Rootlets-informed lumbar registration

[valosekj]

Description

Similarly to the cervical spinal cord (repo, preprint), we could leverage rootlets or spinal levels to inform the registration to the PAM50 template.

Note

Since lumbar rootlet segmentation has proven to be challenging, we may need to manually label the spinal levels based on the rootlet entry zones. Or develop a method to do so automatically. (For the subject below, manually segmented rootlets are available.)

Pseudo-commands:

# 1. Cropping
# I cropped the image manually to reduce its size in FSLeyes using Tools/Crop. I saved it with the suffix _roi

# 2. Cord segmentation
sct_deepseg spinalcord -i sub-CTS04_ses-SPpre_acq-ax_T2w_roi.nii.gz

# 3. Cord segmentation labeling
# I manually labelled the cord segmentation in FSLeyes based on the rootlets entry zones. I saved it with the suffix roi_seg_labeled

# 4. Rootlet midpoints
sct_label_utils -i sub-CTS04_ses-SPpre_acq-ax_T2w_roi_seg_labeled.nii.gz -cubic-to-point -o labels.nii.gz

# 5. Registration
sct_register_to_template -i sub-CTS04_ses-SPpre_acq-ax_T2w_roi.nii.gz -s sub-CTS04_ses-SPpre_acq-ax_T2w_roi_seg.nii.gz -lspinal labels.nii.gz -c t2

TODO

• tweak registration parameters
• try different number of labels (2 or 3+; details)

[sandrinebedard]

Thanks for the issue @valosekj ! From what I have tested, more than 2 labels is indeed relevant as the length of each spinal level also varies! but of course, this depends on how distinguishable the rootlets are that 2 labels may still be useful.

[sandrinebedard]

@valosekj do you think we could also add the rootlets in the PAM50 template?

[valosekj]

@valosekj do you think we could also add the rootlets in the PAM50 template?

There’s currently no automatic method for segmenting rootlets below the Th2 level, so adding these rootlets to the PAM50 template would require segmenting them manually. Although the lumbar rootlets are present in the PAM50, they are blurred and "touching", so I'm not sure how it's feasible.

What would be the rootless usage? We already have PAM50_spinal_midpoint.nii.gz (shown in blue below) spanning the entire spine (though, it is not based on rootlets, and there's shift relative to PAM50_rootlets_midpoint.nii.gz (shown in orange below) in the cervical cord):