Warning caused by sct_process_segmentation

[plbenveniste]

Here is the warning message that I saw in the log file.

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Spinal Cord Toolbox (git-master-72f072555f97e8417260869567b34f8d0c5f5166)

sct_process_segmentation -i sub-HC001_acq-sagCervCube_T2w_seg.nii.gz -vertfile sub-HC001_acq-sagCervCube_T2w_seg_labeled.nii.gz -perslice 1 -o /Users/plbenveniste/Documents/data/ms-mayo/output_pipeline/results/sub-HC001_CSA.csv -append 1 -qc /Users/plbenveniste/Documents/data/ms-mayo/output_pipeline/qc
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/Users/plbenveniste/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/Users/plbenveniste/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
  ret = ret.dtype.type(ret / rcount)
�[33mQC report only available for PMJ-based CSA. QC report not generated.�

I will look into what it is and see whether it we can be easily fixed.

[jcohenadad]

Right, there is no QC for process_segmentation (unless if using PMJ-based CSA), so the warning message is normal. You can simply remove the "-qc" flag.

[plbenveniste]

Removing the QC indeed removed a part of the warning.
However, I still have the following warning message:

/Users/plbenveniste/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/Users/plbenveniste/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
  ret = ret.dtype.type(ret / rcount)