How to test the method

[sandrinebedard]

Description

This issue explains how to run the rootlets-based registration to template

Installation

Update SCT version

cd $SCT_DIR  # Go to SCT directory (if not already there)
git fetch
git pull origin master
./install_sct.  # Rerun installer (if you were in a older version)
sct_register_to_template -h. # Check if the flag -lrootlet is available

Registration to template

1.Rootlets segmentation

Rootlets segmentation method currently works on T2w contrast, and prefered on isotropic resolution. It will segment the dorsal nerve rootlets from levels C2 to C8.

sct_deepseg -i <FILE T2w> -task seg_spinal_rootlets_t2w -qc ./qc

Check results --> look if all the levels form C2-C8 are segmented:

Enregistrement.d.ecran.le.2025-01-24.a.10.58.26.mov

To quickly assess if a level is missing, you can consider running the following:

sct_label_utils -i <FILE ROOTLET> -cubic-to-point -o <FILE ROOTLET>_mid.nii.gz
sct_label_utils -i <FILE SEG> -project-centerline <FILE ROOTLET>_mid.nii.gz  -o <FILE ROOTLET>_mid_center.nii.gz
sct_qc -i <FILE T2w>  -s <FILE ROOTLET>_mid_center.nii.gz -p sct_label_utils -qc $PATH_QC

It will show the center-of-mass of the each levels from the rootlet segmentation, where you can quickly assess if the position is correct, or if a level is missing:

Example of where some levels are missing:

2.Spinal cord segmentation

Run spinal cord segmentation for registration to template

sct_deepseg -i <FILE T2w> -task seg_sc_contrast_agnostic -qc ./qc

Check results : Validate the quality of the spina cord segmentation

3.Registration to template

sct_register_to_template -i <FILE T2w> -s <FILE SEG> -lrootlet <FILE ROOTLET> -qc ./qc

Check results : compare the alignement of the rootlets vs. PAM50

[jingxuangong]

Hi Sandrine!

I've tried all the steps above on my T2w data and everything worked well without any spinal levels missing! The only problem I had was the option -lrootlet was missing. I tried re-downloading the newest version of SCT but it still didn't have the rootlet registration to template. Are there any other steps that you recommend I try?

[sandrinebedard]

Hi Sandrine!

I've tried all the steps above on my T2w data and everything worked well without any spinal levels missing! The only problem I had was the option -lrootlet was missing. I tried re-downloading the newest version of SCT but it still didn't have the rootlet registration to template. Are there any other steps that you recommend I try?

Hi! For now, the method is only available in the master branch of SCT and not in a stable version, have you installed 6.5 or from Github?

I would recommend you install from the master branch as described option-2-install-from-github-development

Let me know if this works!

[jingxuangong]

Hi Sandrine!
I've tried all the steps above on my T2w data and everything worked well without any spinal levels missing! The only problem I had was the option -lrootlet was missing. I tried re-downloading the newest version of SCT but it still didn't have the rootlet registration to template. Are there any other steps that you recommend I try?

Hi! For now, the method is only available in the master branch of SCT and not in a stable version, have you installed 6.5 or from Github?

I would recommend you install from the master branch as described option-2-install-from-github-development

Let me know if this works!

Thanks for the tip! I re-installed the newest development version of SCT and the -lrootlet option worked fine for me!