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= Comprehensive CBU Guide To Scanning At The WBIC =
The following guide is meant to cover all practical steps required to carry out an imaging study at the WBIC. However, it does not cover information regarding neuroimaging design, programming of experiments, or analysis of results. For details of these aspects of scanning, please visit the [wiki:WhoToContact points of contact] page, to find out who to ask, or the appropriate pages on the Imaging Website.


== A) Preparations for your study ==
[[Anchor(1)]] '''1. Access to WBIC (anytime before scanning starts)'''

'''1.1. fMRI testing -'''

 '''1.1.1. [http://www.wbic.cam.ac.uk/courses/index.html?fl=116&flc1=2 Safety Course] '''. Before fMRI testing for the first time in the WBIC each experimenter MUST attend a WBIC course on magnetic safety. These are organised about twice a year (details from the radiographers: radiog@wbic.cam.ac.uk , or Jackie Jenkins (WBIC administrator): jj111@wbic.cam.ac.uk ). There are also very clear rules within the WBIC about who may or may not access what parts of the scanner environment/computer system etc. Please do not be afraid to ask one of the radiographers, to tell you where you may or may not go.

 '''1.1.2. WBIC Induction.''' Before fMRI testing for the first time, you should arrange an induction to the facilities with one of the radiographers (email radiog@wbic.cam.ac.uk for more details). In addition, on first arrival at the WBIC, and periodically, you will need to fill in the WBIC MRI screening form, to ensure you have no metallic substances in your body. This should be carried out at the WBIC immediately prior to entering the MRI scanning suite for the first time, and will be available from the radiographers.

'''1.2. PET testing -'''

 '''1.2.1 POPUMET'''. You need to attend the POPUMET course, run every few months, in order to be allowed into the PET scanning suite for scanning (contact Jackie Jenkins (WBIC administrator): jj111@wbic.cam.ac.uk for details). Note that PET subjects will also normally require a structural MRI to be taken. It would therefore be highly desirable to carry out the MRI safety course even if you don't plan to run any fMRI studies (see 1.1 above).

[[Anchor(2)]] '''2. Debate and approval by Cambridge research community.'''
=== 2. Debate and approval by Cambridge research community. ===
'''2.1 CBU Research group meeting (at least three months before scanning).''' Present your proposal at your own research group meeting for debate about the scientific merits of the study and design. See the organiser of your research group to arrange this.

'''2.2 Cambridge imagers methods meeting (at least three months before scanning).''' Following revision from 2.1 above, present your proposal for scientific and methodological debate at the imagers meeting, which meets on Monday afternoons at 12:30, normally at the CBU lecture theatre. Contact Andrew Lawrence ( andrew.lawrence@mrc-cbu.cam.ac.uk ) or Rik Henson ( rik.henson@mrc-cbu.cam.ac.uk ) for details and request for a talk slot. To see further information about the imagers meeting, please visit the ImagersInterestGroup page.

'''2.3 Fill in [wiki:RequestForScanningSlots request for scan slots form] after imagers methods meeting, and submit to ImagingManagementCommittee (at least two months before scanning). This should contain a detailed summary of the research background, proposed experiment, its hypotheses, and any problems or issues raised in the imagers methods meeting. In the first instance, you can request at most 16 slots. If more slots are required later then you will need to resubmit the request form above, with justification. You will need explicit approval from the management committee, who normally meet twice a month, before being allowed to scan at the WBIC. If you feel there has been a long delay after submission before hearing about the result of your feedback form, then contact Adrian Owen for more details ( adrian.owen@mrc-cbu.cam.ac.uk ).

=== 3. Local Research Ethics Committee (LREC) approval (absolute minimum 2 months before scanning). ===
In order to be given slots at the WBIC, you need official ethics approval from the above body. They meet every six weeks. For more details about what is involved, contact Debbie Davies ( admin-imaging@mrc-cbu.cam.ac.uk) .

=== 4. Obtaining insurance approval and a WBIC protocol number (at least 2 months before scanning). ===
Once LREC approval has come through, you need to send the project, along with the approval letter (in duplicate) to Jackie Jenkins at the WBIC ( jj111@wbic.cam.ac.uk) , and request a certain number of subjects to be insured for the study. As it is a requisition of unit funds, any insurance request should be cc'ed to Anthea Hills (email: anthea.hills@mrc-cbu.cam.ac.uk ). This number should be sufficient to cover your likely numbers for the study (for instance, 12 subjects for a normal group study). Once this is done, she will give you a WBIC protocol number for the LREC project.

=== 5. Booking in slots (normally two months or more before scanning). ===
Once IMC (point 2.3) and LREC (point 3) approval has been given and you have obtained insurance (point 4), you need to contact Debbie Davies in order to be given fMRI slots (email admin-imaging@mrc-cbu.cam.ac.uk) . Before she will give you slots, you need to provide her with copies of i) your LREC application; ii) the letter of approval for your study from LREC; iii) the request for slots form you sent to the IMC (see [#2 2.3] ); and iv) the WBIC protocol number.

=== 6. Computer issues relating to imaging. ===
'''6.1 Subscribing to mailing lists (as early as possible).''' In order to get information about talks, current computer and scanner problems, changes in WBIC setup, etc. you need to subscribe to the following mailing lists: ImagersCbuList (CBU only imaging related information), ImagersTechList (any technical imaging information relating to SPM, scanner issues, methods talks, etc.), and ImagersList (general Cambridge imaging mailing list).

'''6.2 Obtain WBIC ID badge (at least two weeks before scanning).''' Contact Brian Cox (email: brian.cox@mrc-cbu.cam.ac.uk ) to request that he make you a WBIC ID badge. For security reasons, this is required for you to scan at the WBIC and should be worn at all times there.

'''6.3 Request imaging status and disk space from the Imaging Quota Manager, if scanning for the first time (at least a week before scanning).''' Your account needs to be labelled as having imaging status, so that you can access and use the imaging directories. You will also need some imaging space, in order to store and analyse your data. You are likely to need 40 GB per study at least. For approval and a quota, contact imagers-quota-manager@mrc-cbu.cam.ac.uk .

'''6.4. Thoroughly test your experimental program.'''

 '''6.4.1. Testing program at CBU (at least a week before scanning).''' There is a replica of the WBIC fMRI machine in the public computer area of the unit, labelled WBIC Mimic, that is only used to test programs to make sure they will not crash in an fMRI study at the WBIC. You should make full use of this before going to the WBIC. For details about how to simulate scanner pulses, or other issues relating to the WBIC mimic, contact the CBU technical staff or Daniel Bor ( daniel.bor@mrc-cbu.cam.ac.uk) .

 '''6.4.2 Testing program at WBIC (at least a few days before scanning).''' It is also vital that you book some time at the WBIC to install and test your program before you start your experiment. You should contact the radiographers about the best time to carry this out, and to request whether you need them to generate any scanner pulses (note, it is possible to simulate pulses without the scanner generating EPI scans using a pulse button attached to the patch panel - if you use Rhodri's timing routines, make sure you press the button ''less'' frequently than the TR specified in your program or it will crash). Be sure to fully test your program, including its interaction with scanner pulses via the patch panel (contact Gary Chandler for more details on the patch panel: gary.chandler@mrc-cbu.cam.ac.uk) , and with the button box if required. This is also a good time to introduce yourself to the staff (particularly the radiographers) at the WBIC prior to scanning, and could be combined with the WBIC induction and your own MRI screening if you've never visited the WBIC before (see point [#1 1.1.2] ).

=== 7. Recruiting subjects. ===
Given the expense of scanning, it is therefore vital that appropriate subjects turn up to scanning, and all slots are filled. Therefore pay particular attention to the following:

'''7.1. Obtain potential subject list (a month before scanning).''' Normally this will involve going to Jackie Harper (contact jackie.harper@mrc-cbu.cam.ac.uk ) with the details of your study (including LREC approval number), and requesting a list of potential subjects that are appropriate for your study (e.g. age limits, etc.).

'''7.2. Conduct a phone interview with each subject (at least a week before scanning).''' Each interview should include the following:

 '''7.2.1. Introduce yourself and the study.''' Make sure the subject is fully aware who you are, what the study involves and is allowed to ask any questions, in case they feel they would not like to take part.

 '''7.2.2. Go through the [wiki:MriSubjectScreening subject screening questionnaire].''' Make sure you understand the relevance of each question (explained in the notes at the end), and pay particular attention to metal in body questions, and whether or not they have had a significant head injury.

 '''7.2.3. Experiment-specific questions.''' In addition, make sure to ask any experiment-specific questions. For instance, if it is a visual experiment, can the subject see satisfactorily without glasses (glasses include metal)? If it is a language experiment, is the subject a native English speaker?

 '''7.2.4. Is the subject booked in for another study?''' The CBU guidelines are that a subject should not be scanned twice over the same 30 day period, so make sure that the subject isn't also booked into another fMRI study at a date close to yours.

 '''7.2.5. Book the subject in.''' It is desirable to book the subject in to arrive around 15-30 minutes before the slot is due to start (30 if they haven't been scanned before, 15 minutes otherwise), to go through the paperwork, task instructions, etc.

 '''7.2.6. Inform subject what to bring.''' If it is their first time, they should be told to bring a music CD (for the structural scans, which last around 30 minutes), so that they are not bored, and the name and address of their GP for the forms to fill in at the WBIC (see [#10 10.2.1] ).

'''7.3. Sending written/email confirmation to each subject.'''

 '''7.3.1. Send/email subject LREC volunteer information sheet (at least a week before scanning).''' It is an official requirement that they read this before participating, and would save you time at the WBIC if they read it beforehand.

 '''7.3.2. Send/email WBIC map (at least a week before scanning).''' This should include full contact details for you and directions to the WBIC. See [http://imaging.mrc-cbu.cam.ac.uk/text/wbic_recruit_map.doc here] for example.

'''7.4. Remind subject about appointment (1-2 days before scanning).''' Either via phone or email, remind the subject a day or so before that they are due to be scanned, and to contact you if there are any problems. Make certain that the subject knows how to contact the WBIC should they need to on the day. This is to minimise the not infrequent situation of subjects simply not turning up to slots without informing you, which the CBU then still have to pay for, despite not collecting any data. In addition, attempt to secure a usable mobile phone number for the subject, so that you can contact them if you need to cancel at the last minute or they have unexpectedly not turned up.

'''7.5 Obtain MRI subject receipt forms from Jackie Harper (at least a day before).''' Make sure you are given the yellow MRI forms, with all the subject's details. It may be useful to take a few spare blank yellow forms (obtained from beginning of South Wing) in case you use a backup or unexpected subject at the last minute after a booked subject has not turned up.

'''7.6 Also recruit backup subjects (one week before scanning).''' Just in case after all the above the subject still doesn't turn up, it is extremely useful to have a backup either at the WBIC in case there are scanning problems, or only 10 minutes away and readily available, who can fill in at the last minute. This way, you still get the dataset, and the CBU hasn't wasted a large amount of money. You pay backup subjects 10 pounds a day if they are not used, or the usual rate if they are.

'''7.7 Request subject money (by 12 noon on the Wednesday before the week you scan).''' Contact subject-money@mrc-cbu.cam.ac.uk with details of how much you will require, making sure you won't be left short of money. Collect the money on the Monday - you will be given an appointment time.

=== 8. Informing WBIC of scanning slots taken and subjects booked (1 week before). ===
You need to tell the radiographers who you are, and what slots you will be scanning with whom, and under what WBIC 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). Contact [mailto:radiogr@wbic.cam.ac.uk radiog@wbic.cam.ac.uk] with these details. The radiographers will also pass this information to WBIC reception so that they know who is expected on the day and can obtain WBIC subject folders in advance for you (if the person has been scanned before).

== B) Carrying out your study ==
=== 9. List of what to bring with you on the day: ===
 * Contact info for subjects and backup subjects.
 * Details of your WBIC protocol number.
 * Any extra equipment required (for instance, DAT recorder, non-standard button box).
 * A copy of your experimental program on disk.
 * Disk to retrieve behavioural data from (floppy or Zip if large).
 * Your WBIC ID badge.
 * CBU yellow subject receipt forms (for booked subjects and a few blank spares).
 * Subject Money.
 * Notebook to log experiment.
 * This guide.
=== 10. Checklist for time at the WBIC. ===
Arrive approximately 30 minutes before the slot begins, to wait for subject and setup and double check your experiment. It is advisable to bring a friend with to help out on the day, particularly if you are scanning more than one person. For each scanning slot, the following times should be allotted in any calculation of time needed per subject: i) Paperwork (10 minutes if subject has been scanned before, 20 minutes otherwise); ii) placing subject in scanner and calibration (15 mins); iii) structural scans if first time scanned (30 mins), otherwise just phase maps (5 mins); iv) subject leaving scanner and payment (5 mins). Note that if the subject has not had any structural scans in the last 2 years, then they will have to have an additional short (10 minutes) structural scan (a PDT2 scan). 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.

'''10.1 Check experimental program is running (30 mins before slot begins):'''

 '''10.1.1. Reboot PC.''' Given that the operating system is MS Windows 98, this is essential to prevent non-specific problems and crashes.

 '''10.1.2. Boot up and test program.''' Make sure the program is running as it should.

 '''10.1.3. Test extraneous 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 subject before scanning starts. If there are any problems, contact Gary Chandler (355 294, ext. 413) or Maarten Van Casteran (355 294, ext. 261).

'''10.2 On subject arrival (15-30 mins before slot begins):'''

 '''10.2.1. Paperwork.''' When the subject first comes to the WBIC for the first time, they will be assigned a WBIC folder and a unique WBIC subject number (e.g. W030321), which will be used each subsequent time they are scanned. Either you or the radiographer should get them to fill in the relevant papers before scanning. These are '''''i) Subject details sheet''''' (including their name, address, and name and address of their GP), which can be found on the reverse of the MRI scan log form. This only needs to be filled in on the first visit; '''''ii) WBIC fMRI screening form''''' (the same as in 1.1.2), to ensure they have no metal in their body. This needs to be filled in on every visit, and will need to be signed by the subject and radiographer; '''''iii) WBIC Informed consent sheet''''', so that they give permission to be scanned for this particular LREC study. If this is a generic sheet, rather than a specific one (you should preferably bring along the specific one that you sent to LREC), then you can get the LREC details from the red folder which will carry your WBIC protocol number on its spine. The radiographers can tell you where this is, if they haven't already got it out for scanning. This sheet will need to be signed by the subject, a witness (the receptionist or a radiographer are normally good for this), and you as the experimenter. Only when all these signatures have been collected will the subject be ready to enter the scanning suite.

 '''10.2.2. Entering the scanning suite.''' The subject must put in a locker next to the scanning suite all his/her metallic objects (and anything loose that they brought with them, such as bags, a coat, etc.). Make sure they give you the music CD at this point, if they are due for a structural scan. You must wait for the radiographer to guide the subject into the suite (the door with the number code lock) rather than doing this yourself.

 '''10.2.3. Give subject practice.''' If the task requires a practice session, then this can be done outside the scanner within the scanner suite on the PC that controls the stimuli. Alternatively, a laptop outside the suite could be used for this purpose. A laptop is preferable, since there may be delays with the previous subject that prevent the subject entering the suite and mean s/he is simply waiting doing nothing outside in the lobby anyway.

 '''10.2.4. Radiographer place subject in scanner.''' The radiographers will make sure the subject is placed in the scanner, with the headphones, earplugs (if your experiment is audio-critical, it is not necessary that the earplugs are used), microphone and button-box (if required), and will make sure the subject can see the screen clearly before continuing. However, it is vital to double-check that the subject has the button box appropriately placed, knows which button means which response, can see the screen fully and clearly and that the microphone (if necessary for verbal responses during the experiment) is placed in the optimal position.

'''10.3. During scanning:'''

 '''10.3.1. 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 TR of 1.6 or 1.1 secs), if there are any special characteristics of the fMRI protocol, how many runs you plan to give the subject (typically 2-4), and how many scans you will roughly need for each run. For instance, you may request a TR of 1.1 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. In addition, it is usual to collect phasemaps A and C, after the EPI's, which should take an additional 5 minutes. These phasemaps normally significantly increase the quality of the preprocessing.

 '''10.3.2. Regularly tell the subject what is going on.''' In addition to the radiographer, who will regularly warn the subject when loud noises will occur relating to calibration scans, you should inform the subject via the microphone system about experimental scans about to come up, and to ask them 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, keep the subject regularly informed. Otherwise, it can be a very frustrating, boring, and sometimes rather frightening experience for the subject if there are lengthy delays due to malfunctions.

 '''10.3.3. Remind subjects before each scanning run.''' Tell the subjects 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.

 '''10.3.4. 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.

 '''10.3.5. Play the music CD for the subject.''' Once the EPI sequence has finished, inform the subject and (if they are new) play them the music CD they brought with them during the acquisition of the phasemaps and structurals (SPGR and PDT2).

'''10.4. After the subject has been scanned:'''

 '''10.4.1. Retrieve CD and return to subject.'''

 '''10.4.2. Get feedback on experiment from subject.'''

 '''10.4.3. Pay subject.''' Payment is normally 10 pounds per hour, plus travel (2 pounds from within Cambridge, 2.50 pounds from outside Cambridge).

 '''10.4.4. MRI scanning log.''' The radiographer should give you a photocopy of the MRI scanning log for that subject. You will need this sheet in order to analyse the data.

 '''10.4.5. Backup data.''' Any behavioural or scanning data generated should now be backed up either on a floppy or zip disk (don't expect the WBIC to have any disks, so bring these with yourself). These files may be deleted at any time and the PC is so heavily used that it is more likely than normal to develop a hardware fault, so it is vital to do this for each subject ideally, but definitely on each scanning day.

== C) After scanning ==
=== 11. Reporting on the scanning to CBU (as soon as possible after scanning). ===
You need to inform the CBU imaging administrator of everything that happened on the day of scanning each time you scan (contact Debbie Davies, admin-imaging@mrc-cbu.cam.ac.uk ). She needs to know: '''''i) What WBIC protocol you are scanning under'''''; '''''ii) who you scanned''''' (give the WBIC numbers); '''''iii) when you scanned them;''''' '''''iv) any problems that might have occurred''''', for instance with the fMRI machine, or the stimulus delivery system.

=== 12. Retrieving the data. ===
Within a week of scanning, an email should be sent to the mailing list "imagerscbu" informing you that your data is now in the imagers directory (/cbu/imagers/wbic_data/). This data will only remain active for another week, so you should apply the [wiki:AnalysisDefaults first preprocessing steps] to the data within this time. Otherwise, it may take a while for you to retrieve your data from the archives. If the data hasn't arrived within a week, you should contact the computing department about this ( imagers-data@mrc-cbu.cam.ac.uk ).

=== 13. Sending brain picture to subject. ===
Once you have received the data, and it was the first time the subject has been scanned, then you need to generate a picture of their structural image (usually mid-sagittal slice. MRICro is a useful tool for making this) and send this to the subject (Jackie Harper will send you a label with their address on it).

Last revision 24/2/5 - Daniel Bor, Ingrid Johnsrude, Rhodri Cusack.
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