Hierarchizer

Introduction

Docker container containing Python scripts that reorganize DICOM files creating a folder hierarchy using meta-data found in DICOM files and/or external meta-data files (e.g. XML files from PPMI).

Usage

Run: docker run --rm -v <input_folder>:/input_folder -v <output_folder>:/output_folder -v <meta_output_folder>:/meta_output_folder hbpmip/hierarchizer:1.3.8 <incoming_dataset> [options]

where:

• <input_folder> is the folder containing the input DICOM/NIFTI files
• <output_folder> is the folder that will contain the hierarchized DICOM/NIFTI files
• <meta_output_folder> is the folder that will contain the metadata files
• <incoming_dataset> is the dataset name (e.g. CLM, EDSD, PPMI, ADNI)
• options:
  • -h, --help : show help
  • --type TYPE : Type of image files (DICOM, NIFTI)
  • --output_folder_organisation OUTPUT_FOLDER_ORGANISATION : String containing DICOM fields to use to create the output folder hierarchy (default='#PatientID/#StudyID/#SeriesDescription/#SeriesNumber')
  • --unknown_value UNKNOWN_VALUE : value to use if a field cannot be found (default="unknown")
  • --ppmi_xml_extension : try to use meta-data from PPMI XML files if a field cannot be found in the DICOM files
  • --excluded_fields EXCLUDED_FIELDS [EXCLUDED_FIELDS ...]
  • --allowed_field_values FIELD=VALUE1,VALUE2,VALUE3 [FIELD=VALUE1,VALUE2 ...] : ignore input files containing values outside of the range of allowed field values.

Example:

  docker run --rm \
    -v $(pwd)/original:/input_folder
    -v $(pwd)/hierarchized:/output_folder \
    -v $(pwd)/hierarchized/meta:/meta_output_folder \
    hbpmip/hierarchizer:1.3.8 MyDataset --type DICOM

Build

Run: ./build.sh

Publish

Run: ./publish.sh

NOTE

Any '*' symbol in the output path is replaced by an '_' symbol.

Acknowledgements

This work has been funded by the European Union Seventh Framework Program (FP7/2007­2013) under grant agreement no. 604102 (HBP)

This work is part of SP8 of the Human Brain Project (SGA1).