Is segmentation of T1-weighted images of the lumbar spine possible?

SCT
1

Dear SCT team,

Hi.
I am currently performing segmentation of T1-weighted images of the lumbar spine using SCT.
However, I am having trouble with prop_seg and deep_seg not recognizing the spinal cord area well. In the first place, does SCT support segmentation of lumbar spine MRI anatomy images as well as cervical spine?" I would appreciate your answer.

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Hi @amijas:

For lumbar segmentation of T1w images:

  • You are correct that the default traditional SC segmentation tools (sct_propseg, sct_deepseg_sc) tend to perform poorly on the lower regions of the spinal cord.
  • However, sct_propseg does have quite a few options that allow you to customize the approach: Fixing a failed sct_propseg segmentation - Spinal Cord Toolbox documentation. There may be a set of parameters that would work well for your specific data. But, the parameters will depend on exactly how the segmentation has failed (e.g. over- vs. under-segmentation), so I would need to be able to test on your data to make recommendations.
  • We do also have a dedicated lumbar segmentation model (sct_deepseg -task seg_lumbar_sc_t2w). However, unfortunately it is only available for the T2w contrast at this time.
  • SCT is also in the process of working on a contrast-agnostic segmentation model, which may work better on T1w lumbar regions than the traditional sct_propseg/sct_deepseg_sc. I would be happy to update this post once the model is available for testing.

Kind regards,
Joshua

1 Like
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Hi Joshua

Thank you for your kind reply.
I tried the troubleshooting methods listed in the link you posted (Parameter “-init”, Parameter “-init-mask”, Parameter “-init-centerline”, Smoothing the image), but none of them worked.
As you can see in the attached image, only a small portion of the spinal cord is segmented.
At this point, we think that the quality of the image (T2MEDIC) may be too rough, and we are working on a new imaging protocol that will allow us to get a cleaner image.
Do you have any other ideas on this?

image
image4144×876 170 KB

Kind regards,
amijas

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Hi @amijas,

We have recently developed a new model for segmenting the spinal cord, that is more robust across various MRI contrasts. If you send me your image in private, we could give it a try, and if it works well we will give you access to that model before the next public release.

Cheers,
Julien

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Hi Julien,

Thank you for your kind suggestion.
When you say “send image in private,” is it OK to send it to your email address, or is there such a function in this forum?

Kind regards,
amijas

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to my email, yes