Convert issues to project pages, yay! (#78)

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

content/project/project_30.md

@@ -11,22 +11,22 @@
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   "content": "### Title\r\n\r\nClustintime: a toolbox for spatio-temporal clustering of fMRI data\r\n\r\n### Leaders\r\n\r\nCris Tob\u00edas (@cristobias)\r\n\r\n### Collaborators\r\n\r\n_No response_\r\n\r\n### Brainhack Global 2023 Event \r\n\r\nBrainhack Donostia\r\n\r\n### Project Description\r\n\r\n- What are you doing, for whom, and why?\r\nThis project is a toolbox that allows researchers in neuroimage to apply clustering methods to fMRI data on the spatiotemporal domain. Conventional methods of clustering in fMRI allow to see spatial patterns but cannot describe the temporal dynamics of functional activity. \r\n\r\n- What makes your project special and exciting?\r\nProviding a tool for researchers interested in analyzing brain patterns in uncontrolled fmri experiments or clinical settings is a necessity that has not been covered yet and that could be done through clustintime. \r\n\r\n- How to get started?\r\nClustintime has been under development for a few years and has been already tried on data from individual epileptic patients, the skeletton of the project is already done, now there is need to transform it into a proper toolbox to release the first version of the software. \r\n\r\n- Where to find key resources?\r\nThe project already has its repository on GitHub (https://github.com/Cristina-Tobias/clustintime) and a public fMRI data will be used for testing.\r\n\r\n\r\n### Link to project repository/sources\r\n\r\nhttps://github.com/Cristina-Tobias/clustintime\r\n\r\n### Goals for Brainhack Global\r\n\r\nCreate integration testing suite/framework\r\nCreate CI/CD pipeline \r\nPopulate CI/CD pipeline with checks\r\n\r\n**Release version 0.1.0** \r\n\r\nCreate documentation\r\nImprove user experience of adding input\r\nStructure output messages\r\n\r\n**Release version 0.2.0**\r\n\r\nIntroduce new features\r\n- group analysis\r\n- consensus clustering\r\n\r\n**Release version 1.0.0**\r\n\r\n### Good first issues\r\n\r\nIssue 1: Create integration testing suite/framework\r\n- Find usable data\r\n- Execute each algorithm in a reproducible way (fix seed)\r\n- Integrate into CI/CD pipeline\r\n\r\nIssue 2: Create CI/CD pipeline \r\n- Find free tier provider\r\n- e.g., github actions, circleci\r\n\r\nIssue 3: Populate CI/CD pipeline with checks\r\n- Pylint, flake8, black, isort, ...\r\n\r\n\r\n### Communication channels\r\n\r\nhttps://mattermost.brainhack.org/brainhack/channels/clustintime\r\n\r\n### Skills\r\n\r\n- Git: intermediate\r\n- Python: advanced (only for those that want to develop new methods)\r\n- Markdown: intermediate\r\n- Bash: begginer\r\n\r\n### Onboarding documentation\r\n\r\n_No response_\r\n\r\n### What will participants learn?\r\n\r\n- Experience on collaborating with git \r\n- Experience on how to design and build an open-source library\r\n- Different methods of fMRI visualization\r\n- Unsupervised machine learning methods for fMRI\r\n\r\n### Data to use\r\n\r\n_No response_\r\n\r\n### Number of collaborators\r\n\r\nmore\r\n\r\n### Credit to collaborators\r\n\r\nProject contributors will be acknowledged as contributors in GitHub, credit will also be given in future publications (if any) to those who make a major contribution to the toolbox. \r\n\r\n### Image\r\n\r\nLeave this text if you don't have an image yet.\r\n\r\n### Type\r\n\r\ncoding_methods, documentation, method_development, pipeline_development\r\n\r\n### Development status\r\n\r\n1_basic structure\r\n\r\n### Topic\r\n\r\ndata_visualisation, machine_learning\r\n\r\n### Tools\r\n\r\nother\r\n\r\n### Programming language\r\n\r\nPython\r\n\r\n### Modalities\r\n\r\nfMRI\r\n\r\n### Git skills\r\n\r\n2_branches_PRs\r\n\r\n### Anything else?\r\n\r\n_No response_\r\n\r\n### Things to do after the project is submitted and ready to review.\r\n\r\n- [ ] Add a comment below the main post of your issue saying: `Hi @brainhackorg/project-monitors my project is ready!`\r\n- [ ] Twitter-sized summary of your project pitch.",

content/project/project_31.md

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       "name": "topic:ICA",
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   "content": "### Title\r\n\r\nTedana: TE-dependent analysis\r\n\r\n### Leaders \r\n\r\nEneko Uru\u00f1uela (@eurunuela)\r\n\r\n### Collaborators\r\n\r\n_No response_\r\n\r\n### Brainhack Global 2023 Event\r\n\r\nBrainhack Donostia\r\n\r\n### Project Description\r\n\r\n- What are you doing, for whom, and why?\r\n- What makes your project special and exciting?\r\n- How to get started?\r\n- Where to find key resources?\r\n\r\n\r\n### Link to project repository/sources\r\n\r\nhttps://github.com/ME-ICA/tedana\r\n\r\n### Goals for Brainhack Global\r\n\r\nThey are listed in the following GitHub discussion: https://github.com/ME-ICA/tedana/discussions/987\r\n\r\n### Good first issues\r\n\r\n1. issue one: [Fix reference rendering in HTML report](https://github.com/ME-ICA/tedana/issues/986)\r\n\r\n2. issue two: [Documentation to highlight situations or studies where multi-echo or tedana are specifically useful](https://github.com/ME-ICA/tedana/issues/520)\r\n\r\n\r\n### Communication channels\r\n\r\nhttps://mattermost.brainhack.org/brainhack/channels/tedana\r\n\r\n### Skills\r\n\r\n- Python: beginner/medium\r\n- Documentation: beginner\r\n\r\n### Onboarding documentation\r\n\r\nhttps://github.com/ME-ICA/tedana/blob/main/CONTRIBUTING.md\r\n\r\n### What will participants learn?\r\n\r\n- How small scientific open-source software development happens\r\n- How to contribute to such projects\r\n- How tedana works for multi-echo fMRI denoising\r\n- How to use GitHub\r\n\r\n### Data to use\r\n\r\nMulti-echo data we use to test tedana is available in OSF: https://osf.io/bpe8h/\r\n\r\n### Number of collaborators\r\n\r\n2\r\n\r\n### Credit to collaborators\r\n\r\nProject contributors are listed on the project README using the all contributors bot:\r\n\r\nhttps://github.com/ME-ICA/tedana\r\n\r\n### Image\r\n\r\nLeave this text if you don't have an image yet.\r\n\r\n### Type\r\n\r\ndocumentation, method_development, visualization\r\n\r\n### Development status\r\n\r\n2_releases_existing\r\n\r\n### Topic\r\n\r\nICA, PCA\r\n\r\n### Tools\r\n\r\nother\r\n\r\n### Programming language\r\n\r\ndocumentation, Python, html_css\r\n\r\n### Modalities\r\n\r\nfMRI\r\n\r\n### Git skills\r\n\r\n0_no_git_skills\r\n\r\n### Anything else?\r\n\r\n_No response_\r\n\r\n### Things to do after the project is submitted and ready to review.\r\n\r\n- [X] Add a comment below the main post of your issue saying: `Hi @brainhackorg/project-monitors my project is ready!`\r\n- [X] Twitter-sized summary of your project pitch.",

content/project/project_33.md

@@ -11,27 +11,27 @@
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   "content": "### Title\r\n\r\nphys2CVR: a BIDS-compliant python toolbox to compute cerebrovascular reacitvity mapping\r\n\r\n### Leaders \r\n\r\nStefano Moia \r\n\r\nEmail: s.moia.research@gmail.com\r\nTwitter: @SteMoia\r\nMattermost: @smoia\r\n\r\n### Collaborators\r\n\r\n_No response_\r\n\r\n### Brainhack Global 2023 Event\r\n\r\nBrainhack Donostia\r\n\r\n### Project Description\r\n\r\nphys2cvr is a python toolbox that aims at offering various approaches to compute cerebrovascular mapping, starting from at least a functional MRI hypervolume.\r\n\r\nWhile not the first toolbox to compute CVR out there, I'm aiming at making something easy to adopt, a swiss knife to compute all sorts of maps to image cerebral physiology (*not* to denoise fMRI timeseries, for that you can check [phys2denoise](https://github.com/physiopy/phys2denoise)). phys2cvr should become one of the most complete tools for CVR mapping available, easy to adopt through a CLI (and, if possible, a GUI), with nice reports and plots, and allowing the highest automation through BIDS compliance. No repetition allowed thoough: for all python-based approaches out there, phys2cvr should only act as wrap around.\r\nAll contributions are welcome - and all contributions are recognised via all-contributors guidelines (and authorship on publications).\r\n\r\nThe project is already in advanced beta stage - in fact, I'm aiming at writing and publishing a paper about it. There is a list of to-dos left, that I collected [here](https://docs.google.com/document/d/1MFgwIjM5IaT7RlHtc5vzplPXZi8xaW76Fa-dLzknckA/edit?usp=sharing), before submitting a manuscript.\r\n\r\nIf you want to collaborate, yaih! Feel free to reach out to me, and if you are attending Brainhack Donostia, we can get the party started!\r\n\r\n### Link to project repository/sources\r\n\r\nhttps://github.com/smoia/phys2cvr\r\n\r\n### Goals for Brainhack Global\r\n\r\nGo through this list as much as possible:\r\n\r\nhttps://docs.google.com/document/d/1MFgwIjM5IaT7RlHtc5vzplPXZi8xaW76Fa-dLzknckA/edit?usp=sharing\r\n\r\n### Good first issues\r\n\r\n1. issue one:\r\nadd a code of conduct and a contribution guideline\r\n2. issue two:\r\ncheck that licence is valid in all files\r\n3. issue three:\r\nspellcheck CLI help and docstrings\r\n\r\n### Communication channels\r\n\r\nhttps://mattermost.brainhack.org/brainhack/channels/bhg-phys2cvr\r\n\r\n### Skills\r\n\r\nThe list of todos is long, and each part requires different skills.\r\nIn general, no skill is required, beside good will and interest in CVR mapping.\r\n\r\nIn practice, generally speaking git knowledge is welcome. To touch the code, python knowledge is fairly mandatory. For documentation and other parts, knowing markdown or restructured test would be nice, but not mandatory. \r\n\r\n### Onboarding documentation\r\n\r\n_No response_\r\n\r\n### What will participants learn?\r\n\r\ngit, python, CVR mapping, pre-commit, sphinx based documentation writing, datalad, ...\r\n\r\n### Data to use\r\n\r\n_No response_\r\n\r\n### Number of collaborators\r\n\r\nmore\r\n\r\n### Credit to collaborators\r\n\r\nI follow physiopy's CoC, guidelines, and contribution recognition.\r\n\r\nAll contributions are recognised through all-contributors, all contributors are invited to be authors in outreach activities.\r\n\r\n### Image\r\n\r\nLeave this text if you don't have an image yet.\r\n\r\n### Type\r\n\r\npipeline_development\r\n\r\n### Development status\r\n\r\n2_releases_existing\r\n\r\n### Topic\r\n\r\nphysiology\r\n\r\n### Tools\r\n\r\nBIDS\r\n\r\n### Programming language\r\n\r\nPython\r\n\r\n### Modalities\r\n\r\nfMRI\r\n\r\n### Git skills\r\n\r\n2_branches_PRs\r\n\r\n### Anything else?\r\n\r\n_No response_\r\n\r\n### Things to do after the project is submitted and ready to review.\r\n\r\n- [x] Add a comment below the main post of your issue saying: `Hi @brainhackorg/project-monitors my project is ready!`\r\n- [ ] Twitter-sized summary of your project pitch.",

content/project/project_44.md

@@ -16,32 +16,32 @@
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       "name": "modality:DWI",
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   "content": "### Title\r\n\r\nLaunchcontainers: A Python tool for launching containerized analysis on HPC \r\n\r\n\r\n### Leaders\r\n\r\nYongning Lei\r\n\r\nemail: t.lei@bcbl.eu\r\n\r\n### Collaborators\r\n\r\n_No response_\r\n\r\n### Brainhack Global 2023 Event\r\n\r\nBrainhack Donostia\r\n\r\n### Project Description\r\n\r\nLaunchcontainers is a Python-based program built to automatically launch containerlized MRI processing pipelines. This program takes one config.ymal file, one container.json file, and one subject-session-list.txt file as inputs. Using 1 line of bash command, it will automatically send jobs to HPC clusters regarding your computing demands.\r\n\r\nThis program is well-suited for multi-subject, multi-scan datasets. And it will save a lot of time if you need analysis your entire dataset with different parameters multiple times.\r\n\r\nIn future versions, we are trying to add more functionality to this repository so that you can launch all the MRI data analysis pipelines such as Heudiconv, fMRIprep, pRF pipelines and etc. Please keep track of this repo and if you have any questions or suggestions, don't hesitate to contact Gari: [garikoitz@gmail.com](mailto:garikoitz@gmail.com) and Tiger: [t.lei@bcbl.eu](mailto:yongninglei@gmail.com)\r\n\r\n\r\n### Link to project repository/sources\r\n\r\nhttps://github.com/garikoitz/launchcontainers\r\n\r\n### Goals for Brainhack Global\r\n\r\n- Let more people get to know the advantages of using containers to process MRI data to improve the data availability and reproducibility\r\n- Let beginner level users get familiar with the UNIX operation and git operation\r\n- Add new features to launchcontainer so that it supports more MRI processing pipeline (ie. HeuDiconv, fMRIprep, PRF-analyze)\r\n- Make a better documentation on the project Wiki\r\n\r\n### Good first issues\r\n\r\n1. issue one:\r\nhttps://github.com/garikoitz/launchcontainers/issues/28\r\n2. issue two:\r\nhttps://github.com/garikoitz/launchcontainers/issues/32\r\n\r\n### Communication channels\r\n\r\nhttps://mattermost.bcbl.eu/bhdonostia/channels/launchcontainer\r\n\r\n### Skills\r\n\r\n- Python intermediate\r\n- Unix intermediate\r\n\r\n\r\n\r\n### Onboarding documentation\r\n\r\nhttps://docs.google.com/document/d/1XMmMpp3w7i2o8wVyHv_kUgoTgYVJ7n-qvgIQilfEBEU/edit?usp=sharing\r\n\r\n### What will participants learn?\r\n\r\n- How to use Unix to run python script, navigate to directory, and edit files.\r\n- How to use git to collaborate with other's, create branch to fix issues, pull-request\r\n- How to use launchcontainers to launch DWI pipeline on SGE, SLURM and local machine\r\n\r\n\r\n### Data to use\r\n\r\nI will prepare the converted nifti DWI scan folder in BIDS format and zipped it for use\r\n\r\n### Number of collaborators\r\n\r\n3\r\n\r\n### Credit to collaborators\r\n\r\nProject contributers will be listed in the launchcontainer repo\r\n\r\n### Image\r\n\r\n![Launchcontainer logo](https://github.com/brainhackorg/global2023/assets/48440236/776ecfbb-f775-4942-b1cf-77cf89add43a)\r\n\r\n### Type\r\n\r\ndocumentation coding_methods\r\n\r\n### Development status\r\n\r\n2_releases_existing\r\n\r\n### Topic\r\n\r\nreproducible_scientific_methods\r\n\r\n### Tools\r\n\r\nBIDS\r\n\r\n### Programming language\r\n\r\nPython\r\n\r\n### Modalities\r\n\r\nDWI\r\n\r\n### Git skills\r\n\r\n1_commit_push, 2_branches_PRs\r\n\r\n### Anything else?\r\n\r\n_No response_\r\n\r\n### Things to do after the project is submitted and ready to review.\r\n\r\n- [X] Add a comment below the main post of your issue saying: `Hi @brainhackorg/project-monitors my project is ready!`\r\n- [x] Twitter-sized summary of your project pitch.",