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Run the SCI Analysis Pipeline

Source: R/pipeline-run.R
sci_run_pipeline.Rd

Orchestrates all external tool steps in sequence:

  1. DICOM metadata extraction

  2. Anonymization (if requested)

  3. DICOM to NIfTI conversion

  4. Spinal cord segmentation

  5. Lesion segmentation (SCIsegV2)

  6. Vertebral labeling

  7. Parameter extraction

  8. Merge & export

Usage

sci_run_pipeline(
  project_dir,
  steps = 1:8,
  anonymize = FALSE,
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

project_dir

Character. Path to workflowr project root.

steps

Integer vector. Which steps to run. Default 1:8.

anonymize

Logical. Run anonymization step. Default FALSE.

overwrite

Logical. Re-process existing outputs. Default FALSE.

verbose

Logical. Print progress. Default TRUE.

Value

Tibble with pipeline status per step.

Details

Each step checks for existing outputs (idempotent). The pipeline can be interrupted and resumed at any step.

Examples

if (FALSE) { # \dontrun{
sci_run_pipeline("~/projects/my-sci-study", steps = 1:3)
} # }