Analyzing Data

During the Planning Research stage, a Project folder for storing research data is not yet available. Therefore, when dealing with any data (real or simulated) during the Planning Research stage, you will most often want to store it in your Home Drive. This is because, since the Home Drive is mounted on High Performance Storage, you will be able to work with the HPC Cluster which can speed up your analysis time. Otherwise, you would use the local storage on your DCCN-issued PC.

Note

It is essential that data generated in the Planning Research stage that is eventually relevant for the project is moved to the Project folder once this is created after PPM approval.

Let’s see how we would download existing data. Below, we will show three examples of downloading existing data from the RDR or an External Repository.

Closed Access Collection with Repocli

Once you have been added to a collection, you will receive an email to the email account you used when you signed up to the Radboud Data Repository stating that you have been added. Workshop attendees will be added to our workshop’s DAC in the RDR which is Closed Access Others can access our workshop’s Open Access DSC in the Radboud Data Repository to do this exercise. We will practice downloading this DSC onto your Home Drive (replace groupname with your lab group’s name and firlas with your DCCN username)

  1. Establish a Network Connection to Trigon (either eduVPN or hardwired)

  2. Log in on the Radboud Data Repostory

../../_images/RDR_login.png

  • Click Login with your SURFconext account

../../_images/RDR_login2.png

  • Login with the USEZ credentials of the account that has been added to the our workshop’s DAC

  • After loggin in, click on the dropdown with your name, then click Data access credentials

../../_images/RDR_access.png

  • Click the button to copy the password and leave this page open while you do other excercises

  1. Open a TigerVNC session (read how to do that here)

  2. Login to the Radboud Data Repository

  • Open TigerVNC

  • Open the terminal application

  • Type repocli shell and then push enter

  • Type config and then push enter

  • Enter your RU username (u1234567@ru.nl) and then push enter

  • Enter the RDR password you retreived in step 2, then push enter

  1. Download the Data Sharing Collection to Your Home Directory

  • Type get dccn/DAC_3010000.05_873 /home/groupname/firlas for workshop attendees

  • Type get dccn/DSC_3010000.05_519 /home/groupname/firlas for non-workshop attendees

Public Collection with Cyberduck

  1. Establish a Network Connection to Trigon (either eduVPN or hardwired)

  2. Login to the Radboud Data Repository

  • Open Cyberduck

  • Click Open Connection at the top left of the window

  • Click on the dropdown menu (which defaults to File Transfer Protocol (FTP)) and select WebDAV (HTTPS)

  • At the Server: field type in data.ru.nl

  • Click the box next to Anonymous Login and then click Connect at the bottom right side of the window

  1. Download the Data Sharing Collection to Your Folder of Choice

  • Double click on the dccn directory

  • Single click on the DSC_3010000.11_518_v1 directory

  • Locate and click on Action at the top of the window and then select Download To on the dropdown menu

  • Select the folder you want to download the data to and then push Ok

  • Select the disconnect button at the top right of the window

Other Repositories with Cyberduck

Let’s say you have found a data collection you want to analyze on OpenNeuro called Demo. Before you can go about downloading it with Cyberduck or Repocli, you must determine which protocol you must use to interact with the server. Below is a list of the Protocols required by some commonly used Open Access Repositories.

Repository

OpenfMRI

OpenNeuro

OMEGA

Protocol

AWS

AWS

WebDAV

  1. Establish an AWS Connection to the OpenNeuro folder you want to download

  • Open Cyberduck and push Open Connection

  • Click on the dropdown menu which defaults to FTP (File Transfer Protocol) and select Amazon S3

  • Click on the dropdown for more options and copy the domain name and the dataset number, seperated by a forward slash (i.e. openneuro.org/ds004564) into the Path: field

  • In the Access Key ID: field, type anonymous

../../_images/Cyberduck_AWS.png

  • Click connect

  1. Download the fMRI data

  • Control-click the data you want to download (so the subject data folders and the participants.tsv file)

  • Click Action and then Download To in the dropdown

  • Select the directory you want to download the data to and then push OK