Workflow for manual labeling

Identifing problematic vertebral labeling (QC)

Send QC to participants.
Sort QC by subject.
Define the subject range that each participant will help with.
Sort by Function (reverse order) to see vertebral labeling.
Identify problematic labeling following this procedure.
- If C2-3 is not aligned with the disc, mark as ❌.
- Mark as ⚠️ for bad data quality (subjects to exclude) : most likely FOV that cuts C2-C3.
- Here is an example of an adequate labeling ✅:
If some segmentation errors are noticed, mark the segmentation of that subject as ❌ (you can search for the subject to find its segmentation).
Download the lists by clicking on Download QC Fails and on Download Qc Artifacts (at the very bottom of the QC page).
Send both lists to the lead team.
Lead team will package the data (automatic labeling + associated data) and send to the respective participant .
Manually correcting vertebral labeling
Download SCT v5.3, see here for installation instructions.
Identify C1-C2, C2-C3 and C3-C4 by following this procedure. (A tutorial is included)
Package the derivatives folder as a ZIP package and send it to the lead team.
Lead team will quickly review and add to the git-annex centralized repository and add the YML list of subjects to exclude to exclude.yml.