{"id":27241240,"url":"https://github.com/stevenwhitaker/stfr-mwf","last_synced_at":"2025-04-10T19:56:58.736Z","repository":{"id":97987902,"uuid":"207578047","full_name":"StevenWhitaker/STFR-MWF","owner":"StevenWhitaker","description":"Code for reproducing results in \"Myelin Water Fraction Estimation Using Small-Tip Fast Recovery MRI\".","archived":false,"fork":false,"pushed_at":"2020-04-13T13:17:00.000Z","size":93,"stargazers_count":5,"open_issues_count":0,"forks_count":2,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-04-03T21:33:42.847Z","etag":null,"topics":["kernel-learning","mri","myelin-water-fraction","scan-design","small-tip-fast-recovery"],"latest_commit_sha":null,"homepage":null,"language":"Julia","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/StevenWhitaker.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2019-09-10T14:13:11.000Z","updated_at":"2024-05-27T11:35:18.000Z","dependencies_parsed_at":"2023-06-01T11:01:37.923Z","dependency_job_id":null,"html_url":"https://github.com/StevenWhitaker/STFR-MWF","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/StevenWhitaker%2FSTFR-MWF","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/StevenWhitaker%2FSTFR-MWF/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/StevenWhitaker%2FSTFR-MWF/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/StevenWhitaker%2FSTFR-MWF/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/StevenWhitaker","download_url":"https://codeload.github.com/StevenWhitaker/STFR-MWF/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248285759,"owners_count":21078343,"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":["kernel-learning","mri","myelin-water-fraction","scan-design","small-tip-fast-recovery"],"created_at":"2025-04-10T19:56:58.057Z","updated_at":"2025-04-10T19:56:58.728Z","avatar_url":"https://github.com/StevenWhitaker.png","language":"Julia","funding_links":[],"categories":[],"sub_categories":[],"readme":"# STFR-MWF\nThis repository contains code\nfor reproducing the results in the paper:\n\nSteven T. Whitaker, Gopal Nataraj, Jon-Fredrik Nielsen, and Jeffrey A. Fessler. \\\nMyelin water fraction estimation using small-tip fast recovery MRI. \\\nMagnetic Resonance in Medicine. 2020;00:1-14. \\\n\u003chttps://doi.org/10.1002/mrm.28259\u003e\n\n## Getting Started\nThe code in this repository is structured as a Julia module.\nIt was coded using Julia 1.1.1,\nthough other versions may work as well.\n\n1. Download or clone this repository.\n2. Download the BrainWeb dataset [here](https://brainweb.bic.mni.mcgill.ca/cgi/brainweb1?alias=phantom_1.0mm_normal_crisp\u0026download=1).\n   - Choose raw byte (unsigned) for the file format.\n   - Choose none for compression.\n   - Place the downloaded file in `\u003cpath_to_this_repo\u003e/STFR-MWF/src/estimation/data/BrainWeb/`,\n     where `\u003cpath_to_this_repo\u003e` is where you downloaded this repo on your computer.\n     (You will have to create the `data` and `BrainWeb` directories.)\n3. Download Julia 1.1.1 [here](https://julialang.org/downloads/oldreleases/).\n4. Run Julia.\n5. Change directories to this repo with\n   ```julia\n   julia\u003e cd(\"\u003cpath_to_this_repo\u003e\")\n   ```\n6. Install some necessary packages and load the code by running `setup.jl` via\n   ```julia\n   julia\u003e include(\"setup.jl\")\n   ```\n7. Run any function with\n    ```julia\n    julia\u003e STFRMWF.func() # Replace func with actual function name\n    ```\n\nSteps 1 through 3 only need to be done once,\nand steps 4 through 6 only need to be done once each time you start Julia.\n(Note that running `setup.jl` again will not reinstall packages,\nso will run faster after the first time.)\n\n## Reproducing Results\nTo reproduce the results in the paper, call the corresponding function.\nFor example, to reproduce Figure 3 run\n```julia\njulia\u003e STFRMWF.figure3()\n```\nSome results are used for both a figure and a table.\nFor example, Figure 4 and Table 3 use the same data,\nso to reproduce both run\n```julia\njulia\u003e STFRMWF.figure4table3()\n```\nTo get a list of all available functions, run\n```julia\njulia\u003e STFRMWF.reproducible\n```\n\nThe first time calling these functions may take a while\n(especially the biased CRLB and NNLS results),\nbut after running once the results will be saved,\nso future calls will simply load the results and display them.\n\n## Data\nThe data used in the paper and in this code is available at\n[Deep Blue Data](https://doi.org/10.7302/nw6e-1d66).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstevenwhitaker%2Fstfr-mwf","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fstevenwhitaker%2Fstfr-mwf","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstevenwhitaker%2Fstfr-mwf/lists"}