Spinal cord smoothing as a preprocessing operation#

SCT provides a spinal cord smoothing function that takes into account the curvature of the cord, preserving the boundary between the spinal cord and cerebrospinal fluid. This is useful in a variety of situations:

  • It can be used to improve sensitivity of fMRI results while minimizing contamination from CSF

  • It can also be used to obtain more reliable cord segmentations, because smoothing will sharpen the edge of the cord and will blur out possible artifacts at the cord/CSF interface.

Downloading the files for this tutorial#

First, make sure that you have the following files in your working directory:

  • single_subject/data/t1.nii.gz: An anatomical spinal cord scan in the T1 contrast.

  • single_subject/data/t1_seg.nii.gz: 3D segmentation of the spinal cord, corresponding to the T1 image.

    You can get these files by downloading data_spinalcord-smoothing.zip.

Running the command#

Next, open up your terminal and run the following command:

sct_smooth_spinalcord -i t1.nii.gz -s t1_seg.nii.gz
Input arguments:
  • -i : The input image.

  • -s : A spinal cord segmentation mask corresponding to the input image. This is needed as sct_smooth_spinalcord performs a 1D smoothing operation following the cord centerline (as opposed to the cortical surface smoothing in FreeSurfer, which is 2D).

Output files/folders:
  • t1_smooth.nii.gz : The input image, smoothed along the spinal cord.

  • warp_curve2straight.nii.gz : sct_smooth_spinalcord involves an intermediate straightening step, so this is the 4D warping field that defines the transform from the original curved anatomical image to the straightened image.

  • warp_straight2curve.nii.gz : sct_smooth_spinalcord involves an intermediate straightening step, so this is the 4D warping field that defines the inverse transform from the straightened anatomical image back to the original curved image.

  • straight_ref.nii.gz : The straightened input image produced by the intermediate straightening step. Can be re-used by other SCT functions that need a straight reference space.

  • straightening.cache : SCT functions that require straightening will check for this file. If it is present in the working directory, straight_ref.nii.gz and the two warping fields will be re-used, saving processing time.

After smoothing, the apparent noise is reduced, while the cord edges are preserved, allowing a more reliable segmentation on a second pass.