Start Pipeline
start_pipelineLaunch all six Champollion pipeline stages sequentially and get a job ID for tracking, enabling a full MRI-to-sulcal-embedding run without manual stage calls.
Instructions
Launch the full Champollion pipeline (all 6 stages sequentially). Returns a pipeline job_id immediately.
reference_data_dir is optional and forwarded to stage 6 (snapshots) for UMAP plots.
A non-empty masks is forwarded to stages 2, 3 and 4, and names the
<datasets_root>/derivatives/champollion_V1/<masks or canonical_25>/ directory that
stages 5 and 6 read and write (region_embeddings, embeddings, snapshots).
overwrite, run_cka, regions, masks_version and cortical_version
apply to stage 4 (embeddings) only. regions are model names (e.g. SCsylv_left);
cortical_version must name where the stage-2 crops actually are.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| cpu | No | ||
| masks | No | ||
| njobs | No | ||
| dataset | Yes | ||
| regions | No | ||
| run_cka | No | ||
| parallel | No | ||
| crop_path | Yes | ||
| input_dir | Yes | ||
| overwrite | No | ||
| output_dir | Yes | ||
| sk_qc_path | No | ||
| models_path | Yes | ||
| skip_stages | No | ||
| datasets_root | Yes | ||
| masks_version | No | ||
| path_to_graph | Yes | ||
| cortical_version | No | ||
| labelling_session | No | ||
| path_sk_with_hull | Yes | ||
| reference_data_dir | No |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||