Outputs

CSV tables are the pipeline’s audit spine. Each stage preserves existing columns and adds or normalizes the fields needed downstream.

Stage	Main output	Error/auxiliary output	Key additions
`parse`	`dicom_index.csv`	`dicom_index_errors.csv`; optional `dicom_tags_snapshot.ndjson`	IDs, `dicom_path`, selected DICOM tags
`clean`	`<input>_clean.csv`	—	volume grouping, normalized date/time, ordering and geometry fields
`ingest`	`dicom_index_clean.csv`	parse artifacts	parsed and curated volume rows
`convert`	`nifti_index.csv`	`conv_errors.csv`	`nifti_path`
`segment`	input CSV in place, or `--csv_path_out`	`seg_errors.csv` and warning report when applicable	`mask_<output>` paths
`phase`	input CSV in place, or `--csv_path_out`	`phase_errors.csv`	`totalseg_*`, including `totalseg_phase`
`radiomics`	`<input>_radiomics.csv`	`radiomics_errors.csv`	ROI-prefixed PyRadiomics features

Defaults are relative to the input CSV or selected output directory. Explicit paths are recommended in scheduled pipelines.

Identity and traceability

The core identifiers are patient_key, study_id, and series_id. Parse also retains _patient_key_raw when standardization is applied. dicom_path may serialize multiple files for a volume or contain archive-aware locations; consumers should not assume it is a single ordinary filesystem path.

Long-running stages use an internal _source_idx for stable resume and merge behavior. It is removed from finalized user-facing tables.

Image and mask paths

nifti_path identifies the converted CT image. Segmentation outputs are stored in columns beginning with mask_; their exact set follows the manifest tasks. Paths may be absolute depending on the supplied output directory, so moving a dataset can invalidate a table. If portability matters, move artifacts and rewrite paths as one controlled operation.

Error tables

Error CSVs contain the failed source row plus an error message. A command can complete while some rows fail, making these tables part of the expected output rather than disposable logs. Check all of the following before downstream use:

expected input and output row counts;
missing nifti_path or mask_* values;
command-specific error and warning tables;
whether filtering intentionally reduced radiomics rows.

Checkpoint files and JSON state may appear beside the configured main/error outputs during resumable runs. They are implementation artifacts, not cohort tables, and should not be passed to the next stage.