Luna  Hermann

Luna Hermann

1599122460

Visualizing Brains using R

Introduction

Recently, I took an introductory psychology course in my first year of university where among other basic principles of psychology, we were taught about the brain, the ways we can visualize the brain using different kinds of scans, and how doctors use these scans to detect and monitor diseases. It got me wondering- is there a simple way I can visualize and analyze the brain?

A good amount of research led me to the course ‘Introduction to Neurohacking in R’ on Coursera. This course helped me gather the background information and the building blocks needed to visualize the brain using just two things: open-source MRI scans and R. Given Python is generally considered the go-to language for deep learning and image analysis, I wanted to challenge myself to use R and solve the questions I had.

Dataset

I tested my knowledge on a dataset I found on Kaggle called ‘Brain Tumor Progression’. It consists of the MRI scans of 20 patients suffering from Glioblastoma. There are two MRI exams included for each patient taken 90 days apart to monitor the progression of the tumor.

Questions I Answered

Question 1: How do I convert the scans into a format suitable for analysis?

Most hospitals store MRI scan data in a two-dimensional DICOM format where each axial slice of the brain is one DICOM file. This is done to protect health information. To make these images suitable for analysis by R, the first step is to convert DICOM into NifTI format, which combines all the DICOM files into a folder to come up with a 3D image of the brain (the NifTI format!). So say we wanted to take a look at the 11th axial slice of Patient 1’s brain, we get this.

Image for post

Image for post

Axial view of the 11th slice of Patient 1’s brain

Question 2: Is there a way to visualize certain tissues/parts of the brain using intensity values?

When I told R to highlight regions of the 11th slice of the brain with intensity values between 300 and 400 (excluding boundary values), it colored all those regions in red like this.

Image for post

Image for post

Regions colored in red represent intensity values between 300 and 400

#r #data-science #brain-scan #machine-learning #data-visualization

What is GEEK

Buddha Community

Visualizing Brains using R
Luna  Hermann

Luna Hermann

1599122460

Visualizing Brains using R

Introduction

Recently, I took an introductory psychology course in my first year of university where among other basic principles of psychology, we were taught about the brain, the ways we can visualize the brain using different kinds of scans, and how doctors use these scans to detect and monitor diseases. It got me wondering- is there a simple way I can visualize and analyze the brain?

A good amount of research led me to the course ‘Introduction to Neurohacking in R’ on Coursera. This course helped me gather the background information and the building blocks needed to visualize the brain using just two things: open-source MRI scans and R. Given Python is generally considered the go-to language for deep learning and image analysis, I wanted to challenge myself to use R and solve the questions I had.

Dataset

I tested my knowledge on a dataset I found on Kaggle called ‘Brain Tumor Progression’. It consists of the MRI scans of 20 patients suffering from Glioblastoma. There are two MRI exams included for each patient taken 90 days apart to monitor the progression of the tumor.

Questions I Answered

Question 1: How do I convert the scans into a format suitable for analysis?

Most hospitals store MRI scan data in a two-dimensional DICOM format where each axial slice of the brain is one DICOM file. This is done to protect health information. To make these images suitable for analysis by R, the first step is to convert DICOM into NifTI format, which combines all the DICOM files into a folder to come up with a 3D image of the brain (the NifTI format!). So say we wanted to take a look at the 11th axial slice of Patient 1’s brain, we get this.

Image for post

Image for post

Axial view of the 11th slice of Patient 1’s brain

Question 2: Is there a way to visualize certain tissues/parts of the brain using intensity values?

When I told R to highlight regions of the 11th slice of the brain with intensity values between 300 and 400 (excluding boundary values), it colored all those regions in red like this.

Image for post

Image for post

Regions colored in red represent intensity values between 300 and 400

#r #data-science #brain-scan #machine-learning #data-visualization

Why Use WordPress? What Can You Do With WordPress?

Can you use WordPress for anything other than blogging? To your surprise, yes. WordPress is more than just a blogging tool, and it has helped thousands of websites and web applications to thrive. The use of WordPress powers around 40% of online projects, and today in our blog, we would visit some amazing uses of WordPress other than blogging.
What Is The Use Of WordPress?

WordPress is the most popular website platform in the world. It is the first choice of businesses that want to set a feature-rich and dynamic Content Management System. So, if you ask what WordPress is used for, the answer is – everything. It is a super-flexible, feature-rich and secure platform that offers everything to build unique websites and applications. Let’s start knowing them:

1. Multiple Websites Under A Single Installation
WordPress Multisite allows you to develop multiple sites from a single WordPress installation. You can download WordPress and start building websites you want to launch under a single server. Literally speaking, you can handle hundreds of sites from one single dashboard, which now needs applause.
It is a highly efficient platform that allows you to easily run several websites under the same login credentials. One of the best things about WordPress is the themes it has to offer. You can simply download them and plugin for various sites and save space on sites without losing their speed.

2. WordPress Social Network
WordPress can be used for high-end projects such as Social Media Network. If you don’t have the money and patience to hire a coder and invest months in building a feature-rich social media site, go for WordPress. It is one of the most amazing uses of WordPress. Its stunning CMS is unbeatable. And you can build sites as good as Facebook or Reddit etc. It can just make the process a lot easier.
To set up a social media network, you would have to download a WordPress Plugin called BuddyPress. It would allow you to connect a community page with ease and would provide all the necessary features of a community or social media. It has direct messaging, activity stream, user groups, extended profiles, and so much more. You just have to download and configure it.
If BuddyPress doesn’t meet all your needs, don’t give up on your dreams. You can try out WP Symposium or PeepSo. There are also several themes you can use to build a social network.

3. Create A Forum For Your Brand’s Community
Communities are very important for your business. They help you stay in constant connection with your users and consumers. And allow you to turn them into a loyal customer base. Meanwhile, there are many good technologies that can be used for building a community page – the good old WordPress is still the best.
It is the best community development technology. If you want to build your online community, you need to consider all the amazing features you get with WordPress. Plugins such as BB Press is an open-source, template-driven PHP/ MySQL forum software. It is very simple and doesn’t hamper the experience of the website.
Other tools such as wpFoRo and Asgaros Forum are equally good for creating a community blog. They are lightweight tools that are easy to manage and integrate with your WordPress site easily. However, there is only one tiny problem; you need to have some technical knowledge to build a WordPress Community blog page.

4. Shortcodes
Since we gave you a problem in the previous section, we would also give you a perfect solution for it. You might not know to code, but you have shortcodes. Shortcodes help you execute functions without having to code. It is an easy way to build an amazing website, add new features, customize plugins easily. They are short lines of code, and rather than memorizing multiple lines; you can have zero technical knowledge and start building a feature-rich website or application.
There are also plugins like Shortcoder, Shortcodes Ultimate, and the Basics available on WordPress that can be used, and you would not even have to remember the shortcodes.

5. Build Online Stores
If you still think about why to use WordPress, use it to build an online store. You can start selling your goods online and start selling. It is an affordable technology that helps you build a feature-rich eCommerce store with WordPress.
WooCommerce is an extension of WordPress and is one of the most used eCommerce solutions. WooCommerce holds a 28% share of the global market and is one of the best ways to set up an online store. It allows you to build user-friendly and professional online stores and has thousands of free and paid extensions. Moreover as an open-source platform, and you don’t have to pay for the license.
Apart from WooCommerce, there are Easy Digital Downloads, iThemes Exchange, Shopify eCommerce plugin, and so much more available.

6. Security Features
WordPress takes security very seriously. It offers tons of external solutions that help you in safeguarding your WordPress site. While there is no way to ensure 100% security, it provides regular updates with security patches and provides several plugins to help with backups, two-factor authorization, and more.
By choosing hosting providers like WP Engine, you can improve the security of the website. It helps in threat detection, manage patching and updates, and internal security audits for the customers, and so much more.

Read More

#use of wordpress #use wordpress for business website #use wordpress for website #what is use of wordpress #why use wordpress #why use wordpress to build a website

How to use R Shiny for EDA and Prediction

The objective of the present article is to provide a simple guide on how to develop an R Shiny application to analyze, explore, and predict variables within a dataset.

The first segment of the article covers R Shiny basics, such as the explanation fo its functionality. Further, I will develop an exploratory data analysis of bike-sharing data in the form of interactive graphs. Then, I will create a prediction model to help the user of the application predict the number of total bike registration the system by taking into consideration weather conditions and a specific day of the year.

Furthermore, I will describe the data to get in the context of the information that the dataset contains. To put a purpose to the web application, in the data understanding section, I will create several business questions that I will walk through to build the R Shiny.

Then, by using R, I will arrange the data in the correct format to build the machine learning model and the Shiny application. Finally, I will display the code and explain the steps on how to create an R Shiny application.

What is R Shiny?

R Shiny is an R package that is capable of building an interactive web page application straight from R without using any web application languages such as HTML, CSS, or JavaScript knowledge.

One essential feature of Shiny is that these applications are in a way “live” since the output of the web page changes as the user modifies the inputs, without reloading the browser.

#r #bike-sharing #towards-data-science #data-visualization #r-shiny #visual studio code

Marcus  Flatley

Marcus Flatley

1594399440

Getting Started with R Markdown — Guide and Cheatsheet

In this blog post, we’ll look at how to use R Markdown. By the end, you’ll have the skills you need to produce a document or presentation using R Mardown, from scratch!

We’ll show you how to convert the default R Markdown document into a useful reference guide of your own. We encourage you to follow along by building out your own R Markdown guide, but if you prefer to just read along, that works, too!

R Markdown is an open-source tool for producing reproducible reports in R. It enables you to keep all of your code, results, plots, and writing in one place. R Markdown is particularly useful when you are producing a document for an audience that is interested in the results from your analysis, but not your code.

R Markdown is powerful because it can be used for data analysis and data science, collaborating with others, and communicating results to decision makers. With R Markdown, you have the option to export your work to numerous formats including PDF, Microsoft Word, a slideshow, or an HTML document for use in a website.

r markdown tips, tricks, and shortcuts

Turn your data analysis into pretty documents with R Markdown.

We’ll use the RStudio integrated development environment (IDE) to produce our R Markdown reference guide. If you’d like to learn more about RStudio, check out our list of 23 awesome RStudio tips and tricks!

Here at Dataquest, we love using R Markdown for coding in R and authoring content. In fact, we wrote this blog post in R Markdown! Also, learners on the Dataquest platform use R Markdown for completing their R projects.

We included fully-reproducible code examples in this blog post. When you’ve mastered the content in this post, check out our other blog post on R Markdown tips, tricks, and shortcuts.

Okay, let’s get started with building our very own R Markdown reference document!

R Markdown Guide and Cheatsheet: Quick Navigation

1. Install R Markdown

R Markdown is a free, open source tool that is installed like any other R package. Use the following command to install R Markdown:

install.packages("rmarkdown")

Now that R Markdown is installed, open a new R Markdown file in RStudio by navigating to File > New File > R Markdown…. R Markdown files have the file extension “.Rmd”.

2. Default Output Format

When you open a new R Markdown file in RStudio, a pop-up window appears that prompts you to select output format to use for the document.

New Document

The default output format is HTML. With HTML, you can easily view it in a web browser.

We recommend selecting the default HTML setting for now — it can save you time! Why? Because compiling an HTML document is generally faster than generating a PDF or other format. When you near a finished product, you change the output to the format of your choosing and then make the final touches.

One final thing to note is that the title you give your document in the pop-up above is not the file name! Navigate to File > Save As.. to name, and save, the document.

#data science tutorials #beginner #r #r markdown #r tutorial #r tutorials #rstats #rstudio #tutorial #tutorials

How to Enable using R Programming with Visual Studio Code for Beginner

This video showcases VS Code (Visual Studio Code from Microsoft) as an alternative IDE to the most popular RStudio. You'll learn how to enable R in VS Code and also a few R-specific shortcuts that can make your programming faster.

vscode-R - https://github.com/Ikuyadeu/vscode-R

#r #visual-studio