{"id":21765692,"url":"https://github.com/schluppeck/hands-on-brain-data","last_synced_at":"2025-03-21T05:22:07.624Z","repository":{"id":91667010,"uuid":"298375449","full_name":"schluppeck/hands-on-brain-data","owner":"schluppeck","description":"getting started with data analysis with #julialang and sample MRI data","archived":false,"fork":false,"pushed_at":"2024-11-07T13:27:51.000Z","size":48483,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-01-26T01:49:07.589Z","etag":null,"topics":["brains","colormaps","julia","mri"],"latest_commit_sha":null,"homepage":"https://schluppeck.github.io/hands-on-brain-data","language":"Julia","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/schluppeck.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}},"created_at":"2020-09-24T19:24:52.000Z","updated_at":"2022-09-16T13:42:45.000Z","dependencies_parsed_at":null,"dependency_job_id":"bf8fb4a4-8e53-4ea8-9139-7caddc24cb07","html_url":"https://github.com/schluppeck/hands-on-brain-data","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/schluppeck%2Fhands-on-brain-data","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/schluppeck%2Fhands-on-brain-data/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/schluppeck%2Fhands-on-brain-data/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/schluppeck%2Fhands-on-brain-data/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/schluppeck","download_url":"https://codeload.github.com/schluppeck/hands-on-brain-data/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244741087,"owners_count":20502203,"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":["brains","colormaps","julia","mri"],"created_at":"2024-11-26T13:13:26.526Z","updated_at":"2025-03-21T05:22:07.603Z","avatar_url":"https://github.com/schluppeck.png","language":"Julia","funding_links":[],"categories":[],"sub_categories":[],"readme":"# hands-on-brain-data\n\nDenis Schluppeck, started Sept/Oct 2020.\n\nThis material provides some details for reproducing the animations / interactive examples I have used to for teaching in my 2nd year undergraduate lab in **neuroimaging**. \n\nYou could also used this as a starting point for learning a bit of scripting / programming for your  own data analysis with #julialang with sample MRI data shown in class.\n\n\u003cimg src=\"julia-gif.gif\" alt=\"example animation\"\u003e \n\n## Getting set up\n\n- install `julia` and `pluto.jl` as per excellent instructions [in this youtube clip](https://www.youtube.com/watch?v=OOjKEgbt8AI\u0026list=PLP8iPy9hna6Q2Kr16aWPOKE0dz9OnsnIJ\u0026index=21\u0026t=204s)\n\n- clone or download this repository:\n```bash\ncd ~\ngit clone https://github.com/schluppeck/hands-on-brain-data.git\n```\n```bash\n# wait for it to download / clone and then change directory into it\ncd hands-on-brain-data\n# you can now look around at the files in this folder\nls\npwd # print working directory: where are you in the file hierarchy?\n```\n\n- Next, start the `julia` interpreter by double-clicking the app icon or start `julia` in the shell, if you have set it up. You can install dependencies at this point, but if you are going to run the notebooks with `Pluto` you can also do that from within that environment\n\n\u003cimg src=\"./julia.png\" width=\"30%\"/\u003e \u003cimg src=\"./julia-shell.png\" width=\"30%\"/\u003e  \u003cimg src=\"./julia-cd.png\" width=\"30%\"/\u003e\n\nTry and run the Pluto notebook you want to explore. The first time you run it, you will have to be a bit patient, as some additional packages may need to be installed)\n\n```julia\n# change directory to the folder with the downloaded files...\n# using the ; changes the prompt to red / shell\n;  \ncd ~/hands-on-brain-data\n# BACKSPACE to go back to the julia prompt\nusing Pluto\n\n# for versions 1.9 onwards, the julia package manager will ask you if you\n# want to install this package if you don't already have it... say [y]\n\nPluto.run()\n# and open specific notebook in browser\n```\n\n\u003cimg src=\"./pluto-notebook.png\" width=\"50%\"/\u003e\n\n**A good place to start is the notebook `what_are_images.jl`.** Load it, Click `Run Notebook code` at the top of the page... the first time you do this, it may take 30s to a minute to update packages.... you can look at the `Status` (by clicking the status button at the bottom right... this will show you progress of what's happening. Second time aroud, the code will run *much* faster).\n\n## Additional resources\n\n- If you scroll to the bottom of the `Pluto` launch window, you can also find some `Featured Notebooks` which are a good place to find your feet with `julia` and `Pluto`.\n\n\u003cimg src=\"./featured-notebooks.png\" width=\"50%\"/\u003e\n\n- Grant Sanderson has a brilliant video explaining images, etc. [in the second class of this MIT OpenCourseWare lecture](https://www.youtube.com/watch?v=DGojI9xcCfg\u0026list=PLP8iPy9hna6Q2Kr16aWPOKE0dz9OnsnIJ\u0026index=2\n), which is part of a whole course on [Computational Thinking](https://www.youtube.com/playlist?list=PLP8iPy9hna6Q2Kr16aWPOKE0dz9OnsnIJ).\n\nEnjoy!\n\n## update notes\n\nYou can use this snippet of code to get rid of `Pluto.jl` Manifest.toml update warnings\n\n```julia\nbegin\n    using Pkg \n    Pkg.upgrade_manifest()\n    Pkg.resolve()\nend\n```\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fschluppeck%2Fhands-on-brain-data","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fschluppeck%2Fhands-on-brain-data","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fschluppeck%2Fhands-on-brain-data/lists"}