Problem with sct_label_utils; v. 4.3


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)

How would I get this to work? Thank you.

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?


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]

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.

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 ( 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 ( 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?

source /usr/local/apps/SCT/4.3/src/python/bin/activate
pip install pytest

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

Spinal Cord Toolbox (4.3)

Trying URL:
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…

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