itk_extract

Extract specified classes from ITK semantic segmentation maps.

Usage

itk_extract <source_folder> <dest_folder> <mappings...> [options]

Parameters

• source_folder: Folder containing source images
• dest_folder: Destination folder to save extracted label files (created if missing)
• mappings: One or more label mappings in "source:target" format (e.g., "1:0" "5:1")
• -r, --recursive: Recursively process subdirectories and preserve relative paths
• --mp: Enable multiprocessing
• --workers N: Number of worker processes for multiprocessing

Output

• Remapped label files written to dest_folder (extensions normalized to .mha)
• extract_meta.json: Per-sample metadata
• extract_configs.json: Configuration used

Examples

# Extract liver (label 1) and tumor (label 5), renumber to 0 and 1
itk_extract /data/labels /data/extracted "1:0" "5:1" --mp

# Extract specific organs from multi-organ segmentation
itk_extract /data/multi_organ /data/liver_kidney \
    "1:1" "2:2" \
    --recursive --mp