Merge pull request #1475 from softmatterlab/yc-ReadMe

ReadMe updates

Author: giovannivolpe

README.md

@@ -6,37 +6,36 @@
 <p align="center">
   <a href="https://twitter.com/braph2software" alt="tweeter"><img src="https://img.shields.io/twitter/url?label=BRAPH%202&style=social&url=https%3A%2F%2Ftwitter.com%2Fbraph2software"></a>
   <a href="http://braph.org/" alt="website"><img src="https://img.shields.io/website?up_message=braph.org&url=http%3A%2F%2Fbraph.org%2F"></a>
-  <a href="https://doi.org/10.1371/journal.pone.01787981" alt="DOI"><img src="https://img.shields.io/badge/DOI-10.1371%2Fjournal.pone.0178798-blue">
+  <a href="https://doi.org/10.1371/journal.pone.0178798" alt="DOI"><img src="https://img.shields.io/badge/DOI-10.1371%2Fjournal.pone.0178798-blue">
   </a>
 </p>
 <p align="center">
   <a href="#installation">Installation</a> •
-  <a href="#using-braph2">Examples</a> •
-  <a href="#learning-braph-2">Basics</a> •
+  <a href="#braph-2-usage-examples">Examples</a> •
   <a href="#cite-us">Cite us</a> •
-  <a href="https://github.com/softmatterlab/BRAPH-2-Matlab/blob/develop/braph2genesis/LICENSE">License</a> 
+  <a href="https://github.com/softmatterlab/BRAPH-2-Matlab/blob/develop/LICENSE">License</a> 
 </p>
 
 
 An object-oriented software that provides pipelines for conventional brain connectivity analysis as well as more advanced methods, including multilayer networks and deep learning methods.
 
 # Installation
 
-BRAPH 2 requires at least MATLAB 2020b. BRAPH 2 requires Statistics and Machine Learning Toolbox. For deep learning analysis, Deep Learning Toolbox and Deep Learning Toolbox Converter for ONNX Model Format are also needed. We strongly recommend the Parallel Computing Toolbox to speed up BRAPH 2.
+BRAPH 2 requires at least **MATLAB R2021a**. BRAPH 2 requires both **Statistics and Machine Learning Toolbox** and **Parallel Computing Toolbox**. For deep learning analysis, **Deep Learning Toolbox** and **Deep Learning Toolbox Converter for ONNX Model Format** are also needed.
 
-To install BRAPH 2, first clone this repository or download via zip. 
-Once inside MATLAB go to the folder of BRAPH 2 and run braph2genesis (you may have to add it to the path). This will create a braph2 folder with the executable code, it may take a while.
-This will be only needed once, or every time you add a new functionality to BRAPH 2.
+To install BRAPH 2, first download BRAPH 2.
+From our GitHub repository, you can find the latest stable version in the branch <a href="https://github.com/softmatterlab/BRAPH-2-Matlab/tree/master">master</a> and the latest development version in the branch <a href="https://github.com/softmatterlab/BRAPH-2-Matlab/tree/develop">develop</a>.
+You can also download BRAPH 2 from our <a href="http://braph.org/software/braph-2/">website</a>.
 
-# Using-braph2
+After unzipping the downloaded file into the desired directory and launching MATLAB, change the current folder to **braph2genesis** and run *braph2genesis* (you may have to add it to the path). This installation takes around 5 minutes.
+The installation will be only needed once.
+You can also follow the <a href="http://braph.org/software/braph-2/">Installation</a> section from our website.
 
-Each provided pipeline comes with an example folder where you can run the example script that mocks the analysis/comparison of the cohort data using the desired graph measures.
+# BRAPH 2 usage examples
 
-# Learning-braph-2
+BRAPH 2 is a powerful tool that transforms scripts to pipelines. We provide example data in order to test the different analyses and comparisons from the provided pipelines. Please check the <a href="http://braph.org/tutorials/">Tutorials</a> section from our website for the step-by-step instructions and more details.
 
-BRAPH 2 is a powerful tool that transforms scripts to pipelines. Please check the tutorial section on our website <a href="http://braph.org/tutorials/"></a>
-
-## Cite us!
+# Cite us!
 If you use BRAPH 2 in your project, please cite us here:
 
 ```
@@ -52,5 +51,5 @@ See also:
 ```
 Mite Mijalkov, Ehsan Kakaei, Joana B Pereira, Eric Westman, Giovanni Volpe
 BRAPH: A graph theory software for the analysis of brain connectivity.
-PLOS ONE 12, e0178798 (2017)..
+PLOS ONE 12, e0178798 (2017).
 ```