Where is the demo data for `sct_deepseg_sc`?

SCT
1

I’d like to utilize the Spinal Cord Toolbox (SCT) and experiment with it using demo data.

I’ve been following the documentation provided on the official SCT GitHub repository: spinalcordtoolbox/spinalcordtoolbox: Comprehensive and open-source library of analysis tools for MRI of the spinal cord. (github.com).

However, I encountered an issue while trying to locate the demo data necessary to run the following command:

sct_deepseg_sc -i t2.nii.gz -c t2

This command is outlined in the usage section of the documentation, but I couldn’t find the associated demo data to proceed with my experimentation.

Thank you.

2

I’ve located the repository spinalcordtoolbox/sct_tutorial_data: Data and scripts for SCT’s tutorials and courses (github.com).

Could you please confirm if this is the repository I should use for accessing demo data?

Thank you.

3

Hi @Yuexiang_Ji,

My apologies for the late reply. I was out of the office last week.

This command is a very general command, and so it can be used on any T2 image of the spinal cord.

SCT does provide several example datasets, depending on which documentation you are following:

All three of these datasets contain a file called t2.nii.gz. You can use the t2.nii.gz image from any of these datasets – it doesn’t matter too much which one you use, as the results will be similar for each. :slight_smile:

Still, I would recommend downloading sct_tutorial_data and starting with the SCT web tutorials.

Kind regards,
Joshua

2 Likes
4

Dear @joshuacwnewton,

Thank you for your sincere answer.

I have understood the difference and the usage of the three directory.

In addition, I appreciate your advice and will start to study the SCT web tutorial so that I can comprehend more about the tool.

Best regards,
Yuexiang Ji

1 Like