{"id":26766074,"url":"https://github.com/ucl/petmr-resolute","last_synced_at":"2025-09-10T14:18:28.649Z","repository":{"id":81377436,"uuid":"123155931","full_name":"UCL/petmr-RESOLUTE","owner":"UCL","description":" Implementation of RESOLUTE pseudo-CT method for mMR.","archived":false,"fork":false,"pushed_at":"2018-08-21T23:00:44.000Z","size":113,"stargazers_count":2,"open_issues_count":2,"forks_count":1,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-08-14T08:52:50.565Z","etag":null,"topics":["medical-imaging","mrac","pct","pet-mr","positron-emission-tomography"],"latest_commit_sha":null,"homepage":null,"language":"C++","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/UCL.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,"zenodo":null}},"created_at":"2018-02-27T16:22:44.000Z","updated_at":"2023-09-09T19:48:53.000Z","dependencies_parsed_at":null,"dependency_job_id":"b2fcbd10-7d3d-493e-a422-24596f6a825a","html_url":"https://github.com/UCL/petmr-RESOLUTE","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/UCL/petmr-RESOLUTE","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UCL%2Fpetmr-RESOLUTE","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UCL%2Fpetmr-RESOLUTE/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UCL%2Fpetmr-RESOLUTE/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UCL%2Fpetmr-RESOLUTE/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/UCL","download_url":"https://codeload.github.com/UCL/petmr-RESOLUTE/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UCL%2Fpetmr-RESOLUTE/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274477217,"owners_count":25292825,"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","status":"online","status_checked_at":"2025-09-10T02:00:12.551Z","response_time":83,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["medical-imaging","mrac","pct","pet-mr","positron-emission-tomography"],"created_at":"2025-03-28T20:19:02.173Z","updated_at":"2025-09-10T14:18:28.624Z","avatar_url":"https://github.com/UCL.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# petmr-RESOLUTE\n\n[![Build Status](https://travis-ci.org/UCL/petmr-RESOLUTE.svg?branch=master)](https://travis-ci.org/UCL/petmr-RESOLUTE) [![Codacy Badge](https://api.codacy.com/project/badge/Grade/bc66119aefae4628a914e01a2a6f83fa)](https://www.codacy.com/app/bathomas/petmr-RESOLUTE?utm_source=github.com\u0026amp;utm_medium=referral\u0026amp;utm_content=UCL/petmr-RESOLUTE\u0026amp;utm_campaign=Badge_Grade) [![DOI](https://zenodo.org/badge/123155931.svg)](https://zenodo.org/badge/latestdoi/123155931)\n\nImplementation of the RESOLUTE pseudo-CT (pCT) method for the Siemens mMR.\n\nIf you use the RESOLUTE pCT approach in your work, please cite the following paper:\n- \u003ci\u003eRegion specific optimization of continuous linear attenuation coefficients based  on UTE (RESOLUTE): application to PET/MR brain imaging\u003c/i\u003e. Ladefoged, C. N., Benoit, D., Law, I., Holm, S., Kjaer, A., Hojgaard, L., … Andersen, F. L. (2015). Physics in Medicine and Biology, 60(20), 8047–8065. [DOI](https://doi.org/10.1088/0031-9155/60/20/8047)\n\n## Required packages\n- [ANTs](https://github.com/ANTsX/ANTs)\n- [ITK](https://itk.org/) (Note. this can be built when compiling ANTs)\n- [Boost](http://www.boost.org/)\n- [glog](https://github.com/google/glog)\n- [DCMTK](http://dicom.offis.de/). The application `dcmodify` must be available on your path.\n\n## Template and mask images\nThe images that are required to run this application are available on Zenodo:\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1204196.svg)](https://doi.org/10.5281/zenodo.1204196)\n\nPlease extract the zip and amend the JSON file as described below.\n\n## Basic usage\n```shell\n./resolute -i \u003cDICOMDIR\u003e -j \u003cJSON\u003e\n```\nwhere ```\u003cDICOMDIR\u003e``` contains both the UTE and MRAC DICOM data for a given patient and ```\u003cJSON\u003e``` is the JSON configuration file. The application will produce a folder in the output directory specified in the JSON file. The output folder is named using the ```Study UID```, and inside this folder will be a new DICOM series comprising the RESOLUTE MRAC image.\n\n## Configuration file\n\nA skeleton JSON file can be created with the command:\n```\n./resolute --create-json \u003cMYJSONFILE\u003e\n```\nwhere ```\u003cMYJSONFILE\u003e``` is an output filename.\nThe skeleton will look like this:\n```yaml\n{\n    \"MRACSeriesName\": \"Head_MRAC_PET_UTE_UMAP\",\n    \"UTE1SeriesName\": \"Head_MRAC_PET_UTE\",\n    \"UTE1TE\": \"0.07\",\n    \"UTE2SeriesName\": \"Head_MRAC_PET_UTE\",\n    \"UTE2TE\": \"2.46\",\n    \"destDir\": \".\",\n    \"destExportMethod\": \"FILE\",\n    \"destFileType\": \".nii.gz\",\n    \"logDir\": \"./logs\",\n    \"regArgs\": \"3 -m CC[\u003c%%REF%%\u003e,\u003c%%FLOAT%%\u003e,1,4] -i 10x5x2 -o \u003c%%PREFIX%%\u003e -t SyN[0.5] -r Gauss[3,0] -G\",\n    \"regName\": \"ANTS\",\n    \"regTemplatePath\": \"\",\n    \"version\": \"0.0.1\"\n}\n```\nFill in the desired output directory in the variable `destDir`, and the path to the registration template `manifest.json` in `regTemplatePath`, e.g.\n```yaml\n{\n    \"MRACSeriesName\": \"Head_MRAC_PET_UTE_UMAP\",\n    \"UTE1SeriesName\": \"Head_MRAC_PET_UTE\",\n    \"UTE1TE\": \"0.07\",\n    \"UTE2SeriesName\": \"Head_MRAC_PET_UTE\",\n    \"UTE2TE\": \"2.46\",\n    \"destDir\": \"./OUTPUT\",\n    \"destExportMethod\": \"FILE\",\n    \"destFileType\": \".nii.gz\",\n    \"logDir\": \"./logs\",\n    \"regName\": \"ANTS\",\n    \"regTemplatePath\": \"/path/to/template/manifest.json\",\n    \"regArgs\": \"3 -m CC[\u003c%%REF%%\u003e,\u003c%%FLOAT%%\u003e,1,4] -i 10x5x2 -o \u003c%%PREFIX%%\u003e -t SyN[0.5] -r Gauss[3,0] -G\",\n    \"version\": \"0.0.1\"\n}\n\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fucl%2Fpetmr-resolute","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fucl%2Fpetmr-resolute","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fucl%2Fpetmr-resolute/lists"}