├── .all-contributorsrc ├── .github ├── ISSUE_TEMPLATE │ ├── add-a-database.md │ ├── add-a-software.md │ ├── add-a-tutorial.md │ ├── add-a-video.md │ └── add-a-website.md ├── PULL_REQUEST_TEMPLATE │ ├── add-a-database.md │ ├── add-a-software.md │ ├── add-a-tutorial.md │ ├── add-a-video.md │ └── add-a-website.md └── workflows │ ├── check_markdown.yml │ ├── check_md_links.yml │ └── publishdocs.yaml ├── .prettierrc ├── .remarkrc ├── CONTRIBUTING.md ├── LICENSE.md ├── README.md ├── docs ├── 10-before-you-start.md ├── 11-programming.md ├── 12-version-control.md ├── 13-data-code-management.md ├── 14-documentation.md ├── 20-planning-your-study.md ├── 21-reproducible-neuroimaging-research.md ├── 22-preregistration.md ├── 30-getting-data.md ├── 31-data-repositories.md ├── 40-processing.md ├── 41-computing.md ├── 42-analysis-software-MRI.md ├── 43-analysis-software-MEEG.md ├── 44-analysis-software-physio.md ├── 45-learning-neuroimaging.md ├── 46-neuroimaging-resources.md ├── 50-analysis.md ├── 51-statistics.md ├── 52-machine-and-deep-learning.md ├── 53-genetics-software.md ├── 60-quality-control.md ├── 70-reporting-methods-and-results.md ├── 80-sharing-data-code-and-results.md ├── 81-open-science.md ├── 99-appendix.md └── index.md ├── img ├── dogeLove.gif └── dogeLoveScanner_600x400.gif ├── mkdocs.yml ├── npm-requirements.txt ├── requirements.txt └── templates └── README.md /.all-contributorsrc: -------------------------------------------------------------------------------- 1 | { 2 | "files": [ 3 | "README.md" 4 | ], 5 | "imageSize": 100, 6 | "commit": false, 7 | "contributors": [ 8 | { 9 | "login": "Remi-Gau", 10 | "name": "Remi Gau", 11 | "avatar_url": "https://avatars3.githubusercontent.com/u/6961185?v=4", 12 | "profile": "https://remi-gau.github.io/", 13 | "contributions": [ 14 | "code", 15 | "content", 16 | "ideas" 17 | ] 18 | }, 19 | { 20 | "login": "katjaq", 21 | "name": "katja heuer", 22 | "avatar_url": "https://avatars3.githubusercontent.com/u/6297454?v=4", 23 | "profile": "https://katjaq.github.io/graphy/", 24 | "contributions": [ 25 | "code", 26 | "content", 27 | "ideas" 28 | ] 29 | }, 30 | { 31 | "login": "roopa-pai", 32 | "name": "Roopa Pai", 33 | "avatar_url": "https://avatars2.githubusercontent.com/u/33023134?v=4", 34 | "profile": "https://www.linkedin.com/in/roopa-pai/", 35 | "contributions": [ 36 | "code", 37 | "content", 38 | "ideas" 39 | ] 40 | }, 41 | { 42 | "login": "IRuotsa", 43 | "name": "IRuotsa", 44 | "avatar_url": "https://avatars1.githubusercontent.com/u/47354027?v=4", 45 | "profile": "https://github.com/IRuotsa", 46 | "contributions": [ 47 | "code", 48 | "content", 49 | "ideas" 50 | ] 51 | }, 52 | { 53 | "login": "martinagvilas", 54 | "name": "Martina G. 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| title: '' 5 | labels: '' 6 | assignees: '' 7 | 8 | --- 9 | 10 | ??? example "insert database name - insert short description" 11 | - [database repository]( insert URL ) 12 | - [contact](inser URL to mailing list, slack, forum, mattermost) 13 | - data type: {fMRI} {MEG} {EEG} {MRI} 14 | - [paper](https://doi.org/insert_paper_DOI_here) 15 | - RRID: insert_RRID_here 16 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/add-a-software.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Add a software 3 | about: Add a software to this repository 4 | title: '' 5 | labels: '' 6 | assignees: '' 7 | 8 | --- 9 | 10 | ??? example "insert software name - insert short description" 11 | - [code repository](insert GitHub or GitLab URL ) 12 | - [website](insert URL) 13 | - [documentation](insert documentation or wiki URL) 14 | - [contact](insert URL to mailing list, slack, forum, mattermost) 15 | - programming language: {python}, {matlab/octave}, {C}, ... 16 | - tags: {fMRI} {MEG} {EEG} {MRI} {nipype} 17 | - [paper](https://doi.org/insert_paper_DOI_here) 18 | - RRID: insert_RRID_here 19 | - tutorial: 20 | - [URL]( insert URL ) 21 | - programming language: {python}, {matlab/octave}, {C}, ... 22 | - level: {beginner} / {intermediate} / {advanced} 23 | - tags: {video} {notebook} 24 | - date: 25 | - duration: HH:MM 26 | - by: John Doe and Jane Doe 27 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/add-a-tutorial.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Add a course / workshop / tutorial 3 | about: Add a course / workshop / tutorial to this repository 4 | title: '' 5 | labels: '' 6 | assignees: '' 7 | 8 | --- 9 | 10 | ??? example "insert course / workshop / tutorial name - insert short description" 11 | - [URL]( insert URL ) 12 | - programming language: {python}, {matlab/octave}, {C}, ... 13 | - level: {beginner} / {intermediate} / {advanced} 14 | - tags: {video} {notebook} 15 | - date: 16 | - duration: HH:MM 17 | - by: John Doe and Jane Doe 18 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/add-a-video.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Add a video / video series 3 | about: Add a video / video series to this repository 4 | title: '' 5 | labels: '' 6 | assignees: '' 7 | 8 | --- 9 | 10 | ??? example "insert video / video series name - insert short description" 11 | - [URL]( insert URL ) 12 | - programming language: {python}, {matlab/octave}, {C}, ... 13 | - level: {beginner} / {intermediate} / {advanced} 14 | - tags: {video} {MOOC} 15 | - date: 16 | - duration: HH:MM 17 | - by: John Doe and Jane Doe 18 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/add-a-website.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Add a website / blog 3 | about: Add a website or blog or podcast to this repository 4 | title: '' 5 | labels: '' 6 | assignees: '' 7 | 8 | --- 9 | 10 | ??? example "insert website name - insert short description" 11 | - [URL]( insert URL ) 12 | - [RSS](_insert_RSS_feed) 13 | - level: {beginner} / {intermediate} / {advanced} 14 | - tags: {video} {notebook} {fMRI} {MOOC} {blog} {website} {podcast} 15 | - by: John Doe and Jane Doe 16 | -------------------------------------------------------------------------------- /.github/PULL_REQUEST_TEMPLATE/add-a-database.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Add a database 3 | about: Add a database to this repository 4 | title: '' 5 | labels: '' 6 | assignees: '' 7 | 8 | --- 9 | 10 | ??? example "insert database name - insert short description" 11 | - [database repository]( insert URL ) 12 | - [contact](inser URL to mailing list, slack, forum, mattermost) 13 | - data type: {fMRI} {MEG} {EEG} {MRI} 14 | - [paper](https://doi.org/insert_paper_DOI_here) 15 | - RRID: insert_RRID_here 16 | -------------------------------------------------------------------------------- /.github/PULL_REQUEST_TEMPLATE/add-a-software.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Add a software 3 | about: Add a software to this repository 4 | title: '' 5 | labels: '' 6 | assignees: '' 7 | 8 | --- 9 | 10 | ??? example "insert software name - insert short description" 11 | - [code repository](insert GitHub or GitLab URL ) 12 | - [website](insert URL) 13 | - [documentation](insert documentation or wiki URL) 14 | - [contact](insert URL to mailing list, slack, forum, mattermost) 15 | - programming language: {python}, {matlab/octave}, {C}, ... 16 | - tags: {fMRI} {MEG} {EEG} {MRI} {nipype} 17 | - [paper](https://doi.org/insert_paper_DOI_here) 18 | - RRID: insert_RRID_here 19 | - tutorial: 20 | - [URL]( insert URL ) 21 | - programming language: {python}, {matlab/octave}, {C}, ... 22 | - level: {beginner} / {intermediate} / {advanced} 23 | - tags: {video} {notebook} 24 | - date: 25 | - duration: HH:MM 26 | - by: John Doe and Jane Doe 27 | -------------------------------------------------------------------------------- /.github/PULL_REQUEST_TEMPLATE/add-a-tutorial.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Add a course / workshop / tutorial 3 | about: Add a course / workshop / tutorial to this repository 4 | title: '' 5 | labels: '' 6 | assignees: '' 7 | 8 | --- 9 | 10 | ??? example "insert course / workshop / tutorial name - insert short description" 11 | - [URL]( insert URL ) 12 | - programming language: {python}, {matlab/octave}, {C}, ... 13 | - level: {beginner} / {intermediate} / {advanced} 14 | - tags: {video} {notebook} 15 | - date: 16 | - duration: HH:MM 17 | - by: John Doe and Jane Doe 18 | -------------------------------------------------------------------------------- /.github/PULL_REQUEST_TEMPLATE/add-a-video.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Add a video / video series 3 | about: Add a video / video series to this repository 4 | title: '' 5 | labels: '' 6 | assignees: '' 7 | 8 | --- 9 | 10 | ??? example "insert video / video series name - insert short description" 11 | - [URL]( insert URL ) 12 | - programming language: {python}, {matlab/octave}, {C}, ... 13 | - level: {beginner} / {intermediate} / {advanced} 14 | - tags: {video} {notebook} 15 | - date: 16 | - duration: HH:MM 17 | - by: John Doe and Jane Doe 18 | -------------------------------------------------------------------------------- /.github/PULL_REQUEST_TEMPLATE/add-a-website.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Add a website / blog 3 | about: Add a website or blog or podcast to this repository 4 | title: '' 5 | labels: '' 6 | assignees: '' 7 | 8 | --- 9 | 10 | ??? example "insert website name - insert short description" 11 | - [URL]( insert URL ) 12 | - [RSS](_insert_RSS_feed) 13 | - level: {beginner} / {intermediate} / {advanced} 14 | - tags: {video} {notebook} {fMRI} {MOOC} {blog} {website} {podcast} 15 | - by: John Doe and Jane Doe 16 | -------------------------------------------------------------------------------- /.github/workflows/check_markdown.yml: -------------------------------------------------------------------------------- 1 | name: Check Markdown 2 | 3 | on: 4 | push: 5 | branches: 6 | - master 7 | pull_request: 8 | branches: '*' 9 | 10 | jobs: 11 | build: 12 | 13 | runs-on: ubuntu-latest 14 | 15 | steps: 16 | 17 | - uses: actions/checkout@v2 18 | with: 19 | submodules: true 20 | fetch-depth: 1 21 | 22 | - uses: actions/setup-node@v2 23 | with: 24 | node-version: '10' 25 | 26 | - name: Install dependencies and check markdown 27 | run: | 28 | npm install `cat npm-requirements.txt` 29 | npx remark docs/*.md 30 | -------------------------------------------------------------------------------- /.github/workflows/check_md_links.yml: -------------------------------------------------------------------------------- 1 | name: Check Markdown links 2 | 3 | on: 4 | push: 5 | branches: 6 | - master 7 | pull_request: 8 | branches: '*' 9 | 10 | jobs: 11 | markdown-link-check: 12 | runs-on: ubuntu-latest 13 | steps: 14 | - uses: actions/checkout@master 15 | - uses: gaurav-nelson/github-action-markdown-link-check@v1 -------------------------------------------------------------------------------- /.github/workflows/publishdocs.yaml: -------------------------------------------------------------------------------- 1 | name: Publish docs via GitHub Pages 2 | on: 3 | push: 4 | branches: 5 | - master 6 | 7 | jobs: 8 | build: 9 | name: Deploy docs 10 | runs-on: ubuntu-latest 11 | steps: 12 | - name: Checkout master 13 | uses: actions/checkout@v1 14 | 15 | - name: Deploy docs 16 | uses: mhausenblas/mkdocs-deploy-gh-pages@master 17 | env: 18 | GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 19 | -------------------------------------------------------------------------------- /.prettierrc: -------------------------------------------------------------------------------- 1 | { 2 | "parser": "markdown", 3 | "proseWrap": "always", 4 | "tabWidth": 2, 5 | "overrides": [ 6 | { 7 | "files": "*.md", 8 | "options": { 9 | "tabWidth": 4 10 | } 11 | } 12 | ] 13 | } 14 | -------------------------------------------------------------------------------- /.remarkrc: -------------------------------------------------------------------------------- 1 | { 2 | "plugins": [ 3 | "preset-lint-markdown-style-guide", 4 | ["lint-no-duplicate-headings", false], 5 | ["lint-list-item-indent", "tab-size"], 6 | ["lint-emphasis-marker", "consistent"], 7 | ["lint-maximum-line-length", false], 8 | ["lint-maximum-heading-length", false] 9 | ] 10 | } 11 | -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- 1 | # Contributing to this repo 2 | 3 | There are many ways in which to contribute to the ongoing improvement of this list of tutorials and other resources useful for open science and neuroimaging, EEG and MEG. 4 | 5 | 6 | 7 | ## Asking questions or reporting an issue 8 | 9 | You have two ways for asking questions or reporting an issue: 10 | 11 | - Join the [Brainhack Mattermost Team](https://mattermost.brainhack.org/): there is a dedicated channel called [~tutorial-and-resources](https://mattermost.brainhack.org/brainhack/channels/tutorial-and-resources) where you can contact us. 12 | 13 | - [Open an issue on GitHub](https://github.com/learn-neuroimaging/tutorials-and-resources/issues/). 14 | 15 | 16 | 17 | ## Proposing a new resource (software, website, etc.) 18 | 19 | Simply [Open an issue on GitHub](https://github.com/learn-neuroimaging/tutorials-and-resources/issues/). You will see several templates you will need to fill when proposing a new resource. 20 | 21 | If the resource you want to add is not in the list of templates, no worries! Simply try to detail what you would like to add in this project and we will discuss about it. 22 | 23 | If you do not feel comfortable with GitHub, simply contact us on the [~tutorial-and-resources](https://mattermost.brainhack.org/brainhack/channels/tutorial-and-resources) channel of the [Brainhack Mattermost Team](https://mattermost.brainhack.org/). 24 | 25 | 26 | 27 | ## Making direct contributions 28 | 29 | If this is your first time contributing to an open source project, please read this very clear [tutorial](https://github.com/firstcontributions/first-contributions). You will find how to **fork** this project, **clone** your fork, make a **branch**, add modifications and create a **pull request** using command line or [GUI tools](https://github.com/firstcontributions/first-contributions#tutorials-using-other-tools). 30 | 31 | To sum up these steps: 32 | 33 | - Go to the [repository](https://github.com/learn-neuroimaging/tutorials-and-resources) and click 34 | the "Fork" button to create your own copy of the project. 35 | 36 | - Clone the project to your local computer: 37 | ``` 38 | git clone git@github.com:/tutorials-and-resources.git 39 | ``` 40 | where `` is your GitHub username. 41 | 42 | - Create a branch for the feature you want to work on. Since the branch name 43 | will appear on the pull request, use a meaningful name: 44 | ``` 45 | git checkout -b 46 | ``` 47 | (e.g. `git checkout -b fix_title`) 48 | 49 | - Commit locally as you progress (`git add` and `git commit`) 50 | 51 | - To push your changes to your fork on GitHub, type: 52 | ``` 53 | git push origin 54 | ``` 55 | 56 | - Go to GitHub. The new branch will show up with a green Pull Request button. Simply click it. 57 | 58 | - You pull request will be under review. A friendly discussion with the reviewer(s) will be done in order to improve the quality of your contribution if needed. If so, update your pull request until your changes are pushed up. The pull request will update automatically and will finally be merged by the reviewer(s). 59 | 60 | 61 | 62 | ## Coding/style conventions 63 | 64 | Currently, this project does not have a consistent style for Markdown files nor possible lines of code. This is currently [under discussion](https://github.com/learn-neuroimaging/tutorials-and-resources/issues/55). 65 | 66 | 67 | 68 | ## Testing locally 69 | 70 | This project uses [MkDocs](https://www.mkdocs.org/) tool with [Material theme](https://squidfunk.github.io/mkdocs-material/) and extra plugins to generate the website. 71 | 72 | - To test locally, you will need to install the Python dependencies. To do that, type the following commands: 73 | ``` 74 | git clone https://github.com/learn-neuroimaging/tutorials-and-resources.git 75 | cd tutorials-and-resources 76 | pip install -r requirements.txt 77 | ``` 78 | (If you are working on your *fork*, simply replace `https://github.com/learn-neuroimaging/tutorials-and-resources.git` by `git clone git@github.com:/tutorials-and-resources.git` where 79 | `` is your GitHub username) 80 | 81 | - Once done, you need to run MkDocs. Simply type: 82 | ``` 83 | mkdocs serve 84 | ``` 85 | 86 | - Finally, open up [`http://127.0.0.1:8000/`](http://127.0.0.1:8000/) in your browser, and you should see the default home page being displayed. 87 | 88 | We also recommend that you use a virtual environment. For example: 89 | ```bash 90 | virtualenv --python=python3 ~/env/hhg2b 91 | . ~/env/hhg2b/bin/activate 92 | pip install -r requirements.txt 93 | ``` 94 | 95 | 99 | 100 | 101 | 102 | ## Recognizing contributions 103 | 104 | We welcome and recognize all contributions! 105 | 106 | This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind are welcome! 107 | -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- 1 | # LICENSE 2 | 3 | The process documents and data of the Hitchhacker's guide to the brain (H2GB) 4 | are made available under a CC-BY license. 5 | Software are made available under an MIT license. 6 | 7 | The license text listed below (describing both CC-BY and MIT licenses) 8 | is re-used under a CC-BY license from The Carpentries community materials. 9 | (Specifically from the [Reproducible Science Curriculum](https://github.com/Reproducible-Science-Curriculum/sharing-RR-Jupyter/blob/gh-pages/LICENSE.md)). 10 | 11 | ## Process documents and data 12 | 13 | All documentation and chapter materials in this repository are made available 14 | under the [Creative Commons Attribution license][cc-by-human]. 15 | The following is a human-readable summary of (and not a substitute for) 16 | the [full legal text of the CC BY 4.0 license][cc-by-legal]. 17 | 18 | You are free: 19 | 20 | - to **Share**---copy and redistribute the material in any medium or format 21 | 22 | - to **Adapt**---remix, transform, and build upon the material 23 | 24 | for any purpose, even commercially. 25 | 26 | The licensor cannot revoke these freedoms as long as you follow the license terms. 27 | 28 | Under the following terms: 29 | 30 | - **Attribution**---You must give appropriate credit 31 | (mentioning that your work is derived from work that is Copyright © H2GB 32 | and, where practical, linking to the H2GB repository), 33 | provide a [link to the license][cc-by-human], and indicate if changes were made. 34 | You may do so in any reasonable manner, but not in any way that suggests 35 | the licensor endorses you or your use. 36 | 37 | - **No additional restrictions**---You may not apply legal terms or 38 | technological measures that legally restrict others from doing anything the license permits. 39 | 40 | With the understanding that: 41 | 42 | - You do not have to comply with the license for elements of the material 43 | in the public domain or where your use is permitted 44 | by an applicable exception or limitation. 45 | 46 | - No warranties are given. 47 | The license may not give you all of the permissions necessary for your intended use. 48 | For example, other rights such as publicity, privacy, or moral rights may limit how you use the material. 49 | 50 | ## Software 51 | 52 | Except where otherwise noted, the software and infrastructure provided by the 53 | H2GB Community are made available under the [OSI][osi]-approved [MIT license][mit-license]. 54 | 55 | > Permission is hereby granted, free of charge, to any person obtaining 56 | > a copy of this software and associated documentation files (the 57 | > "Software"), to deal in the Software without restriction, including 58 | > without limitation the rights to use, copy, modify, merge, publish, 59 | > distribute, sublicense, and/or sell copies of the Software, and to 60 | > permit persons to whom the Software is furnished to do so, subject to 61 | > the following conditions: 62 | > 63 | > The above copyright notice and this permission notice shall be 64 | > included in all copies or substantial portions of the Software. 65 | > 66 | > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 67 | > EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 68 | > MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND 69 | > NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE 70 | > LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION 71 | > OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION 72 | > WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 73 | 74 | [cc-by-human]: https://creativecommons.org/licenses/by/4.0/ 75 | [cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode 76 | [mit-license]: https://opensource.org/licenses/mit-license.html 77 | [osi]: https://opensource.org 78 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | 3 | [![All Contributors](https://img.shields.io/badge/all_contributors-27-blue.svg?)](#contributors) 4 | 5 | 6 | [![Build Status](https://travis-ci.org/learn-neuroimaging/hitchhackers_guide_brain.svg?branch=master)](https://travis-ci.org/learn-neuroimaging/hitchhackers_guide_brain) 7 | 8 | 9 | 10 | # Welcome ! 11 | 12 | ## Introduction 13 | 14 | This website is full of links and resources for all your neuro-needs! 15 | 16 | https://learn-neuroimaging.github.io/hitchhackers_guide_brain/ 17 | 18 | We currently use mkdocs for our website. The "docs" directory contains ".md" pages containing domain-specific links to resources. 19 | 20 | ## How to add a resource and contribute 21 | See our contributing [guidelines](CONTRIBUTING.md) 22 | 23 | ## Get in touch 24 | 25 | Join our channel on 26 | 27 | ## Contributors ✨ 28 | 29 | Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)): 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 |

Remi Gau
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71 | 72 | 73 | 74 | 75 | 76 | 77 | ## Contributing 78 | 79 | This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. We encourage you to contribute to this project! Please check out the [Contributing guide](CONTRIBUTING.md) for guidelines about how to proceed. Contributions of any kind are welcome! 80 | -------------------------------------------------------------------------------- /docs/10-before-you-start.md: -------------------------------------------------------------------------------- 1 | # Before you start 2 | 3 | Before you start your study, here are some things you might want to consider: 4 | 5 | - [programming](11-programming.md) 6 | - [version control](12-version-control.md) 7 | - [code, data, project management](13-data-code-management.md) 8 | - documentation 9 | 10 | 17 | -------------------------------------------------------------------------------- /docs/11-programming.md: -------------------------------------------------------------------------------- 1 | # Programming 2 | 3 | ## Introduction & Basics 4 | 5 | - [Khan Academy](https://www.khanacademy.org/): Beginners' coursework on 6 | programming, algorithms, and more. 7 | 8 | ## General 9 | 10 | - [The Missing Semester of Your CS Education](https://missing.csail.mit.edu/): 11 | 11 videos ranging from 45min-1h25 about debugging, data wrangling, and 12 | useful tools. By @anishathalye, @jjgo and @jonhoo from MIT. 13 | 14 | ## Shell programming 15 | 16 | - [Conquering the command line](http://conqueringthecommandline.com/book/frontmatter) 17 | 18 | - [Learn shell](https://www.learnshell.org/) 19 | 20 | - [The shell introduction I wish I had](https://dev.to/maxwell_dev/the-shell-introduction-i-wish-i-had-551k) 21 | by Max Antonucci 22 | 23 | - [The Unix shell](http://swcarpentry.github.io/shell-novice/) 24 | 25 | - [Andrew Jahn's Unix introduction](https://www.youtube.com/watch?v=dBDmIhSWfnM&list=PLIQIswOrUH6992C4FDDCNCIaK4R2FIOCB) 26 | 27 | - [Bash cheatsheet](https://devhints.io/bash) 28 | 29 | - [Explain shell commands](https://explainshell.com/) 30 | 31 | - [Check shell scripts](https://www.shellcheck.net/) 32 | 33 | - [Vim interactive tutorial](https://www.openvim.com/) 34 | 35 | ## Python 36 | 37 | ### Introduction 38 | 39 | - [A whirlwind tour of Python](https://jakevdp.github.io/WhirlwindTourOfPython/) 40 | by Jake Vanderplas 2016 (full text of his free O'Reilly book; link to GitHub 41 | with Jupyter Notebooks, Python3) 42 | 43 | - [Introduction to Python](https://www.youtube.com/watch?v=3y55b_Md-N8&list=PLNt4AJV1JZbfq0vdD4vcITV7x3OqGxLKp&t=0s&index=3) 44 | by Chris Gorgolewski within Brainhack Americas 2015 (45 min, Python2, screen 45 | shared live coding in Ipython Notebook) 46 | 47 | - [Introduction to Python](https://neurohackademy.org/course/introduction-to-python-2/) 48 | by Tal Yarkoni within Neurohackademy 2019 (1 hr 42 min, lecture with 49 | [code slides](https://github.com/neurohackademy/introduction-to-python/blob/master/introduction-to-python.ipynb) 50 | and live coding) 51 | 52 | - [Python programming](https://neurohackademy.org/course/python-programming/) 53 | by Valentina Staneva within Neurohackweek 2016 (course material & code 54 | shared) 55 | 56 | - [Python tips and tricks](https://neurohackademy.org/course/python-tips-and-tricks/) 57 | by Tal Yarkoni within Neurohackweek 2016 (58 min, lecture with code slides 58 | and live coding) 59 | 60 | - [Scientific computing with Python](https://www.youtube.com/watch?v=RhNfnQlnCEo&index=18&t=0s&list=PLEE6ggCEJ0H0KOlMKx_PUVB_16VoCfGj9) 61 | by Luke Chang within MIND 2018 (24 min, lecture) 62 | 63 | - [An introduction to Python!](https://cogs18.github.io/intro/) is course made 64 | by Thomas Donoghue 65 | 66 | - [Programming with Python](https://swcarpentry.github.io/python-novice-inflammation/) 67 | Software Carpentry practical lesson (~7h25min) by Bekolay, T., Staneva, V., 68 | Fouilloux, A., Belkin, M., & Ko, L. � 69 | [GitHub repo](https://github.com/swcarpentry/python-novice-inflammation) 70 | 71 | ### Specific topics 72 | 73 | - [Cython and numba](https://neurohackademy.org/course/cython-and-numba/) by 74 | Ariel Rokem within Neurohackweek 2016 75 | 76 | - [Data manipulation in Python/Pandas](https://neurohackademy.org/course/complex-data-structures/) 77 | by Tal Yarkoni within Neurohackademy 2018 (1 hr 21 min) 78 | 79 | - [High-performance Python](https://neurohackademy.org/course/high-performance-python/) 80 | by Ariel Rokem within Neurohackweek 2016 81 | 82 | - [Modular Software Design](https://neurohackademy.org/course/modular-software-design/) 83 | by Jeremy Freeman within Neurohackweek 2016 (48 min) 84 | 85 | - [Python packaging](https://neurohackademy.org/course/python-packaging/) by 86 | Ariel Rokem within Neurohackademy 2018 (1 hr 26 min) 87 | 88 | - [Python Data Science Handbook](https://jakevdp.github.io/PythonDataScienceHandbook/) 89 | by Jake Vanderplas 90 | 91 | - [Science Hacking 101](https://www.youtube.com/watch?v=Gin8_AITmS0) by Jeremy 92 | Manning within MIND 2018 93 | 94 | - [Software testing 1](https://neurohackademy.org/course/software-testing/) by 95 | Chris Gorgolewski within Neurohackweek 96 | 97 | - [Software testing 2](https://neurohackademy.org/course/software-testing-2/) 98 | by Chris Gorgolewski within Neurohackweek 99 | 100 | - [Testing scientific code](https://neurohackademy.org/course/testing-scientific-code/) 101 | by Chris Gorgolewski within Neurohackweek 2017 (43 min) 102 | 103 | - [Porting Python 2 code to Python 3 - official](https://docs.python.org/3/howto/pyporting.html) 104 | 105 | - [guide 2 - another migration guide](http://blog.pyspoken.com/2018/02/13/python-2-to-3-migration-guide/) 106 | 107 | - [guide 3 - migration strategies](http://python3porting.com/strategies.html) 108 | 109 | - [guide 4 - practicalities and packaging](https://python3statement.org/practicalities) 110 | 111 | ## R 112 | 113 | - [Programming with R](https://neurohackademy.org/course/programming-with-r/) 114 | by Jeanette Mumford within Neurohackweek 2016 115 | 116 | - [Introduction to Neurohacking in R](https://www.coursera.org/learn/neurohacking) 117 | MOOC on coursera 118 | 119 | - [Programming with R](http://swcarpentry.github.io/r-novice-inflammation/) 120 | Software Carpentry practical lesson (~6h40min) by Leinweber, K., Das, D., & 121 | Goswami, R. 122 | [GitHub repo](https://github.com/swcarpentry/r-novice-inflammation) 123 | - [R for Reproducible Scientific Analysis](http://swcarpentry.github.io/r-novice-gapminder/) 124 | Software Carpentry lesson (~12h20min) by Wright, T., Zimmerman, N., Oliver, 125 | J., & Mawdsley, D. 126 | [GitHub repo](https://github.com/swcarpentry/r-novice-gapminder) 127 | -------------------------------------------------------------------------------- /docs/12-version-control.md: -------------------------------------------------------------------------------- 1 | # Version control 2 | 3 | ## Code 4 | 5 | Using Git and Github / Gitlab to version control your code 6 | 7 | - [A Quick Introduction to Version Control with Git and GitHub](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004668) 8 | by Bilschak et al. (2016) 9 | 10 | - [Introduction to git and GitHub](https://www.youtube.com/watch?v=XyMCsEGPcjM&list=PLNt4AJV1JZbfq0vdD4vcITV7x3OqGxLKp) 11 | by Chris Gorgolewski within Brainhack Americas (45 min) 12 | 13 | - [Git and GitHub 1 & 2](https://neurohackademy.org/course/git-and-github/) by 14 | Bernease Herman within Neurohackweek 2016 15 | 16 | - [Git tutorial](https://www.youtube.com/watch?v=0DGCnBZBoc0&index=2&t=5s&list=PLEE6ggCEJ0H0KOlMKx_PUVB_16VoCfGj9) 17 | by Eshin Jolly within MIND 2018 (36 min) 18 | 19 | - [Pro Git](https://git-scm.com/book/en/v2) by Scott Chacon and Ben Straub 20 | 21 | - [What is GitHub and how to use it](https://www.youtube.com/watch?v=AnftV9HBPSc) 22 | (17 min) 23 | 24 | - [Learn Git Branching](https://learngitbranching.js.org/) Neat interactive 25 | introduction to Git, like an online game! 26 | 27 | - [Version Control with Git] (http://swcarpentry.github.io/git-novice/) 28 | Software Carpentry practical lesson (~2h57min) by Gonzalez, I., Huang, D., 29 | Hejazi, N., Koziar, K., & Munk, M. � 30 | 31 | [GitHub repo](https://github.com/swcarpentry/git-novice) 32 | 33 | - [Git tutorial](https://psyarxiv.com/6tzh8/) Vuorre, M., & Curley, J. P. 34 | (2017, June 21). Curating Research Assets: A Tutorial on the Git Version 35 | Control System. https://doi.org/10.31234/osf.io/6tzh8 36 | 37 | - [A Friendly Github Intro Workshop](https://kirstiejane.github.io/friendly-github-intro/) 38 | Workshop with presentations, exercises and resources - by Mozilla Science 39 | Lab 40 | 41 | - [Collaborating with Git and GitHub](https://neurohackademy.org/course/collaborating-with-git-and-github/) 42 | by Elizabeth DuPre within Neurohackademy 2019 (2 hr 15 min, lecture with 43 | [code slides](https://emdupre.github.io/git-course/)) 44 | 45 | ## Data 46 | 47 | [Datalad](https://www.datalad.org/for/data-consumers) is to data what git is to 48 | code. It allows curation of data and version controlling of but also lets you 49 | crawl databases to explore and download data from them and it facilitates data 50 | sharing. Several of these features are described 51 | [here](https://www.datalad.org/features.html) with scripts that act as tutorial. 52 | There are videos presentation of it 53 | [there](https://www.youtube.com/watch?v=59CE6iOr45k). 54 | -------------------------------------------------------------------------------- /docs/13-data-code-management.md: -------------------------------------------------------------------------------- 1 | # Organizing your files 2 | 3 | Having a standard way to organize not only your data but also your code, the 4 | results, the documentation... from the beginning of a project can go a long way 5 | to save you a lot of time down the line (when communicating within or outside 6 | your lab, or when you have to wrap things up when moving to a new project/job). 7 | 8 | ## Templates 9 | 10 | Using the the 11 | [Cookiecutter python package](https://github.com/cookiecutter/cookiecutter) is a 12 | good way to get started to use a standardised folder structure. See for example 13 | an example for 14 | [data science](https://drivendata.github.io/cookiecutter-data-science/) 15 | 16 | But there are other possibilities: see 17 | [here](http://nikola.me/folder_structure.html) or 18 | [here](https://eglerean.wordpress.com/2017/05/24/project-management-data-management/). 19 | 20 | And some project template on OSF that can be forked and reused: 21 | 22 | - [Research Template to Start New Project (Confirmatory)](https://osf.io/qpdth/) 23 | - [Research Template to Start New Project (Exploratory)](https://osf.io/nc8ha/) 24 | 25 | ## The Brain Imaging Data Structure (BIDS) 26 | 27 | If you are going to do some MRI, fMRI, MEEG... analysis you will quickly drown 28 | in data if you are not a bit organized, we highly recommend you use the brain 29 | imaging data structure standard ([BIDS](http://bids.neuroimaging.io/)) to 30 | organize your data. 31 | 32 | The current version of BIDS covers raw data and some aspects of derivative data 33 | (e.g preprocessed data). In general BIDS also allows you to more easily share 34 | your data and use plenty of analytical [tools](bids-apps.neuroimaging.io/apps/). 35 | 36 | If you would like to use BIDS but you have no idea what a JSON file and / or the 37 | length of the specification document scares you, head over to the 38 | [BIDS starter kit](https://github.com/bids-standard/bids-starter-kit) to find 39 | tutorials and scripts to help you rearrange your data. 40 | 41 | - [The Brain Imaging Data Structure (BIDS)](https://neurohackademy.org/course/the-brain-imaging-data-structure-bids/) 42 | presented by Chris Gorgolewski within Neurohackademy 2018 43 | - duration: 56 min 44 | - type: [video] 45 | 46 | - [BIDS website](http://bids.neuroimaging.io/) 47 | - [BIDS apps](https://bids-apps.neuroimaging.io/apps/) 48 | - [BIDS starter kit](https://github.com/bids-standard/bids-starter-kit) 49 | 50 | ## KEEPING your files organized 51 | 52 | Not matter how clean your starting point is, it won't help if you don't have 53 | good every day practices to make sure everything stays clean. 54 | 55 | Some suggestions on how to do that from from 56 | [Danielle Navarro](https://twitter.com/djnavarro). 57 | 58 | 59 | 60 | And some more from [Marijn van Vliet](https://twitter.com/wmvanvliet) 61 | 62 | 63 | 64 | 67 | -------------------------------------------------------------------------------- /docs/14-documentation.md: -------------------------------------------------------------------------------- 1 | # Documentation 2 | 3 | There are different types of documentation. 4 | 5 | https://www.divio.com/blog/documentation/ 6 | 7 | Write the docs: 8 | 9 | - website: https://www.writethedocs.org/ 10 | 11 | - slackspace: 12 | https://join.slack.com/t/writethedocs/shared_invite/zt-kiwjl5qr-2P6cY1aU0XEore_8RaF2Bg 13 | 14 | ## Documenting projects and code 15 | 16 | It is often said to: 17 | 18 | > Always code as if the person who ends up maintaining your code is a violent 19 | > psychopath who knows where you live. 20 | 21 | Proper documentation of a project and good commenting of your code will help 22 | others to use it or pick it up later. But there are good selfish reasons to 23 | document your project and comment your code: it will most likely help future you 24 | when you have to respond to reviewers or when you want to check something in 25 | that data set or in that function you used 6 months ago. 26 | 27 | > - Most likely, you will have to re-run your analysis more than once. 28 | > 29 | > - In the future, you or a collaborator may have to re-visit part of the 30 | > project. 31 | > 32 | > - Your most likely collaborator is your future self, and your past self 33 | > doesn’t answer emails. 34 | 35 | See [here](http://bioconnector.github.io/bims8382/r-repres.html) for more. 36 | 37 | ### READMEs 38 | 39 | [list](https://github.com/matiassingers/awesome-readme#tools) 40 | 41 | this [checklist](https://github.com/Remi-Gau/readme-checklist) that are more 42 | specific to README files. 43 | 44 | In terms of code I guess the ideal is 45 | [self-documenting code](http://wiki.c2.com/?SelfDocumentingCode). 46 | 47 | [Read the docs](https://readthedocs.org/) is a good option that also allows for 48 | continuous integration. Python also apparently has this thing called 49 | [Sphinx](http://www.sphinx-doc.org/en/master/) that helps _create intelligent 50 | and beautiful documentation_ (that alone should make matlab users envious). 51 | 52 | There are also ways to make it part of a 53 | [continuous integration](https://predictablynoisy.com/circle-documentation-build). 54 | 55 | - [Write a great project ReadMe](https://mozilla.github.io/open-leadership-training-series/articles/opening-your-project/write-a-great-project-readme/) 56 | - [Documenting Python Code: A Complete Guide](https://realpython.com/documenting-python-code/) 57 | -------------------------------------------------------------------------------- /docs/20-planning-your-study.md: -------------------------------------------------------------------------------- 1 | # Planning your study 2 | 3 | When planning your study, here are some things you might want to consider: 4 | 5 | - [tools for reproducible research](21-reproducible-neuroimaging-research.md) 6 | - [pre-registration](22-preregistration.md) 7 | 8 | 27 | -------------------------------------------------------------------------------- /docs/21-reproducible-neuroimaging-research.md: -------------------------------------------------------------------------------- 1 | # Tools for reproducible research 2 | 3 | - [From interactive exploration to reproducible data science: Jupyter, Binder, Travis and friends.](https://neurohackademy.org/course/from-interactive-exploration-to-reproducible-data-science-jupyter-binder-travis-and-friends/) 4 | by Fernando Perez within Neurohackademy 2018 5 | 6 | - duration: 1 hr 25 min 7 | - type: {video} 8 | 9 | - [Jupyter tutorial](https://www.youtube.com/watch?v=CSkTJRNBTME&index=3&t=4s&list=PLEE6ggCEJ0H0KOlMKx_PUVB_16VoCfGj9) 10 | by Eshin Jolly within MIND 2018 11 | - duration: 31 min 12 | - type: {video} 13 | 14 | ## Containers 15 | 16 | - [Docker for scientists 1](https://neurohackademy.org/course/docker-for-scientists/) 17 | by Chris Gorgolewski within Neurohackweek 2016 18 | 19 | - duration: 1 hr 13 min 20 | - type: {video} 21 | 22 | - [Docker for scientists 2](https://neurohackademy.org/course/docker/) by 23 | Chris Gorgolewski within Neurohackweek 24 | 25 | - [Docker tutorial](https://www.youtube.com/watch?v=hUvYdXo5MfU&index=17&t=0s&list=PLEE6ggCEJ0H0KOlMKx_PUVB_16VoCfGj9) 26 | by Lucy Owen within MIND 2018 27 | 28 | - duration: 20 min 29 | - type: {video} 30 | 31 | - [Neurodocker](https://github.com/kaczmarj/neurodocker) allows you to easily 32 | create containers suited to your neuroimaging needs. Here is a 33 | [tutorial](https://miykael.github.io/nipype_tutorial/notebooks/introduction_neurodocker.html) 34 | on how to use it. 35 | 36 | ## Tools for reproducible neuroimaging 37 | 38 | - [ReproNim](http://www.reproducibleimaging.org/index.html) - A Center for 39 | Reproducible Neuroimaging Computation (a good site to get up to date on 40 | doing reproducible neuroimaging research) 41 | 42 | - [Code-ocean](https://codeocean.com/) - A research collaboration platform 43 | that uses docker containers to let you run your analysis online 44 | 45 | - [NeuroLinks](https://brainhack101.github.io/neurolinks/) - Resources for 46 | computational neuroscience 47 | 48 | ### Presentations 49 | 50 | - [Improving the Reproducibility of Neuroimaging Research](https://neurohackademy.org/course/improving-the-reproducibility-of-neuroimaging-research/) 51 | by Russ Poldrack within Neurohackweek 2016 52 | 53 | - duration: 1 hr 23 min 54 | - type: {video} 55 | 56 | - [GNU Make for Neuroimaging Workflows](https://neurohackademy.org/course/gnu-make-for-neuroimaging-workflows/) 57 | by Tara Madhyastha within Neurohackweek 2016 58 | 59 | - duration: 48 min 60 | - type: {video} 61 | 62 | - [Introduction to web technologies](https://neurohackademy.org/course/introduction-to-web-technologies/) 63 | by Anisha Keshavan within Neurohackademy 2018 64 | 65 | - duration: 56 min 66 | - type: {video} 67 | 68 | - [Neuroimaging pipelines](https://neurohackademy.org/course/neuroimaging-pipelines-2/) 69 | by Satra Ghosh within Neurohackweek 2017 70 | 71 | - duration: 1 hr 33 min 72 | - type: {video} 73 | 74 | - [Reproducibility in fMRI: What is the problem? 1](https://neurohackademy.org/course/reproducibility-in-fmri-what-is-the-problem-2/) 75 | by Russ Poldrack within Neurohackweek 2017 76 | 77 | - duration: 1 hr 40 min 78 | - type: {video} 79 | 80 | - [Same Data - Different Software - Different Results? Analytic Variability of Group fMRI Results](https://www.pathlms.com/ohbm/courses/8246/sections/12541/video_presentations/116000) 81 | by Alexander Bowring 82 | 83 | - duration: 12 min 84 | - type: {video} 85 | 86 | - [Software pipelines for reproducible neuroimaging](https://neurohackademy.org/course/software-pipelines-for-reproducible-neuroimaging/) 87 | by Satra Ghosh and Chris Gorgolewski within Neurohackademy 2016 88 | 89 | - duration: 1 hr 14 min 90 | - type: {video} 91 | 92 | - [Neuroimaging Workflows & Statistics for reproducibility](https://www.pathlms.com/ohbm/courses/8246/sections/12542/video_presentations/115885) 93 | by Dorota Jarecka, Satrajit Ghosh, Celia Greenwood and Jean-Baptiste Poline 94 | at OHBM 95 | 96 | - duration: 3 hr 45 min 97 | - type: {video} 98 | 99 | - [Tools from the Center for Open Neuroscience](https://www.youtube.com/watch?v=RBaJn2Xtqzg&index=8&t=2278s&list=PLEE6ggCEJ0H0KOlMKx_PUVB_16VoCfGj9) 100 | by Yaroslav Halchenko within MIND 2018 101 | 102 | - duration: 59 min 103 | - type: {video} 104 | 105 | - [Allen Institute Data and Software](https://neurohackademy.org/course/allen-institute-data-and-software/) 106 | by Nicolas Cain within Neurohackweek 2017 107 | 108 | - duration: 53 min 109 | - type: {video} 110 | 111 | - [Allen Institute Datasets](https://neurohackademy.org/course/allen-institute-datasets/) 112 | by Terri Gilbert within Neurohackweek 2016 113 | 114 | - duration: 1 hr 8 min 115 | - type: {video} 116 | 117 | - [Allen Institute RNAseq data](https://neurohackademy.org/course/allen-institute-rnaseq-data/) 118 | by Jeremy Miller within Neurohackweek 2016 119 | 120 | - duration: 52 min 121 | - type: {video} 122 | 123 | - [AllenSDK and the Allen Brain Observatory](https://neurohackademy.org/course/allensdk-and-the-allen-brain-observatory/) 124 | by Nicolas Cain and Justin Kiggins within Neurohackademy 2018 125 | 126 | - duration: 1 hr 42 min 127 | - type: {video} 128 | 129 | - [Integrating Allen Institute Datasets with MRI data](https://neurohackademy.org/course/integrating-allen-institute-datasets-with-mri-data/) 130 | by Kirstie Whitaker within Neurohackweek 2016 131 | - duration: 28 min 132 | - type: {video} 133 | 134 | ### Tutorials/instructions/slides 135 | 136 | - [Advance Unix and Make](https://neurohackademy.org/course/advance-unix-and-make/) 137 | by Valentina Staneva and Tara Madhyastha within Neurohackweek 2016 138 | 139 | - [CRN resources](https://neurohackademy.org/course/crn-resources/) by Chris 140 | Gorgolewski within Neurohackweek 141 | 142 | - [Reproducibility in fMRI: What is the problem? 2](https://neurohackademy.org/course/reproducibility-in-fmri-what-is-the-problem-3/) 143 | by Russ Poldrack within Neurohackweek 2017 144 | 145 | - [Reproducible research pipelines](https://neurohackademy.org/course/reproducible-research-pipelines/) 146 | by Chris Gorgolewski and Satra Ghosh within Neurohackweek 2016 147 | 148 | - [Reproducible fMRI analysis with Code Ocean](https://www.fmrwhy.com/2018/10/31/reproducible-fmri-codeocean/) 149 | by [Stephan Heunis](https://twitter.com/fmrwhy) describing how he did that 150 | with an SPM pipeline. 151 | 152 | ### Other 153 | 154 | - [Challenges to open data and how to respond](https://github.com/mozillascience/open-data-training/blob/master/Materials/Handouts/ODChallengesQI.md) 155 | -------------------------------------------------------------------------------- /docs/22-preregistration.md: -------------------------------------------------------------------------------- 1 | # Preregistration 2 | 3 | If your work is not purely exploratory you might want to consider 4 | [pre-registering your study](http://help.osf.io/m/registrations). It can be a 5 | good way to decide in advance how you are going to collect and analyze your 6 | data. It helps make it clear to yourself and to others what part of your study 7 | was predicted (i.e confirmatory) and which part wasn't (i.e exploratory). 8 | 9 | You can also opt for [registered reports](https://osf.io/8mpji/wiki/home/) where 10 | you submit your methods to a journal and get reviews on the protocol before the 11 | data collection and analysis is conducted. At the moment there is a large number 12 | of [journals that accept registered reports](https://cos.io/rr/#journals). 13 | 14 | Pre-registering neuroimaging studies can be quite challenging and comes with a 15 | whole set of constraints that might be absent in other fields. 16 | [Jessica Flannery](https://twitter.com/j_flan) has created a 17 | [preregistration template](https://osf.io/6juft/) based on the OHBM COBIDAS 18 | guidelines for fMRI studies. It is also available 19 | [on Github in an Rmarkdown format](https://github.com/jessicaflannery/fmri-prereg) 20 | 21 | For examples of studies that were pre-registered you can search in the 22 | [zotero libraries](https://www.zotero.org/groups/479248/osf/items?) curated by 23 | the [open science framework](https://osf.io/). 24 | 25 | There is also a communit effort to keep track of the MRI and MEEG 26 | preregistrtions that exist in this 27 | [spreadsheet](https://docs.google.com/spreadsheets/d/1_R3UBKvT4vEDOAPXxR8W98QGvZMhpuyxlvYzIGekf0w/edit?usp=sharing) 28 | and new entry can be added using this 29 | [form](https://docs.google.com/forms/d/e/1FAIpQLSc_l8nTd-gq_WlC7LvpLP5GKChNhD_mok1EnPX48xD3MYzdWA/viewform). 30 | 31 | You can find more information in 32 | [this google drive](https://drive.google.com/drive/folders/1p0Tr38HJ2tKAUIoTh-xGPHye3Y6oe8Q-?usp=sharing) 33 | on the effort to develop more templates for pre-reg in neuroimaging. 34 | -------------------------------------------------------------------------------- /docs/30-getting-data.md: -------------------------------------------------------------------------------- 1 | # Getting data 2 | 3 | Before you go off and acquire new data, you might want to check if there is not 4 | already a data set out there that might be suited to answer your question. 5 | 6 | So you might want to check some open data repositories 7 | [here](31-data-repositories.md#Data repositories). 8 | -------------------------------------------------------------------------------- /docs/31-data-repositories.md: -------------------------------------------------------------------------------- 1 | # Data repositories 2 | 3 | This section contains links to "open" data resources, that can be accessed for research purposes. 4 | For some of them, a formal request to the organization or to the data curation team may be required. 5 | 6 | This [Wikipedia](https://en.wikipedia.org/wiki/List_of_neuroscience_databases) also has a nice list with some more suggestions. 7 | 8 | ## Generic 9 | 10 | 11 | 12 | ??? example "GIN - The equivalent of github but for data. Based in Europe." 13 | - [database repository](https://gin.g-node.org/) 14 | - contact 15 | - data type: {MRI} {EEG} {iEEG} {ECoG} {human} {non-human} 16 | - datalad compatible: yes 17 | - paper: [10.12751/incf.ni2017.0040](https://doi.org/10.12751/incf.ni2017.0040) 18 | - RRID: [SCR_015864](https://scicrunch.org/resources/Tools/record/nlx_144509-1/SCR_015864/resolver?q=GIN&l=GIN) 19 | - The G-Node Data Infrastructure Services provides a platform for comprehensive and reproducible management and sharing of neuroscience data. Building on well established versioning technology, GIN offers the power of a web based repository management service combined with a distributed file storage. 20 | - Very similar to github but for data. 21 | - As it is based in Europe, this can an interesting option for GDPR compliance. 22 | 23 | 24 | 25 | ??? example "OSF - The interface can be slow and clunky but it can definitely be used to host and share data... and many other things." 26 | - [database repository](https://osf.io/) 27 | - contact 28 | - data type: pretty much anything goes 29 | - datalad compatible: 30 | - paper 31 | - RRID: [SCR_017419](https://scicrunch.org/resources/Tools/record/nlx_144509-1/SCR_017419/resolver?q=open%20science%20framework&l=open%20science%20framework) 32 | - OSF is a platform to support research and enable collaboration. Used to discover projects, data, materials, and collaborators helpful to your own research. 33 | 34 | 35 | 36 | ??? example "eBrains - For human & non-human data sets matching specific criteria" 37 | - [database repository](https://ebrains.eu/) 38 | - contact 39 | - data type: {human} {non-human} {fMRI} {MRI} {EEG} {DWI} {histology} 40 | - datalad compatible: 41 | - paper 42 | - RRID: 43 | 44 | ## NeuroImaging 45 | 46 | To get an exhaustive list of the datasets and databases available out there, 47 | you should first go to the [data section](https://www.nitrc.org/search/?type_of_search=group&q=category%3A%27Data%27) of the [Neuroimaging Tools 48 | an Resources Collaboratory](https://www.nitrc.org/). 49 | 50 | ### MRI/fMRI 51 | 52 | 53 | 54 | ??? example "OpenNeuro - A go to for MRI, MEG, EEG, iEEG, and ECoG data" 55 | - [database repository](https://openneuro.org/) 56 | - contact 57 | - data type: {MRI} {EEG} {iEEG} {ECoG} {human} 58 | - datalad compatible: yes 59 | - paper 60 | - RRID: [SCR_005031](https://scicrunch.org/resources/Any/record/nlx_144509-1/SCR_005031/resolver?q=openneuro&l=openneuro) 61 | - Open platform for analyzing and sharing neuroimaging data from human brain imaging research studies. Brain Imaging Data Structure (BIDS) compliant database. Formerly known as OpenfMRI. Platform for sharing MRI, MEG, EEG, iEEG, and ECoG data. 62 | 63 | 64 | 65 | ??? example "Neurovault - The place for your group results." 66 | - [database repository](https://neurovault.org/) 67 | - contact 68 | - data type: {MRI} {PET} {human} {non-human} 69 | - datalad compatible: yes 70 | - paper: 71 | - RRID: [SCR_003806](https://scicrunch.org/resources/Tools/record/nlx_144509-1/SCR_003806/resolver?q=Neurovault&l=Neurovault) 72 | - A data repository where researchers can publicly store and share unthresholded statistical brain activation maps produced by MRI and PET studies. 73 | 74 | 75 | 76 | ??? example "INDI - International Neuroimaging Data-Sharing Initiative for rawdata" 77 | - [database repository](http://fcon_1000.projects.nitrc.org/) 78 | - contact 79 | - data type: {MRI} {PET} {human} {non-human} {EEG} 80 | - datalad compatible: yes 81 | - paper: 82 | - RRID: [SCR_015771] 83 | - A data repository containing the 1000 Functional Connectomes project with more than 1200 resting state fMRI indenpendently collected at 33 sites. Age, sex and imaging center information are provided for each of the datasets. In accordance with HIPAA guidelines, all datasets are anonymous, with no protected health information included. The repository also provides INDI prospective and retrospective data Sharing Samples (resting state fMRI, behavioural, DTI, PET,...). 84 | 85 | 86 | 87 | ??? example "ACPI - Addiction Connectome Preprocessed Initiative" 88 | - [database repository](http://fcon_1000.projects.nitrc.org/indi/ACPI/html/index.html) 89 | - contact 90 | - data type: {MRI} {resting state} {ADHD} {human} 91 | - datalad compatible: yes 92 | - paper: 93 | - The Addiction Connectome Preprocessed Initiative (ACPI) aims to facilitate the image processing and analysis of datasets generated by NIDA investigators, with a particular focus on the determination of robustness to preprocessing decisions. In this regard, we are providing 8 preprocessed versions of the resting state fMRI datasets. ACPI includes 2 datasets, raw and preprocessed data (158 Subjects, 129 Anatomicla Scans, 185 Resting Functional Scans). 94 | 95 | 96 | 97 | 98 | ??? example "BALSA (Brain Analysis Library of Spatial Maps and Atlases) - A database for neuroimaging and neuroanatomical datasets for human and primate species." 99 | - [database repository](https://balsa.wustl.edu/) 100 | - contact 101 | - data type:{MRI} {PET} {human} {non-human} {DTI} 102 | - datalad compatible: 103 | - paper: 104 | - BALSA hosts two types of extensively analyzed neuroimaging data. BALSA Studies: extensively analyzed neuroimaging data associated with published figures. BALSA Reference: reference data mapped to brain atlas surfaces and volumes in humans and nonhuman primates 105 | 106 | 107 | 108 | ??? example "MCP (Mouse Connectome Project)." 109 | - [database repository](https://cic.ini.usc.edu) 110 | - contact 111 | - data type: {mouse} {fluorescent label} 112 | - datalad compatible: 113 | - paper: 114 | - RRID: [SCR_004096] (https://www.nitrc.org/projects/mcp/) 115 | - The CIC, home of the Mouse Connectome Project (MCP) seeks to create a complete mesoscale connectivity atlas of the C57Black/6 mouse brain and to subsequently generate its global neural networks. Multiple fluorescent neural dyes are used to trace all of the connections of the roughly 800 identified structures of the mouse brain. Our crossdisciplinary group develops neuroanatomic and neuroinformatic approaches to understand connectivity patterns in both health and disease. 116 | 117 | 118 | 119 | ??? example "ABIDE - the Autism Brain Imaging Data Exchange" 120 | - [database repository](http://fcon_1000.projects.nitrc.org/indi/abide/) 121 | - contact 122 | - data type: {human} {healthy} {autism} {fMRI} {MRI} {resting state} 123 | - paper 124 | - RRID: [SCR_003612](https://scicrunch.org/resources/Any/record/nlx_144509-1/SCR_003612/resolver?q=abide&l=abide) 125 | - Resting state functional magnetic resonance imaging (R-fMRI) datasets from 539 individuals with autism spectrum disorder (ASD) and 573 typical controls. This initiative involved 16 international sites, sharing 20 samples yielding 1112 datasets composed of both MRI data and an extensive array of phenotypic information common across nearly all sites. This effort is expected to facilitate discovery science and comparisons across samples. All datasets are anonymous, with no protected health information included. 126 | 127 | 128 | 129 | ??? example "ADNI - Alzheimer's Disease Neuroimaging Initiative" 130 | - [database repository](http://adni.loni.usc.edu/data-samples/access-data/) 131 | - contact 132 | - data type: {human} {alzheimer} {MRI} {fMRI} {PET} 133 | - paper 134 | - RRID: [SCR_003007](https://scicrunch.org/resources/Any/record/nlx_144509-1/SCR_003007/resolver?q=adni&l=adni) 135 | - Database of the results of the Alzheimer's Disease Neuroimaging Initiative study. ADNI is an initiative to develop biomarker-based methods to detect and track the progression of Alzheimer's disease (AD) that provides access to qualified scientists to their database of imaging, clinical, genomic, and biomarker data. 136 | 137 | 138 | 139 | 140 | ??? example "IXI Dataset - Brain Development from ICL" 141 | - [database repository](https://brain-development.org/ixi-dataset/) 142 | - contact: Biomedical Image Analysis Group, Imperial College London 143 | - data type: {human} {MRI} {DTI} 144 | - RRID: [SCR_005839](https://scicrunch.org/resources/Any/record/nlx_144509-1/SCR_005839/resolver?q=*&l=) 145 | - Nearly 600 MR images from normal, healthy subjects. The MR image acquisition protocol for each subject includes: T1, T2 and PD-weighted images, MRA images, and Diffusion-weighted images (15 directions). 146 | 147 | 148 | #### fNIRS 149 | 150 | ## Electrophysiology 151 | 152 | You definitely want to check this [list openly available electrophysiological data](https://github.com/openlists/ElectrophysiologyData), including EEG, MEG, ECoG/iEEG, and LFP data compiled by [Tom Donoghue](https://twitter.com/tomdonoghue) 153 | 154 | ### Surface (EEG/MEG) 155 | 156 | ### Intracranial (ECoG / iEEG / LFP / Single cell) 157 | 158 | 169 | -------------------------------------------------------------------------------- /docs/40-processing.md: -------------------------------------------------------------------------------- 1 | # Processing 2 | 3 | ## Processing infrastructure 4 | 5 | Resources currently [here](41-computing.md#Computing-Resources). 6 | 7 | ## Preprocessing data 8 | 9 | Processing has several stages, and can vary depending on which image modality 10 | (or type of data in general) you want to use. 11 | 12 | If you are interested in processing a specific type of data, you can refer to 13 | the links below. 14 | 15 | ## Single-modality Processing 16 | 17 | ### MRI 18 | 19 | Resources currently 20 | [here](42-analysis-software-MRI.md#Neuroimaging-analysis-software-for-MRI) 21 | 22 | #### Structural 23 | 24 | - T1w 25 | - T2w 26 | - Diffusion MRI 27 | - Laminar and high-resolution MRI 28 | 29 | #### Functional MRI 30 | 31 | - resting state fMRI 32 | - task-related fMRI 33 | 34 | ### EEG 35 | 36 | ### MEG 37 | 38 | Resources currently 39 | [here](43-analysis-software-MEEG.md#Neuroimaging-analysis-software-for-MEEG). 40 | 41 | ## Multi-modal Processing 42 | 43 | Some processing pipelines require multiple types of data. 44 | 45 | 46 | 47 | ### Meta analysis 48 | 49 | ### Modeling / Computational neuroscience 50 | 51 | ## More 52 | 53 | [Here](45-learning-neuroimaging.md#Neuroimaging) and 54 | [here](46-neuroimaging-resources.md#Neuroimaging-resources). 55 | -------------------------------------------------------------------------------- /docs/41-computing.md: -------------------------------------------------------------------------------- 1 | # Computing Resources 2 | 3 | - [Cloud Computing for Neuroimaging 1](https://neurohackademy.org/course/cloud-computing-for-neuroimaging/) 4 | by Amanda Tan and Ariel Rokem within Neurohackademy 2018 (3 hr 9 min) 5 | - [Cloud Computing for Neuroimaging 2](https://neurohackademy.org/course/cloud-computing/) 6 | by Tara Madhyastha within Neurohackweek 2016 7 | - [Using cloud computing for neuroimaging](https://neurohackademy.org/course/using-cloud-computing-for-neuroimaging/) 8 | by Cameron Craddock within Neurohackweek 2016 9 | -------------------------------------------------------------------------------- /docs/42-analysis-software-MRI.md: -------------------------------------------------------------------------------- 1 | # Analysis software for MRI 2 | 3 | ## Generic 4 | 5 | ??? example "SPM - Software package for the analysis of brain imaging data sequences" 6 | - [code repository]( ) 7 | - [website](https://www.fil.ion.ucl.ac.uk/spm/) 8 | - [documentation](https://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf) 9 | - [contact](https://www.fil.ion.ucl.ac.uk/spm/support/) 10 | - programming language: {matlab} {octave} 11 | - tags: {fMRI} {MEG} {EEG} {SPECT} {PET} {nipype} 12 | - [paper](https://doi.org/insert_paper_DOI_here) 13 | - RRID: 14 | - tutorial: 15 | - [URL](http://www.fil.ion.ucl.ac.uk/spm/course/) 16 | - programming language: {matlab} 17 | - level: 18 | - tags: 19 | - date: 20 | - duration: 21 | - by: 22 | 23 | 24 | 25 | 40 | 41 | ??? example "AFNI - A software suite primarily developed for the analysis and display of anatomical and fMRI data." 42 | - [website](https://afni.nimh.nih.gov/) 43 | - [documentation](https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/index.html) 44 | - [contact](https://afni.nimh.nih.gov/afni/community/board/list.php?1) 45 | - programming language: {C}, {python}, {R}, {shell} 46 | - tags: {fMRI} {MRI} {nipype} 47 | - [paper](https://doi.org/insert_paper_DOI_here) 48 | - RRID: 49 | - tutorial: 50 | - [URL](https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/main_toc.html) 51 | - [AFNI bootcamp](https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/educational/bootcamp_recordings.html) 52 | - [example data](https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/unix_tutorial/misc/install.data.html) 53 | - programming language: {shell} 54 | 55 | ??? example "FreeSurfer - An open source software suite for processing and analyzing (human) brain MRI images." 56 | - [code repository](https://github.com/freesurfer/freesurfer) 57 | - [website](https://surfer.nmr.mgh.harvard.edu/) 58 | - [documentation](https://surfer.nmr.mgh.harvard.edu/fswiki) 59 | - [contact](https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSupport) 60 | - programming language: {C}, {C++}, {shell} 61 | - tags: {fMRI} {MRI} {nipype} 62 | - [paper] 63 | - RRID: 64 | - tutorial: 65 | - [URL](https://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials 66 | - [videos](https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription) 67 | - programming language: {shell} 68 | 69 | ??? example "FSL - A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data." 70 | - [code repository](insert GitHub or GitLab URL ) 71 | - [website](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki) 72 | - [documentation](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Support) 73 | - [contact](https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=fsl) 74 | - programming language: 75 | - tags: {fMRI} {MRI} {nipype} 76 | - [paper] 77 | - RRID: 78 | - tutorial: 79 | - [URL](https://fsl.fmrib.ox.ac.uk/fslcourse/) 80 | 81 | ## Diffusion MRI 82 | 83 | ??? example "MRtrix3 - Advanced tools for the analysis of diffusion MRI data." 84 | - [GitHub]([insert GitHub or GitLab URL ](https://github.com/MRtrix3)) 85 | - [website]([insert URL](http://www.mrtrix.org/)) 86 | - [documentation](https://mrtrix.readthedocs.io/en/latest/) 87 | - [developer documentation](http://www.mrtrix.org/developer-documentation/) 88 | - [discussion forum](https://community.mrtrix.org/) 89 | - programming language: {C++}, {python} 90 | - tags: {dMRI} 91 | - [paper](doi: 10.1016/j.neuroimage.2019.116137) 92 | - RRID: insert_RRID_here 93 | - tutorial: 94 | - [beginner DWI tutorial](https://mrtrix.readthedocs.io/en/latest/getting_started/beginner_dwi_tutorial.html) 95 | - programming language: 96 | - level: beginner 97 | - tags: 98 | - date: 99 | - duration: 100 | - by: 101 | - tutorial: 102 | - [basic and advanced tractography with MRtrix tutorial](https://osf.io/fkyht/) 103 | - programming language: 104 | - level: 105 | - tags: 106 | - date: 107 | - duration: 108 | - by: 109 | - [tutorial video1](https://osf.io/fkyht/), 110 | - [tutorial video2](https://www.youtube.com/watch?v=lQWucXuAXR8) 111 | 112 | ??? example "DIPY - a free and open source software project for computational neuroanatomy, focusing mainly on dMRI analysis" 113 | - [gitHub](https://github.com/dipy/dipy) 114 | - [website](https://dipy.org/) 115 | - [documentation](https://dipy.org/documentation/1.1.1./documentation/) 116 | - [contact](https://mail.python.org/mailman/listinfo/neuroimaging) 117 | - programming language: {python} 118 | - tags: {dMRI} 119 | - paper: https://doi.org/10.3389/fninf.2014.00008 120 | - RRID: 121 | - [tutorial](https://dipy.org/tutorials/) 122 | 123 | ## Pipelines 124 | 125 | ??? example "Nipype - provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow." 126 | - [website](https://nipype.readthedocs.io/en/latest/) - 127 | - [GitHub](https://github.com/nipy/nipype) 128 | - [documentation](https://nipype.readthedocs.io/en/latest/) 129 | - [contact](https://gitter.im/nipy/nipype) 130 | - programming language: {python} 131 | - tags: {fMRI} {MRI} 132 | - paper DOI: 133 | - RRID: 134 | - tutorial: 135 | - [tutorial 1](https://nipype.readthedocs.io/en/0.11.0/users/pipeline_tutorial.html), 136 | - [tutorial 2](https://miykael.github.io/nipype_tutorial/), 137 | - [examples](https://nipype.readthedocs.io/en/latest/examples.html) 138 | - programming language: 139 | - level: 140 | - tags: 141 | - date: 142 | - duration: 143 | - by: 144 | 145 | ??? example "Automatic Analysis - multimodal MATLAB toolbox processing fMRI, DTI/DKI, and M/EEG" 146 | - [code repository](https://github.com/automaticanalysis/automaticanalysis) 147 | - [website](https://automaticanalysis.org) 148 | - [documentation](https://github.com/automaticanalysis/automaticanalysis/wiki) 149 | - [contact]() 150 | - programming language: {matlab} 151 | - tags: {MRI} {MEG} {EEG} {fMRI} {DTI} {DKI} {MATLAB} 152 | - [paper](http://doi.org/10.3389/fninf.2014.00090) 153 | - RRID: 154 | - tutorial: 155 | - [URL](http://www.cubic.rhul.ac.uk/wiki/doku.php?id=aa:aa_workshop) 156 | - programming language: {matlab} 157 | - level: {beginner} / {intermediate} 158 | - tags: {PDF} 159 | - date: 160 | - duration: 161 | - by: Tibor Auer 162 | 163 | 164 | ??? example "fMRIPrep - A Robust Preprocessing Pipeline for fMRI Data" 165 | - [GitHub](https://github.com/poldracklab/fmriprep) 166 | - [website](https://fmriprep.readthedocs.io/en/stable/) 167 | - [documentation] : 168 | - [contact] : 169 | - [tutorial](http://reproducibility.stanford.edu/fmriprep-tutorial-running-the-docker-image/) 170 | - programming language: {python} 171 | - tags: {fMRI} {nipype} 172 | - paper DOI: [https://doi.org/10.1038/s41592-018-0235-4](https://doi.org/10.1038/s41592-018-0235-4) 173 | - RRID: SCR_001362 174 | - tutorial: 175 | - [URL]( insert URL ) 176 | - programming language: 177 | - level: 178 | - tags: 179 | - date: 180 | - duration: 181 | - by: 182 | 183 | ## High-resolution 184 | 185 | ??? example "Nighres - Neuroimaging at high resolution" 186 | - [code repository](https://github.com/nighres/nighres) 187 | - [documentation](https://nighres.readthedocs.io/) 188 | - programming language: {python}, {java} 189 | - tags: {fMRI} {MRI} 190 | - [paper](https://doi.org/10.1093/gigascience/giy082) 191 | - RRID: SCR_016287 192 | - tutorial: 193 | - [URL](https://nighres.readthedocs.io/en/latest/auto_examples/index.html) 194 | - programming language: {python} 195 | - level: {beginner} 196 | - tags: {notebook} 197 | - by: the Nighres team 198 | 199 | ## Misc 200 | 201 | ??? example "ANTs - To compute high-dimensional mappings to capture the statistics of brain structure and function" 202 | - [GitHub](https://github.com/ANTsX/ANTs) 203 | - [website](http://stnava.github.io/ANTs/) 204 | - [documentation](https://github.com/ANTsX/ANTs/wiki) 205 | - [contact](https://sourceforge.net/p/advants/discussion/) 206 | - programming language: 207 | - tags: {fMRI} {MRI} {nipype} 208 | - paper DOI: 209 | - RRID: 210 | - tutorial: 211 | - [URL](https://github.com/stnava/ANTsTutorial) 212 | - programming language: 213 | - level: 214 | - tags: 215 | - date: 216 | - duration: 217 | - by: 218 | 219 | ??? example "BrainSuite - A collection of open source software tools that enable largely automated processing of MRI of the human brain." 220 | - [website](http://brainsuite.org/) 221 | - documentation: 222 | - [contact](http://forums.brainsuite.org/) 223 | - programming language: 224 | - tags: 225 | - paper DOI: 226 | - RRID: 227 | - tutorial 228 | - [URL](http://brainsuite.org/tutorials/) 229 | - programming language: 230 | - level: 231 | - tags: 232 | - date: 233 | - duration: 234 | - by: 235 | -------------------------------------------------------------------------------- /docs/43-analysis-software-MEEG.md: -------------------------------------------------------------------------------- 1 | # Neuroimaging analysis software for EEG and MEG 2 | 3 | The following list has been shamelessly taken from the excellent repo [Open Software for Human Electrophysiology](https://github.com/voytekresearch/OpenTools). Do check it out as it also includes plugins that are not listed here. 4 | 5 | ## General Purpose Tools 6 | 7 | The following are general purpose platforms, with functionality including: loading data, pre-processing, visualization, standard analysis, and making figures. 8 | 9 | ??? example "MNE - Open-source Python software for exploring, visualizing, and analyzing human neurophysiological data" 10 | - [code repository](https://github.com/mne-tools/mne-python) 11 | - [website](http://martinos.org/mne/stable/index.html) 12 | - [documentation](https://mne.tools/dev/overview/index.html) 13 | - [contact](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) 14 | - programming language: {python} 15 | - tags: {MEG} {EEG} {sEEG} {ECoG} 16 | - [paper](https://doi.org/10.1016/j.neuroimage.2013.10.027) 17 | - RRID: 18 | - tutorial: 19 | - [URL](https://mne.tools/stable/auto_tutorials/index.html) 20 | - programming language: {python} 21 | - level: 22 | - tags: 23 | - date: 24 | - duration: 25 | - by: 26 | 27 | ??? example "Wonambi - A general purpose tool for processing, analyzing and visualizing EEG, ECoG and other electrophysiology formats data, including specific tools focused on sleep scoring and analysis." 28 | - [code repository](https://github.com/wonambi-python/wonambi) 29 | - [website](https://wonambi-python.github.io) 30 | - [documentation]( ) 31 | - [contact]( ) 32 | - programming language: {python} 33 | - tags: {MEG} {EEG} {sleep} {ECoG} 34 | - [paper](https://doi.org/insert_paper_DOI_here) 35 | - RRID: 36 | - tutorial: 37 | - [URL](https://wonambi-python.github.io/analysis/index.html) 38 | - programming language: {python} 39 | - level: 40 | - tags: 41 | - date: 42 | - duration: 43 | - by: 44 | 45 | ??? example "FieldTrip - A general purpose tool for processing, analyzing and visualizing toolbox for MEG, EEG, iEEG and NIRS data" 46 | - repository URL: [Github](https://github.com/fieldtrip/fieldtrip) 47 | - website URL: [http://www.fieldtriptoolbox.org](http://www.fieldtriptoolbox.org) 48 | - tutorial URL: [http://www.fieldtriptoolbox.org/tutorial/](http://www.fieldtriptoolbox.org/tutorial/) 49 | - documentation: [http://www.fieldtriptoolbox.org/documentation/](http://www.fieldtriptoolbox.org/documentation/) 50 | - programming language: {matlab} 51 | - paper DOI: [https://doi.org/10.1155/2011/156869](https://doi.org/10.1155/2011/156869) 52 | - RRID: 53 | - contact: [mailing list](http://www.fieldtriptoolbox.org/discussion_list/) 54 | 70 | 71 | ??? example "BrainStorm - A collaborative, open-source application dedicated to the analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal invasive neurophysiology." 72 | - [BrainStorm](https://neuroimage.usc.edu/brainstorm/) - 73 | - repository URL: [Github](https://github.com/brainstorm-tools/brainstorm3) 74 | - website URL: [https://neuroimage.usc.edu/brainstorm/](https://neuroimage.usc.edu/brainstorm/) 75 | - tutorial URL: [https://neuroimage.usc.edu/brainstorm/Tutorials](https://neuroimage.usc.edu/brainstorm/Tutorials) 76 | - documentation: 77 | - programming language: {matlab}, {Java} 78 | - paper DOI: [https://doi.org/10.1155/2011/879716](https://doi.org/10.1155/2011/879716) 79 | - RRID: 80 | - contact: [discussion forum](https://neuroimage.usc.edu/forums/) 81 | 97 | 98 | ??? example "EEGLab - A general purpose tool for processing, analyzing and visualizing EEG data." 99 | - repository URL: 100 | - [website](https://sccn.ucsd.edu/eeglab/index.php) 101 | - tutorial URL: [https://sccn.ucsd.edu/wiki/EEGLAB_TUTORIAL_OUTLINE](https://sccn.ucsd.edu/wiki/EEGLAB_TUTORIAL_OUTLINE) 102 | - documentation: [https://sccn.ucsd.edu/wiki/EEGLAB_Wiki](https://sccn.ucsd.edu/wiki/EEGLAB_Wiki) 103 | - programming language: {matlab} 104 | - paper DOI: [https://doi.org/10.1016/j.jneumeth.2003.10.009](https://doi.org/10.1016/j.jneumeth.2003.10.009) 105 | - RRID: 106 | - contact: [mailing list](https://sccn.ucsd.edu/contact/mailinglists.php) 107 | 123 | 124 | ??? example "SPM - Software package for the analysis of brain imaging data sequences" 125 | - [code repository]( ) 126 | - [website](https://www.fil.ion.ucl.ac.uk/spm/) 127 | - [documentation](https://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf) 128 | - [contact](https://www.fil.ion.ucl.ac.uk/spm/support/) 129 | - programming language: {matlab} {octave} 130 | - tags: {fMRI} {MEG} {EEG} {SPECT} {PET} {nipype} 131 | - [paper](https://doi.org/insert_paper_DOI_here) 132 | - RRID: 133 | - tutorial: 134 | - [URL](http://www.fil.ion.ucl.ac.uk/spm/course/) 135 | - programming language: {matlab} 136 | - level: 137 | - tags: 138 | - date: 139 | - duration: 140 | - by: 141 | 142 | ??? example "NutMEG - A general purpose tool for processing, analyzing and visualizing MEG data." 143 | - [website](https://www.nitrc.org/plugins/mwiki/index.php/nutmeg:MainPage) - 144 | - [Github](https://github.com/UCSFBiomagneticImagingLab/nutmeg) 145 | - tutorial URL: 146 | - documentation: 147 | - programming language: {R} 148 | - paper DOI: [https://doi.org/10.1155/2011/758973](https://doi.org/10.1155/2011/758973) 149 | - RRID: 150 | - contact: 151 | 167 | 168 | ??? example "EEGUtils - A general purpose tool for processing, analyzing and visualizing EEG data." 169 | - [Github](https://github.com/craddm/eegUtils) 170 | - [website](https://craddm.github.io/eegUtils/) 171 | - tutorial URL: 172 | - documentation: 173 | - programming language: {Julia} 174 | - paper DOI: 175 | - RRID: 176 | - contact: 177 | 193 | 194 | ??? example "EEG.jl - An EEG processing library." 195 | - [EEG.jl](https://eegjl.readthedocs.io/en/latest/) - 196 | - repository URL: [Github](https://github.com/rob-luke/EEG.jl) 197 | - website URL: [https://eegjl.readthedocs.io/en/latest/](https://eegjl.readthedocs.io/en/latest/) 198 | - tutorial URL: 199 | - documentation: 200 | - programming language: {C++} 201 | - paper DOI: 202 | - RRID: 203 | - contact: 204 | 220 | 221 | ??? example "CarTool - An EEG analysis toolbox." 222 | - repository URL: 223 | - [website](https://sites.google.com/site/cartoolcommunity/) 224 | - tutorial URL: [tutorial videos](https://www.youtube.com/watch?v=xxfotUryojM&list=PLsWOKfVt5ZtIzPy6QZ1u_5c6M2Zs3wM4k) 225 | - documentation: 226 | - programming language: {C++} 227 | - paper DOI: [https://doi.org/10.1155/2011/813870](https://doi.org/10.1155/2011/813870) 228 | - RRID: 229 | - contact: [discussion forum](https://sites.google.com/site/cartoolcommunity/forum) 230 | 245 | - by: John Doe and Jane Doe 246 | 247 | ## Standalone Tools - Specific Purposes 248 | 249 | ??? example "NeuroDSP - A package for calculating a broad range of measures on neural time series, including a range of time-domain measures such as waveform shape analyses." 250 | - [Github](https://github.com/voytekresearch/neurodsp) 251 | - [website](https://neurodsp-tools.github.io/neurodsp/index.html) 252 | - tutorial URL: [https://neurodsp-tools.github.io/neurodsp/auto_tutorials/index.html](https://neurodsp-tools.github.io/neurodsp/auto_tutorials/index.html) 253 | - documentation: 254 | - programming language: {python} 255 | - paper DOI: [https://doi.org/10.21105/joss.01272](https://doi.org/10.21105/joss.01272) 256 | - RRID: 257 | - contact: 258 | 274 | 275 | ??? example "FOOOF - A package for parameterizing neural power spectra." 276 | - [Github](https://github.com/voytekresearch/fooof) 277 | - [website](https://fooof-tools.github.io/fooof/index.html) 278 | - tutorial URL: 279 | - documentation: [https://fooof-tools.github.io/fooof/index.html](https://fooof-tools.github.io/fooof/index.html) 280 | - programming language: {python} 281 | - paper DOI: [https://doi.org/10.1101/299859](https://doi.org/10.1101/299859) 282 | - RRID: 283 | - contact: 284 | 300 | 301 | ??? example "Spectral Connectivity - A package including a group of functional connectivity and coherence related measures." 302 | - [Github](https://github.com/Eden-Kramer-Lab/spectral_connectivity) 303 | - website URL: 304 | - tutorial URL: 305 | - [documentation](http://spectral-connectivity.readthedocs.io/en/latest/index.html) 306 | - programming language: {python} 307 | - paper DOI: 308 | - RRID: 309 | - contact: 310 | 326 | 327 | ??? example "pactools - Provides tools to estimate phase-amplitude coupling (PAC) in neural time series." 328 | - [Github](https://github.com/pactools/pactools) 329 | - website URL: [https://pactools.github.io](https://pactools.github.io) 330 | - tutorial URL: 331 | - documentation: 332 | - programming language: 333 | - paper DOI: [https://doi.org/10.1371/journal.pcbi.1005893](https://doi.org/10.1371/journal.pcbi.1005893) 334 | - RRID: 335 | - contact: 336 | 352 | 353 | ??? example "Tensor PAC - A tool for calculating phase-amplitude coupling measures, using tensors and parallel computing." 354 | - repository URL: [Github](https://github.com/EtienneCmb/tensorpac) 355 | - website URL: [https://etiennecmb.github.io/tensorpac/](https://etiennecmb.github.io/tensorpac/) 356 | - tutorial URL: 357 | - documentation: 358 | - programming language: {python} 359 | - paper DOI: 360 | - RRID: 361 | - contact: [chat](https://etiennecmb.github.io/tensorpac/community.html#chat) 362 | 378 | 379 | 380 | ??? example "PyEEG - A Python module with many functions for time series analysis, including brain physiological signals" 381 | - [Github](https://github.com/forrestbao/pyeeg) 382 | - website URL: 383 | - tutorial URL: 384 | - documentation: 385 | - programming language: {python} 386 | - paper DOI: [https://doi.org/10.1155/2011/406391](https://doi.org/10.1155/2011/406391) 387 | - RRID: 388 | - contact: 389 | 405 | 406 | ??? example "ECoGTools - A collection of tools for analyzing ECoG data" 407 | - [Github](https://github.com/choldgraf/ecogtools) 408 | - website URL: 409 | - tutorial URL: 410 | - documentation: 411 | - programming language: 412 | - paper DOI: 413 | - RRID: 414 | - contact: 415 | 431 | 432 | ??? example "restingIAF - A tool for estimating the peak individual alpha frequency" 433 | - [Github](https://github.com/corcorana/restingIAF) 434 | - website URL: 435 | - tutorial URL: [https://github.com/corcorana/restingIAF/blob/master/tutorial/tute_README.md](https://github.com/corcorana/restingIAF/blob/master/tutorial/tute_README.md) 436 | - documentation: 437 | - programming language: 438 | - paper DOI: [https://doi.org/10.1111/psyp.13064](https://doi.org/10.1111/psyp.13064) 439 | - RRID: 440 | - contact: 441 | 457 | 458 | ??? example "Phase Opposition Code - A collection of functions for calculating phase opposition measures" 459 | - [website](http://www.cerco.ups-tlse.fr/~rufin/PhaseOppositionCode/) - . 460 | - repository URL: 461 | - website URL: 462 | - tutorial URL: 463 | - documentation: 464 | - programming language: 465 | - paper DOI: [https://doi.org/10.3389/fnins.2016.00426](https://doi.org/10.3389/fnins.2016.00426) 466 | - RRID: 467 | - contact: 468 | 483 | 484 | ??? example "ADAM - Amsterdam Decoding and Modeling Toolbox" 485 | - [ADAM](https://github.com/fahrenfort/ADAM) - An open source Matlab Toolbox that allows you to perform multivariate analyses on your M/EEG data using BDM and FEM. 486 | - repository URL: [Github](https://github.com/fahrenfort/ADAM) 487 | - website URL: 488 | - tutorial URL: [http://doi.org/10.3389/fnins.2018.00368](http://doi.org/10.3389/fnins.2018.00368) 489 | - documentation: 490 | - programming language: {matlab} 491 | - paper DOI: [https://doi.org/10.1007/s12021-013-9186-1](https://doi.org/10.1007/s12021-013-9186-1) 492 | - RRID: 493 | - contact: 494 | 510 | 511 | ??? example "HERMES - A tool for estimating connectivity measures between M/EEG signals" 512 | - repository URL: [Github](https://github.com/guiomar/HERMES) 513 | - website URL: [http://hermes.ctb.upm.es](http://hermes.ctb.upm.es) 514 | - tutorial URL: 515 | - documentation: 516 | - programming language: 517 | - paper DOI: [https://doi.org/10.3389/fnins.2018.00368](https://doi.org/10.3389/fnins.2018.00368) 518 | - RRID: 519 | - contact: [http://hermes.ctb.upm.es/contact/](http://hermes.ctb.upm.es/contact/) 520 | 536 | 537 | ??? example "SEREEGA - A package for simulating synthetic data that mimic event-related EEG activity." 538 | - [Github](https://github.com/lrkrol/SEREEGA) 539 | - website URL: 540 | - tutorial URL: [https://github.com/lrkrol/SEREEGA#tutorial](https://github.com/lrkrol/SEREEGA#tutorial) 541 | - documentation: 542 | - programming language: {matlab} 543 | - paper DOI: [https://doi.org/10.1101/326066](https://doi.org/10.1101/326066) 544 | - RRID: 545 | - contact: 546 | 562 | 563 | ??? example "Unfold - A tool for deconvolving overlapping EEG signals and for non-linear modelling" 564 | - [Unfold](https://www.unfoldtoolbox.org) - 565 | - repository URL: [Github](https://github.com/unfoldtoolbox/unfold) 566 | - website URL: [https://www.unfoldtoolbox.org/](https://www.unfoldtoolbox.org/) 567 | - tutorial URL: 568 | - documentation: 569 | - programming language: 570 | - paper DOI: [https://doi.org/10.7717/peerj.7838](https://doi.org/10.7717/peerj.7838) 571 | - RRID: 572 | - contact: 573 | 589 | 590 | ??? example "ept-TFCE - A tool for statistical analysis of already pre-processed M/EEG data, focused mainly around the 'threshold-free cluster enhancement' method" 591 | - [ept-TFCE](https://github.com/Mensen/ept_TFCE-matlab) - . 592 | - [Github](https://github.com/Mensen/ept_TFCE-matlab) 593 | - website URL: 594 | - tutorial URL: 595 | - documentation: 596 | - programming language: 597 | - paper DOI: [https://doi.org/10.1016/j.neuroimage.2012.10.027](https://doi.org/10.1016/j.neuroimage.2012.10.027) 598 | - RRID: 599 | - contact: 600 | 616 | 617 | ??? example "ERP Reliability Analysis - an open-source Matlab program that uses generalizability theory to evaluate the reliability of ERP data" 618 | - repository URL: [Github](https://github.com/peclayson/ERA_Toolbox) 619 | - website URL: [http://peterclayson.com/era-toolbox/](http://peterclayson.com/era-toolbox/) 620 | - tutorial URL: 621 | - documentation: [https://github.com/peclayson/ERA_Toolbox/wiki](https://github.com/peclayson/ERA_Toolbox/wiki) 622 | - programming language: {matlab} 623 | - paper DOI: [https://doi.org/10.1016/j.ijpsycho.2016.10.012](https://doi.org/10.1016/j.ijpsycho.2016.10.012) 624 | - RRID: 625 | - contact: 626 | 642 | 643 | ??? example "OpenMEEG - A package for solving forward problems for EEG & MEG data." 644 | - [Github](https://github.com/openmeeg/openmeeg) 645 | - [website](http://openmeeg.github.io) 646 | - tutorial URL: [https://openmeeg.github.io/tutorial.html](https://openmeeg.github.io/tutorial.html) 647 | - documentation: 648 | - programming language: 649 | - paper DOI: [https://doi.org/10.1186/1475-925X-9-45](https://doi.org/10.1186/1475-925X-9-45) 650 | - RRID: 651 | - contact: [mailing list](https://lists.gforge.inria.fr/mailman/listinfo/openmeeg-info) 652 | 668 | 669 | 670 | ## Pipelines 671 | 672 | 691 | 692 | ??? example "Automatic Analysis - multimodal MATLAB toolbox processing fMRI, DTI/DKI, and M/EEG" 693 | - [code repository](https://github.com/automaticanalysis/automaticanalysis) 694 | - [website](https://automaticanalysis.org) 695 | - [documentation](https://github.com/automaticanalysis/automaticanalysis/wiki) 696 | - [contact]() 697 | - programming language: {matlab} 698 | - tags: {MRI} {MEG} {EEG} {fMRI} {DTI} {DKI} {MATLAB} 699 | - [paper](http://doi.org/10.3389/fninf.2014.00090) 700 | - RRID: 701 | - tutorial: 702 | - [URL](http://www.cubic.rhul.ac.uk/wiki/doku.php?id=aa:aa_workshop) 703 | - programming language: {matlab} 704 | - level: {beginner} / {intermediate} 705 | - tags: {PDF} 706 | - date: 707 | - duration: 708 | - by: Tibor Auer 709 | -------------------------------------------------------------------------------- /docs/44-analysis-software-physio.md: -------------------------------------------------------------------------------- 1 | # Analysis software for physiological signals (ECG, PPG, EDA, EMG...) 2 | 3 | ??? example "NeuroKit2 - A python toolbox for statistics and neurophysiological signal processing" 4 | - [code repository](https://github.com/neuropsychology/NeuroKit) 5 | - [website](https://neurokit2.readthedocs.io/en/latest/introduction.html) 6 | - [documentation](https://neurokit2.readthedocs.io/en/latest/introduction.html) 7 | - [contact](https://github.com/neuropsychology/NeuroKit/issues) 8 | - programming language: {python} 9 | - tags: {EDA} {EMG} {ECG} {PPG} {RSP} {EEG} 10 | - [paper] 11 | - RRID: 12 | - tutorial: 13 | - [URL](https://neurokit.readthedocs.io/en/latest/tutorials/index.html) 14 | - programming language: {python} 15 | -------------------------------------------------------------------------------- /docs/45-learning-neuroimaging.md: -------------------------------------------------------------------------------- 1 | # Neuroimaging 2 | 3 | ## MOOC on neuroimaging 4 | 5 | - description: MOOC on neuroimaging 6 | - URL: [part 1](https://en.coursera.org/learn/functional-mri) and 7 | [part 2](https://en.coursera.org/learn/functional-mri-2) 8 | - date: 9 | - tags: [video] [fMRI] [MOOC] 10 | - duration: 11 | - level: [intermediate] [meta-analysis] 12 | - event: 13 | - reference: 14 | - by:[Tor Wager](https://twitter.com/torwager) and Martin Lindquist 15 | 16 | ## Quality control 17 | 18 | ### Neuroimaging quality control task force 19 | 20 | - description: 21 | - URL: 22 | [URL](https://crossinvalidation.com/2018/07/31/neuroimaging-quality-control-niqc-task-force-to-develop-protocols-tools-and-manuals/) 23 | - date: 2018 24 | - tags: 25 | - duration: 26 | - level: [intermediate] 27 | - event: 28 | - reference: 29 | - by: 30 | 31 | ### quality control on MRI and fMRI 32 | 33 | - description: 34 | - URL: 35 | [URL](https://practicalfmri.blogspot.com/2014/08/qa-for-fmri-part-3-facility-qa-what-to.html) 36 | - date: 37 | - tags: 38 | - duration: 39 | - level: 40 | - event: 41 | - reference: 42 | - by: 43 | 44 | ### COBIDacq 45 | 46 | - description: 47 | - URL: [URL](https://practicalfmri.blogspot.com/2017/12/cobidacq.html) 48 | - date: 49 | - tags: 50 | - duration: 51 | - level: 52 | - event: 53 | - reference: 54 | - by: 55 | 56 | ### wikibook neuroimaging data processing 57 | 58 | - description: 59 | - URL: 60 | [URL](https://en.wikibooks.org/wiki/Neuroimaging_Data_Processing/Data_Quality) 61 | - date: 62 | - tags: 63 | - duration: 64 | - level: 65 | - event: 66 | - reference: 67 | - by: 68 | 69 | ### References for quality control 70 | 71 | - description: 72 | - URL: [URL](https://www.zotero.org/groups/2221093/niqc) 73 | - date: 74 | - tags: 75 | - duration: 76 | - level: 77 | - event: 78 | - reference: 79 | - by: 80 | 81 | ### MRIQC 82 | 83 | - description: MRI quality control. A BIDS app that runs a pipeline to assess 84 | the quality of your data. 85 | - URL: [URL](https://mriqc.readthedocs.io/en/stable/) 86 | - date: 87 | - tags: 88 | - duration: 89 | - level: 90 | - event: 91 | - reference: 92 | - by: 93 | 94 | ### the PCP Quality Assessment Protocol 95 | 96 | - description: BIDS app based on the protocol of the connectome project data 97 | - URL: [URL1](https://github.com/BIDS-Apps/QAP) , 98 | [URL2](http://preprocessed-connectomes-project.org/quality-assessment-protocol/) 99 | - date: 100 | - tags: 101 | - duration: 102 | - level: 103 | - event: 104 | - reference: 105 | - by: 106 | 107 | ### Scripts for quality control of diffusion data 108 | 109 | [Scripts](http://davidroalf.com/script_download/) 110 | 111 | - description: 112 | - URL: [URL](https://practicalfmri.blogspot.com/2017/12/cobidacq.html) 113 | - date: 114 | - tags: [software] 115 | - duration: 116 | - level: 117 | - event: 118 | - reference: 119 | - by: 120 | 121 | ### Qoala-t 122 | 123 | - description: QA for freesurfer segmentations 124 | - URL: [URL](https://github.com/Qoala-T/Qoala-T) 125 | - date: 126 | - tags: 127 | - duration: 128 | - level: 129 | - event: 130 | - reference: 131 | - by: 132 | - shinyapp 133 | - description: QA for freesurfer segmentations 134 | - URL: [URL](https://qoala-t.shinyapps.io/qoala-t_app/) 135 | - date: 136 | - tags: 137 | - duration: 138 | - level: 139 | - event: 140 | - reference: 141 | - by: 142 | 143 | ### Visual QC 144 | 145 | - description: 146 | - URL: [URL](https://github.com/raamana/visualqc) 147 | - date: 2018 148 | - tags: 149 | - duration: 150 | - level: [intermediate] 151 | - event: 152 | - reference: 153 | - by:[Pradeep](https://twitter.com/raamana_) 154 | 155 | ## Diffusion Microstructure Imaging in Python (Dmipy) 156 | 157 | - description: The Dmipy software project is dedicated to fasciliting 158 | high-level, reproducible diffusion microstructure research. The Dmipy 159 | open-source repository has many examples on implementing and fitting 160 | microstructure models. 161 | - URL: [URL](https://github.com/AthenaEPI/dmipy) 162 | - date: 2018 163 | - tags: [software] [image processing] 164 | - duration: 165 | - level: [intermediate] 166 | - event: 167 | - reference: 168 | [reference](https://hal.inria.fr/hal-01873353/file/dmipy-diffusion-microstructure.pdf) 169 | - by: 170 | 171 | ## Other specific topics 172 | 173 | ### Computer Vision 174 | 175 | - description: Lecture on Computer Vision by Michael Beyeler within 176 | Neurohackademy 2018. 177 | - URL: [URL](https://neurohackademy.org/course/computer-vision/) 178 | - date: 2018 179 | - tags: [video] [summer school] [image processing] [machine learning] 180 | - duration: 00:53 181 | - level: [intermediate] 182 | - event: Neurohackademy 2018 183 | - by: Michael Beyeler 184 | 185 | ### Finding low-dimensional structure in large-scale neural recordings 186 | 187 | - description: 188 | - URL: 189 | [URL](https://neurohackademy.org/course/finding-low-dimensional-structure-in-large-scale-neural-recordings/) 190 | - date: 2018 191 | - tags: [video] [summer school] 192 | - duration: 00:36 193 | - level: [intermediate] 194 | - event: Neurohackademy 2018 195 | - reference: 196 | - by: Eva Dyer 197 | 198 | ### Interactive Data Visualization with D3 199 | 200 | - description: 201 | - URL: 202 | [URL](https://neurohackademy.org/course/interactive-data-visualization-with-d3/) 203 | - date: 2018 204 | - tags: [video] [summer school] 205 | - duration: 00:49 206 | - level: [intermediate] 207 | - event: Neurohackweek 2017 208 | - reference: 209 | - by: Anisha Keshavan 210 | 211 | ### Neuroethics 212 | 213 | - description: 214 | - URL: https://neurohackademy.org/course/neuroethics/ 215 | - date: 2018 216 | - tags: [video] [summer school] 217 | - duration: 00:58 218 | - level: [intermediate] 219 | - event: Neurohackademy 2018 220 | - reference: 221 | - by: Eran Klein 222 | 223 | ### Quantitative and diffusion MRI modeling of developmental data 224 | 225 | - description: 226 | - URL: 227 | [URL](https://neurohackademy.org/course/quantitative-and-diffusion-mri-modeling-of-developmental-data/) 228 | - date: 2018 229 | - tags: [video] [summer school] 230 | - duration: 231 | - level: [intermediate] 232 | - event: Neurohackademy 233 | - reference: 234 | - by: by Yason Yeatman 235 | 236 | ## Meta analysis 237 | 238 | ### Overview_of_Meta-Analysis_Approaches 239 | 240 | #### video 241 | 242 | - description: Overview of Meta Analysis Approaches 243 | - URL: 244 | [URL](https://www.pathlms.com/ohbm/courses/8246/sections/12542/video_presentations/116072) 245 | - date: 2018 246 | - tags: 247 | - duration: 00:18 248 | - level: [intermediate] 249 | - event: OHBM 2018 250 | - reference: 251 | - by: [Tom Nichols](https://twitter.com/ten_photos) 252 | 253 | #### slides 254 | 255 | - description: Overview of Meta Analysis Approaches 256 | - URL: 257 | [URL](https://figshare.com/articles/Overview_of_Meta-Analysis_Approaches/6723839) 258 | - date: 2018 259 | - tags: [slides] 260 | - duration: 261 | - level: [intermediate] 262 | - event: OHBM 2018 263 | - reference: 264 | 265 | #### ALE and BrainMap 266 | 267 | - description: Overview of Meta Analysis Approaches 268 | - URL: 269 | [URL](https://www.pathlms.com/ohbm/courses/8246/sections/12542/video_presentations/116066) 270 | - date: 2018 271 | - tags: [video] 272 | - duration: 00:22 273 | - level: [intermediate] 274 | - event: OHBM 2018 275 | - reference: 276 | - by: Simon B. Eickhoff 277 | 278 | #### NiMARE 279 | 280 | - description: NiMARE is a Python library for coordinate- and image-based 281 | meta-analysis. 282 | - URL: [URL](https://github.com/neurostuff/NiMARE) 283 | - type: [software] [python] [meta-analysis] 284 | - level: [intermediate] 285 | - tutorial 286 | - URL: 287 | [URL](https://www.kaggle.com/chrisfilo/coordinate-and-image-metaanalysis-with-nimare) 288 | - type: [tutorial] [juptyer] [meta-analysis] 289 | - level: [intermediate] 290 | - by: Chris Gorgolewski 291 | 292 | ### coordinate based meta-analysis 293 | 294 | #### brainmap 295 | 296 | - description: 297 | - URL: [URL](http://www.brainmap.org/) 298 | - date: 299 | - tags: 300 | - duration: 301 | - level: [intermediate] [meta-analysis] 302 | - event: 303 | - reference: 304 | - by: 305 | 306 | #### Sleuth 307 | 308 | - description: 309 | - URL: [URL](http://www.brainmap.org/software.html#Sleuth) 310 | - date: 2018 311 | - tags: [software] [meta-analysis] 312 | - duration: 313 | - level: [intermediate] 314 | - event: 315 | - reference: 316 | - by: 317 | 318 | #### GingerALE 319 | 320 | - [description](http://www.brainmap.org/) 321 | - URL: [URL](http://www.brainmap.org/software.html#GingerALE) 322 | - date: 323 | - tags: [software] [meta-analysis] 324 | - duration: 325 | - level: [intermediate] 326 | - event: 327 | - reference: 328 | - by: 329 | 330 | ### image based meta-analysis 331 | 332 | #### IBMA 333 | 334 | - description: IBMA is the Image-Based Meta-Analysis toolbox for SPM. 335 | - URL: [URL](https://github.com/NeuroimagingMetaAnalysis/ibma) 336 | - date: 337 | - tags: [software] [meta-analysis] 338 | - duration: 339 | - level: [intermediate] 340 | - event: 341 | - reference: 342 | - by: 343 | -------------------------------------------------------------------------------- /docs/46-neuroimaging-resources.md: -------------------------------------------------------------------------------- 1 | # Neuroimaging resources 2 | 3 | ## Neuroimaging video series 4 | 5 | Either on youtube or on some other platform 6 | 7 | ### Neurohackademy Lectures 8 | 9 | Lecture series on neuroimaging and electrophysiology from the 10 | [Neurohackademy](https://neurohackademy.org/course_type/lectures/) summer 11 | school. 12 | 13 | ### Mike Cohen's Lectures on Time Series Analysis 14 | 15 | Mike Cohen's lecturelets on time series data analysis 16 | [here](https://mikexcohen.com/lectures.html). 17 | 18 | ### Mumford brainstats 19 | 20 | Jeanette Mumford series of videos on neuroimaging analysis on 21 | [youtube](https://www.youtube.com/channel/UCZ7gF0zm35FwrFpDND6DWeA). The channel 22 | also has [Facebook group](https://www.facebook.com/groups/mumfordbrainstats/). 23 | 24 | ### Andrew Jahn 25 | 26 | [Here](https://www.youtube.com/user/Shala5ha5ka) for the videos with 'tutorials' 27 | for FSL, SPM, Freesurfer and AFNI amongst other things. 28 | 29 | ### Exploring the Human Connectome 2019 30 | 31 | HCP 2019 course lecture slides can be found 32 | [here](https://store.humanconnectome.org/courses/2019/exploring-the-human-connectome.php) 33 | 34 | ### Center for Brains, Minds and Machines 35 | 36 | [Here](https://www.youtube.com/channel/UCGoxKRfTs0jQP52cfHCyyRQ) 37 | 38 | ### Organization from human brain mapping (OHBM) 39 | 40 | The videos of the lectures and workshops from the previous HBM conferences are 41 | available online [here](https://www.pathlms.com/ohbm/courses). 42 | 43 | ### fMRIf summer courses from the NIH 44 | 45 | [Here](https://fmrif.nimh.nih.gov/public/fmri-course/) 46 | 47 | ### Conference on Cognitive Computational Neuroscience (CCN) 48 | 49 | This [conference](https://ccneuro.org/) has the videos from its first edition 50 | [here](https://ccneuro.org/2017/index.html@p=602.html) 51 | 52 | ### INCF 53 | 54 | [Here](https://www.youtube.com/channel/UC6FYCVath84rVzs99Ecfxyw) 55 | 56 | ### TVB made easy 57 | 58 | Lectures showing how to use The Virtual Brain software in a clinical context can 59 | be found [here](https://training.incf.org/course/tvb-made-easy) 60 | 61 | ### Computational and Systems Neuroscience (Cosyne) 2018 62 | 63 | [Here](https://www.youtube.com/playlist?list=PL9YzmV9joj3FNsAV2S_cKxY8Ik_-YlQfu) 64 | 65 | ### Cambridge University MRC Cognition and Brain Sciences Unit Method Seminars 2017 66 | 67 | [Here](http://www.mrc-cbu.cam.ac.uk/conferences/methods-day-2017/) 68 | 69 | ### Cambridge University MRC Cognition and Brain Sciences Unit Method Seminars 2018 70 | 71 | [Here](http://www.mrc-cbu.cam.ac.uk/conferences/methods-day-2018/) 72 | 73 | ### ISMRM Educational Materials 74 | 75 | [Here](https://www.youtube.com/user/ISMRM/playlists) 76 | 77 | ### fMRIF NIMH fMRI Course - from 2014 to 2018 78 | 79 | [Here](https://fmrif.nimh.nih.gov/public/fmri-course/fmri-course-summer-2014) 80 | 81 | ### Rad229: MRI Signals and Sequences – Stanford University 2020 course 82 | 83 | [Here](https://www.youtube.com/playlist?list=PLscv4NA0bNSOWYDILwQPuXURMVkSaGuEU) 84 | 85 | The above list is by far not exhaustive, you will be able to find more resources 86 | in the following: 87 | 88 | - the 89 | [Neuroimaging Informatics Tools and Resources Clearinghouse](https://www.nitrc.org/) 90 | - [Mariam Aly's](https://twitter.com/mariam_s_aly) 91 | [lab wiki](https://osf.io/kgd9b/wiki/home/) 92 | - [Jonathan Peelle's](@jpeelle) 93 | [list of resources for beignners](http://jonathanpeelle.net/mri-resources-for-beginners) 94 | - [Stephan Heunis](https://twitter.com/fmrwhy) has a 95 | [list](https://www.fmrwhy.com/2018/06/28/spm12-matlab-scripting-tutorial-4/) 96 | to many SPM and matlab material. 97 | - [https://github.com/brainhack101](https://github.com/brainhack101) also has 98 | a [collections or links](https://brainhack101.github.io/neurolinks/) to 99 | courses, data... 100 | - a 101 | [list](https://docs.google.com/document/d/1Wt6sZUavq4oQf4t3tpQARcajf-6i4TtHlx_lw-WJD1U/edit#heading=h.rgwbys315r9s) 102 | of Scientific Coding Resource put together by neuroconscience. 103 | - [Aya Ben-Yakov](@aya_ben_yakov) compiled a great list of 104 | [open-science resources](http://www.mrc-cbu.cam.ac.uk/openscience/resources/) 105 | for the CBU in Cambridge. 106 | - [LabHacks](https://github.com/pbeukema/LabHacks) is a list of resources for 107 | data driven neuroscientists put together by Patrick Beukema 108 | - a list of [open computational neuroscience resources](‏ 109 | https://github.com/asoplata/open-computational-neuroscience-resources/blob/master/README.md) 110 | put together by [Austin Soplata](https://twitter.com/austinsoplata) 111 | - a list of 112 | [Computational resources](https://github.com/martinagvilas/lists/blob/master/computational_resources.md) 113 | put together by [Martina Vilas](https://twitter.com/martinagvilas) 114 | 115 | ### Interactive Brain Atlases 116 | 117 | - [15 pcw - Whole Brain Atlas](http://atlas.brain-map.org/atlas?atlas=138322603&_ga=2.75462097.21923152.1555421610-1429565100.1555421610) 118 | 119 | - [21 pcw - Cerebrum](http://atlas.brain-map.org/atlas?atlas=3&_ga=2.106387264.21923152.1555421610-1429565100.1555421610#atlas=3&_ga=2.106387264.21923152.1555421610-1429565100.1555421610&plate=101892610&structure=10390&x=10112&y=23872&zoom=-6&resolution=64.04&z=3) 120 | 121 | - [21 pcw - Brain Stem](http://atlas.brain-map.org/atlas?atlas=287730656&_ga=2.6657777.21923152.1555421610-1429565100.1555421610) 122 | 123 | - [34 years old - Whole Brain](http://atlas.brain-map.org/atlas?atlas=138322605&_ga=2.6657777.21923152.1555421610-1429565100.1555421610) 124 | 125 | - [Brainnetome Atlas](http://atlas.brainnetome.org/bnatlas.html) 126 | 127 | - [Anatomy Explorer](https://www.innerbody.com/anatomy/nervous/medial-frontal-gyrus) 128 | 129 | ### Analysis 130 | 131 | - [Advanced time-series analysis (Dynamic Mode Decomposition)](https://neurohackademy.org/course/advanced-time-series-analysis-dynamic-mode-decomposition/) 132 | by Bing Brunton within Neurohackweek 2017 (1 hr 1 min) 133 | - [Advanced time-series analysis](https://neurohackademy.org/course/advanced-time-series-analysis/) 134 | by Bing Brunton within Neurohackweek 2016 (1 hr 8 min) 135 | - [Data visualization](https://neurohackademy.org/course/data-visualization/) 136 | by Tal Yarkoni within Neurohackademy 2018 137 | - [Efficiency and Design Optimization for fMRI](https://neurohackademy.org/course/efficiency-and-design-optimization-for-fmri/) 138 | by Jeanette Mumford within Neurohackweek 2017 (51 min) 139 | - [Image processing](https://neurohackademy.org/course/image-processing/) by 140 | Ariel Rokem within Neurohackweek 2016 141 | - [Modeling fMRI data](https://neurohackademy.org/course/modeling-fmri-data/) 142 | by Kendrick Kay within Neurohackweek 2016 (1 hr 2 min) 143 | - [NiBabel 101](https://www.youtube.com/watch?v=9ffUQo2mF6w&list=PLNt4AJV1JZbfq0vdD4vcITV7x3OqGxLKp&t=0s&index=4) 144 | by Dan Lurie within Brainhack Americas (18 min) 145 | - [Numerical computing for neuroimaging](https://neurohackademy.org/course/numerical-computing-for-neuroimaging/) 146 | by JB Poline within Neurohackademy 2018 147 | - [R for statistical analysis of fMRI data](https://neurohackademy.org/course/r-for-statistical-analysis-of-fmri-data/) 148 | by Tara Madhyastha within Neurohackademy 2018 (1 hr 26 min) 149 | - [A video series on dynamic causal modeling](https://www.youtube.com/watch?v=q-yypnHgCII&list=PLwiAO9Cs0Tb8wUGAnYY5yIMckB9tc4T3_) 150 | by [Kevin Aquino](https://twitter.com/kevin_m_aquino) [6 hrs] 151 | - A blog post 152 | [tutorial](https://medium.com/@solopchuk/tutorial-on-active-inference-30edcf50f5dc) 153 | on active inference (to get a better grasp on what free energy is) 154 | 155 | ## Brainhack 156 | 157 | - [Brainhacking](https://neurohackademy.org/course/brain-hacking/) by Cameron 158 | Craddock within Neurohackademy 2018 (59 min) 159 | - Craddock, R. C., Margulies, D. S., Bellec, P., Nichols, B. N., Alcauter, S., 160 | Barrios, F. A., … Xu, T. (2016). 161 | [Brainhack: a collaborative workshop for the open neuroscience community.](https://doi.org/10.1186/s13742-016-0121-x) 162 | GigaScience, 5(1). 163 | - [Introduction to Brainhack](https://www.youtube.com/watch?v=JLJFKV7p74A) by 164 | Cameron Craddock within Brainhack Proceedings 2017 (30 min) 165 | - [Introduction to Neurohackweek 2017](https://neurohackademy.org/course/introduction-to-neurohackweek-4/) 166 | by Ariel Rokem within Neurohackweek 2017 167 | -------------------------------------------------------------------------------- /docs/50-analysis.md: -------------------------------------------------------------------------------- 1 | # Analysis 2 | 3 | Once your data has been processed, you probably want to analyze it. 4 | 5 | ## Statistics 6 | 7 | Resources currently [here](51-statistics.md#Statistics). 8 | 9 | ## Machine learning applications 10 | 11 | Resources currently 12 | [here](52-machine-and-deep-learning.md#Machine-learning-and-deep-learning) 13 | 14 | ## Genetics sotfware 15 | 16 | Resources currently [here](53-genetics-software.md#genetics-software) 17 | 18 | 30 | -------------------------------------------------------------------------------- /docs/51-statistics.md: -------------------------------------------------------------------------------- 1 | # Statistics 2 | 3 | - [P-values and reproducibility issues](https://neurohackademy.org/course/p-values-and-reproducibility-issues/) 4 | by JB Poline within Neurohackademy 2018 (1 hr 1 min) 5 | - [The evil p value](https://neurohackademy.org/course/the-evil-p-value/) by 6 | JB Poline within Neurohackweek 2017 (1 hr 2 min) 7 | - [Statistical Decision Theory](https://www.youtube.com/watch?v=OT1i2SKfGPM&index=2&t=0s&list=PLNt4AJV1JZbcCs84XEbN9XdXBXN9U-kyT) 8 | by Joshua Vogelstein within Brainhack-Vienna (starts at 8 min, ends at 48 9 | min) 10 | - A reminder on how random field theory is used to correct for multiple 11 | comparison 12 | [here](http://imaging.mrc-cbu.cam.ac.uk/imaging/PrinciplesRandomFields). 13 | - [A primer on permutation testing (not only) for MVPA](https://www.pathlms.com/ohbm/courses/8246/sections/12542/video_presentations/116074) 14 | by [Carsten Allefeld](https://twitter.com/c_allefeld) at OHBM 2018 (36 min) 15 | - [Cross-validation: what, which and how?](https://www.pathlms.com/ohbm/courses/8246/sections/12542/video_presentations/116075) 16 | by [Pradeep Reedy Raamana](https://twitter.com/raamana_) at OHBM 2018 (30 17 | min) 18 | - [Daniel Lakens](https://twitter.com/lakens) MOOC on coursera on 19 | [how to improve your statistical inferences](https://www.coursera.org/learn/statistical-inferences) 20 | - [Statistical thinking for the 21st century](http://statsthinking21.org/) by 21 | Russ Poldrack: "I am trained as a psychologist and neuroscientist, not a 22 | statistician. However, my research on brain imaging for the last 20 years 23 | has required the use of sophisticated statistical and computational tools, 24 | and this has required me to teach myself many of the fundamental concepts of 25 | statistics. Thus, I think that I have a solid feel for what kinds of 26 | statistical methods are important in the scientific trenches." 27 | - [Principles, Statistical and Computational Tools for Reproducible Data Science](https://www.edx.org/course/principles-statistical-and-computational-tools-for) 28 | Intermediate-level course by Harvard University in edX 29 | - [Gentle Introduction to Bayesian Stats](https://easystats.github.io/bayestestR/articles/bayestestR.html) 30 | from _bayestestR_ by [easystats](https://github.com/easystats) 31 | 32 | A list of R based web based apps from [shiny apps](http://shinyapps.org/) and 33 | [R psychologist](http://rpsychologist.com/) to help better understand: 34 | 35 | - [p-values](https://www.shinyapps.org/apps/vs-mpr/) 36 | - [confidence intervals](http://rpsychologist.com/d3/CI/) 37 | - [p curves](https://shinyapps.org/apps/p-checker/) and 38 | [why with a decent power and a large effect size, it is relatively unlikely to find a value between p<.01 and p<.05](http://rpsychologist.com/d3/pdist/) 39 | - [null hypothesis significance testing](http://rpsychologist.com/d3/NHST/) 40 | - [p hacking](https://www.shinyapps.org/apps/p-hacker/) 41 | - [positive predictive values](http://shinyapps.org/showapp.php?app=https://tellmi.psy.lmu.de/felix/PPV&by=Michael%20Zehetleitner%20and%20Felix%20Sch%C3%B6nbrodt&title=When%20does%20a%20significant%20p-value%20indicate%20a%20true%20effect?&shorttitle=When%20does%20a%20significant%20p-value%20indicate%20a%20true%20effect?) 42 | 43 | Partial least squares regression: 44 | 45 | This is particularly useful for highdimensional neuroimaging data (particularly 46 | when correlating with genetic/transcriptome data). It finds a linear regression 47 | model by projecting the predicted variables and the observable variables to a 48 | new space. Useful resources if you are new to PLS-R: 49 | 50 | - [A beginner's guide to PLS](https://www.researchgate.net/publication/228861711_A_Beginner's_Guide_to_Partial_Least_Squares_Analysis) 51 | - [python package](https://hoggorm.readthedocs.io/en/latest/) 52 | - [r package](https://cran.r-project.org/web/packages/pls/) 53 | - [matlab](https://uk.mathworks.com/help/stats/examples/partial-least-squares-regression-and-principal-components-regression.html) 54 | -------------------------------------------------------------------------------- /docs/52-machine-and-deep-learning.md: -------------------------------------------------------------------------------- 1 | # Machine learning and deep learning 2 | 3 | ## Workshops and Videos 4 | 5 | ### General 6 | 7 | - [Deep learning with Keras part 1](https://neurohackademy.org/course/deep-learning-with-keras/) 8 | by Ariel Rokem [Video, ca. 2 hrs] 9 | - [Deep learning with Keras part 2](https://neurohackademy.org/course/neural-networks-part-2/) 10 | by Ariel Rokem [Video, ca. 2 hrs] 11 | - [Machine learning with scikit-learn 1](https://neurohackademy.org/course/machine-learning-with-scikit-learn/) 12 | by Jake Vanderplas within Neurohackweek [Jupyter Notebook] 13 | - [Machine learning with scikit-learn 2](https://neurohackademy.org/course/machine-learning-with-scikit-learn-2/) 14 | by Jake Vanderplas within Neurohackweek 2017 [Video, ca. 80 mins] 15 | - [Machine learning with scikit-learn 3](https://neurohackademy.org/course/machine-learning-with-scikit-learn-3/) 16 | by Jake Vanderplas within Neurohackademy [Video, ca. 140 mins] 17 | - [Deep learning and machine learing tutorials](https://github.com/brainhack101/introML) 18 | from the Montreal Artificial Intelligence and Neuroscience conference, 19 | Montreal 2018 by many authors. [Jupyter notebook, 2 days] 20 | - [TensorFlow 2.0 Complete Course - Python Neural Networks for Beginners](https://www.youtube.com/watch?time_continue=13&v=tPYj3fFJGjk) 21 | by Tim Ruscica (Tech with Tim) [Video, 7 hrs] 22 | 23 | 26 | 27 | ### Neuroimaging-related 28 | 29 | #### Machine learning in general 30 | 31 | - [Machine learning for neuroimaging](https://neurohackademy.org/course/machine-learning-for-neuroimaging/) 32 | by Chris Holdgraf within Neurohackweek 2017 [Video, ca. 1 hr] 33 | - [Machine learning in neuroimaging](https://neurohackademy.org/course/machine-learning-in-neuroimaging/) 34 | by Gael Varoquaux within Neurohackademy 2018 [Video, ca. 2hrs 40 mins] 35 | - [Synthesizing fMRI using generative adversarial networks: cognitive neuroscience applications, promises and pitfalls](https://neurohackademy.org/course/gans-for-brain-imaging/) 36 | by Sanmi Koyejo within Neurohackademy 2018 [Video, ca. 1 hr] 37 | 38 | #### Deep learning 39 | 40 | - OHBM DL Educational Course 2018-2020 41 | (https://brainhack101.github.io/IntroDL/) [Video and Jupyter Notebook, 3 42 | days] 43 | - [Introduction to Keras & Interpretability Methods](https://colab.research.google.com/drive/1EgdnWZeNqmzqEmnSR9PUnYXlTjeu1wAU) 44 | by Andrew Doyle within 45 | [MAIN 2018 Hands-on DL course](https://brainhack101.github.io/introML/dl-course-outline.html) 46 | [Jupyter notebook] 47 | - [Brain Segmentation in Keras](https://colab.research.google.com/github/tfunck/minc_keras/blob/master/main2018.ipynb) 48 | by Thomas Funck within MAIN 2018 Hands-on DL course [Jupyter notebook] 49 | 50 | ## Software 51 | 52 | They are divided in sub-sections depending on the language they use. 53 | 54 | ![Language](https://img.shields.io/badge/Language-Python-blue.svg) 55 | 56 | ### pyMVPA 57 | 58 | ??? example "pyMVPA - Intended to ease statistical learning analyses of large 59 | datasets." - [code repository](https://github.com/PyMVPA/PyMVPA) - 60 | [website](http://www.pymvpa.org/) - 61 | [documentation](http://www.pymvpa.org/docoverview.html) - programming language: 62 | [python] - tags: - [paper] - RRID:SCR_006099 - tutorial: - 63 | [URL](http://www.pymvpa.org/tutorial.html) - level: [beginner] - type: 64 | [notebook] 65 | 66 | ### nilearn 67 | 68 | Nilearn is a Python module for fast and easy statistical learning on 69 | NeuroImaging data. 70 | 71 | - [GitHub](http://nilearn.github.io/) 72 | - [manual](http://nilearn.github.io/user_guide.html) 73 | - [course/tutorial](http://nilearn.github.io/introduction.html#python-for-neuroimaging-a-quick-start) 74 | 75 | ### neuropredict 76 | 77 | neuropredict is an easy to use Python tool for comprehensive evaluation of 78 | predictive power of popular ML techniques for features-to-target prediction 79 | (such as biomarkers to disease and similar variations) 80 | 81 | - [GitHub](http://github.com/raamana/neuropredict) 82 | - [docs](http://raamana.github.io/neuropredict) 83 | 84 | ### brainIAK 85 | 86 | BrainIAK applies advanced machine learning methods and high-performance 87 | computing to analyzing neuroimaging data. We also have tutorials that cover 88 | topics from basics to advanced techniques. 89 | 90 | - [website](http://brainiak.org/) 91 | - [GitHub](https://github.com/brainiak/brainiak) 92 | - [tutorials](http://brainiak.org/tutorials) 93 | 94 | ![Language](https://img.shields.io/badge/Language-Matlab-orange.svg) 95 | 96 | ### The Decoding Toolbox (TDT) 97 | 98 | TDT is an easy to use, fast and versatile Matlab toolbox for the multivariate 99 | analysis of functional and structural MRI data. It contains searchlight, 100 | region-of-interest, and whole-brain analyses, as well as many feature selection 101 | and parameter selection methods including recursive feature elimination. 102 | 103 | - [website](https://sites.google.com/site/tdtdecodingtoolbox/) 104 | 105 | ### ProNTo 106 | 107 | PRoNTo is the Pattern Recognition for Neuroimaging Toolbox developed at UCL 108 | (UK). The toolbox is based on pattern recognition techniques for the analysis of 109 | neuroimaging data. 110 | 111 | - [website](http://www.mlnl.cs.ucl.ac.uk/pronto/prtsoftware.html) 112 | - [manual](http://www.mlnl.cs.ucl.ac.uk/pronto/prtdocs.html) 113 | - [course/tutorial](http://www.mlnl.cs.ucl.ac.uk/pronto/prtcourses.html) 114 | 115 | ### RSA toolbox 116 | 117 | A Matlab toolbox for representational similarity analysis 118 | 119 | - [GitHub](https://github.com/rsagroup/rsatoolbox) 120 | - [manual](https://github.com/rsagroup/rsatoolbox/blob/develop/Documentation/toolbox%20documentation.pdf) 121 | 122 | ### Pattern components modelling (PCM) toolbox 123 | 124 | Pattern component modeling (PCM) is a practical Bayesian approach for evaluating 125 | representational models - models that specify how complex patterns of neural 126 | activity relate to visual stimuli, motor actions, or abstract thoughts. 127 | 128 | - [GitHub](https://github.com/jdiedrichsen/pcm_toolbox) 129 | - [manual](https://github.com/jdiedrichsen/pcm_toolbox/blob/master/documentation/pcm_toolbox_manual.pdf) 130 | 131 | ### cvMANOVA 132 | 133 | MVPA by cross-validated MANOVA, which is proposed as a replacement of 134 | classification. 135 | 136 | - [GitHub](https://github.com/allefeld/cvmanova) 137 | - [reference](https://www.sciencedirect.com/science/article/abs/pii/S1053811913011920) 138 | -------------------------------------------------------------------------------- /docs/53-genetics-software.md: -------------------------------------------------------------------------------- 1 | # Genetics sotfware 2 | 3 | ## Extracting data from the Allen atlas 4 | 5 | The Allen atlas is an amazing resource of regional gene expression in the human 6 | brain. It contains a database of expression levels of 20,737 genes represented 7 | by 58,692 probes across the complete cortical mantle and is constructed 8 | postmortem from the brains of 6 human donors with no history of psychiatric or 9 | neuropathological disorders. The donor brains also underwent MRI postmortem and 10 | the probe locations mapped into each donor's MRI data in MNI space, providing a 11 | great opportunity to correlate regional gene expression with imaging findings! 12 | 13 | Data is freely available to download from AIBS 14 | [AIBS](http://human.brain-map.org/static/download). Extracting appropriate gene 15 | expression data from the Allen Atlas has many caveats, detailed in the excellent 16 | paper [here](https://doi.org/10.1016/j.neuroimage.2019.01.011) but tools have 17 | now been developed to make gene extraction easier. 18 | 19 | The following list includes software/packages and useful resources that can be 20 | used to extract gene expression data in imaging space. 21 | 22 | ### Abagen 23 | 24 | - Open-source Python software for extracting gene expression data from the 25 | ALlen atlas. 26 | - repository URL: [Github](https://github.com/rmarkello/abagen/) 27 | - website URL: 28 | [http://martinos.org/mne/stable/index.html](http://martinos.org/mne/stable/index.html) 29 | - tutorial URL: 30 | - documentation: 31 | [https://abagen.readthedocs.io/en/stable/index.html](https://abagen.readthedocs.io/en/stable/index.html) 32 | - programming language: {python} 33 | - paper DOI: 34 | [https://doi.org/10.5281/zenodo.3726257.](https://doi.org/10.5281/zenodo.3726257.) 35 | 36 | ### Matlab repository from Aurina Arnatkeviciute 37 | 38 | - Repository from the Aurina's paper describing best practice when extracting 39 | data from the Allen atlas. 40 | - repository URL: [Github](https://github.com/BMHLab/AHBAprocessing) 41 | - programming language: {matlab} 42 | - paper DOI: 43 | [https://doi.org/10.1016/j.neuroimage.2019.01.011](https://doi.org/10.1016/j.neuroimage.2019.01.011) 44 | - contact: aurina.arnatkeviciute@monash.edu 45 | -------------------------------------------------------------------------------- /docs/60-quality-control.md: -------------------------------------------------------------------------------- 1 | # Quality control 2 | 3 | When processing data, it is considered good practice (and is also very useful!) 4 | to inspect the intermediate output files/data created after every few steps. 5 | Here are some resources that can guide you through this process. 6 | 7 | ## Introduction 8 | 9 | ### Introduction about quality assessment process 10 | 11 | 1. Looking for susceptibility and pathological artifacts 12 | 13 | 2. Checking whether motion exceeds your lab's thresholds 14 | 15 | 3. Keeping records to make sure you have the data that you should have. 16 | 17 | ??? example "Quality Checks for fMRI Data - Lecture on quality control for neuroimaging data, especially fMRI data" 18 | - [URL](https://www.youtube.com/watch?v=fvv2dr3pT7I) 19 | - programming language: {python}, {matlab/octave}, {C}, ... 20 | - level: {beginner} 21 | - tags: {video} {MOOC} 22 | - date: 23 | - duration: 00:31 24 | - by: Andrew Jahn 25 | 26 | ## Interesting paper for understanding QA 27 | 28 | ??? example "Basic quality control in routine MRI - Scientific research about the steps of QA" 29 | - [URL](https://www.sciencedirect.com/science/article/abs/pii/S112017971630401X) 30 | - level: {beginner} 31 | - tags: {video} {notebook} {fMRI} {MOOC} {blog} {website} {podcast} 32 | - by: Thomas Maris 33 | 34 | ## Python libraries for QA 35 | 36 | ??? example "INCF Tools for quality assessment - This website has a list of QA libraries in python for different modalities with their documentation" 37 | - [URL](https://incf.github.io/niQC/tools) 38 | - level: {beginner} / {intermediate} / {advanced} 39 | - tags: {video} {notebook} {fMRI} {MOOC} {blog} {website} {podcast} 40 | - by: INCF 41 | -------------------------------------------------------------------------------- /docs/70-reporting-methods-and-results.md: -------------------------------------------------------------------------------- 1 | # Reporting Methods and Results 2 | 3 | Resources for writing and reviewing papers: 4 | 5 | 11 | -------------------------------------------------------------------------------- /docs/80-sharing-data-code-and-results.md: -------------------------------------------------------------------------------- 1 | # Sharing your code, data and your results 2 | 3 | Once you're done with your project, you might want to share your data, code, 4 | results, or all of the above, whether just with a collaborator, or to further 5 | [open science](./81-open-science.md#databases). 6 | 7 | Here are some resources that may help with that: 8 | 9 | 15 | -------------------------------------------------------------------------------- /docs/81-open-science.md: -------------------------------------------------------------------------------- 1 | # Open Science 2 | 3 | ## Databases 4 | 5 | - [The Open Science MOOC](https://opensciencemooc.eu/) 6 | 7 | - [Panel discussion: fostering open communities](https://neurohackademy.org/course/panel-discussion-fostering-open-communities/) within Neurohackademy 2018 (1 hr 30 min) 8 | 9 | - [Science: open for all](https://neurohackademy.org/course/science-open-for-all/) by Kirstie Whitaker within Neurohackademy 2018 10 | 11 | - [Surviving and thriving as an open scientist](https://neurohackademy.org/course/surviving-and-thriving-as-an-open-scientist/) by Tal Yarkoni within Neurohackweek 2016 12 | 13 | - MRC Cognition and Brain Sciences Unit Open Science Day 2018 14 | [Here](https://www.youtube.com/watch?list=PLp67eqWCj2f-SsbYZFQVb-ecjxqr1CpRu&v=jKmv3-Nk8iE) 15 | 16 | - Orthogonal Research and Education Laboratory's [Open Science Database] (https://orthogonal-research.weebly.com/open-science-and-data.html) 17 | -------------------------------------------------------------------------------- /docs/99-appendix.md: -------------------------------------------------------------------------------- 1 | # Appendix 2 | 3 | General resources. 4 | 5 | ## Introductory neuroscience resources 6 | 7 | ## Miscellaneous 8 | 9 | 10 | -------------------------------------------------------------------------------- /docs/index.md: -------------------------------------------------------------------------------- 1 | # Welcome to the hitchhacker's guide to the brain! 2 | 3 | This is a place where you will find your way around the multiverse of resources and methods 4 | that have almost, but not quite, entirely everything to do about the brain. 5 | 6 | So in case you get lost and you don't know where to find something 7 | or in case you are not sure what you were looking for in the first place... 8 | 9 | _Just remember..._ 10 | 11 | [![DON'T PANIC](https://upload.wikimedia.org/wikipedia/commons/thumb/6/6b/Don%27t_Panic.svg/1280px-Don%27t_Panic.svg.png)](https://upload.wikimedia.org/wikipedia/commons/thumb/6/6b/Don%27t_Panic.svg/1280px-Don%27t_Panic.svg.png) 12 | 13 | And come back here. 14 | 15 | --- 16 | 17 | --- 18 | 19 | ## Introduction 20 | 21 | This website is full of links and resources for all your neuro-needs! 22 | 23 | Use the links on the left to discover resources belonging to a particular category. 24 | 25 | If you're not sure what you're looking for, or you'd like to get an overview, 26 | start [here](10-before-you-start.md#Before-you-start). 27 | 28 | General introductory resources can be found [here](99-appendix.md#Appendix). 29 | 30 | ## Contribute 31 | 32 | To add new resources, [start an issue on GitHub](https://github.com/learn-neuroimaging/tutorials-and-resources/issues/new/choose), 33 | by selecting the type of resource you want add and this should open an issue 34 | with a template of code similar the ones listed below. 35 | Edit it to add details of your resource and open the issue and you're done! 36 | We will get back to you to finalize things and add the resource to our list. 37 | 38 | If you want to get touch directly, you can find us on 39 | [our channel on the mattermost Brainhack](https://mattermost.brainhack.org/brainhack/channels/hitchhackers_guide_to_the_brain). 40 | 41 | 42 | ### Software 43 | 44 | The following code: 45 | 46 | ```markdown 47 | ??? example "insert software name - insert short description" 48 | - [code repository](insert GitHub or GitLab URL ) 49 | - [website](insert URL) 50 | - [documentation](insert documentation or wiki URL) 51 | - [contact](insert URL to mailing list, slack, forum, mattermost) 52 | - programming language: {python}, {matlab/octave}, {C}, ... 53 | - tags: {fMRI} {MEG} {EEG} {MRI} {nipype} 54 | - [paper](https://doi.org/insert_paper_DOI_here) 55 | - RRID: insert_RRID_here 56 | - tutorial: 57 | - [URL]( insert URL ) 58 | - programming language: {python}, {matlab/octave}, {C}, ... 59 | - level: {beginner} / {intermediate} / {advanced} 60 | - tags: {video} {notebook} 61 | - date: 62 | - duration: HH:MM 63 | - by: John Doe and Jane Doe 64 | ``` 65 | 66 | will render as: 67 | 68 | ??? example "insert software name - insert short description" 69 | - [code repository](insert GitHub or GitLab URL) 70 | - [website](insert URL) 71 | - [documentation](insert documentation or wiki URL) 72 | - [contact](insert URL to mailing list, slack, forum, mattermost) 73 | - programming language: {python}, {matlab/octave}, {C}, ... 74 | - tags: {fMRI} {MEG} {EEG} {MRI} {nipype} 75 | - [paper](https://doi.org/insert_paper_DOI_here) 76 | - RRID: insert_RRID_here 77 | - tutorial: 78 | - [URL](insert URL) 79 | - programming language: {python}, {matlab/octave}, {C}, ... 80 | - level: {beginner} / {intermediate} / {advanced} 81 | - tags: {video} {notebook} 82 | - date: 83 | - duration: HH:MM 84 | - by: John Doe and Jane Doe 85 | 86 | ### Course / Workshop / Tutorial 87 | 88 | The following code: 89 | 90 | ```markdown 91 | ??? example "insert course / workshop / tutorial name - insert short description" 92 | - [URL](insert URL) 93 | - programming language: {python}, {matlab/octave}, {C}, ... 94 | - level: {beginner} / {intermediate} / {advanced} 95 | - tags: {video} {notebook} 96 | - date: 97 | - duration: HH:MM 98 | - by: John Doe and Jane Doe 99 | ``` 100 | 101 | will render as: 102 | 103 | ??? example "insert course / workshop / tutorial name - insert short description" 104 | - [URL](insert URL) 105 | - programming language: {python}, {matlab/octave}, {C}, ... 106 | - level: {beginner} / {intermediate} / {advanced} 107 | - tags: {video} {notebook} 108 | - date: 109 | - duration: HH:MM 110 | - by: John Doe and Jane Doe 111 | 112 | ### Website / Blog / Podcast 113 | 114 | The following code: 115 | 116 | ```markdown 117 | ??? example "insert website name - insert short description" 118 | - [URL](insert URL) 119 | - [RSS](insert_RSS_feed) 120 | - level: {beginner} / {intermediate} / {advanced} 121 | - tags: {video} {notebook} {fMRI} {MOOC} {blog} {website} {podcast} 122 | - by: John Doe and Jane Doe 123 | ``` 124 | 125 | will render as: 126 | 127 | ??? example "insert website name - insert short description" 128 | - [URL](insert URL) 129 | - [RSS](insert_RSS_feed) 130 | - level: {beginner} / {intermediate} / {advanced} 131 | - tags: {video} {notebook} {fMRI} {MOOC} {blog} {website} {podcast} 132 | - by: John Doe and Jane Doe 133 | 134 | ### Video / Video series 135 | 136 | The following code: 137 | 138 | ```markdown 139 | ??? example "insert video / video series name - insert short description" 140 | - [URL](insert URL) 141 | - programming language: {python}, {matlab/octave}, {C}, ... 142 | - level: {beginner} / {intermediate} / {advanced} 143 | - tags: {video} {MOOC} 144 | - date: 145 | - duration: HH:MM 146 | - by: John Doe and Jane Doe 147 | ``` 148 | 149 | will render as: 150 | 151 | ??? example "insert video / video series name - insert short description" 152 | - [URL]( insert URL ) 153 | - programming language: {python}, {matlab/octave}, {C}, ... 154 | - level: {beginner} / {intermediate} / {advanced} 155 | - tags: {video} {MOOC} 156 | - date: 157 | - duration: HH:MM 158 | - by: John Doe and Jane Doe 159 | 160 | ### Database 161 | 162 | The following code: 163 | 164 | ```markdown 165 | ??? example "insert database name - insert short description" 166 | - [database repository](insert URL) 167 | - [documentation](insert documentation or wiki URL) 168 | - [contact](inser URL to mailing list, slack, forum, mattermost) 169 | - data type: {fMRI} {MEG} {EEG} {MRI} 170 | - tags: 171 | - [paper](https://doi.org/insert_paper_DOI_here) 172 | - RRID: insert_RRID_here 173 | ``` 174 | 175 | will render as: 176 | 177 | ??? example "insert database name - insert short description" 178 | - [database repository](insert URL) 179 | - [documentation](insert documentation or wiki URL) 180 | - [contact](inser URL to mailing list, slack, forum, mattermost) 181 | - data type: {fMRI} {MEG} {EEG} {MRI} 182 | - tags: 183 | - [paper](https://doi.org/insert_paper_DOI_here) 184 | - RRID: insert_RRID_here 185 | 186 | ## Licence 187 | 188 | Creative Commons License 189 |
This work is licensed under a Creative Commons Attribution 4.0 International License. 190 | -------------------------------------------------------------------------------- /img/dogeLove.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/learn-neuroimaging/hitchhackers_guide_brain/3133ed83982561bb924d3dfcf859ccd1405d6d2a/img/dogeLove.gif -------------------------------------------------------------------------------- /img/dogeLoveScanner_600x400.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/learn-neuroimaging/hitchhackers_guide_brain/3133ed83982561bb924d3dfcf859ccd1405d6d2a/img/dogeLoveScanner_600x400.gif -------------------------------------------------------------------------------- /mkdocs.yml: -------------------------------------------------------------------------------- 1 | # Project information 2 | site_name: "Hitchhacker's guide to the brain" 3 | repo_name: 'learn-neuroimaging/hitchhackers_guide_brain' 4 | repo_url: 'https://github.com/learn-neuroimaging/hitchhackers_guide_brain' 5 | # docs_dir: alternative_path # docs/ is the default folder 6 | copyright: "CC-BY 4.0" 7 | 8 | # This will use Material them 9 | theme: 10 | name: 'material' 11 | language: 'en' 12 | palette: 13 | primary: 'light blue' 14 | accent: 'light blue' 15 | 16 | # Pages 17 | nav: 18 | - Welcome: "index.md" 19 | - Before you start: 20 | - About: "10-before-you-start.md" 21 | - Programming: "11-programming.md" 22 | - Version control: "12-version-control.md" 23 | - Organizing your files: "13-data-code-management.md" 24 | - Planning your study: 25 | - About: "20-planning-your-study.md" 26 | - Reproducible research: "21-reproducible-neuroimaging-research.md" 27 | - Preregistration: "22-preregistration.md" 28 | - Getting data: 29 | - About: "30-getting-data.md" 30 | - Data repositories: "31-data-repositories.md" 31 | - Processing: 32 | - About: "40-processing.md" 33 | - Computing: "41-computing.md" 34 | - MRI: "42-analysis-software-MRI.md" 35 | - MEEG: "43-analysis-software-MEEG.md" 36 | - Other physiological signals: "44-analysis-software-physio.md" 37 | - Learning neuroimaging: "45-learning-neuroimaging.md" 38 | - Neuroimaging resources: "46-neuroimaging-resources.md" 39 | - Analysis: 40 | - About: "50-analysis.md" 41 | - Statistics: "51-statistics.md" 42 | - Machine learning and Deep learning: "52-machine-and-deep-learning.md" 43 | - Genetic software: "53-genetics-software.md" 44 | - Quality control: 45 | - About: "60-quality-control.md" 46 | - Reporting methods and results: 47 | - About: "70-reporting-methods-and-results.md" 48 | - Sharing data, code and results: 49 | - About: "80-sharing-data-code-and-results.md" 50 | - Open science: "81-open-science.md" 51 | - Appendix: "99-appendix.md" 52 | 53 | # list of extension 54 | markdown_extensions: 55 | - admonition 56 | - pymdownx.details 57 | -------------------------------------------------------------------------------- /npm-requirements.txt: -------------------------------------------------------------------------------- 1 | remark-cli@5.0.0 2 | remark-lint@6.0.2 3 | remark-preset-lint-recommended@3.0.2 4 | remark-preset-lint-markdown-style-guide@2.1.2 5 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | mkdocs-material 2 | pymdown-extensions 3 | -------------------------------------------------------------------------------- /templates/README.md: -------------------------------------------------------------------------------- 1 | # README 2 | 3 | This folder lists the different templates we used for the different types of resources listed on this repository. 4 | 5 | Some of those templates can be nested. 6 | 7 | Many of those templates use some [MKDOCS Material extensions](https://squidfunk.github.io/mkdocs-material/extensions/admonition/) like: 8 | - [admonition](https://squidfunk.github.io/mkdocs-material/extensions/admonition/) 9 | - [PyMdownExtensions](https://squidfunk.github.io/mkdocs-material/extensions/pymdown/) like [details](https://facelessuser.github.io/pymdown-extensions/extensions/details/) that need to be installed with `pip install pymdown-extensions` 10 | 11 | 12 | 13 | ## Templates list 14 | 15 | - [software](../.github/ISSUE_TEMPLATE/add-a-software.md) 16 | - [course / workshop / tutorial](../.github/ISSUE_TEMPLATE/add-a-tutorial.md) 17 | - [website / podcast](../.github/ISSUE_TEMPLATE/add-a-website.md) 18 | - [video / series](../.github/ISSUE_TEMPLATE/add-a-video.md) 19 | - [database](../.github/ISSUE_TEMPLATE/add-a-database.md) 20 | - paper / slides / poster 21 | 22 | 23 | ## Tags list 24 | 25 | [video] [notebook] [fMRI] [MOOC] [machine learning] [summer school] [meta-analysis] [nipype] [course] [blog] [website] [tutorial] [software] [slides] [EEG] [MEG] [pipeline] [tractography] 26 | 27 | 28 | ## RRID 29 | 30 | For software and databases search if they have an research resource identifier ([RRID](https://scicrunch.org/resources)) associated with it and add it where necessary. 31 | --------------------------------------------------------------------------------