Updating the documentation (#125)

* Shorten intro

* Add inria support

* Add intro contrib

* move content to new file (developer doc)

* Contrib as main title

* Add two profiles

* Separate in two issues

* fix typo

* Remove toc

* Remove duplicate ref

* Add link to nipype

* Remove direct links to step 2

* Add wip to user doc

CONTENT.md

@@ -0,0 +1,7 @@
+### Contents overview
+
+- :snake: :package: `narps_open/` contains the Python package with all the pipelines logic.
+- :brain: `data/` contains data that is used by the pipelines, as well as the (intermediate or final) results data. Instructions to download data are available in [INSTALL.md](/INSTALL.md#data-download-instructions).
+- :blue_book: `docs/` contains the documentation for the project. Start browsing it with the entry point [docs/README.md](/docs/README.md)
+- :orange_book: `examples/` contains notebooks examples to launch of the reproduced pipelines.
+- :microscope: `tests/` contains the tests of the narps_open package.

CONTRIBUTING.md

@@ -1,15 +1,19 @@
 # How to contribute to NARPS Open Pipelines ? 
 
-General guidelines can be found [here](https://docs.github.com/en/get-started/quickstart/contributing-to-projects) in the GitHub documentation. 
+For the reproductions, we are especially looking for contributors with the following profiles:
+ - 👩‍🎤 SPM, FSL, AFNI or nistats has no secrets for you? You know this fMRI analysis software by heart 💓. Please help us by reproducing the corresponding NARPS pipelines. 👣 after step 1, follow the fMRI expert trail.
+ - 🧑‍🎤 You are a nipype guru? 👣 after step 1, follow the nipype expert trail.
 
-## Reproduce a pipeline :keyboard:
-:thinking: Not sure which one to start with ? You can have a look on [this table](https://github.com/Inria-Empenn/narps_open_pipelines/wiki/pipeline_status) giving the work progress status for each pipeline. This will help choosing the one that best suits you!
+# Step 1: Choose a pipeline to reproduce :keyboard:
+:thinking: Not sure which pipeline to start with ? 🚦The [pipeline dashboard](https://github.com/Inria-Empenn/narps_open_pipelines/wiki/pipeline_status) provides the progress status for each pipeline. You can pick any pipeline that is in red (not started).
 
-Need more information ? You can have a look to the pipeline description [here](https://docs.google.com/spreadsheets/d/1FU_F6kdxOD4PRQDIHXGHS4zTi_jEVaUqY_Zwg0z6S64/edit?usp=sharing). Also feel free to use the `narps_open.utils.description` module of the project, as described [in the documentation](/docs/description.md).
+Need more information to make a decision? The `narps_open.utils.description` module of the project, as described [in the documentation](/docs/description.md) provides easy access to all the info we have on each pipeline.
 
 When you are ready, [start an issue](https://github.com/Inria-Empenn/narps_open_pipelines/issues/new/choose) and choose **Pipeline reproduction**!
 
-### If you have experience with NiPype
+# Step 2: Reproduction 
+
+## 🧑‍🎤 NiPype trail
 
 We created templates with modifications to make and holes to fill to create a pipeline. You can find them in [`narps_open/pipelines/templates`](/narps_open/pipelines/templates).
 
@@ -21,9 +25,9 @@ Feel free to have a look to the following pipelines, these are examples :
 | 2T6S | SPM | Yes | [/narps_open/pipelines/team_2T6S.py](/narps_open/pipelines/team_2T6S.py) |
 | X19V | FSL | Yes | [/narps_open/pipelines/team_X19V.py](/narps_open/pipelines/team_2T6S.py) |
 
-### If you have experience with the original software package but not with NiPype
+## 👩‍🎤 fMRI software trail
 
-A fantastic tool named [Giraffe](https://giraffe.tools/porcupine/TimVanMourik/GiraffePlayground/master) is available. It allows you to create a graph of your pipeline using NiPype functions but without coding! Just save your NiPype script in a .py file and send it as a new issue, we will convert this script to a script which works with our specific parameters. 
+...
 
 ## Find or propose an issue :clipboard:
 Issues are very important for this project. If you want to contribute, you can either **comment an existing issue** or **proposing a new issue**. 
@@ -64,3 +68,7 @@ Once your PR is ready, you may add a reviewer to your PR, as described [here](ht
 Please turn your Draft Pull Request into a "regular" Pull Request, by clicking **Ready for review** in the Pull Request page.
 
 **:wave: Thank you in advance for contributing to the project!**
+
+## Additional resources
+
+ - git and Gitub: general guidelines can be found [here](https://docs.github.com/en/get-started/quickstart/contributing-to-projects) in the GitHub documentation. 

README.md

@@ -15,45 +15,26 @@
         <img src="https://img.shields.io/github/commit-activity/m/Inria-Empenn/narps_open_pipelines" /></a>
 </p>
 
-## Table of contents
-
-- [Project presentation](#project-presentation)
-- [Getting Started](#getting-started)
-	- [Contents overview](#contents-overview)
-	- [Installation](#installation)
-	- [Contributing](#contributing)
-- [References](#references)
-- [Funding](#funding)
-
 ## Project presentation
 
-Neuroimaging workflows are highly flexible, leaving researchers with multiple possible options to analyze a dataset [(Carp, 2012)](https://www.frontiersin.org/articles/10.3389/fnins.2012.00149/full).
-However, different analytical choices can cause variation in the results [(Botvinik-Nezer et al., 2020)](https://www.nature.com/articles/s41586-020-2314-9), leading to what was called a "vibration of effects" [(Ioannidis, 2008)](https://pubmed.ncbi.nlm.nih.gov/18633328/) also known as analytical variability. 
-
 **The goal of the NARPS Open Pipelines project is to create a codebase reproducing the 70 pipelines of the NARPS project (Botvinik-Nezer et al., 2020) and share this as an open resource for the community**. 
 
-To perform the reproduction, we are lucky to be able to use the [descriptions provided by the teams](https://github.com/poldrack/narps/blob/1.0.1/ImageAnalyses/metadata_files/analysis_pipelines_for_analysis.xlsx).
-We also created a [shared spreadsheet](https://docs.google.com/spreadsheets/d/1FU_F6kdxOD4PRQDIHXGHS4zTi_jEVaUqY_Zwg0z6S64/edit?usp=sharing) that can be used to add comments on pipelines (e.g.: identify the ones that are not reproducible with NiPype).
+We base our reproductions on the [original descriptions provided by the teams](https://github.com/poldrack/narps/blob/1.0.1/ImageAnalyses/metadata_files/analysis_pipelines_for_analysis.xlsx) and test the quality of the reproductions by comparing our results with the original results published on NeuroVault.
 
-:vertical_traffic_light: Lastly, please find [here in the project's wiki](https://github.com/Inria-Empenn/narps_open_pipelines/wiki/pipeline_status) a dashboard to see pipelines work progresses at first glance.
+:vertical_traffic_light: See [the pipeline dashboard](https://github.com/Inria-Empenn/narps_open_pipelines/wiki/pipeline_status) to view our current progress at a glance.
 
-## Getting Started
+## Contributing
 
-### Contents overview
+NARPS open pipelines uses [nipype](https://nipype.readthedocs.io/en/latest/index.html) as a workflow manager and provides a series of templates and examples to help reproduce the different teams’ analysis. 
 
-- :snake: :package: `narps_open/` contains the Python package with all the pipelines logic.
-- :brain: `data/` contains data that is used by the pipelines, as well as the (intermediate or final) results data. Instructions to download data are available in [INSTALL.md](/INSTALL.md#data-download-instructions).
-- :blue_book: `docs/` contains the documentation for the project. Start browsing it with the entry point [docs/README.md](/docs/README.md)
-- :orange_book: `examples/` contains notebooks examples to launch of the reproduced pipelines.
-- :microscope: `tests/` contains the tests of the narps_open package.
+There are many ways you can contribute 🤗 :wave: Any help is welcome ! Follow the guidelines in [CONTRIBUTING.md](/CONTRIBUTING.md) if you wish to get involved !
 
 ### Installation
 
 To get the pipelines running, please follow the installation steps in [INSTALL.md](/INSTALL.md)
 
-### Contributing 
-
-:wave: Any help is welcome ! Follow the guidelines in [CONTRIBUTING.md](/CONTRIBUTING.md) if you wish to get involved !
+## Getting started
+If you are interested in using the codebase to run the pipelines, see the [user documentation (work-in-progress)].
 
 ## References
 
@@ -64,7 +45,7 @@ To get the pipelines running, please follow the installation steps in [INSTALL.m
 
 ## Funding
 
-This project is supported by Région Bretagne (Boost MIND). 
+This project is supported by Région Bretagne (Boost MIND) and by Inria (Exploratory action GRASP). 
 
 ## Credits