I have been trying to make a reconstruction on the virtual box, but ran into an error at the Slice Outlier rejection.
I can imagine it is a memory error, since my memory was already at 97% up to this point.
If that is indeed the case, I can hopefully fix it by expanding my memory. But otherwise, perhaps I need to change some settings.
I ran it with a resolution of 2.0 mm as a first test if the code worked.

Thanks in advance.

The output is as follows (last part of running and the error):

--- Cycle 1/3: Slice-to-Volume Registration -- Stack 3/3 (cor) -- Slice 30/33
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 3/3 (cor) -- Slice 31/33
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 3/3 (cor) -- Slice 32/33
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 3/3 (cor) -- Slice 33/33

*** Slice Outlier Rejection (NCC < 0.5) ***
Traceback (most recent call last):
File "/home/niftymic/Software/PythonVirtualenv/py3venv/bin/niftymic_reconstruct_volume", line 11, in
load_entry_point('NiftyMIC', 'console_scripts', 'niftymic_reconstruct_volume')()
File "/home/niftymic/Software/NiftyMIC/niftymic/application/reconstruct_volume.py", line 450, in main
two_step_s2v_reg_recon.run()
File "/home/niftymic/Software/NiftyMIC/niftymic/utilities/volumetric_reconstruction_pipeline.py", line 64, in run
self._run()
File "/home/niftymic/Software/NiftyMIC/niftymic/utilities/volumetric_reconstruction_pipeline.py", line 596, in _run
outlier_rejector.run()
File "/home/niftymic/Software/NiftyMIC/niftymic/utilities/outlier_rejector.py", line 56, in run
residual_evaluator.compute_slice_projections()
File "/home/niftymic/Software/NiftyMIC/niftymic/validation/residual_evaluator.py", line 170, in compute_slice_projections
self._reference, slice)
File "/home/niftymic/Software/NiftyMIC/niftymic/reconstruction/linear_operators.py", line 167, in A
stack_slice.sitk, interpolator=interpolator_mask)
File "/home/niftymic/Software/NiftyMIC/niftymic/base/stack.py", line 933, in get_resampled_stack
image_sitk_mask=resampled_stack_sitk_mask,
File "/home/niftymic/Software/NiftyMIC/niftymic/base/stack.py", line 332, in from_sitk_image
slice_thickness=slice_thickness,
File "/home/niftymic/Software/NiftyMIC/niftymic/base/stack.py", line 1278, in _extract_slices
slice_thickness=slice_thickness,
File "/home/niftymic/Software/NiftyMIC/niftymic/base/slice.py", line 59, in from_sitk_image
slice.sitk_mask = sitk.Cast(slice_sitk_mask, sitk.sitkUInt8)
File "/home/niftymic/Software/PythonVirtualenv/py3venv/lib/python3.6/site-packages/SimpleITK/SimpleITK.py", line 10215, in Cast
return _SimpleITK.Cast(image, pixelID)
RuntimeError: Exception thrown in SimpleITK Cast: /tmp/SimpleITK-build/ITK/Modules/Core/Common/src/itkMultiThreader.cxx:399:
itk::ERROR: MultiThreader(0x386762c60): Exception occurred during SingleMethodExecute
/tmp/SimpleITK-build/ITK/Modules/Core/Common/src/itkMultiThreaderPThreads.cxx:187:
itk::ERROR: MultiThreader(0x386762c60): Unable to join thread.