Accessing MRI Data

Introduction

​Once you complete an MRI scan on either the 3T or 7T the DICOM data is copied to a central file store where it is then archived onto tape (and cloned).  

Requesting Sc​​ans

Scan recovery is via a web interface that is accessed through the Calpendo scan booking web pages: 

https://calpendo.fmrib.ox.ac.uk/bookings/

Once logged in (using your University SSO username/password - NOT the same password as your WIN computer account) go to  Projects > My Scans. 

This will open a separate window with a list of the projects you are associated with on the left. Clicking on the project of interest will allow you to select a particular scan session, with the details of the project in the top right and the scans from this session listed in the bottom right section. There you can select which scans to retrieve and an which format - Nifti (probably what you want) or Dicom (normally not what you want) - by ticking the appropriate box in the Nifti or Dicom columns. Where you want all scans from the session you can tick the box in the Nifti or Dicom header to automatically select everything. 

Now click on Retrieve selected to begin the retrieval process, which can take a few minutes. The status of the retrieve is indicated in the status column as an animated icon - grey for pending tasks and blue for running tasks. 

Once complete, you will be notified by email and the scans will remain available for collection for 7 days before being removed, so you should take a copy of the data as soon as possible. 

To be able to transfer your scans off of the system you need either a SFTP Only Account (issued free of charge) or a full FMRIB computer account (charged, which provides access to other FMRIB computer resources). 

With either of these account types, the retrieved scans are available via SFTP (not scp) from the computer scans.fmrib.ox.ac.uk (see below). For those with a full computer account, you can find the data in the folder /vols/Data/MRdata/<myusername> on jalapeno.fmrib.ox.ac.uk. ​

SFTP Ac​​cess to Scans

​NB Make sure to request your MRI data from Calpendo BEFORE attempting to connect via SFTP. SFTP access is permitted only when there is data waiting for you to collect. If there is no MRI data downloaded for you, your SFTP connection will FAIL even if you have put in the correct username, password and other connection details. If your SFTP connection fails, the first thing to check is whether you have requested your data from Calpendo and received the email confirming it is ready to collect.​​

We recommend the use of the program Cyberduck (available for macOS [also in the Mac app store] and Windows) or the command line sftp program (macOS and Linux). 

Cyberd​​uck

When you launch Cyberduck you will be presented with a view of your bookmarks - we recommend you create a bookmark for easy connection in the future (if you've already done this then just double-click on the bookmark and get your scans). If you don't see the bookmarks window, choose File > New Browser from the Cyberduck menu. 

Creating a bookmark

In the bottom left of the window you will find three icons, +, a pen and -, click the +. 

In the resulting window choose SFTP (SSH File Transfer Protocol), provide a nickname (if you wish) and enter the server name: 

      scans.fmrib.ox.ac.uk

Then enter your FMRIB username in the Username box. If you are have a SFTP Only Account you can now close the bookmark editor (changes are saved automatically). 

For those with full computer accounts you then need to click on More Options and enter the path 

      /vols/Data/MRdata/username

(replacing username with your username) and then you can close the bookmark. 

Opening a c​onnection

Double-click on the scans bookmark in the main Cyberduck window, the first time you connect you may be presented with a request to allow an Unknown fingerprint. Confirm that the fingerprint is: 

      b1:9a:e3:34:57:0d:f9:3c:ac:7e:b1:59:5a:c8:0b:3d

then select Always and click Allow. 

​ 

You should then be presented with a window showing the contents of your MRdata folder, you can drag folders out of there onto your computer. 

SFTP Comma​​ndline

You can copy scans off using the sftp program. This can be used in both an interactive and non-interactive manner. 

Interac​​​tive

To open a connection with a SFTP Only Account, use the command: 

      sftp username@scans.fmrib.ox.ac.uk

For those with full computer accounts, use the command: 

      sftp username@scans.fmrib.ox.ac.uk:/vols/Data/MRdata/username

replacing both usernames with your username. You will then be given a command prompt, type ls to show a folder listing. To get the folder AF, storing in the folder you were in when you ran the sftp, type get -r AF, individual files with get afile. 

To change to a different folder, use cd, to change to a different folder on your computer, use !cd and list files on your computer with !ls. 

Non-interactive

You can also use the sftp program in a similar manner to scp as long as you know the 'scan' folder name. With a SFTP Only Account use: 

      sftp -r username@scans.fmrib.ox.ac.uk:/F3T_XYZ1 .

to copy to the current folder (replace . with a local folder path if you wish to put the folder somewhere else). With a full computer account use: 

      sftp -r username@scans.fmrib.ox.ac.uk:/vols/Data/MRdata/username/F3T_XYZ1 .

to copy to the current folder (replace . with a local folder path if you wish to put the folder somewhere else).