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 -a 0 -qc ~/qc_singleSubj

Input arguments:

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

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

• -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. In particular, we care about the PAM50_spinal_levels.nii.gz and PAM50_spinal_midpoint.nii.gz files, which contain the spinal level “full body labels” and “single-voxel point labels” respectively.