This is technically not a graphic design question, but it is technically not not a graphic design question either, so here I go.

I have a set of MRI scans of my head. They are 5mm slices in x,y,z (or if you prefer med-speak: saggital, coronal, axial). (I also have some sets in 1.5mm slices, but they are incomplete. I.e. only a section, not the entire brain.). enter image description here My ultimate goal is to extract the brain only, and have it 3D printed. I am using Osirix (though I have Slicer, but have not tried it yet).

I could hand-draw the outline of the brain in each individual slice, but apart from taking weeks to do properly, I am not sure the resulting slices will add up to anything near good enough (If I knew it would turn out good, I would consider it). But there have to be a better way.

I have tried to make a 3D model of the entire head using 3D surface rendering, and the result even of that is rather disappointing: enter image description here

I have also tried using the "growing" tool, where, as far as I understand, I should be able to select a colour/density and then removing everything else.

As I see it, there are two ideas, but they both boil down to the same: How to select one organ, when the other organs and tissue close to it are much of the same density? (the inverse approach would be; instead of extracting something spesific, then delete what is not needed).

I realise that if I am ever successful in extracting the brain, there will be the voxel lego-effect (albeit in x, y, z), and I would also need to set some smoothing parameters.

So. In short:

  • What settings (for contrast/density/tissue type/bone) do I set, to make the extraction possible?
  • Do I use the "grow" tool, and if so, how do I get it to select all voxels in all three series?
  • If not the grow tool... then what?

  • If I get it extracted, where and how do I determine smooting options?

  • This really boils down to: how do I create a mask from this imagery? You are only interested in the outer edge of the brain. In the sample images--in the narrow band which can be loosely described as an ellipse--I see a high contrast bewteen the part you want and the part you don't. If you mask quickly mask the inner part you don't want and the outer part you don't want, the problem of edge detection becomes a lot easier, especially using a threshold filter.
    – horatio
    Commented Dec 10, 2013 at 18:20
  • 1
    A similar question was asked here on Stack Overflow. Commented Dec 10, 2013 at 18:24
  • @horatio, yes you are technically right, but the images you see does not show the slices where the contrast is very, very low. Technically, dicom files are not really concerned with colour as such, but density. There must be a density-difference in those low-contrast areas that might well have a default "extract organ" tool. I am just a noob in Osirix.
    – benteh
    Commented Dec 10, 2013 at 19:47
  • @AlexBlackwood yes, I have been past that post a long while ago, and I will look into it again, but what I found then, was not helpful. It might just boil down to my Royal Noobness regarding Osirix and medical jargon.
    – benteh
    Commented Dec 10, 2013 at 19:48
  • I do not know what medium the data is stored as: is it fixed pixel data; is it a raw data map which has a color gradient applied to it; can the visualization be weighted/adjusted/multiplied rescaled? If you can get the boundary that you are interested in to be well-demarcated via color-ramping/threshold/etc, you can use any graphic tool to silhouette the shape.
    – horatio
    Commented Dec 10, 2013 at 19:58

2 Answers 2


In order to render just the brain you need to perform a volume render (it's different from a surface render), better if after a semi-automatic segmentation.

The segmentation provides the set of the data with the needed density. Without a segmentation you can use built-in volumetric filters and obtain a rough reconstruction. This is possible in ImageJ too.

I've more experience with Slicer (see a tutorial here), but I'm sure that OsiriX can perform a correct segmentation as well.

There are a lot of tutorials on brain segmentation with OsiriX, for example here (CT brain data) or here (head). There is a segmentation plugin for OsiriX (not tried).

Be aware that segmentation is a slow technique and needs a certain time to be properly used.

  • Hurray - I will dig into it in a little later: will report back.
    – benteh
    Commented Dec 11, 2013 at 16:16
  • Give also a look to this tool, I have not yet tested it, but it seems to be able to open the slices and export them in DF3 format. Commented Feb 12, 2018 at 8:11

As a layman (a physician by profession but not a 3D modeling guy), I like the 3D-Doctor. Maybe it'll give some clue to your question: http://www.ablesw.com/3d-doctor/tutor.html

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