Segment SCI Lesion

Runs SCIsegV2 lesion segmentation model via SCT.

Usage

sct_segment_lesion(
  input,
  output = NULL,
  output_dir = NULL,
  overwrite = FALSE,
  verbose = TRUE,
  qc_dir = NULL
)

Arguments

input

Character. Path to T2w NIfTI file (.nii.gz).

output

Character. Path for output segmentation. Auto-generated if NULL.

output_dir

Character. Directory for output. Alternative to output.

overwrite

Logical. Re-run if output exists? Default FALSE.

verbose

Logical. Print progress. Default TRUE.

qc_dir

Character. If provided, auto-generate QC report.

Value

Character. Path to output lesion segmentation, or NA on failure.

Examples

if (FALSE) { # \dontrun{
sct_segment_lesion("sub-01_T2w.nii.gz")
} # }