We are releasing the new version of T2w dog template generated using all the 5 subjects. We provide the cord segmentation, vertebral levels and disc labels along with the template.
What has changed from the previous release:
- Centerlines on the subjects were improved to create a perfectly straight template and avoid any wiggling.
- The new template has 24 discs when compared to r20240112.
- The spacing in between the discs is kept intact w.r.t. to the 5 subjects used for the template creation process.
- More precise cord segmentation.
- The template along with it's derivatives (in the PAM50 format) can be found in the link above. Here's how they are named:
templatedog_t2w.nii.gz --> T2w template using the 5 subjects
templatedog_level.nii.gz --> T2w spinal cord mask with discrete vertebral levels
templatedog_label_disc.nii.gz --> point-wise intervertebral disc labels
templatedog_cord.nii.gz --> spinal cord mask
Protocol to generate the above derivatives
- templatedog_t2w.nii.gz
Use the SCT template creation framework along with the initially mentioned parameters: https://github.com/neuropoly/template
- templatedog_cord.nii.gz
2.1. Command used: sct_deepseg_sc -i templatedog_t2w.nii.gz -c t2s -o templatedog_cord.nii.gz
2.2. Manual correction was done by Rohan Banerjee on the output from sct_deepseg_sc on just the right side.
2.3. Use script from scripts/symmetrize_cord_segmentation.py to make symmetric spinal cord segmentation.
- templatedog_label_disc.nii.gz
sct_label_utils -i templatedog_t2w.nii.gz -create-viewer 1:24 -o templatedog_label_disc.nii.gz -qc qc_templatedog_label_disc
- templatedog_level.nii.gz
sct_label_vertebrae -i templatedog_t2w.nii.gz -s templatedog_cord.nii.gz -c t2 -discfile templatedog_label_disc.nii.gz