Integrating Dog Template

How do you integrate the dog template (Releases · spinalcordtoolbox/template-dog · GitHub) instead of the PAM50 template? Additionally, how do you go about adding the vertebral levels, cord segments, etc?

Thank you for posting this, @Richard_Shinn.

Firstly, we need to properly package the dog template. We will take care of this ASAP. More details here.

Once the template is properly packaged, you will be able to use sct_register_to_template with the flag -t PATH_TEMPLATE, with PATH_TEMPLATE being the path to the dog template. For convenience, you can place it under $SCT_DIR/data/

Please note that the current plan is to add the spinal cord segmentation and the vertebral levels, which you will be able to use with sct_register_to_template. That way, you will be able to do groupwise analysis (eg: mapping of quantitative MRI metrics in the template space).

Not all of the features that are currently in the PAM50 template will be available in the dog template. For example, there is currently no white and gray matter atlases in the dog template, so it won’t be possible to do white or gray matter based analyses.