Segmenting out a brain in an MRI

Hello all,

I’d like to segment out my brain from an MRI and 3D print it. I had been trying to segment it following this tutorial but have not been able to isolate my brain - it makes contact with my skull so I haven’t been able to use the island tool, and their signals are close enough that I can’t isolate it with a threshold either. Does anyone have suggestions on how to do this?

This is my first time using 3D Slicer and it’s an amazing tool to have. Thank you to everyone who has made this software available!

If you are only interested in the brain (not in the skull or skin surface) then remove the skull using one of the automatic skull stripping modules. I would recommend to use SwissSkullStripper extension.

Thank you very much for your help! This is exactly the sort of thing I was looking for and it worked very well.

I was able to use the output image to a segment and then export that to an STL file following these instructions, but the STL file is empty or at least invisible when I try to view it in either FreeCAD or Microsoft’s Print 3D. Unless I think of an alternative way to export it, I will post a new question about this later.

After you stripped the skull, you still need to segment the volume. Segmentation of brain surface should be possible using thresholding (optionally followed by smoothing).

Thank you again!

That’s exactly the tool I used - the threshold, that is. I was able to construct a segment by using a threshold that encompassed my entire brain, and then export that as an STL.

I tried again, and apparently I had not clicked “apply” or something, so that the thresholding was not actually applied to and I was exporting an empty file. I now have a successful export.

Oddly enough, it seems to have been smoothed automatically.

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