S0: Setup

Environment validation, container bootstrapping, and policy gate verification.

Purpose

S0 ensures the processing environment is properly configured before any data processing begins. It validates:

1. Container runtime availability (Docker or Apptainer)
2. Required container images are present and functional
3. Dataset policy passes the v1 gate
4. Template data (PAM50) is accessible

Inputs

Outputs

Algorithm

1. Policy Gate

Loads policy/datasets.yaml and validates against the v1 schema:

• All required fields present
• Dataset keys are unique
• Selection constraints are valid
• Spec fields (has_fmap, has_physio) are boolean

2. Container Runtime Detection

Checks for available container runtimes in order:

1. docker — preferred
2. apptainer — fallback for HPC environments

3. Container Image Verification

For each required image, verifies:

4. PAM50 Template Check

Searches for PAM50 templates in order:

1. $PAM50_PATH environment variable
2. $SCT_DIR/data/PAM50
3. ~/sct_7.1/data/PAM50

CLI Usage

# Run S0 setup
spinalfmriprep run S0_SETUP --project-root /path/to/project

# Check S0 (verify artifacts exist)
spinalfmriprep check S0_SETUP --project-root /path/to/project

QC Status Schema

{
  "step": "S0_SETUP",
  "status": "PASS | FAIL",
  "failure_message": null,
  "checks": [
    {
      "name": "dataset_policy_gate",
      "passed": true,
      "message": "Dataset policy gate passed.",
      "details": { ... }
    },
    {
      "name": "container_runtime",
      "passed": true,
      "message": "Container runtime available.",
      "info": { "runtime": "docker", "version": "24.0.7" }
    }
  ]
}

Edge Cases

Dependencies

• Docker Engine ≥ 20.10 or Apptainer ≥ 1.0
• Python 3.11+
• Valid policy/datasets.yaml