{"id":20911082,"url":"https://github.com/lren-chuv/hierarchizer","last_synced_at":"2026-04-27T10:31:25.203Z","repository":{"id":144914445,"uuid":"82545624","full_name":"LREN-CHUV/hierarchizer","owner":"LREN-CHUV","description":"Reorganize DICOM files following a hierarchy based on meta-data fields","archived":false,"fork":false,"pushed_at":"2018-08-07T09:22:03.000Z","size":49,"stargazers_count":0,"open_issues_count":1,"forks_count":1,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-01-19T15:34:54.462Z","etag":null,"topics":["data-factory","dicom","docker-image","mri","python-3"],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/LREN-CHUV.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-02-20T10:27:14.000Z","updated_at":"2018-08-07T09:22:04.000Z","dependencies_parsed_at":null,"dependency_job_id":"76791fa6-a337-4338-9e22-92d468dde5ec","html_url":"https://github.com/LREN-CHUV/hierarchizer","commit_stats":null,"previous_names":[],"tags_count":36,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LREN-CHUV%2Fhierarchizer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LREN-CHUV%2Fhierarchizer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LREN-CHUV%2Fhierarchizer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LREN-CHUV%2Fhierarchizer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LREN-CHUV","download_url":"https://codeload.github.com/LREN-CHUV/hierarchizer/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243301123,"owners_count":20269287,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["data-factory","dicom","docker-image","mri","python-3"],"created_at":"2024-11-18T14:19:10.540Z","updated_at":"2025-12-26T10:49:23.857Z","avatar_url":"https://github.com/LREN-CHUV.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![CHUV](https://img.shields.io/badge/CHUV-LREN-AF4C64.svg)](https://www.unil.ch/lren/en/home.html) [![License](https://img.shields.io/badge/license-Apache--2.0-blue.svg)](https://github.com/LREN-CHUV/hierarchizer/blob/master/LICENSE) [![DockerHub](https://img.shields.io/badge/docker-hbpmip%2Fhierarchizer-008bb8.svg)](https://hub.docker.com/r/hbpmip/hierarchizer/) [![Codacy Badge](https://api.codacy.com/project/badge/Grade/830355fa4faa47169b44572ec43f6fea)](https://www.codacy.com/app/hbp-mip/hierarchizer?utm_source=github.com\u0026amp;utm_medium=referral\u0026amp;utm_content=LREN-CHUV/hierarchizer\u0026amp;utm_campaign=Badge_Grade)\n[![CircleCI](https://circleci.com/gh/LREN-CHUV/hierarchizer.svg?style=svg)](https://circleci.com/gh/LREN-CHUV/hierarchizer)\n\n# Hierarchizer\n\n## Introduction\n\nDocker container containing Python scripts that reorganize DICOM files creating a folder hierarchy using meta-data found in DICOM files\nand/or external meta-data files (e.g. XML files from PPMI).\n\n## Usage\n\nRun: `docker run --rm -v \u003cinput_folder\u003e:/input_folder -v \u003coutput_folder\u003e:/output_folder -v \u003cmeta_output_folder\u003e:/meta_output_folder hbpmip/hierarchizer:1.3.8 \u003cincoming_dataset\u003e [options]`\n\nwhere:\n* \u003cinput_folder\u003e is the folder containing the input DICOM/NIFTI files\n* \u003coutput_folder\u003e is the folder that will contain the hierarchized DICOM/NIFTI files\n* \u003cmeta_output_folder\u003e is the folder that will contain the metadata files\n* \u003cincoming_dataset\u003e is the dataset name (e.g. CLM, EDSD, PPMI, ADNI)\n* options:\n  * -h, --help : show help\n  * --type TYPE : Type of image files (DICOM, NIFTI)\n  * --output_folder_organisation OUTPUT_FOLDER_ORGANISATION : String containing DICOM fields to use to create\n  the output folder hierarchy (default='#PatientID/#StudyID/#SeriesDescription/#SeriesNumber')\n  * --unknown_value UNKNOWN_VALUE : value to use if a field cannot be found (default=\"unknown\")\n  * --ppmi_xml_extension : try to use meta-data from PPMI XML files if a field cannot be found in the DICOM files\n  * --excluded_fields EXCLUDED_FIELDS [EXCLUDED_FIELDS ...]\n  * --allowed_field_values FIELD=VALUE1,VALUE2,VALUE3 [FIELD=VALUE1,VALUE2 ...] : ignore input files containing values outside of the range of allowed field values.\n\nExample:\n```\n  docker run --rm \\\n    -v $(pwd)/original:/input_folder\n    -v $(pwd)/hierarchized:/output_folder \\\n    -v $(pwd)/hierarchized/meta:/meta_output_folder \\\n    hbpmip/hierarchizer:1.3.8 MyDataset --type DICOM\n```\n\n## Build\n\nRun: `./build.sh`\n\n\n## Publish\n\nRun: `./publish.sh`\n\n\n## NOTE\n\n`Any '*' symbol in the output path is replaced by an '_' symbol.`\n\n# Acknowledgements\n\nThis work has been funded by the European Union Seventh Framework Program (FP7/2007­2013) under grant agreement no. 604102 (HBP)\n\nThis work is part of SP8 of the Human Brain Project (SGA1).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flren-chuv%2Fhierarchizer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flren-chuv%2Fhierarchizer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flren-chuv%2Fhierarchizer/lists"}