Medical Scan Data to 3d Object

Scan data to 3d object

There is an instructables item covering the procedure with some screenshots.

  • Download and install OsiriX , Meshlab, Netfabb Basic and a slicer of your choice. I used bleeding edge Slic3r.
  • Get some scan data either from a public source (OsiriX has some samples) or your friendly hospital where you need to ask for the PACS Team where you'll need to fill in a form and pay some money.
  • Start Osirix and import your scan data. Double click a series image to get to the 2D viewer then using the 2D/3D reconstruction tools menu select '3d Surface Rendering'. This is the one to use if you are reconstructing a surface like bone for example but there are other types of reconstruction relevant to different scan types.
  • Export as .obj or .stl
  • Start Meshlab and Edit -> Select Vertexes that you clearly don't want. Use Filters -> Selection -> Delete Selected Verticies to get rid of them.
  • There seems to be rather a lot of point artifacts floating in mid air around the place. I used Filters -> Cleaning and Repairing -> Remove Isolated Pieces (wrt Diameter) with the maximum piece size to be 1.5% of the object size.
  • Rotate to correct for the adjustment that OsiriX informed you of when exporting 'Warning gantry was used, points rotated by 2.5 degrees' or similar. Do this with Filters -> Normals, Curvatures and Orientation -> Transform:Rotate where you'll be able to find which axis using Render -> Show Axes. For some reason, you can't enter a '-' sign in the UI textbox so you need to use the slider and edit if you want -ve angles (!!!! am I doing something wrong?) Remember to check the Freeze Matrix box otherwise it'll store the transformation only and not apply it to your mesh.
  • Export to .stl
  • Import in Netfabb Basic which will most likely give you a big red warning triangle.
  • Select the part and Part -> Auto Repair then using the dialog on the right click Auto Repair. Don't forget to 'Apply repair' otherwise you won't export the modified mesh.
  • Export to .stl

Plate up and slice as usual. Slic3r struggled before I used Netfabb Basic's Auto Repair. Sclic3r's repair features have improved recently and it is worth checking to avoid the additional step.

I haven't tried this on anything other than X-ray CT scan DICOM input involving the Osirix software but the subsequent steps I imagine might be a starting point for other types of 3d scan cleanup.


Here are some I made earlier:


Investigate water soluble support and multiple materials.

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