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itk_convert

Convert ITKIT datasets between different formats and frameworks.

Subcommands

  • format: Convert medical image file formats
  • monai: Convert to MONAI Decathlon format
  • torchio: Convert to TorchIO format

Format Conversion

Convert medical image files between different formats while preserving metadata.

Usage

itk_convert format <target_format> <source_folder> <dest_folder> [options]

Supported Formats

  • mha: MetaImage (single file)
  • mhd: MetaImage Header (with separate .raw file)
  • nii.gz: Compressed NIfTI
  • nii: NIfTI (uncompressed)
  • nrrd: Nearly Raw Raster Data

Parameters

  • target_format: Target file format
  • source_folder: Path to ITKIT dataset
  • dest_folder: Path to output dataset
  • --mp: Enable multiprocessing
  • --workers N: Number of worker processes

Examples

# Convert MHA to compressed NIfTI
itk_convert format nii.gz /data/mha_dataset /data/nifti_dataset

# Convert to NRRD with multiprocessing
itk_convert format nrrd /data/input /data/output --mp --workers 8

# Convert MHD to MHA
itk_convert format mha /data/mhd_dataset /data/mha_dataset

MONAI Conversion

Convert ITKIT dataset to MONAI Decathlon format.

Usage

itk_convert monai <source_folder> <dest_folder> [options]

Parameters

  • source_folder: Path to ITKIT dataset
  • dest_folder: Path to output dataset in MONAI format
  • --name: Dataset name for the manifest file (default: ITKITDataset)
  • --description: Dataset description for the manifest file
  • --modality: Primary imaging modality (default: CT)
  • --split: Which split to treat the data as: train | val | test | all (default: train)
  • --labels: Label names in order (e.g., background liver tumor). Index 0 is background
  • --mp: Enable multiprocessing
  • --workers N: Number of worker processes

Output

  • Converted files in .nii.gz format
  • dataset.json manifest file
  • meta.json ITKIT-style metadata

Examples

itk_convert monai /data/itkit_dataset /data/monai_dataset \
    --name MyDataset \
    --modality CT \
    --labels background liver tumor \
    --mp

TorchIO Conversion

Convert ITKIT dataset to TorchIO format.

Usage

itk_convert torchio <source_folder> <dest_folder> [options]

Parameters

  • source_folder: Path to ITKIT dataset
  • dest_folder: Path to output dataset in TorchIO format
  • --no-csv: Skip creating subjects.csv manifest file
  • --mp: Enable multiprocessing
  • --workers N: Number of worker processes

Output

  • Converted files in .nii.gz format
  • subjects.csv manifest file (unless --no-csv is specified)
  • meta.json ITKIT-style metadata

Examples

itk_convert torchio /data/itkit_dataset /data/torchio_dataset --mp