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        <dc:date>2023-02-27T15:07:18+00:00</dc:date>
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        <title>adult-forms</title>
        <link>http://54.236.43.240/doku.php?id=adult-forms&amp;rev=1677510438&amp;do=diff</link>
        <description>Forms for adult participants

	*    [Information Sheet] 

	*    [Intial Screening Form] 

	*    [Secondary Screening Form]  

	*    [Consent Form]</description>
    </item>
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        <dc:date>2025-03-26T14:02:51+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>ap-list</title>
        <link>http://54.236.43.240/doku.php?id=ap-list&amp;rev=1742997771&amp;do=diff</link>
        <description>List of Approved Persons

Full APs

	*  Ari Lingeswaran
	*  Jonas Larsson
	*  Kyle Jasmin

Provisional APs

	*  Carl Hodgetts
	*  Francesco Scaramozzino
	*  Gabriele Bellucci
	*  Kavishini Appasamy
	*  Irena Arslanova
	*  Olaf Borghi
	*  Narender Ramnani</description>
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        <dc:date>2024-02-22T09:15:39+00:00</dc:date>
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        <title>ap-training</title>
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        <description>How to become an Authorised Person (AP) at CUBIC

PIs, Postdocs, and PhD students as well as RAs (with undergraduate degree) with staff contracts of
one of the Four partner universities can all become an Authorised Person (AP), which allows you to
become an AP and undertake scanning duty. This user guide summarises what is involved in
becoming a</description>
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        <description>BIDS (Brain Imaging Data Structure)

BIDS is a data format intended to facilitate data sharing and replication of neuroimaging data. For more information, please consult the BIDS website.

CUBIC users are strongly encouraged to store their MRI data in BIDS format to allow data sharing and replication.</description>
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        <title>booking-policy</title>
        <link>http://54.236.43.240/doku.php?id=booking-policy&amp;rev=1743499939&amp;do=diff</link>
        <description>CUBIC Scanner Booking Policy

How to book scans at CUBIC

Researchers can book scanning time directly in the CUBIC Calendar. The CUBIC booking calendar can be accessed here:  

&lt;https://www.supersaas.com/schedule/cubic/Scanner_Booking_System?view=month&gt;

Starting a new project

Note: Before scans can be booked for a new project, users must follow the steps outlined in the</description>
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        <dc:format>text/html</dc:format>
        <dc:date>2023-05-04T11:34:08+00:00</dc:date>
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        <title>brain_anatomy</title>
        <link>http://54.236.43.240/doku.php?id=brain_anatomy&amp;rev=1683200048&amp;do=diff</link>
        <description>Brain anatomy resources

Allen Brain Atlas

HBP Brain Atlas

Harvard Brain Atlas

Portal to more than twenty online brain atlases

 The D99 macaque atlas</description>
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        <dc:date>2023-02-24T14:18:50+00:00</dc:date>
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        <title>brunel-internal</title>
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        <description>Information for Brunel users</description>
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        <dc:format>text/html</dc:format>
        <dc:date>2024-02-08T12:51:04+00:00</dc:date>
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        <title>charges-cancellation-policy</title>
        <link>http://54.236.43.240/doku.php?id=charges-cancellation-policy&amp;rev=1707396664&amp;do=diff</link>
        <description>CUBIC RHUL Charges and Cancellation Policy

This document sets out the scanner charges and cancellation policies for RHUL CUBIC users. Please consult the Scanner booking policy for guidance on how to book scans in the calendar. 

Scanner charges

RHUL users with external grant funding are charged a flat rate (currently £550/h) for use of the scanner at any time (weekdays, evenings and weekends). Users without current grant funding can scan at a reduced rate (currently 10% of the full rate), subj…</description>
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        <dc:date>2023-03-06T15:32:26+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>child-forms</title>
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        <description>Forms for children (participants under 18)

	*  [Parent/Guardian Information Form]

	*  [Parent/Guardian Consent form]

	*  [Participant Information form for Under 18]

	*  [Participant Consent form for Under 18]</description>
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        <dc:date>2026-03-06T14:36:39+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>cluster-access</title>
        <link>http://54.236.43.240/doku.php?id=cluster-access&amp;rev=1772807799&amp;do=diff</link>
        <description>CLUSTER MANUAL

Cluster Access

What's on this page:


	*  VPN connection
	*  Log in with SSH
	*  GUI access

After you have registered up for HPC access, you will be provided with a local USERID and PASSWORD, different from your college login credentials, which you can use to log into psychp01 using</description>
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        <dc:format>text/html</dc:format>
        <dc:date>2024-05-09T12:51:00+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>cluster-advanced_slurm</title>
        <link>http://54.236.43.240/doku.php?id=cluster-advanced_slurm&amp;rev=1715259060&amp;do=diff</link>
        <description>CLUSTER MANUAL

Advanced SLURM

Please have a look at page 26 of the pdf version of the manual on the main page and on the SLURM webpage for advanced SLURM options.

cluster-softwarescluster-jobs

cluster-toccluster-guide</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=cluster-analyses&amp;rev=1715258834&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-05-09T12:47:14+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>cluster-analyses</title>
        <link>http://54.236.43.240/doku.php?id=cluster-analyses&amp;rev=1715258834&amp;do=diff</link>
        <description>CLUSTER MANUAL

Running analyses on psychp01

To run analyses, you:

	*  need access to the cluster
		*  No access? Go to How can I access the cluster?

	*  need your data and code on the cluster
		*  To see how you can transfer them go to How can I transfer files to the cluster?

	*  need your job file on the cluster</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=cluster-batch&amp;rev=1715258942&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-05-09T12:49:02+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>cluster-batch</title>
        <link>http://54.236.43.240/doku.php?id=cluster-batch&amp;rev=1715258942&amp;do=diff</link>
        <description>CLUSTER MANUAL

Bash files and Batch system

What's on this page:


	*  Dos and don'ts
	*  Batch System
	*  Creating a job script
	*  How to pass command-line parameters to the job script

1. Dos and don'ts

	*  Never run calculations on the home disk</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=cluster-faq&amp;rev=1715259250&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-05-09T12:54:10+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>cluster-faq</title>
        <link>http://54.236.43.240/doku.php?id=cluster-faq&amp;rev=1715259250&amp;do=diff</link>
        <description>CLUSTER MANUAL

Frequently Asked Questions

What are you looking for?


	*  How do I access the cluster?
	*  How do I transfer data and code to the cluster?
	*  How do I run analyses on the cluster?
	*  Which software is installed on the cluster?
	*  How does SLURM work?

cluster-toccluster-guide</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=cluster-file_transfer&amp;rev=1715258883&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-05-09T12:48:03+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>cluster-file_transfer</title>
        <link>http://54.236.43.240/doku.php?id=cluster-file_transfer&amp;rev=1715258883&amp;do=diff</link>
        <description>CLUSTER MANUAL

Transferring files to/from psychp01

What's on this page:


	*  Transferring data
	*  Transferring code
	*  File Transfer Clients

1. Transferring data

You need to upload your data into the folder that was created by the IT for you within the</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=cluster-guide&amp;rev=1747140229&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2025-05-13T12:43:49+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>cluster-guide</title>
        <link>http://54.236.43.240/doku.php?id=cluster-guide&amp;rev=1747140229&amp;do=diff</link>
        <description>Psychp01: RHUL Psychology Cluster Manual

Gabriele Bellucci

v.1
(2024)

:!: The Cluster Manual is still under construction, so many sections might contain errors/mistake; please bear with us and feel free to contribute!

For questions, please use the discussion forum on each page of the cluster manual. To report any issues or errors with the cluster manual, email</description>
    </item>
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        <dc:format>text/html</dc:format>
        <dc:date>2024-05-09T12:52:51+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>cluster-ijobs</title>
        <link>http://54.236.43.240/doku.php?id=cluster-ijobs&amp;rev=1715259171&amp;do=diff</link>
        <description>CLUSTER MANUAL

Interactive jobs

What's on this page:


	*  Starting an interactive job
	*  Keep interactive jobs alive

1. Starting an interactive job

You can run an interactive job like this:
$ srun --nodes=1 --ntasks-per-node=1 --time=01:00:00 --pty bash -i</description>
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    <item rdf:about="http://54.236.43.240/doku.php?id=cluster-jobs&amp;rev=1721126833&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-07-16T10:47:13+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>cluster-jobs</title>
        <link>http://54.236.43.240/doku.php?id=cluster-jobs&amp;rev=1721126833&amp;do=diff</link>
        <description>CLUSTER MANUAL

Running jobs

What's on this page:


	*  General information
	*  Job Blueprint
	*  R example
	*  Python example
	*  MATLAB example

1. General information

Below here, there are a few introductory sections for your general information on SLURM workload management system. For more details on SLURM visit the</description>
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    <item rdf:about="http://54.236.43.240/doku.php?id=cluster-linux&amp;rev=1716722252&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-05-26T11:17:32+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>cluster-linux</title>
        <link>http://54.236.43.240/doku.php?id=cluster-linux&amp;rev=1716722252&amp;do=diff</link>
        <description>CLUSTER MANUAL

Linux Quickstart

What's on this page:


	*  New on Linux systems?
	*  Common Commands
	*  Text editing in command line
	*  Displaying images in command line
	*  Displaying images from command line (using X11 forwarding)
	*  Displaying NIFTI images in command line</description>
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    <item rdf:about="http://54.236.43.240/doku.php?id=cluster-prerequisites&amp;rev=1715258749&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-05-09T12:45:49+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>cluster-prerequisites</title>
        <link>http://54.236.43.240/doku.php?id=cluster-prerequisites&amp;rev=1715258749&amp;do=diff</link>
        <description>CLUSTER MANUAL

Getting Started with HPC on psychp01

What's on this page:


	*  Prerequisites
	*  High Performance Computing on psychp01
	*  First Steps on psychp01

1. Prerequisites

Psychp01 is a High Performance Computing (HPC) cluster as a vitualized system that runs</description>
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    <item rdf:about="http://54.236.43.240/doku.php?id=cluster-softwares&amp;rev=1737495208&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2025-01-21T21:33:28+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>cluster-softwares</title>
        <link>http://54.236.43.240/doku.php?id=cluster-softwares&amp;rev=1737495208&amp;do=diff</link>
        <description>CLUSTER MANUAL

Softwares on psychp01

Psychp01 is a Linux based platform and has a variety of softwares installed on it. The software suite installed on the cluster is continuously evolving according to user needs and requirements. If an user needs a particular software for a study, the user is encouraged to get in touch with the IT team or Gabriele Bellucci at the earliest convenience. They will run a feasibility analysis and install the required software as soon as possible. Following is a li…</description>
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    <item rdf:about="http://54.236.43.240/doku.php?id=cluster-toc&amp;rev=1716722524&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-05-26T11:22:04+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>cluster-toc</title>
        <link>http://54.236.43.240/doku.php?id=cluster-toc&amp;rev=1716722524&amp;do=diff</link>
        <description>CLUSTER MANUAL

Table of Contents

	*  Getting Started with HPC on psychp01
		*  Prerequisites
		*  High Performance Computing on psychp01
		*  First Steps on psychp01

	*  Linux QuickStart
		*  New on Linux systems?
		*  Common Commands
		*  Text editing in command line
		*  Displaying images in command line</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=cluster-vpn_install&amp;rev=1715259216&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-05-09T12:53:36+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>cluster-vpn_install</title>
        <link>http://54.236.43.240/doku.php?id=cluster-vpn_install&amp;rev=1715259216&amp;do=diff</link>
        <description>CLUSTER MANUAL

Installing VPN Client – GlobalProtect

See [this pdf file] and this RHUL intranet page for a step-by-step guide to install the VPN client GlobalProtect.

cluster-ijobscluster-faq

cluster-toccluster-guide</description>
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    <item rdf:about="http://54.236.43.240/doku.php?id=covid-forms&amp;rev=1677168741&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2023-02-23T16:12:21+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>covid-forms</title>
        <link>http://54.236.43.240/doku.php?id=covid-forms&amp;rev=1677168741&amp;do=diff</link>
        <description>COVID related forms

FIXME

	*  [COVID Working Protocol]

	*  [COVID Questionnaire]</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=cubic-conference&amp;rev=1759509602&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2025-10-03T16:40:02+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>cubic-conference</title>
        <link>http://54.236.43.240/doku.php?id=cubic-conference&amp;rev=1759509602&amp;do=diff</link>
        <description>CUBIC Conference

Every summer, the CUBIC conference is hosted by one of the collaborating universities. This is an opportunity to share new work across the four institutions and develop new links within CUBIC. Each year, we also invite a prestigious external speaker, who has made significant discoveries within the areas of research areas tackled at CUBIC.</description>
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    <item rdf:about="http://54.236.43.240/doku.php?id=cubic-induction-meeting&amp;rev=1698686521&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2023-10-30T17:22:01+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>cubic-induction-meeting</title>
        <link>http://54.236.43.240/doku.php?id=cubic-induction-meeting&amp;rev=1698686521&amp;do=diff</link>
        <description>CUBIC induction

Every October, we hold a CUBIC induction session to introduce new staff and PGRs to CUBIC procedures and personnel. Feel free to take a look at the slides below!

[RHUL MRI induction slides 2023]</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=cubic-monthly&amp;rev=1759509024&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2025-10-03T16:30:24+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>cubic-monthly</title>
        <link>http://54.236.43.240/doku.php?id=cubic-monthly&amp;rev=1759509024&amp;do=diff</link>
        <description>Monthly neuroscience meetings

Starting on Wednesday 15th October 2025 (JBB105, 3-4pm), we will hold the first of our revamped monthly neuroscience meetings, which we are provisionally calling “Neuro Natter” (feedback welcome!). These meetings will be informal and community-focused, providing a space for staff to discuss centre-specific matters but also ongoing challenges in their work (e.g., with preprocessing/analysis), ideas for new projects and grants, recent developments in the field, etc. …</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=cubic-roles&amp;rev=1761741704&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2025-10-29T12:41:44+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>cubic-roles</title>
        <link>http://54.236.43.240/doku.php?id=cubic-roles&amp;rev=1761741704&amp;do=diff</link>
        <description>People and Roles

Carl Hodgetts

Email: &lt;carl.hodgetts@rhul.ac.uk&gt;

Role: CUBIC Director

Key tasks:

	*  Chair of the CUBIC management committee.
	*  Foster and maintain strong relationships with partner institutions and external stakeholders.
	*  Develop and promote the Centre as a research facility within the University, as well as nationally and internationally, engaging with both academic and non-academic partners.</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=cubic-skills&amp;rev=1759501684&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2025-10-03T14:28:04+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>cubic-skills</title>
        <link>http://54.236.43.240/doku.php?id=cubic-skills&amp;rev=1759501684&amp;do=diff</link>
        <description>CUBIC skills database

 Please add your name and any relevant specialist skills you have and are willing to share with other users below. 
 Name       Email  Skill/Expertise        Level (beginner/intermediate/expert)           Jonas Larsson  &lt;jonas.larsson@rhul.ac.uk&gt;     Matlab</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=data-download&amp;rev=1680100090&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2023-03-29T14:28:10+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>data-download</title>
        <link>http://54.236.43.240/doku.php?id=data-download&amp;rev=1680100090&amp;do=diff</link>
        <description>Downloading raw data from the scanner

Non-RHUL users: due to the Siemens PC running an outdated version of Samba, it is not possible to access the MRI raw storage from off-campus. Non-RHUL users need to bring a portable hard drive or USB stick to download data on-site. We are working on a solution to this issue.</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=data-storage&amp;rev=1677591074&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2023-02-28T13:31:14+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>data-storage</title>
        <link>http://54.236.43.240/doku.php?id=data-storage&amp;rev=1677591074&amp;do=diff</link>
        <description>Data storage facilities

Raw MRI data

Archiving/Backup

Processed MRI data

Data sharing</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=find-us&amp;rev=1707394631&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-02-08T12:17:11+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>find-us</title>
        <link>http://54.236.43.240/doku.php?id=find-us&amp;rev=1707394631&amp;do=diff</link>
        <description>How to find us

The Combined Universities Brain Imaging Centre (CUBIC) can be found 40 minutes by train from central London and just seven miles from Heathrow Airport, with excellent road and transport links. 

Combined Universities Brain Imaging Centre (CUBIC)
Royal Holloway, University of London
Egham Hill
Egham
Surrey
TW20 0EX</description>
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    <item rdf:about="http://54.236.43.240/doku.php?id=first-aid-courses&amp;rev=1677590910&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2023-02-28T13:28:30+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>first-aid-courses</title>
        <link>http://54.236.43.240/doku.php?id=first-aid-courses&amp;rev=1677590910&amp;do=diff</link>
        <description>First Aid Requirement

All Authorised persons need to be trained in First aid.

Suitable courses in Emergency First Aid at Work are available from these providers.

 St John Ambulance

 Red Cross

First aid courses are organised periodically at RHUL, so please check if there is one coming up! These will be announced here and on the</description>
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    <item rdf:about="http://54.236.43.240/doku.php?id=high-performance-computing&amp;rev=1705582707&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-01-18T12:58:27+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>high-performance-computing</title>
        <link>http://54.236.43.240/doku.php?id=high-performance-computing&amp;rev=1705582707&amp;do=diff</link>
        <description>High performance computing facilities at RHUL

Note these facilities are managed by the Psychology department and are available to RHUL users only.

The RHUL Psychology department has two facilities for high performance computing (HPC), suitable for processing neuroimaging data:</description>
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    <item rdf:about="http://54.236.43.240/doku.php?id=incidental-finding&amp;rev=1707398167&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-02-08T13:16:07+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>incidental-finding</title>
        <link>http://54.236.43.240/doku.php?id=incidental-finding&amp;rev=1707398167&amp;do=diff</link>
        <description>In the event that a scan reveals a suspected abnormality the MRI Safety Officer ari.lingeswaran@rhul.ac.uk must be notified immediately and will forward the relevant images to a Consultant Radiologist who will provide a report on the findings. 

If this reports indicates that further action is needed, the participant's GP will be sent a copy of the report by CUBIC staff and advised to contact the participant for any further procedures. The participant will not be contacted directly by CUBIC staf…</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=key-guidelines&amp;rev=1678296822&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2023-03-08T17:33:42+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>key-guidelines</title>
        <link>http://54.236.43.240/doku.php?id=key-guidelines&amp;rev=1678296822&amp;do=diff</link>
        <description>Summary of key rules and procedures

Please note that the full rules are detailed in the official [CUBIC Rules of Operation] - the below should be considered as guidelines only. 

Authorised Persons are required to have knowledge of the rules and procedures in the Rules of Operation - these guidelines are not intended as a replacement for AP training.</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=linux-survival&amp;rev=1760022718&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2025-10-09T15:11:58+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>linux-survival</title>
        <link>http://54.236.43.240/doku.php?id=linux-survival&amp;rev=1760022718&amp;do=diff</link>
        <description>Linux survival guide

Why Linux?

Linux is the de facto operating system for scientific computing thanks to its high performance and extensive customisability, and most of the software used for processing and analysing neuroimaging data runs under Linux. There are good reasons for this - Linux is fast and powerful (all of the 500 fastest supercomputers in the world run Linux and most CGI effects in films are made on Linux computers), widely used (major online providers like Amazon and Google run…</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=methods-training&amp;rev=1734365147&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-12-16T16:05:47+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>methods-training</title>
        <link>http://54.236.43.240/doku.php?id=methods-training&amp;rev=1734365147&amp;do=diff</link>
        <description>Methods training

Based on user requests, there are tentative plans to provide training in the following topics for RHUL users (CUBIC partners welcome):

* Basics of MRI data analysis

* MRI methods - BOLD, MRS, DTI &amp; tractography, multiband imaging</description>
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    <item rdf:about="http://54.236.43.240/doku.php?id=mri-sequences&amp;rev=1708354360&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-02-19T14:52:40+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>mri-sequences</title>
        <link>http://54.236.43.240/doku.php?id=mri-sequences&amp;rev=1708354360&amp;do=diff</link>
        <description>Structural

T1-weighted

MPRAGE

High resolution, T1-weighted, structural MRI
 Parameter                 Value                                                          Acquisition time          4 min 32 s</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=new-starter&amp;rev=1678206855&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2023-03-07T16:34:15+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>new-starter</title>
        <link>http://54.236.43.240/doku.php?id=new-starter&amp;rev=1678206855&amp;do=diff</link>
        <description>Guide for new starters

	*  If you are new to neuroimaging or MRI, please consider collaborating with someone experienced to learn the ropes.
	*  Read and follow the guidelines in the new starter guide for  RHUL users or for non-RHUL users.
	*  Attend an Emergency First Aid at Work training course.
	*  Read the [Procedure for becoming an approved MRI operator (AP)] document and contact Ari</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=new-study-partners&amp;rev=1678206544&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2023-03-07T16:29:04+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>new-study-partners</title>
        <link>http://54.236.43.240/doku.php?id=new-study-partners&amp;rev=1678206544&amp;do=diff</link>
        <description>How to start a new study at CUBIC (non-RHUL users)

Please read and follow the steps outlined in the [Starting a new MRI study] guide, except for step 3 (project presentation).</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=new-study-rhul&amp;rev=1708593472&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-02-22T09:17:52+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>new-study-rhul</title>
        <link>http://54.236.43.240/doku.php?id=new-study-rhul&amp;rev=1708593472&amp;do=diff</link>
        <description>How to start a new study at CUBIC

To start a new study at CUBIC the following steps need to be taken:

1) Check that the study can feasibly be carried out using CUBIC facilities. This needs to be done before submitting a grant application to support the study.</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=news-updates&amp;rev=1707729419&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-02-12T09:16:59+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>news-updates</title>
        <link>http://54.236.43.240/doku.php?id=news-updates&amp;rev=1707729419&amp;do=diff</link>
        <description>This page is for important news and updates, including error reports. Please date any contributions and add your name or initials so the admin team can contact you for further information, if necessary

20/2/2023

Some users have reported not receiving the first trigger from the scanner through the mouse connected to the Siemens PC. This is because the mouse is a passive device that some operating systems don't recognise until it sends a signal (such as a mouse click). To avoid this issue, after…</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=open-datasets&amp;rev=1707399204&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-02-08T13:33:24+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>open-datasets</title>
        <link>http://54.236.43.240/doku.php?id=open-datasets&amp;rev=1707399204&amp;do=diff</link>
        <description>Open MRI datasets

This is an (incomplete) list of publicly available MRI data sets for download. Please feel free to add any others!

You may want to check a hitchhiker's guide to work on large neuroimaging databases [Horien et al., 2021].

Another paper is useful to check different databases [Madan, 2021].</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=participants-aps-forum&amp;rev=1677071874&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2023-02-22T13:17:54+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>participants-aps-forum</title>
        <link>http://54.236.43.240/doku.php?id=participants-aps-forum&amp;rev=1677071874&amp;do=diff</link>
        <description></description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=peripheral-equipment&amp;rev=1716539805&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-05-24T08:36:45+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>peripheral-equipment</title>
        <link>http://54.236.43.240/doku.php?id=peripheral-equipment&amp;rev=1716539805&amp;do=diff</link>
        <description>Peripheral equipment and user guides

[List of peripheral equipment]

User guides

Please add useful information about the use of the below equipment (and feel free to add equipment not listed)

USB scanner trigger

This is connected through an optical mouse to the scanner control PC, and sends a simulated mouse click when the scanner starts. If you use DDAs - discarded initial acquisitions - it will not send a click until the first acquired volume. Trigger pulses will only be sent out for funct…</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=piloting-guide&amp;rev=1707396482&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-02-08T12:48:02+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>piloting-guide</title>
        <link>http://54.236.43.240/doku.php?id=piloting-guide&amp;rev=1707396482&amp;do=diff</link>
        <description>Piloting guide

New studies will generally require a certain amount of piloting before “real” data can be acquired. This can be thought of in two phases: 

	*  The programming, debugging, and piloting of your behavioural task. This part does not depend on interaction with the scanner or peripherals other than button presses.</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=recruitment&amp;rev=1707398733&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-02-08T13:25:33+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>recruitment</title>
        <link>http://54.236.43.240/doku.php?id=recruitment&amp;rev=1707398733&amp;do=diff</link>
        <description>The Experiment Management System is used to administer our participant pool. There is a credit pool of 1st year students and restrictions apply to advertising in this pool (your entire study and all credits must be available to the entire cohort of students). There is also a 'paid pool' of RHUL students, staff and general public. Use of the paid pool is not restricted and studies do not have to offer cash payment. Details of the credit scheme are in the</description>
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    <item rdf:about="http://54.236.43.240/doku.php?id=reproducibilitea&amp;rev=1677171314&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2023-02-23T16:55:14+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>reproducibilitea</title>
        <link>http://54.236.43.240/doku.php?id=reproducibilitea&amp;rev=1677171314&amp;do=diff</link>
        <description>ReproducibiliTea Journal Club

These are a series of informal meetings held at Royal Holloway to discuss issues related to research methods. We will discuss some recent papers and ideas on reproducibility and open science, however, our “journal club</description>
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    <item rdf:about="http://54.236.43.240/doku.php?id=rhul-internal&amp;rev=1716978186&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-05-29T10:23:06+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>rhul-internal</title>
        <link>http://54.236.43.240/doku.php?id=rhul-internal&amp;rev=1716978186&amp;do=diff</link>
        <description>Information for Royal Holloway users

Data management

FIXME

Data management policy

How to write a data management plan for neuroimaging

Example data management plans

Open science and reproducibility

Resources for transparent research

ReproducibiliTea at RHUL

Public engagement

FIXME

Publication engagement strategy

Publication engagement contacts

CUBIC Credits Application

[ cubic_credits_application.doc]</description>
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    <item rdf:about="http://54.236.43.240/doku.php?id=roehampton-internal&amp;rev=1677248348&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2023-02-24T14:19:08+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>roehampton-internal</title>
        <link>http://54.236.43.240/doku.php?id=roehampton-internal&amp;rev=1677248348&amp;do=diff</link>
        <description>Information for Roehampton users</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=scanner_description&amp;rev=1678116676&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2023-03-06T15:31:16+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>scanner_description</title>
        <link>http://54.236.43.240/doku.php?id=scanner_description&amp;rev=1678116676&amp;do=diff</link>
        <description>Scanner

Siemens Tim Trio

System Software – Syngo MR B17

RF Coils

32 channel head array

12 channel head array

Birdcage coil

Neck coil

Spine coil

QA testing

Ari runs a weekly Q&amp;A pipeline, testing standard sequences and checking for spikes (among other potential issues). Any anomalies will be reported to potentially affected users, and posted on the</description>
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    <item rdf:about="http://54.236.43.240/doku.php?id=sequence-development&amp;rev=1678103965&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2023-03-06T11:59:25+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>sequence-development</title>
        <link>http://54.236.43.240/doku.php?id=sequence-development&amp;rev=1678103965&amp;do=diff</link>
        <description>Development and installation of new sequences

As CUBIC does not employ an in-house MRI physicist, sequence development on the scanner is limited to a) tweaking parameters on existing sequences (e.g., TR, slice thickness, FOV etc) or b) installing sequences developed elsewhere for the Siemens Trio or compatible systems through our Siemens research agreement. If you want to have an externally developed sequence installed, please contact</description>
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        <dc:format>text/html</dc:format>
        <dc:date>2023-04-21T09:45:34+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>software-list</title>
        <link>http://54.236.43.240/doku.php?id=software-list&amp;rev=1682070334&amp;do=diff</link>
        <description>Software for neuroimaging

 This is a list of commonly used software packages for analysis of neuroimaging data.
Please feel free to expand.

FSL: Software for analysis of neuroimaging data for Linux and Mac (can be run on Windows on a virtual machine)</description>
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    <item rdf:about="http://54.236.43.240/doku.php?id=start&amp;rev=1759509883&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2025-10-03T16:44:43+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>start</title>
        <link>http://54.236.43.240/doku.php?id=start&amp;rev=1759509883&amp;do=diff</link>
        <description>Welcome to the CUBIC Wiki

The CUBIC wiki hosts a wealth of information to help you design, run, analyse and share your MRI experiments. General information on the centre can be found on the CUBIC website.

This wiki is a shared resource for knowledge exchange which</description>
    </item>
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        <dc:format>text/html</dc:format>
        <dc:date>2023-03-14T16:26:25+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>stimulus-generation</title>
        <link>http://54.236.43.240/doku.php?id=stimulus-generation&amp;rev=1678811185&amp;do=diff</link>
        <description>Software for stimulus generation and presentation

Psychtoolbox: Matlab-or Octave-based stimulus presentation library.

Pros:

	*  Multi-platform (Linux, Mac, Windows). 
	*  Very powerful and with comprehensive support for numerous hardware peripherals (e.g. eye tracking, data recording).</description>
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    <item rdf:about="http://54.236.43.240/doku.php?id=stimulus-presentation&amp;rev=1743093448&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2025-03-27T16:37:28+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>stimulus-presentation</title>
        <link>http://54.236.43.240/doku.php?id=stimulus-presentation&amp;rev=1743093448&amp;do=diff</link>
        <description>Stimulus Presentation

Stimulus PC

We now have a new stimulus PC in the MRI control room, which runs Windows X and Ubuntu X. Installed software on the Windows partition include: Matlab XXX, Psychophysics Toolbox XXXX, Presentation version XXXX, and PsychoPy.</description>
    </item>
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        <dc:format>text/html</dc:format>
        <dc:date>2023-02-24T14:19:25+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>surrey-internal</title>
        <link>http://54.236.43.240/doku.php?id=surrey-internal&amp;rev=1677248365&amp;do=diff</link>
        <description>Information for Surrey users</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=tips-tricks&amp;rev=1678881923&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2023-03-15T12:05:23+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>tips-tricks</title>
        <link>http://54.236.43.240/doku.php?id=tips-tricks&amp;rev=1678881923&amp;do=diff</link>
        <description></description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=useful-contacts&amp;rev=1759509713&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2025-10-03T16:41:53+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>useful-contacts</title>
        <link>http://54.236.43.240/doku.php?id=useful-contacts&amp;rev=1759509713&amp;do=diff</link>
        <description>Operations

MRI Operations &amp; Safety Officer: Ari Lingeswaran &lt;ari.lingeswaran@rhul.ac.uk&gt;

Control room telephone:  01784 41 4429

Management

CUBIC Director: Carl Hodgetts &lt;carl.hodgetts@rhul.ac.uk&gt;

Technical Lead (RHUL): Jonas Larsson &lt;jonas.larsson@rhul.ac.uk&gt;

Environment Lead (RHUL): Rikki Lissaman &lt;rikki.lissaman@rhul.ac.uk&gt;

CUBIC partner representatives:</description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=user-forum&amp;rev=1676911584&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2023-02-20T16:46:24+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>user-forum</title>
        <link>http://54.236.43.240/doku.php?id=user-forum&amp;rev=1676911584&amp;do=diff</link>
        <description></description>
    </item>
    <item rdf:about="http://54.236.43.240/doku.php?id=wiki-guide&amp;rev=1707393761&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2024-02-08T12:02:41+00:00</dc:date>
        <dc:creator>Anonymous (anonymous@undisclosed.example.com)</dc:creator>
        <title>wiki-guide</title>
        <link>http://54.236.43.240/doku.php?id=wiki-guide&amp;rev=1707393761&amp;do=diff</link>
        <description>How to use this wiki

Please put comments, queries, help requests, or general items for discussion in the User discussion forum.

If you have any useful tips or tricks for using the scanner or analysing data that don't fit into any of the sectiions below, please post them in the</description>
    </item>
</rdf:RDF>
