Rootlet-informed regsitration to PAM50 template

[sandrinebedard]

Description

This issue is a follow-up on #13. More precisly, the aim is to use the spinal nerve rootlets for registration to the template. The aim is to provide more accurate alinement of spinal levels, for example for groupe-level analysis in spinal cord fMRI.

(TODO: add more details)

[sandrinebedard]

Some points to consider:

• It takes ~ 15 min for the z b-spline reg of the rootlets with the PAM50 rootlets (on abbey)

  • Try to play with shrink factor of 4, then 2, 1 (with fewer steps for each)

• Maybe project in coronal plane to get a 2D image and estimate transfo on a 2D plane, and then ‘repmap’ the transformation into 3D by copying the values slicewise– cons: loss of precision (because of projection on single plane)

• We only dorsal rootlets --> could help adding to the PAM50 (but we don't really see them)

• Testing all discs vs C2,C7 vs C3,C5 for first registraton to the template → effect on last seg

[sandrinebedard]

Here are some premilinary results of sub-007_ses-headNormal and sub-007_ses-headDown (same subject, 2 head positions)of resgistration to the template using the nerve rootlets. here are the steps: Code version

1. Resgistration to the template using 2 mid-vertebrae labels
2. Bringing nerve rootlets to the template space
3. Z-regsitration of the rootlets with PAM50rootlets
4. Bringing spinal levels (PAM50) to native space using concatenated transforms of template reg + z-reg of rootlets
5. Getting midpoints of the spinal levels in the native space (form the registered PAM50 spinal levels)
6. Registration to the template using flag -lspinal using midpoints

Results

Traditional registration 2 template using 2 mid vertebrae labels (C2 and C7) (in PAM50 space):

https://github.com/user-attachments/assets/8598e05f-d187-4d68-b060-bab4a2c110ef

Regsitration to template using spinal nerve rootlets (in PAM50 space):

https://github.com/user-attachments/assets/0e7475df-9342-4d1b-941d-6a52240ff97c

I think this looks very promissing! Next steps:

• explore the impact of the first registration using 2 vs all discs
• try improve registration of nerve rootlets to reduce time of the resgistration