https://github.com/lren-chuv/hierarchizer

Reorganize DICOM files following a hierarchy based on meta-data fields
https://github.com/lren-chuv/hierarchizer

data-factory dicom docker-image mri python-3

Last synced: 3 months ago
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Reorganize DICOM files following a hierarchy based on meta-data fields

• Host: GitHub
• URL: https://github.com/lren-chuv/hierarchizer
• Owner: LREN-CHUV
• License: apache-2.0
• Created: 2017-02-20T10:27:14.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2018-08-07T09:22:03.000Z (almost 7 years ago)
• Last Synced: 2025-01-19T15:34:54.462Z (5 months ago)
• Topics: data-factory, dicom, docker-image, mri, python-3
• Language: Python
• Size: 47.9 KB
• Stars: 0
• Watchers: 5
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE

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# 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 -v :/output_folder -v :/meta_output_folder hbpmip/hierarchizer:1.3.8  [options]`

where:

*  is the folder containing the input DICOM/NIFTI files

*  is the folder that will contain the hierarchized DICOM/NIFTI files

*  is the folder that will contain the metadata files

*  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).