Problem with sct_label_utils; v. 4.3

SCT
1

Hello,

I am having trouble with running sct_label_utils. When I first run sct_label_vertebrae, I get an error ‘Automatic C2-C3 detection failed. Please provide manual label with sct_label_utils.’ After running the sct_label_utils command, I get the output:
‘Cannot mix compatible Qt library (version 0x50b03) with this library (version 0x50b02)
Aborted’.

How would I get this to work? Thank you.

2

hi,
looks like there is a problem with display in your station. Are you connecting with ssh to a remote station? Can you copy/paste the output of sct_check_dependencies?
thanks

3

Hello,

I apologize for the late response. Yes, I am connecting with ssh to a remote station. I have copied the output below:
Spinal Cord Toolbox (4.3)

SCT info:

  • version: 4.3
  • path: /usr/local/apps/SCT/4.3/src
    OS: linux (Linux-3.10.0-862.14.4.el7.x86_64-x86_64-with-centos-7.5.1804-Core)
    CPU cores: Available: 72, Used by SCT: 72
    Swap: 2047 14 2033
    Check Python executable…[OK]
    Using bundled python 3.6.10 |Anaconda, Inc.| (default, May 8 2020, 02:54:21)
    [GCC 7.3.0] at /usr/local/apps/SCT/4.3/src/python/envs/venv_sct/bin/python
    Check if data are installed…[OK]
    Check if numpy is installed…[OK] (1.18.5)
    Check if colored is installed…[OK] (1.4.2)
    Check if dipy is installed…[OK] (1.1.1)
    Check if futures is installed…[OK]
    Check if h5py is installed…[OK] (2.10.0)
    Check if ivadomed (1.2.1) is installed…[OK] (1.2.1)
    Check if Keras (2.1.5) is installed…[OK] (2.1.5)
    Check if matplotlib is installed…[OK] (3.2.1)
    Check if nibabel is installed…[OK] (3.1.0)
    Check if pandas is installed…[OK] (1.0.4)
    Check if pyqt5 (5.11.3) is installed…[OK] (5.11.3)
    Check if pytest is installed…[OK] (5.4.3)
    Check if pytest-cov is installed…[OK] (2.9.0)
    Check if raven is installed…[OK]
    Check if requests is installed…[OK] (2.23.0)
    Check if requirements-parser is installed…[OK] (0.2.0)
    Check if scipy is installed…[OK] (1.4.1)
    Check if scikit-image is installed…[OK] (0.17.2)
    Check if scikit-learn is installed…[OK] (0.23.1)
    Check if tensorflow (1.5.0) is installed…[OK] (1.5.0)
    Check if torch (1.5.0+cpu) is installed…[OK] (1.5.0+cpu)
    Check if torchvision (0.6.0+cpu) is installed…[OK] (0.6.0+cpu)
    Check if xlwt is installed…[OK] (1.3.0)
    Check if tqdm is installed…[OK] (4.46.1)
    Check if transforms3d is installed…[OK] (0.3.1)
    Check if urllib3 is installed…[OK] (1.25.9)
    Check if spinalcordtoolbox is installed…[OK]
    Check ANTs compatibility with OS …[OK]
    Check PropSeg compatibility with OS …[OK]
    Check if DISPLAY variable is set…[OK]
    Check if figure can be opened with PyQt…[OK]
4

Hi @kim, surprisingly PyQt appears to be working during sct_check_dependencies so we are working to figure out what is different between that sct_label_utils.

Would you be able to run

echo $LD_LIBRARY_PATH and report the outcome.

Also I notice this is a centos machine, is this a compute canada cluster that you’re using? If so this will be much easier to debug because we have access to the system.

5

Assuming you are running on ComputeCanada, I think it’s likely this was induced by anaconda somehow. They don’t support running conda on their systems (https://docs.computecanada.ca/wiki/Anaconda/en). I see you have 72 cores, so I assume you’re on an HPC system even if it’s not ComputeCanada.

I think this is a bug on our end, caused by only testing against conda which doesn’t fairly represent the diversity of systems, especially HPC systems like yours. We have a longstanding task (https://github.com/neuropoly/spinalcordtoolbox/issues/1526) to make this better.

I am curious about exactly what is failing. I would also like to see $LD_LIBRARY_PATH, and to see what our tests say. If you have a moment, can you launch this and upload the output here?

echo $LD_LIBRARY_PATH;
source /usr/local/apps/SCT/4.3/src/python/bin/activate
echo $LD_LIBRARY_PATH;
pip install pytest
pytest
sct_testing

I’ll make some time this week to log onto ComputeCanada and try to investigate your issue. Thanks for bringing it to our attention!

6

Spinal Cord Toolbox (4.3)

Trying URL: https://osf.io/yutrj/?action=download
Downloading: 20191031_sct_testing_data.zip
Status: 100%|██████████████████████████████| 6.78M/6.78M [00:00<00:00, 52.6MB/s]
Creating temporary folder (/tmp/sct-20200904120321.172689-2pkj0nbl)
Unzip data to: /tmp/sct-20200904120321.172689-2pkj0nbl
Destination folder: /spin1/home/linux/-----/Desktop
Checking if folder already exists…
Removing temporary folders…
Done!

Will run through the following tests:

  • sequentially: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc
  • in parallel with 72 jobs: sct_analyze_lesion sct_analyze_texture sct_apply_transfo sct_convert sct_compute_ernst_angle sct_compute_hausdorff_distance sct_compute_mtr sct_compute_mscc sct_compute_snr sct_concat_transfo sct_create_mask sct_crop_image sct_dice_coefficient sct_detect_pmj sct_dmri_compute_dti sct_dmri_concat_b0_and_dwi sct_dmri_concat_bvals sct_dmri_concat_bvecs sct_dmri_create_noisemask sct_dmri_compute_bvalue sct_dmri_moco sct_dmri_separate_b0_and_dwi sct_dmri_transpose_bvecs sct_extract_metric sct_flatten_sagittal sct_fmri_compute_tsnr sct_fmri_moco sct_get_centerline sct_image sct_label_utils sct_label_vertebrae sct_maths sct_merge_images sct_process_segmentation sct_propseg sct_qc sct_register_multimodal sct_register_to_template sct_resample sct_smooth_spinalcord sct_straighten_spinalcord sct_warp_template
    Checking sct_deepseg_gm…[OK]
    Checking sct_deepseg_lesion…[OK]
    Checking sct_deepseg_sc…[OK]
    Checking sct_analyze_lesion…[OK]
    Checking sct_analyze_texture…[OK]
    Checking sct_apply_transfo…[OK]
    Checking sct_convert…[OK]
    Checking sct_compute_ernst_angle…[OK]
    Checking sct_compute_hausdorff_distance…[OK]
    Checking sct_compute_mtr…[OK]
    Checking sct_compute_mscc…[OK]
    Checking sct_compute_snr…[OK]
    Checking sct_concat_transfo…[OK]
    Checking sct_create_mask…[OK]
    Checking sct_crop_image…[OK]
    Checking sct_dice_coefficient…[OK]
    Checking sct_detect_pmj…[OK]
    Checking sct_dmri_compute_dti…[OK]
    Checking sct_dmri_concat_b0_and_dwi…[OK]
    Checking sct_dmri_concat_bvals…[OK]
    Checking sct_dmri_concat_bvecs…[OK]
    Checking sct_dmri_create_noisemask…[OK]
    Checking sct_dmri_compute_bvalue…[OK]
    Checking sct_dmri_moco…[OK]
    Checking sct_dmri_separate_b0_and_dwi…[OK]
    Checking sct_dmri_transpose_bvecs…[OK]
    Checking sct_extract_metric…[OK]
    Checking sct_flatten_sagittal…[OK]
    Checking sct_fmri_compute_tsnr…[OK]
    Checking sct_fmri_moco…[OK]
    Checking sct_get_centerline…[OK]
    Checking sct_image…[OK]
    Checking sct_label_utils…[OK]
    Checking sct_label_vertebrae…[OK]
    Checking sct_maths…[OK]
    Checking sct_merge_images…[OK]
    Checking sct_process_segmentation…[OK]
    Checking sct_propseg…[OK]
    Checking sct_qc…[OK]
    Checking sct_register_multimodal…[OK]
    Checking sct_register_to_template…[OK]
    Checking sct_resample…[OK]
    Checking sct_smooth_spinalcord…[OK]
    Checking sct_straighten_spinalcord…[OK]
    Checking sct_warp_template…[OK]
    status: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
    Finished! Elapsed time: 247s