[Jules-GP]

Why

A cohort run showed two problems with the AREG IOS-CBCT results.

1. The patient folders used the matching key as their name. The key keeps only the digits of a file name, so the arches of case_042_T1_U.stl landed in a folder called 42. Nothing on disk ties 42 back to case_042.
2. In Fully-Automated mode, the meshes were in a frame the reader could not open. ASO orients the CBCT first, and every arch is registered onto that oriented scan. That scan stayed in the job's work directory and was deleted with it. Opened over the original CBCT, the registered meshes were off by the whole rotation ASO applied. The landmark residuals were good (0.7 to 3.7 mm on every arch), so the registration itself was right: only its target was missing from the results.

Change

Folder names

• New pipeline.patient_name(): it keeps the name up to the end of its first word that holds a digit, skipping a timepoint word.
  • case_042_T1_L.stl gives case_042
  • P_0001_T2.nii.gz gives P_0001
  • a name with no digit is kept whole
• discover() still pairs on patient_key, and the landmark files are still matched on it. Each pair now also carries its name, taken from the patient's first intraoral mesh (the files the folder holds).
• The output folder and the patients / unpaired keys of AREG_report.json use the name.
• Two keys that would share a name are kept apart: the second gets its key appended, so one patient can never overwrite another's arches.

The oriented CBCT

• When the CBCT came from ASO (Fully-Automated mode), each patient's folder now also receives:
  • the oriented scan, <scan>_Or.nii.gz;
  • ASO's <scan>_Or_transform.tfm (original scan to oriented one), for a reader who wants the meshes on the original scan instead.
• The report names both files (oriented_cbct, cbct_transform).
• A patient whose arches all failed gets no copy, and a missing file is a warning, not a failure.
• Semi-Automated and Registration register onto the caller's own scan, so nothing is copied back in those modes.

Compatibility

The report's patient keys change from the digit key ("1") to the name ("P001"). Nothing in the server or the Slicer client reads those keys.

Tests

• New tests for patient_name, for two keys that would share a name, and for Fully-Automated handing back the oriented CBCT and its transform, while Semi-Automated does not.
• The existing tests now expect the named folders and report keys.
• AREG_IOSCBCT: 217 passed.

[Copilot]

Copilot was unable to review this pull request because the user who requested the review has insufficient remaining quota.

An organization owner can choose the repository organization as the billing source for reviews requested by members with a paid Copilot license. Learn about Copilot code review billing.