SCT Interface

Overview

scimagR provides R wrappers for the Spinal Cord Toolbox (SCT) command-line tools. These wrappers handle: - Path resolution (respects SCT_DIR environment variable) - Input validation - Idempotent execution (skip if output exists) - Structured error reporting - Optional QC report generation

Configuration

Set the SCT_DIR environment variable if SCT is not on your PATH:

Sys.setenv(SCT_DIR = "/path/to/sct")

Or add it to your .Renviron:

SCT_DIR=/path/to/sct

Spinal Cord Segmentation

library(scimagR)

sc_seg <- sct_segment_sc(
  input = "sub-01_T2w.nii.gz",
  qc_dir = "qc/"
)

Lesion Segmentation (SCIsegV2)

lesion_seg <- sct_segment_lesion(
  input = "sub-01_T2w.nii.gz",
  qc_dir = "qc/"
)

Vertebral Labeling

vert_labels <- sct_label_vertebrae(
  input = "sub-01_T2w.nii.gz",
  segmentation = sc_seg
)

Parameter Extraction

# Lesion parameters (volume, length, tissue bridges)
lesion_csv <- sct_analyze_lesion(
  lesion_seg = lesion_seg,
  sc_seg = sc_seg
)

# Morphometric parameters (CSA, diameters per level)
csa_csv <- sct_process_segmentation(
  sc_seg = sc_seg,
  vert_labels = vert_labels
)

QC Reports

Generate HTML QC reports to visually verify segmentations:

sct_generate_qc(
  input = "sub-01_T2w.nii.gz",
  segmentation = sc_seg,
  qc_dir = "qc/"
)

Idempotent Execution

All SCT wrappers are idempotent by default. If the output file already exists, the function returns the existing path without re-running:

# First call: runs segmentation
sct_segment_sc("sub-01_T2w.nii.gz")

# Second call: skips, returns existing path
sct_segment_sc("sub-01_T2w.nii.gz")

# Force re-run:
sct_segment_sc("sub-01_T2w.nii.gz", overwrite = TRUE)

Troubleshooting

Common issues:

• “Cannot find sct_deepseg on PATH”: Set SCT_DIR or add SCT bin/ to PATH
• Segmentation fails silently: Check stderr output in the returned result
• Python errors: Ensure the correct Python environment is activated