OnTheDayOfScanning - CBU MRI facility Wiki
location: OnTheDayOfScanning

Procedure on the day of scanning

List of what to bring with you on the day

  • Contact information for participants and backup participants.
  • Details of your ethics protocol number.
  • Any extra equipment required (for instance, DAT recorder, non-standard button box).
  • A copy of your experimental program on USB Key, CD or floppy disk.
  • Disk to retrieve behavioural data from (floppy, or USB Key or Zip if larger).
  • CBU studies only: CBU yellow participant receipt forms (for booked participants and a few blank spares).

  • Participant Money.
  • Notebook to log experiment.
  • This guide.

Checklist for time at the CBU Scanner

If scanning for the first time, arrive approximately 45 minutes before the slot begins, to wait for the participant and setup and double check your experiment. If you are inexperienced, it is advisable to bring a 'buddy' with you to help out on the day, particularly if you are scanning more than one person, or have not scanned before. For each scanning slot, the following times should be allowed in any calculation of time needed per participant: i) Paperwork (10 minutes if participant has been scanned before, 20 minutes otherwise); ii) placing participant in scanner and calibration (5 mins); iii) structural and fieldmap scans (7 mins); iv) participant leaving scanner and payment (5 mins). In addition to this, there will be the EPI time for the actual experiment, the length of which you should know in advance, from the details of your experiment.

Check experimental program is running (20 mins before slot begins)

Reboot PC

This is HIGHLY recommended to prevent non-specific problems and crashes.

Boot up and test program

Make sure the program is running as it should.

Test equipment

Test that visual presentation is appropriately appearing on the screen in the scanner room. Make sure the button box responses will be recorded by your program. There is a program called "Scanner Input Test," which gives a visual display of the button presses and scanner pulses (pulses can be simulated by a button on the wall). This is an excellent way of verifying correct input. If audio stimuli are used, first verify that the Windows settings are appropriately set: i) double click on the yellow loudspeaker, in system tray at the bottom right of the screen; ii) check to ensure that the master and wave/line levels are set to maximum; iii) ensure that the balance is set centrally. Make sure that the headphones are working properly. If there are two experimenters present, one should listen on the headphones while the other plays tones into each ear. Make sure that the tones are clearly audible and that the input is balanced between ears. If only one experimenter is present, test this procedure on the participant before scanning starts. If there are any problems, contact Gary Chandler (ext. 413) or Rhodri Cusack (ext. 850).

On participant arrival (30 mins before slot begins)


Each participant is given a unique scan number for each session that they take part in. Each session file needs to contain a signed Consent Form and a signed Volunteer Screening form. The researcher should make sure that the volunteer has read the Volunteer Information Sheet prior to the scan and retain this for their records. The Consent Form and Volunteer Information sheet need to be the same forms that were submitted to and approved by the LREC. The radiographer will already have your CBU Ethics protocol number and a label with this number will be attached to the back of the Screening form by the radiographer.

Entering the scanning suite

The researcher should ask the volunteer to complete all of the forms described above. Please then introduce the volunteer to the radiographer who is on duty. Once the volunteer has been screened and cleared for scanning by the radiographer they will be asked to place all their items into one of the lockers beside the staff kitchen. Bulky items not fitting into the lockers (such as sports bags) may be taken into the Control Room by the researcher at the radiographer's discretion. The volunteer will be checked for metal by the radiographer who will escort them into the Controlled Zone/Magnet Room.

Give participant practice

If the task requires a practice session, then this should be done in the Scanner Office next to the Control room (the Control room is out of bounds to participants). The office has a PC identical to the stimulus PCs, along with a button box, except that (at the present time) no scanner pulses can be simulated.

Radiographer places participant in scanner

The radiographer will make sure the participant is placed in the scanner, with the headphones, earplugs (if your experiment is audio-critical, it is not essential that the earplugs are used), microphone and button-box (if required), and will make sure the participant can see the screen clearly before continuing. The pulse oximeter is attached to an available finger and the call button is placed on either a free hand or the chest. It is emphasized at this point that if the volunteer becomes uncomfortable they are able to press the call button at any time during the study to attract the radiographer's attention. On re-entering the Control Room, the radiographer will ask the volunteer to press the call button to make sure it works. It is vital for the researcher to double-check (via the intercom) that the participant has the button box appropriately placed, knows which button means which response and can see the screen fully and clearly before starting.

During scanning

Give radiographer details of the study

Based on the details of your experiment, you should already know what fMRI protocol you are running (for instance, the 'standard' CBU TR 2 secs), if there are any special characteristics of the fMRI protocol, how many runs you plan to give the participant (typically 2-4), and how many scans you will roughly need for each run. For instance, you may request a TR of 2 seconds, with three runs, and each run having 850 scans in it. Remember to factor in the "dummy scans" for each run, to allow the signal to stabilise sufficiently.

Regularly tell the participant what is going on

In addition to the radiographer, who will usually warn the participant when loud noises will occur before calibration scans and other 'standard' events, you should inform the participant via the microphone system about experimental scans which are about to start. Also, ask them regularly if they are still comfortable, whether everything is alright, and if there are any stimulus presentation problems. If there are any problems with the scanner which may cause delays or unusual events (e.g. noises, people entering the scanning room), keep the participant regularly informed. It can be a frustrating, boring, and sometimes rather frightening experience for the participant if there are lengthy delays due to malfunctions and this can be alleviated considerably by keeping them informed.

Remind participants before each scanning run

Tell the participants again, via the microphone system, that they should keep their heads as still as possible (even if the radiographer has already done this), and remind them of the details of the task they are about to carry out. Make sure again that they can see the screen fully and clearly (and can hear clearly if the experiment is auditory). Ask them if there is anything they don't understand or have forgotten, to make absolutely sure they will do the task appropriately during the scan.

Keep careful note of experimental details

Not only should you write down all details of the study (e.g. condition order, etc.), but also any problems that occurred, such as the scanner crashing, etc.

After the participant has been scanned

Get feedback on experiment from participant

Give subject scan photo

The radiographer should at this point give the participant a photo of their structural scan.

Pay participant

MRI scanning log

Please make sure you keep a note during the scanning session of how the various scans were named (EPI Run 1, Run 2, structural etc.) You will need this information in order to identify and analyse your data.

Backup data

Any behavioural or scanning data generated should now be backed up either on a floppy, CD, USB or zip disk (don't expect the Imaging Facility to have any spare disks available). The computers on which these data have been acquired are deleted at regular intervals and you may lose data if you do not take it away on the day of scanning. In addition, these PCs are heavily used and can develop hardware faults, which may mean the loss of your data if it is left there.

After scanning

Retrieving the data.

For CBU studies

At the end of each day, the radiographers transfer the day's data to the /mridata/cbu. It is kept here permanently, so there is no need to copy the data to your own directory. If you feel the need to do this, you should delete the data at some later point to avoid unnecessary duplication. If your data has not arrived at this location within a couple of days, you should email the radiographers to get this issue resolved.

For non-CBU studies

You will have to make arrangements to copy the data to your own system.

Scanning Feedback.

If there are any problems during your study and/or any queries regarding procedures it is important that this information is fed back directly to the Facility Administrator, Lucille Murby. This is particularly important with regard to scheduling (for example, if problems have occurred which mean that you will require more slots. A Scanning Feedback form is available within the Imaging Facility or from Lucille Murby for this purpose. The IMC will regularly review these forms in order to try to address any difficulties and modify our procedures as necessary.

None: OnTheDayOfScanning (last edited 2013-03-08 10:21:22 by localhost)