Launch Stage 1: generate sulcal graphs with Morphologist from raw T1 MRI data.

Launch Stage 2: extract 28 sulcal region crops with cortical_tiles.

Launch Stage 3: generate Champollion dataset YAML configuration files.

Launch encoder training: train a champollion_V1 self-supervised encoder for one sulcal region.

Dataset configs must exist before calling this tool — run start_config first (or supply config_dir if configs live outside the champollion_V1 submodule).

Launch Stage 4: compute sulcal embeddings across all 56 model folds (28 regions × 2 hemispheres).

Launch Stage 5: collect all per-region embedding CSVs into a single output directory.

Launch Stage 6: render sulcal graph meshes, cortical tile masks, and UMAP scatter plots.

Launch the full Champollion pipeline (all 6 stages sequentially). Returns a pipeline job_id immediately.

Launch scan-centric streaming pipeline: one worker per scan runs stages 2-4 in parallel.

Each worker owns one ScanId and processes cortical_tiles → config → embeddings sequentially for its scan, using file-presence barriers between stages. Stage 5 (combine) runs once after all workers drain.

Requires embeddings_only mode (training aggregates all subjects and cannot be parallelised per-scan).

Remove all cortical_tiles derivatives for a single subject.

Deletes per-subject NIfTI files (crops, labels, extremities, distbottom), per-subject subdirectories (skeletons/, foldlabels/, transforms/, distmaps/), and filters the subject's row from aggregated .npy arrays and their subject CSVs.

Use dry_run=True to preview what would be deleted without modifying anything.

Remove cortical_tiles outputs for all subjects that failed QC.

Reads a QC TSV/CSV file with 'participant_id' and 'qc' columns and deletes all files belonging to subjects with qc==0 or absent from the QC file. Equivalent to having run cortical_tiles with --sk_qc_path from the start.

Use dry_run=True to preview what would be deleted without modifying anything.

Get the current status and progress of a running or completed job.

List all jobs for a given output directory, optionally filtered by status.

Cancel a running job by sending SIGTERM to its process.

Retrieve the last N lines of a job's log output.

Get metadata about the Champollion pipeline and available MCP tools.

Check whether the Champollion pipeline is correctly configured and accessible.