r20240709

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

1. templatedog_t2w.nii.gz

Use the SCT template creation framework along with the initially mentioned parameters: https://github.com/neuropoly/template

2. 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.

3. 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

4. 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

r20240112

What's changed

• Added cord segmentation - templatedog_cord.nii.gz
• Added intervertebral discs - templatedog_label_disc.nii.gz
• Added spinal cord segmentation labeled for vertebral level - templatedog_levels.nii.gz
• Added TXT file describing each file present in the template package - info_label.txt

T1w and T2w dog templates

Initial templates generated the structural MRI data of 5 subjects. The T1w and T2w templates were created separately and averaging was stopped after 12 iterations. Both the templates are In the same voxel and world space coordinates.

r20240112

What's changed:

• Fixed typo in the info_label.txt txt file: from templatedog_levels.nii.gz to templatedog_level.nii.gz