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_spinalcordperforms 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.
sct_smooth_spinalcordinvolves 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.
sct_smooth_spinalcordinvolves 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.gzand 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.