1. A description of the problem: When reviewing the csa.csv output using the whole/cropped T1 as input, we needed some spurious slices being included in the calculations. For example, C1:C2 average used slices 33:60;62:63;65;75:76, rather than 33:60. Upon visual inspection, I noted: (a) spurious voxels in the label_seg away from the spinal cord (seg image); and (b) voxels in the label_seg image adjacent to the cord and also not seg image. I was expecting that the label_seg would be constrained to only include voxels in the seg mask image. This does not happen in all cases and doesnāt happen with test case on this forum using the whole brain.
2. Commands and terminal output.
sct_deepseg_sc -i t1_crop.nii -c t1 -brain 1 -centerline cnn;
sct_label_vertebrae -i t1_crop.nii -s t1_crop_seg.nii -c t1;
sct_process_segmentation -i t1_crop_seg.nii -vertfile t1_crop_seg_labeled.nii -vert 1:2 -o my_csa.csv -append 1;
3. System information.
Spinal Cord Toolbox (5.5)
sct_check_dependencies
SCT info:
- version: 5.5
- path: /Users/dmclaren/sct_5.5
OS: osx (Darwin-20.6.0-x86_64-i386-64bit)
CPU cores: Available: 12, Used by ITK functions: 12
RAM: Total: 16384MB, Used: 10034MB, Available: 5259MB
Check Python executableā¦[OK]
Using bundled python 3.7.11 (default, Jul 27 2021, 07:03:16)
[Clang 10.0.0 ] at /Users/dmclaren/sct_5.5/python/envs/venv_sct/bin/python
Check if data are installedā¦[OK]
Check if colored is installedā¦[OK] (1.4.3)
Check if dipy is installedā¦[OK] (1.4.1)
Check if h5py is installedā¦[OK] (2.10.0)
Check if Keras (2.3.1) is installedā¦[OK] (2.3.1)
Check if ivadomed is installedā¦[OK] (2.9.2)
Check if matplotlib is installedā¦[OK] (3.5.1)
Check if nibabel is installedā¦[OK] (3.2.1)
Check if numpy is installedā¦[OK] (1.18.5)
Check if onnxruntime is installedā¦[OK] (1.7.0)
Check if pandas is installedā¦[OK] (1.3.5)
Check if psutil is installedā¦[OK] (5.9.0)
Check if pyqt5 (5.11.3) is installedā¦[OK] (5.11.3)
Check if pytest is installedā¦[OK] (6.2.5)
Check if pytest-cov is installedā¦[OK] (3.0.0)
Check if raven is installedā¦[OK]
Check if requests is installedā¦[OK] (2.27.1)
Check if requirements-parser is installedā¦[OK]
Check if scipy is installedā¦[OK] (1.7.3)
Check if scikit-image is installedā¦[OK] (0.19.1)
Check if scikit-learn is installedā¦[OK] (1.0.2)
Check if tensorflow is installedā¦[OK] (1.15.5)
Check if torch (1.5.0) is installedā¦[OK] (1.5.0)
Check if torchvision (0.6.0) is installedā¦[OK] (0.6.0)
Check if xlwt is installedā¦[OK] (1.3.0)
Check if tqdm is installedā¦[OK] (4.62.3)
Check if transforms3d is installedā¦[OK] (0.3.1)
Check if urllib3 is installedā¦[OK] (1.26.8)
Check if pytest_console_scripts is installedā¦[OK]
Check if wquantiles is installedā¦[OK] (0.4)
Check if spinalcordtoolbox is installedā¦[OK]
Check ANTs compatibility with OS ā¦[OK]
Check PropSeg compatibility with OS ā¦[OK]
Check if figure can be opened with matplotlibā¦[OK] (Using GUI backend: āMacOSXā)
Check if figure can be opened with PyQtā¦[OK]
Check FSLeyes versionā¦Command not found
- File upload. (Please upload any data or scripts needed to reproduce your issue, if there are any.) ā
