Is there a way to segment nerve roots L1–S1 in spinal MRI using SCT

MRI Processing
1

Hi,
I’m working with 3D T2-weighted MRI scans of the lumbar spine (L1–S1), and I’m interested in segmenting the nerve roots coming out of the spinal canal (e.g., exiting through the neural foramina).

I’ve reviewed SCT’s documentation and found excellent tools for spinal cord and vertebral labeling, but I couldn’t find specific support for nerve root segmentation.

  • Is there an existing pipeline, module, or pretrained model that can help with this?
  • If not, do you recommend a strategy for customizing SCT to segment nerve roots (e.g., using spinal cord masks as a base, or integrating external U-Net models)?
  • Are there annotated datasets or atlases you recommend for this task?

Thank you very much!

Miri

2

Dear @mirit,

Thank you so much for your insightful questions! It is refreshing to see posts with such excellent detail. :slight_smile:

SCT does have a segmentation tool for segmenting roolets (sct_deepseg rootlets), however it focuses on just the rootlets, and is limited to the C2-T1 range, rather than the lumbar/sacral regions as requested.

I’ll check in with my colleagues who developed this approach, as they may have insight into approaches and challenges regarding the roots/rootlets problem domain. :slight_smile:

Kind regards,
Joshua