RunningStudiesComputing - CBU MRI facility Wiki

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location: RunningStudiesComputing

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.