Enzymind Labs

The process of surface extraction will likely need to be done several times to get the desired surface qualities -- sulcal features that are deep, but not too deep, with a manageable number of polygon flaws.

Software and file format

The 3D printer uses Rhino software and the STL (stereolithography) file format. Rhino can read most polygonal mesh formats, and (I assume) converts these to STL and validate the model. The website for Rhino allows a free download with 25 saves.

The Marching Cubes algorithm is the standard way to generate a polygon mesh from raster isosurface date, and is well known. I can't find inexpensive software that implements it.

Analyze can do surface extraction from raster volume data and output to polygon mesh format. Unfortuately it is several $K. Several other commercial packages, and freeware that was designed long ago for Sun/Unix systems are available.

Space Software does surface extraction, and Greg Scott wrote code for generating a polygonal mesh from the surface data. It needs some work and validation, and the code to write to a polygonal mesh format needs work. This might be the best option, as I know the code and can debug and troubleshoot.

[ To Do: Software specific to brains -- Freesurfer and Brainvoyager. These have tools that "shrink-wrap" a polygonal mesh sphere around a brain to insure that the surfaces are topologically correct (or manageable). This could be used on the cortical surface and white matter surface to construct a thin shell spheroid.]

List of 3D software and utilities

Volume data

The MNI Colin data set (Montreal Neurological Institute) is very good for a model, clean and good resolution -- it is also a standard brain that researchers use for comparing subject brains to. The brainstem is truncated at the bottom, and it may be better to "add" an extended brainstem, as a sort of stand and perhaps casting sprue.

Also, I think that the interior portions may need to be masked -- so the 3D model is a shell and not a solid chunk. I can do this without too much trouble, but it will take a bit of work [ To Do: Describe isoluminant threshold masking, and think about morphological erosion. ]. How thick should the surface be?

Available and validated surfaces from volume data

There are some surface models derived from volume data that have been cleaned up, topographically validated, documented to some degree, and are available for download.

This brain is available from the Aim@Shape Project:

References

Rapid Prototyping Applications in Medicine. Part 2: STL File Generation and Case Studies

D. Ma¹, F. Lin¹ and C. K. Chua²

The International Journal of Advanced Manufacturing Technology

Volume 18, Number 2 / July, 2001

Rapid prototyping (RP) technology has extended traditional manufacturing applications in areas other than product engineering. Using RP to fabricate custom implants and prosthesis for surgical planning and education is now an important area of research. Although, in theory, RP is capable of producing objects of any complexity, designing freeform shapes is difficult using current CAD systems. These CAD systems are geared toward the design of parts manufactured by traditional methods; they do not help designers exploit the expanded opportunities offered by RP technology. Medical data cannot be input into these CAD systems directly for further modification and manipulation. The purpose of this project is to explore a new approach for modelling and prototyping biomedical objects. The work extends from volume modelling to RP and medicine. In Part 1 of two papers, a new approach to modelling complex objects, NURBS-based volume modelling, is proposed. A NURBS representation of volumes is developed to represent not only the surface boundary but also the interior of a 3D object. NURBS-based volume modelling inherits advantages from both NURBS modelling and voxel-based modelling. The key idea of the NURBS-based volume modelling is to exploit the flexibility of NURBS modelling and use the voxelised NURBS volumes as components for constructing complex objects. This paper, Part 2, deals mainly with issues of interfacing volume models to RP systems. A new approach to generate STL files through volume modelling and iso-surface extraction is proposed. This approach guarantees the validity of the final STL file inherently. Software development and case studies are also given.  

Keywords:Marching cubes; NURBS (non-uniform rational B-spline); Rapid prototyping (RP); Volume modelling; Voxel