learn-neuroimaging / hitchhackers_guide_brain Goto Github PK

@all-contributors please add @Remi-Gau for code content ideas

[video] [notebook] [fMRI] [MOOC] [machine learning] [summer school] [meta-analysis] [nipype] [course] [blog] [website] [tutorial] [software] [slides] [EEG [MEG] [pipeline] [tractography]

Working to edit machine_and_deep_learning.md -file

??? example "Nighres - Neuroimaging at high resolution"
- [code repository]https://github.com/nighres/nighres
- [documentation]https://nighres.readthedocs.io/
- programming language: {python}, {java}
- tags: {fMRI} {MRI}
- [paper]https://doi.org/10.1093/gigascience/giy082
- RRID: SCR_016287
- tutorial:
- [URL]https://nighres.readthedocs.io/en/latest/auto_examples/index.html
- programming language: {python}
- level: {beginner}
- tags: {notebook}
- by: the Nighres team

We are trying to categorize all the resources and would be great to hear your thoughts and ideas. So what do you think about the categories and terms used, please give your comments. Here's the first draft:
Neuroimaging resources?
      Workshops/Video series
      Quality control
      Brainhack
      Meta-analysis
      Interactive brain atlases
      Analysis
Neuroimaging analysis software
      MRI
      MEG/EEG
Open Science
Reproducible neuroimaging/research??
      Reproducible neuroimaging tools
      Tools for reproducible data-science
      Open-data platforms
      Documenting projects and code??
      BIDS
Programming
      Shell
      Python
      R
      GitHub
Computing
      Cloud computing
      Containers
Statistics
Machine learning and deep learning

tags: fMRI, MRI, --> add dMRI? you also said electrophysiology is already there (just not yet linked IIRC)

maybe it would be great to either have a complete choice list of tags in a TAGs.md file, where people can see all used ones (for max consistency) and make a PR to add a missing one which in turn can then be used by future submissions.

Comment from @katjaq in #142

??? example "rsHRF - retrieve and deconvolve a proxy of the hemodynamic response function from BOLD signal without explicit event timings (resting state or other)"
- code repository
- code repository
- website
- documentation
- documentation
- contact
- programming language: {python}, {matlab}
- tags: {fMRI} {BIDS} {SPM}
- paper
- tutorial:
- URL
- programming language: {python}, {matlab}
- level: {beginner}
- tags: {video} {notebook}

In the Contributing to this repo instructions :
We could organise the instructions or simply add an explanatory sentence, in order to clarify that the third suggested way of contributing (i.e. Making direct contributions) is the preferable/fastest one for the evolution of the project, instead of opening an issue on GitHub (as suggested in the 1st and 2nd contributing alternatives), so that it's clearer for all contributors to follow.

When a pull-request is created, continuous integration failed.

I think either the linter found reasons to fail so we should fix this or it is not setted correcly.

??? example "The Missing Semester of Your CS Education - aka finally teaching the tools your professors skipped over"
- URL
- level: {beginner} / {intermediate}
- tags: {video} {website}
- by: Anish, Jon and Jose at MIT

Goal

Come up with a specification for information sharing between NITRC and other resources that, keyed by a NITRC Resource ID, would return a specified set of content (website, license, version, etc.) in a specified format for injection into the repo

Opening this thread to start a discussion.

Tagging: @dnkennedy

To have the mkdocs up and running only 'pip-requirements.txt' is required for the installation of necessary packages leaving behind redundant 'requirements.txt'.

I was browsing through our files and I think we should set up a linter that makes sure that our markdown code is standardized so that we all "write" the same way.

I do use codacy on my repo : https://github.com/marketplace/codacy

But we could also set up remark the way it is used by the BIDS specification: https://github.com/remarkjs/remark-lint

Any other suggestions?

Any thoughts?

https://github.com/learn-neuroimaging/tutorials-and-resources/blob/master/.CONTRIBUTING.md

This link appears to not be working on the main readme. Should it be this way? I also made a pull request abuot this.

??? example "ReproNim Webinar Series - Monthly webinar series devoted to topics in reproducible neuroimaging computation"
- [https://www.youtube.com/playlist?list=PLs3CA4ShM1DUX0nTMKfoB8Z6kdrZpByLa]
- programming language: {not applicable},
- level: {varied}
- tags: {video}
- date: First Friday of month, 2pm eastern, since Nov 1, 2019
- duration: ~1 hour each
- by: The ReproNim Team and Collaborators

Any idea?

Create a bunch of zotero groups?

While going through the listed resources, I thought about a category/section that could be added: workshops. This would be complete workshops focusing open neuroscience. For example (sorry for the biased example), the materials of the workshop series @miykael and I started are freely available, e.g. the latest iteration: https://github.com/PeerHerholz/workshop_marburg. I'm pretty sure that there are much more workshops which materials are publicly available.

What do you think folks?

It could be helpful for people new to the field (or to this website) to navigate it if the website were structured along the lines of a pipeline, e.g.:

1. Introduction / General neuroscience introductory resources
2. Getting data
3. Processing
   3.1 modality
   3.1.1 software
   3.1.2 tutorial
4. QC
5. Analysis
   5.1 Statistics/ML

I suggest we create a mindmap / storyboard to have a rough sketch of what we'd want the organization to look like, using something like miro: www.miro.com
‎
Let me know what you think!

I just realized that there should be a way to rely on RRID to collect metadata about some resources.

For example SPM has the following RRID : SCR_007037.

And if you check what is linked to this there is plenty of info we would not have to enter manually if you could grab them there.

https://scicrunch.org/resources/Tools/record/nlx_144509-1/SCR_007037/resolver?q=%22Statistical%20Parametric%20Mapping%22&l=%22Statistical%20Parametric%20Mapping%22

From @Remi-Gau in Mattermost:

One idea I had last night that can be done quickly for this project: set up the welcome bot we used on the website of the Brainhack. It replies an automatic message when:

• you open your first issue on the repo
• you submit your first pull request
• your first pull request is merged.
  It could be a good way to ensure that people contributing ressources followe the templates.

A list of Visualization resources compiled during the OHBM hackthon 2020

https://hackmd.io/vKSitiQaSwiGFrm_sTS_MQ

These could be interesting to add. :-)

Current "index.md" page is not a "table of contents". Create a landing page with introduction/welcome message and that orients website visitors.

MKdocs (https://www.mkdocs.org/) ables to generate static wiki from Markdown files. The default theme is not very lovely but people developed a great theme called Material with a set of predefined colors: https://squidfunk.github.io/mkdocs-material/ (play with Primary colors section)

(For an overview of themes, see e.g. https://github.com/mkdocs/mkdocs/wiki/MkDocs-Themes)

How to install mkdocs with Material theme?

pip install mkdocs-material

How do I generate a Wiki from my markdown file(s) ?

See Getting Started for details.

MKdocs needs a YAML file to understand which files be on the Wiki and following which hierarchy. MKdocs expects 2 minimum things:

• Markdown files to be located in a default folder named docs (can be changed using docs_dir value)
• The main page will be named index.md

Assuming the following files:

├── docs
│   ├── ReadMe.md
│   └── index.md
└── mkdocs.yml

The resulting configuration file will look like:

# Project information
site_name: 'Tutorials and resources'
repo_name: 'learn-neuroimaging/tutorials-and-resources'
repo_url: 'https://github.com/learn-neuroimaging/tutorials-and-resources'
# docs_dir: alternative_path # docs/ is the default folder

# This will use Material them
theme:
  name: 'material'
  language: 'en'
  palette:
    primary: 'light blue'
    accent: 'light blue'

# Pages
nav:
  - Learning neuroimaging: "ReadMe.md"

Examples

BIDS

Wiki: https://bids-specification.readthedocs.io/
Source: https://github.com/bids-standard/bids-specification

An example of wiki project with Clinica:

Wiki: http://www.clinica.run/doc/
Source:

git clone https://github.com/aramis-lab/clinica.wiki.git
cd  clinica.wiki
pip install -r requirements.txt # will install mkdocs-material and other few things
# Test locally
mkdocs serve

??? example "Rocker - docker for R programming"
- website

Pipeline
"Automatic Analysis - multimodal MATLAB toolbox processing fMRI, DTI/DKI, and M/EEG"
- code repository
- website
- documentation
- contact
- programming language: {matlab}
- tags: {MRI} {MEG} {EEG} {fMRI} {DTI} {DKI} {MATLAB}
- paper
- RRID:
- tutorial:
- URL
- programming language: {matlab}
- level: {beginner} / {intermediate}
- tags: {PDF}
- date:
- duration:
- by: Tibor Auer

It is usually good to have a badge in the Readme that informs the users, contributors as well as the maintainers the status of the build.

I think we will need to change the title of this repo because right now it is WAY too generic and uninformative. Any ideas?

Suggestions of templates for new resources

- a software: NAME
  - description: one line description
  - repository URL: on gtihub, gitlab... 
  - website URL:
  - tutorial URL : 
  - documentation: 
  - programming language: [python], [matlab/octave], [C], ...
  - paper DOI: 
  - RRID: see https://scicrunch.org/resources  

- workshop:
 - description: one line description
 - URL:
 - date: 
 - type: [video], [juptyer], ...
 - duration: HH:MM
 - level: [beginner] / [advanced]

• a website:

• a video

• podcast:

Hi,

I'm finishing the upcoming CONTRIBUTING.md file. I was wondering if would add a requirements.txt file to install dependencies. Currently, we only need to type:

pip install mkdocs-material

to test locally the Wiki.

Alex

Adding here other lists that either were used to create the list of this repository, or for ideas for this project.

• Martina's list
• Hitchhacker's brain to the universe
• Rémi's list
• neurolinks
• from @complexbrains :
  • network analysis
  • fMRI quality analysis
  • podcasts

Hi,

MKDocs allows to deploy Wiki on GitHub pages (see https://www.mkdocs.org/user-guide/deploying-your-docs/).

We need to automate this procedure.

I can volunteer for this task :)

Alex

Working to edit reproducible_neuroimaging_research.md -file

A few things to do to get started:

• rename readme into main.md
• remove unnecessary files left over from the parent repo
• create an actual readme
• add contributors into readme
• add contributing guidelines
• add contributors as collaborators
• severe fork link from OHBM hackathon 2019 repo