYXOYpO-10w8gdMTjNZETYmyPJy0liipFm0?feat=directlink awesome errors].

==3D Printing==
What formats can we easily feed to a makerbot, laser-cutter, or CNC mill? -- [[User:Hurtstotouchfire|Hurtstotouchfire]] 00:02, 30 May 2012 (UTC)

File Formats:
*[http://en.wikipedia.org/wiki/Wavefront_.obj_file .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."
*[http://en.wikipedia.org/wiki/STL_(file_format) .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."
*[http://en.wikipedia.org/wiki/PLY_(file_format) .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."

==Software==
*[http://neuro.debian.net/pkgs/invesalius.html InVesalius]
**exports to [http://en.wikipedia.org/wiki/STL_(file_format) STL]
**packaged by the nice guys at Debian who are trying to get more medical software packaged for linux. I met them at a conference once, they are well-meaning zealots. --[[User:Hurtstotouchfire|Hurtstotouchfire]] 00:02, 30 May 2012 (UTC)
*[http://www.fmrib.ox.ac.uk/fsl/ FSL]
**Also [http://neuro.debian.net/pkgs/fsl.html packaged by neuro-debian].
*[http://www.osirix-viewer.com/ Osirix]
** Semi-opensource and free (the 64-bit functions are proprietary and for pay - not needed)
** Exports to STL (very well)

[[Category:Neuro]]