Warping the spinal levels to the fMRI space

Now that we’ve registered the PAM50 template with the motion-corrected fMRI data, we can use the resulting warping field to transform the full template to the space of the dMRI data.

sct_warp_template -d fmri_moco_mean.nii.gz -w warp_template2fmri.nii.gz -s 1 -a 0 -qc ~/qc_singleSubj

Input arguments

• -d : Destination image the template will be warped to.

• -w : Warping field (template space to anatomical space).

• -s : Because -s 1 is specified, spinal levels will be warped.

• -a : Because -a 0 is specified, the white and gray matter atlas will not be warped.

• -qc : Directory for Quality Control reporting. QC reports allow us to evaluate the results slice-by-slice.

Output files/folders

• label/template/ : This directory contains the entirety of the PAM50 template, transformed into the fMRI space.

• label/spinal_levels/ : This direct contains 20 label images corresponding to different spinal cord levels, spanning both C1:C8 and T1:T12, transformed into the fMRI space. In each NIfTI file, the value of each voxel is the probability for this voxel to belong to the spinal level.

Visualizing the spinal levels

If you have fsleyes installed, you can visualize the warped spinal levels together using the following syntax:

fsleyes --scene lightbox --hideCursor fmri_moco_mean.nii.gz -cm greyscale -dr 0 1000 \
                                      label/spinal_levels/spinal_level_03 -cm red \
                                      label/spinal_levels/spinal_level_04 -cm blue \
                                      label/spinal_levels/spinal_level_05 -cm green \
                                      label/spinal_levels/spinal_level_06 -cm yellow