Preparing to run your CBU-based imaging study
Note that - if you do not have CBU wiki permissions, some important parts of this document will not be included in the page you see. For users outside the CBU, without CBU wiki permissions, see ExternalPreparingYourStudy.
- Preparing to run your CBU-based imaging study
Access to CBU Scanner
(You will need to do this well in advance of your study)
In order to have access to the MRI Facility and to be able to scan volunteers at the CBU you need to have a Panel Induction and become an MRI Certified User. Please arrange to attend a Panel Induction with the Panel Manager (firstname.lastname@example.org) as you are unable to make contact with any of our volunteers until you have attended this induction. Becoming an MRI Certified User is a two stage process and involves booking yourself on 1) an MRI Video Presentation course and, 2) an MRI Practical session (please note that the courses must be attended in sequence). For further information on these courses, contact LucilleMurby. These courses will take place periodically throughout the year, and specific details will be announced in advance via the Imagers Emailing List.
Certified Users based at the CBU will have their access card updated to incorporate access to the external doors of the MRI Facility between 8.15am and 8.15pm. This allows them into Reception where they can meet their volunteers, access the internet and have use of a telephone as well as being able to access the washroom and kitchen. The radiographers will ask them to sign for a card allowing internal door access for their period of scanning which will need to be returned by the end of the day. Imagers based at other sites who attain CBU certification will be logged as Certified Guests and will be eligible for a daily access card to the above areas on each visit. This card must be handed in before exiting the MRI Facility at the end of each day. Access privileges to all types of card are updated by LucilleMurby and any CBU users needing to query their access status should contact Lucille. Temporary cards (for periods when you are scanning) are available from the radiographers.
Please ensure that the OPEN sign on the outer door is visible before you attempt to access the MRI Facility. At the present time the building alarm and the access system are not co-ordinated so you will activate the alrm if you enter when the CLOSED sign is visible.
Before scanning, imagers should familiarise themselves with the CBU Standard Operating Procedures. This is available online for authorized wiki users (see UsingThisWiki) at StandardOperatingProcedure.
Local Research Ethics Committee (LREC) approval
(absolute minimum 2 months before scanning)
In order to be allocated slots on the CBU scanner, you need official ethics approval either from the Cambridge Local Research Ethics Committee (LREC) or another LREC within the region. Applications to Cambridge are likely to be processed more smoothly than applications elsewhere as the Cambridge Committee are aware of, and have formerly approved, our Standard Operating Procedures. However, the Cambridge LREC can only review a relatively small number of applications per month and they are usually over subscribed several months in advance. Therefore, we recommend that you contact the Cambridge LREC in order to book a slot on their agenda as early as you possibly can. If they do not have a slot within a reasonable time frame they can advise you which Committee does have slots available and provide you with contact details.
It is possible that someone in your research group has already acquired LREC permission for your study and to run your experiment you only need to become an additional named investigator on that application. This is now usually done via the Principal Investigator contacting LucilleMurby with an instruction to add you to their protocol (no contact with LREC is normally required). If your study is not included on an existing protocol then you need to submit a full application, which is a substantial document available online at the Central Office for Research Ethics Committees (COREC). For more details about what is involved, contact someone who has recently submitted a protocol in your group, or contact LucilleMurby. There are standard forms available (already approved by LREC) that will need to be included in your application and you can find these at http://imaging.mrc-cbu.cam.ac.uk/mri/InternalAdmin and please follow the instructions there carefully. Only these standard forms will be acceptable for use within the MRI Facility. Please contact LucilleMurby for more information.
Booking scanner slots
(normally one month or more before scanning)
Once you have attained MRI user certification, had a Panel Induction, received LREC approval (or been added as a user to someone else's approval), had your project reviewed by the Cambridge community, logged your project with LucilleMurby and received approval for scanning from the IMC then you are ready to book slots on the scanner. The CBU scanning schedule is available online at http://imaging.mrc-cbu.cam.ac.uk/scanbooker/ via the web browser Mozilla Firefox. Take a look at the schedule then arrange to meet with Lucille Murby to discuss the allocation of available slots. Please remember that just because the scanning time appears to be available, it does not necessarily mean you can have it. Lucille allocates slots according to the current demands on scanner time from the Unit as a whole.
Computer issues for running imaging studies
Subscribing to mailing lists
(as early as possible). In order to get information about talks, current computer and scanner problems, changes in CBU Scanner setup, etc. you need to subscribe to the following mailing lists: ImagersCbuList (for CBU staff only), ImagersTechList (any technical imaging information relating to SPM, scanner issues, methods talks, etc.), and ImagersList (general Cambridge imaging mailing list). Contact Sian Miller for more details and to subscribe.
Thoroughly test your experimental program
Testing program at CBU
(at least a week before scanning). There is a replica of the CBU MRI stimulus delivery computer in the public computer area of the main Unit, labeled CBU Mimic. This is used exclusively to test programs for compatibility and to make sure they will not crash during an fMRI study. You should make full use of this before starting your study. CBU users can book the CBU Mimic on the Resource Scheduler. If you are outside the CBU, please contact CBU reception to ask them to book the machine for you.
Please note that there is currently no guarantee that the CBU mimic will do any kind of a job at replicating the setup in the WBIC - so if you are planning a study at the WBIC, please use the WBIC mimic machine instead - based at Addenbrookes.
For details about how to simulate scanner pulses, or other issues relating to the CBU Mimic, contact the technical support staff. Note, that should you require any programs to be installed that are not already available, you should ask Gary Chandler to install this for you, rather than doing it yourself.
At this point you should mention any non-standard equipment or paradigms to radiographers, in case these need to be approved for the scanner, or the paradigms require the presence of a physicist to run them (this is not necessary for standard protocols). Contact the radiographers with these details.
Piloting your program on the CBU Scanner
(at least a few days before scanning). It is also highly recommended that you book some time at the CBU Scanner to install and test your program onsite. You should contact LucilleMurby about booking a 15 minute pilot slot, and to request whether you need the radiographers to generate any scanner pulses. Note that it is possible to generate simulated pulses, via the panel in the computer cupboard in the corner. There are three stimulus PCs permanently available in the scanner room. You should ask the radiographers about how to switch between PCs if this is unclear. Be sure to fully test your program, including its interaction with scanner pulses and with the button box if required, as well as the correct presentation of stimuli. For more information on stimulus presentation in the CBU scanner, visit CbuStimulusDelivery. Remember to install your program and store your data on the D drive, as the C drive is wiped and refreshed every month with a new image. This is also a good time to tell the radiographers who you are, what slots you will be scanning with whom, and under what CBU Scanner protocol number. In addition, you should mention any non-standard equipment or paradigms, in case these need to be approved for the scanner, or the paradigms require the presence of a physicist to run them (this is not necessary for standard protocols). If any problems are unable to be resolved during the pilot session/s then the main scanning slots (if booked at this point) need to be reviewed and possibly re-allocated.