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itk_resample

Resample ITK image-label sample pairs to a target spacing or size.

Usage

itk_resample <field> <source_folder> <dest_folder> [options]

Field Types

  • image: For image data (uses linear interpolation, preserves data type)
  • label: For label/segmentation data (uses nearest neighbor interpolation)
  • dataset: Processes both image/ and label/ subfolders with appropriate settings

Parameters

  • source_folder: Folder containing source image files
  • dest_folder: Destination folder for resampled files (created if missing)
  • --spacing Z Y X: Target spacing per dimension (ZYX order). Use -1 to ignore a dimension
  • --size Z Y X: Target size per dimension (ZYX order). Use -1 to ignore a dimension
  • --target-folder PATH: Folder of reference images (mutually exclusive with --spacing/--size)
  • -r, --recursive: Recursively process subdirectories, preserving layout
  • --mp: Enable multiprocessing
  • --workers N: Number of worker processes for multiprocessing

Output

  • Resampled files in dest_folder
  • resample_configs.json: Configuration used for resampling
  • meta.json: Metadata for the resampled dataset

Examples

# Resample entire dataset to 1.0mm isotropic spacing
itk_resample dataset /data/source /data/resampled \
    --spacing 1.0 1.0 1.0 --mp

# Resample only in-plane, keep Z spacing
itk_resample image /data/source /data/resampled \
    --spacing -1 0.5 0.5

# Resample to match reference dataset
itk_resample dataset /data/source /data/resampled \
    --target-folder /data/reference --mp