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/sctSpinal 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)