Final installation step 6.0: sct check dependencies

SCT
1

Hello,

I’ve just finished installing sct 6.0 on my computer. I have no computer science background. On the sct check dependencies step this is what I see:

MANDATORY DEPENDENCIES

Check if data are installed…[OK]
Check if dipy is installed…[OK] (1.7.0)
Check if ivadomed is installed…[OK] (2.9.8)
Check if matplotlib is installed…[OK] (3.7.2)
Check if msvc-runtime (14.29.30133) is installed…[OK]
Check if nibabel is installed…[OK] (3.2.2)
Check if nilearn is installed…[OK] (0.10.1)
Check if numpy is installed…[OK] (1.23.5)
Check if onnxruntime is installed…[OK] (1.15.1)
Check if pandas is installed…[OK] (1.4.4)
Check if portalocker is installed…[OK] (2.7.0)
Check if psutil is installed…[OK] (5.9.5)
Check if pyqt5 (5.12.3) is installed…[OK] (5.12.3)
Check if pytest is installed…[OK] (7.4.0)
Check if pytest-cov is installed…[OK] (4.1.0)
Check if requests is installed…[OK] (2.31.0)
Check if requirements-parser is installed…[OK]
Check if scipy is installed…[OK] (1.11.1)
Check if scikit-image is installed…[OK] (0.21.0)
Check if scikit-learn is installed…[OK] (1.3.0)
Check if xlwt is installed…[OK] (1.3.0)
Check if tqdm is installed…[OK] (4.65.0)
Check if transforms3d is installed…[OK] (0.4.1)
Check if urllib3 is installed…[OK] (1.26.16)
Check if pytest_console_scripts is installed…[OK]
Check if pyyaml is installed…[OK] (6.0)
Check if voxelmorph is installed…[OK] (0.2)
Check if wquantiles is installed…[OK] (0.4)
Check if xlsxwriter is installed…[OK] (3.1.2)
Check if spinalcordtoolbox is installed…[OK]
Check ANTs compatibility with OS …[OK]
Skipping PropSeg compatibility check …[ ] (Not supported on ‘native’ Windows (without WSL))
Check if figure can be opened with PyQt…[OK]
Check if figure can be opened with matplotlib…[OK] (Using GUI backend: ‘QtAgg’)

Is there something I can do to fix the Skipping PropSeg compatability check finding? Does it matter or can I still go ahead and start processing my data? Thanks!

Claire

2

When I tried an example it told me in the terminal that I can’t use the Propseg command and should use deepseg instead so I will do that unless I hear otherwise from you, thanks:

sct_propseg: error: sct_propseg is not currently supported on native Windows installations.

For spinal cord segmentation, please migrate to the new and improved sct_deepseg_sc tool, or consider using WSL to install SCT instead.

For further updates on sct_propseg Windows support, please visit:

3

One final question: Is it necessary that I use sagittal images to do my segmentation/registration steps, as I have only really been collecting axial images from my cases. Thanks for your time.

Claire

4

Hi Claire,

Yes, exactly! For now, using sct_deepseg_sc is our recommendation for Windows users. :slight_smile:

I will follow up shortly regarding your question about sagittal/axial images.

Kind regards,
Joshua

5

Axial images can be used for SCT tools that work on a slicewise basis (e.g. sct_deepseg_sc which uses a 2D kernel by default, sct_dmri/fmri_moco). However, there are some steps in the registration pipeline where thick, axially-acquired slices can be prohibitive.

For example, we use the sct_label_vertebrae command to accurately label vertebrae + discs, which are then used in the “vertebrae matching” step during sct_register_to_template. Without sufficient resolution in the sagittal plane, it may be difficult to accurately identify the vertebrae/discs, hence the benefit of having sagittal images.

Kind regards,
Joshua

1 Like
6

Thank you very much!