Question about SCT and spinereport

[MerveKaptan]

Hi @NathanMolinier,

Very excited to try this! I was wondering:

• whether it is possible to get the nice outputs related to disc, vertebrae etc. you put together within SCT?
• what canal model is used here? Is it from totalspineseg?
• what spinal cord segmentation model is used here? Is it from totalspineseg?

[NathanMolinier]

Hey @MerveKaptan ! Thank you for testing SpineReport !

What do you mean by the nice outputs related to the discs or vertebrae? Do you mean QC reports?

Regarding the canal and spinal cord segmentation, I am currently using TotalSpineSeg as the segmentation tool, but I plan to develop custom segmentation models that can be used instead. I will try to work on this as soon as possible.

[MerveKaptan]

Hi @NathanMolinier , thank you, very excited to try!

I mean these outputs related to morphometry of vertebrae, etc.- are they called QC reports?

1. Is there a way to get this output within SCT? For instance, we can run totalspineseg through SCT deepseg- is there a function which we can use in SCT based on the totalspineseg outputs that generates the outputs above (vertebrae volume etc etc) as a CSV?

Regarding canal and spinal cord segmentation, I am currently using TotalSpineSeg as the segmentation tool, but I plan to develop custom segmentation models to use instead. I will try to work on this as soon as possible.

2. Great! Based on your experience, what do you recommend? I also know there is a new canal model that we use - would you recommend comparing different segmentation models within SCT?

Thank you!
Merve

[NathanMolinier]

1. Is there a way to get this output within SCT? For instance, we can run totalspineseg through SCT deepseg- is there a function which we can use in SCT based on the totalspineseg outputs that generates the outputs above (vertebrae volume etc etc) as a CSV?

Oh, I misread your message, sorry! Right now, since SpineReport is not integrated into SCT, I haven’t implemented a way to use this repository directly with the outputs generated by SCT. However, I could add support for allowing users to provide their own segmentation as input.
For the time being, you could try installing both TotalSpineSeg and SpineReport separately? If that’s not convenient, I can let you know once it’s possible to use SpineReport directly with an SCT-based workflow.

2. Great! Based on your experience, what do you recommend? I also know there is a new canal model that we use - would you recommend comparing different segmentation models within SCT?

I think the canal model in SCT will still provide the best segmentation, although the latest TotalSpineSeg model has improved considerably. So, it might be best to wait until I add support for custom segmentations before using it for your project.

[MerveKaptan]

1. Is there a way to get this output within SCT? For instance, we can run totalspineseg through SCT deepseg- is there a function which we can use in SCT based on the totalspineseg outputs that generates the outputs above (vertebrae volume etc etc) as a CSV?

Oh, I misread your message, sorry! Right now, since SpineReport is not integrated into SCT, I haven’t implemented a way to use this repository directly with the outputs generated by SCT. However, I could add support for allowing users to provide their own segmentation as input.
For the time being, you could try installing both TotalSpineSeg and SpineReport separately? If that’s not convenient, I can let you know once it’s possible to use SpineReport directly with an SCT-based workflow.

2. Great! Based on your experience, what do you recommend? I also know there is a new canal model that we use - would you recommend comparing different segmentation models within SCT?

I think the canal model in SCT will still provide the best segmentation, although the latest TotalSpineSeg model has improved considerably. So, it might be best to wait until I add support for custom segmentations before using it for your project.

Thanks so much! I completely understand that integrating something like this into SCT would take additional development work, and I really appreciate you considering it.

Eventually, though, it would be amazing to have everything accessible within SCT — perhaps something along the lines of a --spinereport option that could take the segmentation outputs and generate the SpineReport-derived metrics directly (with SpineReport appropriately cited, of course!). From a workflow perspective, having segmentation and quantitative outputs available within a single SCT-based script would be incredibly convenient.

That being said, we will ofc SpineReport as a standalone tool for now!

Support for custom segmentations would also be extremely helpful! That would give us a lot more flexibility, particularly if we start systematically comparing different segmentation approaches/models. If we do end up doing that, we’d also be very happy to report back and share what we find.

Thanks again for all your work on this!