{"id":13695912,"url":"https://github.com/viswanath-lab/RadQy","last_synced_at":"2025-05-03T13:34:12.435Z","repository":{"id":37207258,"uuid":"213640827","full_name":"ccipd/MRQy","owner":"ccipd","description":"MRQy is a quality assurance and checking tool for quantitative assessment of magnetic resonance imaging (MRI) data. ","archived":false,"fork":false,"pushed_at":"2024-03-16T14:03:53.000Z","size":240449,"stargazers_count":88,"open_issues_count":7,"forks_count":27,"subscribers_count":5,"default_branch":"master","last_synced_at":"2024-05-08T05:41:45.844Z","etag":null,"topics":["imaging","machine-learning","medical-image-processing","medical-imaging","medical-physics","mri","python","quality-assurance","quality-control","quality-metrics"],"latest_commit_sha":null,"homepage":"","language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause-clear","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ccipd.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"ContributingGuidelines.md","funding":null,"license":"LICENSE.txt","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":"2019-10-08T12:49:45.000Z","updated_at":"2024-05-30T04:17:11.144Z","dependencies_parsed_at":"2023-01-31T05:00:57.694Z","dependency_job_id":"b3196e99-c06c-459b-9b23-a659c788d840","html_url":"https://github.com/ccipd/MRQy","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ccipd%2FMRQy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ccipd%2FMRQy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ccipd%2FMRQy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ccipd%2FMRQy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ccipd","download_url":"https://codeload.github.com/ccipd/MRQy/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224364472,"owners_count":17299079,"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":["imaging","machine-learning","medical-image-processing","medical-imaging","medical-physics","mri","python","quality-assurance","quality-control","quality-metrics"],"created_at":"2024-08-02T18:00:34.640Z","updated_at":"2025-05-03T13:34:12.422Z","avatar_url":"https://github.com/ccipd.png","language":"JavaScript","funding_links":[],"categories":["Tools"],"sub_categories":["QC metric and report generation"],"readme":"\u003c!-- ![Picture1](https://user-images.githubusercontent.com/50635618/77593997-b1492a00-6ecb-11ea-939c-c8962f371e5a.png) --\u003e\n\n![alt text](image.png)\n\n## Front-end View\n![gbm_mrqy](https://user-images.githubusercontent.com/50635618/77496601-b6519f00-6e21-11ea-8f52-16f33d4c66cc.gif)\n\n## Backend View\n![gbm_mrqy](https://user-images.githubusercontent.com/50635618/77506445-43095680-6e3c-11ea-9376-7be6f7cdc5d8.gif)\n \n\n\n# Table of Contents\n\n\n\n\n\n\n## Description\n\n\nThis tool takes **MRI** or **CT** datasets in the file formats as the input. \\\nA CLI command is used to generate several tags and noise/information measurements for quality assessment. These scripts save the calculated measures in a  _.tsv_ file as well as generate _.png_ thumbnails for all images in a subject volume. These are then fed to _.js_ scripts to create the user interface (_index.html_) output. A schematic illustrating the framework of the tool is as follows.\n\n\n\n![Picture1](https://user-images.githubusercontent.com/50635618/76675455-07df6b80-6590-11ea-85f7-13b71a9a1ec3.png)\n\n\n\n\n## Installation\n\nRadQy can be installed via `pip` or `conda`.\n\n### Using pip\n\n```bash\npip install radqy\n```\n\n### Using conda\n\n```bash\nconda create -n radqy python=3.10\nconda activate radqy\npip install radqy\n```\n\n## Running\n\nDisplay the help message:\n  \n```bash\nradqy --help\n```\nExpected Output:\n\n```\nusage: radqy [-h] [--ui-download] [--ui-run] [-s S] [-b B] [-u U] [-t {MRI,CT}]\n             output_folder_name inputdir [inputdir ...]\n\npositional arguments:\n  output_folder_name    The subfolder name in the '...\\UserInterface\\Data\\output_folder_name' directory.\n  inputdir              Input folder(s) containing *.dcm, *.mha, *.nii, or *.mat files.\n                        Example: 'E:\\Data\\Rectal\\input_data_folder'\n\noptional arguments:\n  -h, --help            Show this help message and exit\n  --ui-download         Download the UserInterface.zip file\n  --ui-run              Run the User Interface\n  -s S                  Save foreground masks (default: False)\n  -b B                  Number of samples (default: 1)\n  -u U                  Percent of middle images to process (default: 100)\n  -t {MRI,CT}           Type of scan (MRI or CT) \n```\n\n\n\n### Running the Quality Control Script\n\nRun the **radqy** command using the following syntax:\n\n```bash\nradqy output_folder_name \"input_directory\" [options]\n```\n\nExample:\n\n```bash\nradqy output_results \"E:\\Data\\Rectal\\input_data_folder\" -s True -b 5 -u 50 -t CT\n```\n\nArguments:\n\n- **output_folder_name (required)**: The subfolder name in the `...\\UserInterface\\Data\\output_folder_name` directory.\n- **input_directory (required)**: Path to the input directory containing image files.\n\nOptions:\n\n- **-s**: Save foreground masks (`True` or `False`). Default is `False`.\n- **-b**: Number of samples. Default is `1`.\n- **-u**: Percent of middle images to process. Default is `100`.\n- **-t** (required): Type of scan (`MRI` or `CT`). \n\nNotes:\n\n- There is no need to manually create a subfolder in the Data directory; specifying its name in the command is sufficient.\n- All actions will be printed in the output console for transparency.\n- Thumbnail images in .png format will be saved in `...\\UserInterface\\Data\\output_folder_name`, with each original filename as a subfolder name.\n\n### Running the User Interface\n\n#### Download the User Interface\n\nTo download the User Interface, run the following command:\n\n```bash\nradqy --ui-download\n```\n\nThis command will download and unzip the User Interface into the appropriate directory.\n\n\n#### Run the User Interface\nTo run the User Interface, execute:\n  \n```bash\nradqy --ui-run\n```\n\nIf the User Interface is not already downloaded, this command will download it automatically before launching.\n\n#### Accessing the Front-End Interface Manually\nIf you prefer to access the User Interface without using the **--ui-run** command:\n\n1. Open the Interface:\nNavigate to the UserInterface directory (e.g., `C:\\Users\\YourUserName\\.radqy\\UserInterface`).\nDouble-click on `index.html` to open the front-end user interface.\n\n2. Load Results:\n\nIn the interface, select the appropriate **results.tsv** file from the `...\\UserInterface\\Data\\output_folder_name directory`.\n\n\n### Measurements\n\nThe measures of the MRQy tool are listed in the following table.\n\n![Picture1](https://user-images.githubusercontent.com/50635618/76733243-cb9a3f80-6736-11ea-8100-a1bdb6f60d3f.png)\n\n\n### User Interface\n\nThe following figures show the user interface of the tool (index.html). \n\n![C1](https://user-images.githubusercontent.com/50635618/78467306-3ce76580-76d9-11ea-8dbd-d43f82cd29a6.PNG)\n![C2](https://user-images.githubusercontent.com/50635618/78467302-3bb63880-76d9-11ea-84ff-ce44f5f8a822.PNG)\n![C3](https://user-images.githubusercontent.com/50635618/78467305-3ce76580-76d9-11ea-96a8-7574042c14c6.PNG)\n\n## Feedback and usage\n\nPlease report and issues, bugfixes, ideas for enhancements via the \"[Issues](https://github.com/ccipd/MRQy/issues)\" tab.\n\nDetailed usage instructions and an example of using MRQy to analyze TCIA datasets are in the [Wiki](https://github.com/ccipd/MRQy/wiki).\n\nYou can cite this in any associated publication as:  \nSadri, AR, Janowczyk, A, Zou, R, Verma, R, Beig, N, Antunes, J, Madabhushi, A, Tiwari, P, Viswanath, SE, \"Technical Note: MRQy — An open-source tool for quality control of MR imaging data\", Med. Phys., 2020, 47: 6029-6038. https://doi.org/10.1002/mp.14593\n\nArXiv: https://arxiv.org/abs/2004.04871\n\nIf you do use the tool in your own work, please drop us a line to let us know.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fviswanath-lab%2FRadQy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fviswanath-lab%2FRadQy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fviswanath-lab%2FRadQy/lists"}