Fail to export geometry based on DTI images to .stl file

I have generated the geometry of the brain fibers based on DTI, but when I saved the file as the *.stl file and opened it in another 3D software, I saw nothing. How can I solve this problem?

Please try the Export tractography to PLY (mesh) module, available in the SlicerDMRI extension since early April.

Note that we use PLY specifically because it supports color.

Most software with STL import also supports PLY, but if you specifically need OBJ (supports color) or STL (no color) you can convert in MeshLab.

Hi Isaiah,
Thanks for your reply. I tried based on your advice, however, when I opened the *ply file exported from 3D slicer in the MeshLab. I just saw points (not the geometry of the fibers), and the *.stl file converted from the MeshLab still contained nothing.

Hi Kewei. I’ve used this module with a variety of tractography, on a mac, and meshlab 2016.12. If you want to send me a small, sample .vtk file, I can take a quick look. Save it from the vtkMRMLFiberBundleNode with the usual Save Data interface.


inorton -at- partners -.- org

Hi isaiah,
Thanks for your advice. I need to get the permission to send my file to you. I will tell you since I get the permission done.

You can test this with public data:

  • go to Sample Data module, download DTI Brain
  • use Tractography Seeding module, place a seed point (fiducial) inside the brain to generate a fiberbundle see this tutorial, page 59
  • export the resulting vtkMRMLFiberBundle as PLY and load to MeshLab.

If the above steps don’t work, then send me the VTK from the sample data. Also please mention the OS, Slicer version, and MeshLab version.

Kewei Bian ÒÑÓëÄã¹²Ïí OneDrive for Business Îļþ¡£ÈôÒª²é¿´£¬Çëµ¥»÷ÏÂÃæµÄÁ´½Ó¡£



Hi Isaiah,

I have attached the geometry based on part of sample case in *.ply and *.stl format. There are points in MeshLab when I open *.ply, which is the same as I met of my own file; the *.stl is still 1 kb, same as that of my data as well.

I can reproduce this kind of result if I use Save Data, then select “.stl” or “.ply” as the output format in the dropdown.

However, I have just tested the Export tractography to PLY (mesh) tool again in the latest Slicer nightly (2018-06-11), and it works as expected. I include a screenshot below; please make sure you are using that module.


Hi Isaiah ,
I will try the way you suggested. However, where can we get the Export tractography to PLY (mesh) tool? I can’t find it in the slicer (4.8.1, 4.9.0 and 4.5.0-1).

Hi Kewei, it is available in the SlicerDMRI extension in nightly builds since early April. Sorry for the confusion, I thought it was installed already based on earlier discussion. Please see install instructions here.

Hi Isaiah,
I have successfully gotten the geometry based on the way you suggested.
Thanks for your help!

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