Confused segmentation for thoracic spine

Thank you for support.
I have some problems with my image.
I execute the command sct_propseg t1.nii.gz -c t1, but then the output image is incorrect, (attached)
please guide me on how to fix it.

I really appreciate any help you can provide.

Hi @Phuong_Hoai_Dinh

Thank you for reaching out. Few comments:

  • The image you are trying to segment has relatively poor resolution in the right-left direction, hence it will be difficult to obtain a reliable and precise segmentation
  • The cord/CSF contrast seems fairly low, hence the initialization of the algorithm failed. Providing a few manual labels could help. See tutorials
  • There is another function than PropSeg to segment the cord, which could work better for you. It is called sct_deepseg_sc.
  • If you send us a representative image, we could help you figure out the best parameter for your data.