Scanning procedure (MR11)¶

This page walks through a scan session at MR11 (Siemens Cima.X 3T, UZ Leuven Gasthuisberg), from the participant's arrival to getting your data. For the hardware, see the MR11 equipment reference. For the 7T, see Flanders 7T.

Before your first scan

Make sure you have completed all prerequisites: MRI safety course, ethical approval, card access, an XNAT account and project, and a booked slot. See First steps.

For detailed information, go to the radiology wiki

The official step-by-step guide is on the radiology wiki: Scanners › MR11 - Cima.X 3T › Main User Guide, with Troubleshooting below it, and the Standard Procedures poster under Safety, Rules & Procedures (the poster also hangs in the console room). This page follows them and adds what we learned in the lab.

Open the radiology wiki (MR11)

You need an account: ask Rodrigo Trevisan Massera (rodrigo.trevisanmassera@kuleuven.be).

Emergency procedures

Keep this information in mind at all times when working in the MR suite.

Stopping a scan¶

Press stop scanning on the console or the red button on the intercom.
Take the participant out of the scanner.
Call Ron Peeters (41103), another MR Safety Officer, or the MR technicians (40526).

Equipment malfunction or system failure¶

If part of the system fails and puts the participant at risk, first take the participant out of the scanner, then get help from the MR technicians or the radiologist.
If equipment causes an accident, immediately notify the MR technicians (or radiologist) and the MRI Safety Officer.

Emergency magnet shutdown (quench)¶

The big red button with the magnet symbol shuts the magnet down. Use it only if:

a person is in a life-threatening situation caused directly by the magnetic field, or
emergency services need to enter the magnet room with ferromagnetic equipment.

Emergency electrical shutdown¶

Use the emergency power switch in case of fire, smoke, flooding, sparks or another electrical malfunction.

Phone numbers¶

	Internal number
Fire	2580
Resuscitation	1000
MR technician	40526 (backups 47770, 47771)
MR11 console room	43755
Ron Peeters, MR Safety Officer	41103
Stefan Sunaert, head of KUL Radiology	47754

When you call, give the location: MR11, Beeldvorming 2, Gele straat, Poort 2, niveau 0.

Fire

Never bring a standard (ferromagnetic) fire extinguisher into the magnet room. Use only the MR-safe extinguishers.

Seeing an abnormality on brain images¶

Do not disclose concerns to the participant

Avoid causing unnecessary distress. False alarms are common.

All structural scans are checked for incidental findings by the radiology team. If you see something that worries you, e-mail Prof. Stefan Sunaert (stefan.sunaert@uzleuven.be) with the participant's first name, surname and patient ID (from the console), and call 47754 or the internal number 44191 if it is urgent.

General information¶

Important notes

After 6 pm and in the weekend, two certified MR users (MRRUs) must be present. At other times this is strongly advised too, so that one person can stay with the participant while the other calls for help.
Do not enter the console room before your slot starts: the previous user may still be scanning. Use preparation rooms 1 and 2 to instruct and prepare your participant.
Before 7 am the system may still be off. Start it with the blue system on button below the quench button (the key below it turned to unlock); starting takes 10 to 15 minutes, inside your slot.
There is mobile phone coverage and Wi-Fi in the console room.
Contact details and logins for the console-room PCs are in this file in the Hoplab Teams folder.

Required forms¶

Have these ready before you go to the hospital:

Informed consent form: the approved ICF of your study, signed by the participant and by you before the participant enters the controlled area. Keep it safe after the session.
MRI Safety Checklist (English version; see also the radiology Google Drive folder): filled in by the participant, and by everyone who accompanies them into the controlled area. You can send it in advance to save time. The signed checklist goes into the box in the console room.

Before the scan¶

Participant arrival and registration¶

Recruitment and compensation

For details on recruiting participants and compensation rates, see the participant recruitment and reimbursement guide.

Participants register at the main entrance of the hospital:

Belgian eID card: at the self-service kiosks (or with the Mynexuzhealth app).
No Belgian eID card: at the registration desk with their foreign ID (open 7:00 to 18:30).
Children under 12: with a Kids-ID or ISI+ card.
After 17:30: participants can go directly to the MR11 waiting room.
At the weekend: participants do not register at the reception and come straight to the waiting room.

After registering, participants go to the Beeldvorming 2 waiting room (Gele straat, Poort 2, niveau 0). Meet them there: they fill in the MRI Safety Checklist and the consent form, and then you go together to the scanner area. Ask participants to arrive at least 30 minutes before the scan slot.

Text for your participant invitation

When you arrive at UZ Leuven Gasthuisberg, register at the main entrance at the self-service kiosks with your Belgian eID, or with the Mynexuzhealth app (without a Belgian eID, go to the registration desk). Then go to the Beeldvorming 2 waiting room: Gele straat, Poort 2, niveau 0. The researcher will meet you there. Please arrive 30 minutes before your appointment.

Give participants the MR11 location

Participants sometimes go to the wrong waiting area, where there is no phone connection, so you have to go and look for them. Give the exact location in your invitation: Beeldvorming 2, Gele straat, Poort 2, niveau 0, MR11.

Let the participant sign the consent form and the MRI Safety Checklist in the waiting room or in preparation room 1 or 2, before they enter the controlled area.
Show both forms to an MRI technician or radiologist for approval. If any item on the checklist is answered yes, call the MR technician (40526) before going further.
Store your own keys, phone, watch, jewellery, hairpins etc. in preparation room 1 or 2.

Controlled area

Access to the controlled area requires an activated KU Leuven card. Nobody enters it before their MRI Safety Checklist has been checked, including parents and other accompanying persons.

Instruct the participant¶

In the preparation room:

Explain the task, and let the participant practise a few trials if needed.
Ask them to go to the toilet.
Screen them from head to toe for metal (watches, hair clips, bank cards, belts, phones, festival bracelets; if they keep a festival bracelet, cover the metal part with tape).
Belongings: participants can leave their belongings in the changing room attached to the magnet room, or in one of the preparation rooms (onderzoekslokalen) next to the console room.
Glasses: participants cannot wear their own glasses in the scanner. MRI-compatible glasses are available at the hospital; ask the participant their prescription in advance. Contact lenses are fine.
If the session is long, offer water or a snack before they go in.
Explain what will happen: they may feel nerve or muscle twitches, must not cross hands or feet, must not touch the scanner, the scanner is loud and changes sound, you can talk through the intercom, and they can press the communication (panic) button at any time. They can stop the scan at any moment without giving a reason.

Scanning children

Children need extra preparation: see Scanning children for the planning, the preparation game, the team roles and the checks.

Prepare the console room¶

Stimulus PC

log in, open your experiment and check that it loads. See Stimulus PC.

In-room screen

switch it on and check that the input is the stimulus PC and L/R flip is on. See In-room screen.

Trigger box

press the knob and check that it is in mode 002 (HID NAR BYGRT). Press each button you will use and check that your script receives the right keys. See Trigger box and buttons.

Audio

if you use sound, switch on the audio system and check the volume. See Audio system.

Register the participant at the console¶

Do this before the participant goes into the magnet room.

Select the participant from the RIS list (scheduler). Name and date of birth are filled in automatically; check them. If the participant name is not visible, refresh the list.
Fill in height and weight from the MRI Safety Checklist, and implants if applicable.
Click Program selection › others and select your protocol.
Check that the Study description contains your XNAT project ID: your S-number followed by a letter (e.g., S12345a). This sends the images to your XNAT project.
Fill in the Study comment as Subject:<subject ID> Session:<session ID>, for example:
```
Subject:sub-01 Session:sub-01_ses-01
```
- Use your pseudonymised participant ID, never the participant's name.
- Only letters, digits, _ and - are allowed. No space inside an ID; one space between the two fields.
- The session ID must be unique within the whole project, not just for that subject. Hence sub-01_ses-01 rather than ses-01. Otherwise the data of an earlier session can be overwritten.
- Get it exactly right. With a wrong study comment the data do not land in your project, and Ron has to move them on the server by hand before you can download them.
Select the patient orientation.
Check all examination information again. Errors here send your data to the wrong place in XNAT or break the de-identification.

Pilots, phantoms, or a participant who is not in the RIS list

For pilot runs, follow the same booking procedure as for regular participants (i.e., book through radiology). In addition, notify Ron by email that this is a pilot run, to avoid being charged for the run. At the console, the Study description (XNAT project ID) and Study comment still matter, so the data reach your XNAT project. Label your data as pilot data, so they are not confused with your experiment data on the server, for example:

Subject:PIL001 Session:PIL001_MR1

For a phantom run (for example to test the trigger), click New examination and fill in the details by hand (pseudo data for a phantom). For the scanning, use one of the phantom bottles in the fMRI lab. Before you start, switch off the data transfer: right-click the run, choose Edit properties and disable PACS.

If a booked participant is missing from the list, call the MR2 desk (internal 45351) or go there: the receptionist then takes the participant's order out by hand and loads it again.

Getting the participant ready¶

On the scanner table¶

Earplugs

give the participant earplugs and show them how to roll them small so they expand in the ear. Participants who refuse hearing protection cannot be scanned.

Positioning

let them lie down with the head in the coil (watch that they do not hit their head). Put the knee cushion under their legs.

Communication button

give them the panic button, explain it, and test it at the start of the session.

Response buttons

hand them the button pads and repeat which buttons to use.

Headphones

with the 64-channel coil, use the small ear shells of the dedicated audio system. Put cushions or the ear shells around the ears; they also limit head motion. Do not press on the head.

Coil

put the top of the coil on. The participant's eyebrows should be at the calibration line on the coil, so the head ends up at the centre of the magnet. Clip the coil with the handle at the back. Check that the participant can see the screen in the mirror. This can feel claustrophobic: check that they are OK.

Moving the table in¶

Turn the round knob to raise the table. Ask the participant to close their eyes.
Use the same knob to align the light marker with the calibration line on the coil. Hold the knob to save the position: the table moves to the magnet centre by itself. Instead of the light marker, you can also tap head (or brain) on the touch screen at the scanner and hold the big wheel until the table has moved the participant into the bore.
If the table goes too far into the scanner, the calibration did not work: bring the table out and calibrate again.

Before you leave the magnet room, check that:

the participant is comfortable and has not crossed arms or legs (no current loops);
no cable crosses the participant, no metal or cable touches their skin, and their skin does not touch the bore or the coil; no cable forms a loop in the bore;
they can see the screen correctly.

Close the magnet room door, and the door to the technical room, with the magnetic lock.

Scanning¶

Once the participant is inside¶

Stay in the console room. Never leave the console room unattended until the end of the session.

Talk to the participant: press the intercom button to talk, release it to listen. Set the volume to maximum. Ask whether they are OK and can hear you, and tell them the scans will start.
Lights: use the in-room settings at the bottom left of the console to switch off the scanner lights. For fMRI, keep the same light settings throughout the whole study (outer circle on the scanner, lights in the bore).
Test the buttons again: ask the participant to press each button and check the responses in your script.

Run your sequences¶

Your protocol is set up with Ron Peeters when you prepare the study. The lab's standard fMRI protocol at MR11 will be documented here. The exam cards of lab studies that started before June 2026 were transferred to MR11 in May 2026; if your study continues one of them, ask Ron for the MR11 version. In general:

Run the localiser, then set the imaging and shim volumes.
Start your experiment on the stimulus PC so it waits for the trigger, then start the functional sequence on the console: select it and press Go.
After each scan, check the images for movement (see Check head motion) and artefacts.

A small "working men" icon in front of a sequence means that you start it by hand. Without the icon, the sequences run one after the other on their own. Ron normally sets manual starting for everyone, especially for task-based fMRI.

Starting a sequence on the MR11 console: the working-men icon (left circle) means manual start; select the sequence and press Go.

During the session, regularly ask the participant (by intercom) how they are doing, and watch the console for warnings.

Keep settings constant

Keep TR, slices, coverage and all other sequence settings the same within and between participants.

Scanning children

For tips during the scan, see Scanning children.

the screen on the scanner is dark

If you are the first to scan in the morning, and the scanner was not shut down correctly the night before (e.g., due to a scan running overnight), you may experience a black screen on the scanner. In this case, you will need to reboot the system (see MR11 wiki). Thus, if you are the first person to scan in the morning, it may be wise to come early to check whether a reboot is necessary (this can take ~15-20 min).

Door not closed properly

The magnet room door and the door from the magnet room to the technical room must both be closed (use the lock). Closing the changing-room door quickly can make the MR door open again: close it slowly. An open door can cause zipper or spike artefacts in your images.

Patient position on the table is unknown

The calibration was not saved. Go back into the magnet room and calibrate again with the light marker.

Medical supervision of the patient is required

The expected peripheral nerve stimulation of the sequence is between 80 and 100%. Press Confirm and Start.

Table movement must be allowed

Press For this scan only. The table moves a bit further into the scanner before the scan starts.

Pixelated image with only the contours of the skull

The top of the coil is probably not mounted properly. Bring the participant out, close the coil properly, and restart from the calibration.

No trigger or button presses

See the trigger troubleshooting. Never touch the fibre-optic cables.

Participant needs a break in the middle of the session

If the participant has to come out (to stretch, go to the toilet...) and agrees to continue, bring them out, then put them back in as before (including the calibration). The head position will have changed, so repeat the localiser and re-plan your volumes before you continue with the remaining runs.

No key press seems to be recorded

Always press every button you will use before the participant goes in. A good way to check during the session is an instruction screen that waits for a button press. If no key presses arrive, check the LEDs on the trigger box: if they light up, the problem is on the PC side; if not, check that the participant holds the right pad and call the MR technician.

Check head motion¶

Drag the run you want to check into one of the image boxes.
Click the small head icon at the top left of the box.
Choose Movie: the run plays frame by frame.

The movie plays slowly, and we have not found yet how to speed it up, but it gives a good first check of motion.

Checking motion on the MR11 console: the head icon at the top left of the image box (left) opens a menu with Movie (right).

Anatomical scan¶

Schedule the anatomical scan at the end of the session or between functional runs (as a break). During the anatomical run, participants can close their eyes or watch a video on the in-room screen.

Getting your data (XNAT)¶

MR11 sends all images automatically to the radiology research image server RADXNAT (prdaradxnat01.uz.kuleuven.ac.be). There is no export to USB at the console.

Wait about 30 minutes after the session, then check your project page in XNAT.
If the session is not there, look in the prearchive of your project. A conflict status usually means a wrong or duplicate session ID: fix it in XNAT (see the XNAT FAQ on the radiology wiki).
Download the DICOMs (step by step below):
- at the XNAT PC in preparation room 1, one of the onderzoekslokalen next to the console room (generic login, see the radiology wiki), to your encrypted SSD or USB drive; the browser does not remember the address, so type it each time;
- or from anywhere inside the hospital network, or with a UZ Leuven VPN (only for people with a UZ Leuven account).
Move the data to the lab storage as described in the RDM study workflow.

Download from XNAT step by step¶

Log in

Go to prdaradxnat01.uz.kuleuven.ac.be and log in with your KU Leuven number or your UZ Leuven username. The home page shows your projects. If you do not have a project yet, request one through the radiology wiki (Request a new project).

Open your project

Click the project you want to download data from. The project page shows the project description and all subjects and sessions completed in the project.

Open the subject

Click the subject whose data you want. It can take up to 30 minutes after the scan before the data are in XNAT. On the subject page, click Download Images under Actions.

Choose what to download

Choose the session (if there are several; this is why the session ID at the console must be unique, otherwise data are overwritten), select the scans you want, and choose Option 2: ZIP download to get the DICOMs in one .zip file. Then click Submit.

Save to your drive

A pop-up opens to choose where to save the file. On the UZ Leuven computers you cannot reach your own folders from the desktop, but in this pop-up you can go to your own drive and make new folders. You can also use an encrypted drive: selecting it opens the usual prompt to unlock it.

Archive your data quickly

The XNAT prearchive is not backed up, and images older than 30 days that are not archived to a project are deleted. Check after every session that your data arrived in your project.

XNAT Desktop Client

The XNAT Desktop Client is not supported (it interferes with the de-identification). Use the web interface.

Personal information in your images

Images in XNAT should be pseudonymised. If you find a name or other personal information in the subject or session labels, correct it in XNAT. If it is in the DICOM header, contact the XNAT team (Rodrigo Trevisan Massera) right away with the project, session and label.

Also take your behavioural log files from the stimulus PC (on your encrypted drive). Use the same participant code as in XNAT.

After scanning¶

Participant and magnet room¶

Bring the participant out with the round knob, lower the table, and let them get up slowly (children especially).
Debrief the participant and return their belongings.
Clean up:
- Throw away earplugs and paper towels.
- Disinfect all surfaces that were touched, and put fresh paper towels on the table.
- Leave the scanner in a clean state, with fresh paper and earplugs ready on the table.
- Put the 64-channel head coil in place on the table, without plugging it in.
- Put cushions and equipment on the shelves, never on the floor.

Console room¶

Switch off the in-room screen and the audio system.
Close all software on the stimulus PC, but leave the PC on.
Check that your data arrived in XNAT (see above).
Report technical problems or artefacts by e-mail to Ron Peeters (ronald.peeters@uzleuven.be).
Incidental finding suspected? See Seeing an abnormality in the emergency procedures above. Do not tell the participant.

If you are the last user of the day¶

Clean the patient table with alcohol wipes.
Shut down the scanner: on the console, go to Home (top left) › Shut down system (bottom right). Wait until the screens are black and the lights on the intercom flicker. Then press system off below the quench button (key turned to unlock); the last blinking light on the intercom goes out.
Switch off all screens (including the stimulus PC monitor) and the lights in the magnet room, the console room and the rooms next to it.
Put the cover on the in-room screen (the cover lies on its base).
Close all doors.

Next steps

Now that you're familiar with the scanning procedure, see the Analysis workflow to learn how to process and analyze your fMRI data.

October 16, 2026