{"id":20361127,"url":"https://github.com/reubendo/remind","last_synced_at":"2026-05-21T16:46:38.819Z","repository":{"id":174806274,"uuid":"652753944","full_name":"ReubenDo/ReMIND","owner":"ReubenDo","description":"Scripts used for the conversion of the NRRD data to DICOM data","archived":false,"fork":false,"pushed_at":"2023-12-11T18:46:36.000Z","size":17,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-04T18:44:53.424Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ReubenDo.png","metadata":{"files":{"readme":"README.md","changelog":null,"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":"2023-06-12T18:17:56.000Z","updated_at":"2024-09-24T03:34:51.000Z","dependencies_parsed_at":null,"dependency_job_id":"f13e0181-d795-417c-8867-28dbc23abd7d","html_url":"https://github.com/ReubenDo/ReMIND","commit_stats":null,"previous_names":["reubendo/remind"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/ReubenDo/ReMIND","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ReubenDo%2FReMIND","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ReubenDo%2FReMIND/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ReubenDo%2FReMIND/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ReubenDo%2FReMIND/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ReubenDo","download_url":"https://codeload.github.com/ReubenDo/ReMIND/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ReubenDo%2FReMIND/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33307370,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-21T12:23:38.849Z","status":"ssl_error","status_checked_at":"2026-05-21T12:22:11.673Z","response_time":62,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":[],"created_at":"2024-11-14T23:46:37.378Z","updated_at":"2026-05-21T16:46:38.799Z","avatar_url":"https://github.com/ReubenDo.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ReMIND Data Conversion Scripts\n\nThis repository includes scripts designed for the conversion of ReMIND data between NRRD and DICOM formats. The scripts serve two primary purposes:\n\n1. **Conversion from NRRD to DICOM for TCIA:**\n    - Step 1: Conversion of NRRD images to DICOM images for ultrasound and MR data.\n    - Step 2: Conversion of NRRD SEG to DICOM SEG for segmentation files.\n\n2. **Conversion of TCIA Imaging Data from DICOM to NRRD:**\n    - Convert DICOM imaging data downloaded from TCIA into NIfTI or NRRD formats.\n\n## Example Output\nBelow is an example of a DICOM folder loaded in 3D Slicer:\n![image](https://github.com/ReubenDo/ReMIND/assets/17268715/8b057d4c-ab50-4884-b509-a615b7206c1c)\n\n## Conversion from NRRD to DICOM for TCIA\n### Step 1: Conversion of NRRD images to DICOM images\n- Ultrasound images are converted using the [Dicom3tools software](https://www.dclunie.com/dicom3tools.html) as multi-frame DICOM files.\n- MR data is converted using [3D Slicer](https://download.slicer.org/).\n\n#### Requirements\n1. Java: Download from [here](https://www.oracle.com/java/technologies/downloads/)\n2. 3D Slicer: Download from [here](https://download.slicer.org/)\n\n#### Command\nOn MacOS:\n```bash\n/Applications/Slicer.app/Contents/MacOS/Slicer --no-splash --python-script conversion_imaging.py --path_nrrd [PATH_TCIA_NRRD] --path_dicom ./dicom\n```\n\nOn Windows:\n```bash\nSlicer.exe  --no-splash --python-script nrrd_to_dicom_img.py --path_nrrd [PATH_TCIA_NRRD] --path_dicom ./dicom\n```\n\n### Step 2: Conversion of NRRD SEG to DICOM SEG\nNRRD segmentation files are converted with dcmqi using DICOM images as a reference.\n\n#### Requirements\n1. dcmqi: binaries for your operating system are available [here](https://qiicr.gitbook.io/dcmqi-guide/opening/installation/binary_packages)\n\n#### Command\nTo process segmentations:\n\n```python nrrd_to_dicom_seg.py--path_nrrd [PATH_TCIA_NRRD] --path_dicom ./dicom --img2seg ../dcmqi-1.2.4-mac/bin/itkimage2segimage```\n\n# Conversion of the imaging data from DICOM to NRRD\nTo convert DICOM imaging data downloaded from TCIA into NIfTI or NRRD formats, follow these guidelines:\n\n#### Requirements\n1. Download imaging data from [TCIA](https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=157288106)\n2. Python with the required packages (install with ```pip install -r requirements.txt```)\n\n#### Command\nTo convert DICOM images into NIfTI format:\n```python dicom_to_nifti-nrrd_img.py --path_dicom [PATH_REMIND_DATA] --nifti  ```\n\nTo convert DICOM images into NRRD format:\n```python dicom_to_nifti-nrrd_img.py --path_dicom [PATH_REMIND_DATA] --nrrd  ```\n\nReplace `[PATH_REMIND_DATA]` with the path to the downloaded ReMIND imaging data (e.g., `data/ReMIND_TCIA/manifest-1695134609823/ReMIND/`).\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Freubendo%2Fremind","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Freubendo%2Fremind","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Freubendo%2Fremind/lists"}