The strange thing is that it is built as both .so and CLP, so there is both libDiffusionTensorEstimationLib.so and DiffusionTensorEstimation executable in Slicer-build///Plugins.

When I remove the .so, the module is no longer loaded. I tried copying DiffusionTensorEstimation to Slicer-build/bin, but it is not recognized from there either.

This is fixed. There is an unrelated issue with creating the DiffusionTensorVolumeNode automagically from the drop-down menu. Here is my email for reference:

"""
Thanks a lot for this change. I looked at the DTI estimation again and the module is now compiled and called as a CLI. However, there seems to be a problem with reading the output DiffusionTensorVolume back into Slicer after execution - the volume ends up blank. Here's some debugging info:

1. The "Output Baseline Volume" and "Otsu Threshold Mask" volumes are read back in ok.

2. if I set DeleteTemporaryFiles=0 in vtkSlicerCLIModuleLogic.cxx, then run the estimation, I can manually load the (temp) output DiffusionTensorVolume back into Slicer ok from File->Add Volume (and it looks fine).

3. the relevant call is vtkSlicerCLIModuleLogic.cxx:1811, where it calls:
   this->GetApplicationLogic()->RequestReadData(...)

4. In the Volumes Module:
   --if i use the selector to select a manually-loaded DiffusionTensorVolume then it works fine.
   --If I select a node auto-created by the "Create New DiffusionTensorVolume" option in the dropdown menu in DiffusionTensorEstimation, then Slicer segfaults.

5. This sequence gives the correct result:
   -- I manually load helix-DTI from the test data
   -- then run the estimation on my real data with the Output DTI Volume set to existing helix-DTI

From 4 and 5 it seems that the menu auto-create is not setting up the node correctly, and this causes RequestReadData to fail (though without any error, oddly...).

Test data is located in: ./Libs/MRML/Testing/TestData/
helix-DWI should produce helix-DTI
"""

Thanks!

As of today, it seems that 4. doesn't crash anymore.

Can you close this issue if it is resolved, and open another one if needed?

Thanks.

Thanks Julien. Submitted a bug for the other problem:
http://na-mic.org/Mantis/view.php?id=1161

I don't have permission to close on mantis, but I think this is resolved.