PAM50_t2 template contains signal outside spinal cord - impact on fMRI registration quality?

Selma · February 19, 2026, 2:04pm

Hi,

I’m analysing spinal MRI images for the first time and ran into something that might not be a problem at all but that I wanted to check to be sure.

SCT version: 7.0 OS: macOS

Pipeline:

T1 processing: sct_register_to_template → sct_warp_template
T2s processing: sct_register_multimodal (PAM50_t2 → T2s, initialised with T1 warp via -initwarp) → sct_warp_template (T2s space)
fMRI processing: sct_register_multimodal using warped PAM50_t2.nii.gz as source image → sct_warp_template (fMRI space)

When viewing the original PAM50_t2 template, it contains substantial signal outside the spinal cord itself - vertebral bodies and surrounding tissue are clearly visible. After warping to subject T2s space, these surrounding structures are also present in the warped template.

In our fMRI pipeline, we use the warped PAM50_t2.nii.gz as the source image for registration to fMRI space:

bash:

sct_register_multimodal -i PAM50_t2.nii.gz \
                        -d fmri_mean.nii.gz \
                        -iseg PAM50_cord.nii.gz \
                        -dseg fmri_seg.nii.gz \
                        -param step=1,type=seg,algo=affine,slicewise=1,metric=MeanSquares,smooth=3:step=2,type=seg,algo=syn,metric=MeanSquares,smooth=1,iter=5

Questions

Does the presence of surrounding anatomy in PAM50_t2.nii.gz negatively affect the quality of registration to fMRI space?
Would it be better to mask PAM50_t2.nii.gz with the cord segmentation (PAM50_cord.nii.gz) before using it as a registration source, so that only cord signal is used for matching?