Is there a command line to straighten a spinal cord segment?

MRI Processing & SCT
1

I’m aware this is a component of the segmentation process (straighten the native mri → segment), but is there a command line to extract that straightened image?

2

Dear @Matthew_Kirshner,

My deepest apologies for the late reply.

There are a few different paths to straightening the spinal cord outside of other processes:

  • Any process that straightens the spinal cord should produce a warp_curve2straight.nii.gz warping field image. This warping field can be re-used alongside the input image using sct_apply_transfo to reproduce a straightened image.
  • If you don’t have any existing curve2straight warping field, you can use the CLI script sct_straighten_spinalcord directly to produce this output (sct_straighten_spinalcord - Spinal Cord Toolbox documentation).

Please don’t hesitate to ask any further questions.

Kindly,
Joshua