Beginner issues segmenting brain to stl for 3d print


My aim is to take MRI brain scan data to an .stl for 3D print, for a student I’m working with. I have 3 questions, hopefully pretty basic! :slight_smile:

  1. Organs vs bone
    I created an .stl very successfully for a skull a few years ago but trying again with a brain, it seems to be more tricky (or I’m missing a few tricks). Should it be possible to get as good a result for the brain (MRI) as with the skull - is it just a harder workflow or perhaps the MRI wasn’t very high resolution and the problem lies in the data acquisition itself and the student needs to get a dye-enchanced or higher res scan?

  2. Working with data from multiple planes.
    I have these multiple volumes and only seem to be able to work on one at a time to make each segmentation.
    all MRI data
    The axial volume segmentation looks good of course from the top but terrible from the side and therefore in 3D:

    I’m assuming I can work on the sagittal and coronal data in the same way and combine them to get an overall good result - but at what stage do I combine them and how?

  3. Paint effect on sagittal
    I started to work on the segmentation of the sagittal volume, with the hope of later combining with the axial segmentation but despite the sagittal clearly being higher resolution from that angle as I work with the Paint tool on it, the result is super large ‘pixels’ to the scale of the voxels of the previous axial volume on that same sagittal plane:

It feels like there should be a way to work on the segmentation of the combined volumes of all planes at the same time…?

Perhaps this is stupid obvious in which case apologies in adance! I have looked through a lot of videos and documentation but not found the answer.

Thanks for any help!!!


I’d suggest using SynthSeg. It’s not available directly in Slicer but you can load the results and use that to do any further edits and STL export.

1 Like