Segmentation and CSA on T1w vs FLAIR

Marco10 · February 4, 2025, 2:04pm

Dear SCT Community,

I am seeking advice on the most appropriate imaging modality for segmenting the upper cervical cord, vertebral labeling, and estimating cross-sectional area (CSA). Given that I have both T1-weighted and FLAIR images, which modality would be preferable for CSA estimation?

The contrast appears similar in both images, as the cerebrospinal fluid (CSF) is hypointense in relation to the cord in both modalities.

Thank you for your insights.

Best regards,

Marco

jcohenadad · February 4, 2025, 10:14pm

Hi Marco,

I would definitely pick the one that has the best axial resolution. Obviously, contrast should also be sufficient for a reliable automated spinal cord segmentation. Can you show some examples?

Marco10 · February 5, 2025, 9:21am

The images have the same resolution. Which segmentation module would you recommend, since FLAIR is not a modality that can selected in sct_deepseg_sc ?