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FMRIB IT Resources

The aim of this document it to give you a short overview of the available IT facilities in the FMRIB Centre. More detailed information is available for browsing this web site.

Table of Contents

  1. Getting a Computer Account
  2. Computing Equipment Overview
    1. Centralised analysis computing
    2. Data storage (central hard disk)
    3. Desktop computing resources
  3. Using FMRIB's Resources
    1. Accessing FMRIB's computers
    2. Web/Email
    3. Computing Presentation
    4. Getting Help
  4. Computing Staff

Getting a Computing Account

Before you can use the FMRIB IT resources you will need a computing account. New users are issued with a "Centre Welcome Pack" by our Administrator. In this you will find a form for applying for a FMRIB comuting account. Should you be an external collaborator who cannot visit the Centre, you can get a copy of the form below. Alternatively, if you have worked/collaborated with the Centre in the past and/or your account has expired, then please contact computing-help@fmrib.ox.ac.uk to request it's reactivation.

Account Application Form [PDF] - Please fill in and Fax to the Centre Administrator.

Computing Equipment Overview

Centralised analysis computing

The FMRIB Centre provides a computer running scheduling software for researchers to carry-out their MRI analysis tasks. This computer is accessed using terminal software to connect to jalapeno.fmrib.ox.ac.uk. Please see: Using Jalapeno [Internal] for detailed usage instructions.

Data storage (central hard disk)

To support the cluster and other computing requirements in the Centre, we provide centralised disc storage for a users home directory and separate space for MRI data and temporary ("scratch") working space. All centralised storage is allocated using an enforced quota system, i.e., you will have N GB of each area allocated to your account.

Home directories and Centre scanner output are automatically backed up nightly. The scratch space is not backed up but can be archived on-demand. See: Data Management for further details.

Desktop computing resources

Within the Centre, we provide desktop based workstations (Mac OS X and Linux), which are integrated into the shared storage network. MRI/scientific analysis software installed on machines includes FSL, Freesurfer, Matlab, SPSS, Endnote and Microsoft Office (subject to operating system compatibility).

We have limited support for Microsoft Windows based computers and have a policy of not purchasing such computers unless absolutely necessary (for example for controlling a particular piece of hardware). Where you have been allocated a desktop computer we are able to install a virtual machine to enable you to run Microsoft Windows specific software.

Using FMRIB's resources

How to access FMRIB's compute resources

All access to the Centre's analysis computer is via jalapeno.fmrib.ox.ac.uk. You must connect to jalapeno.fmrib.ox.ac.uk using a SSH program, please see the SSH page for details. You can also use a graphical connection such as X11 or VNC.

SSH, X11 and VNC services are also available from remote sites. Where direct access to the FMRIB network is necessary we also provide a VPN service.

Files may be copied to and from your FMRIB data folders using a SCP/SFTP client.

If you have an external collaborator who needs to send you files we provide an anonymous file upload service, which allows them to upload a file through a web interface.

Web/Email

The FMRIB Centre maintains its own web and email services, all users being provided with a personal web page and an email address which may be forwarded to another email account if you so wish.

Computing Presentation

In addition to the web based information we also provide a lecture on Computing at FMRIB as part of the Themes lecture series. For those unable to attend, the slides are available from the internal Computing web pages under the title Computing Themes Slides [PDF].

Getting Help

Further information on accessing services and running analysis software is available on the internal Computing site, the FAQ (Frequently Asked Questions) and User Guides being particularly useful, but if this information does not help, please feel free to request help by sending an email to computing-help@fmrib.ox.ac.uk. This is a ticketed system, so on submission, you will receive a reply with a reference number for this request. Please reply to this acknowledgement email when you wish to add information to this help request.

Computing Staff

  • IT Manager David Flitney
  • Computing Officer Duncan Mortimer
  • Technical Support Officer Iain Wilson
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