How to plan an MRCP protocol

This step-by-step guide is for MRI students, radiographers, and technologists who wish to improve their planning skills and master the MRCP protocol.

What you will learn:

1. Key factors in MRCP, including trade-offs.
2. Patient and scanner setup tips.
3. Best pulse sequences and planning techniques.
4. Ways to avoid common artifacts.
5. What great MRCP images should look like.

MRCP, or magnetic resonance cholangiopancreatography, evaluates the biliary and pancreatic duct systems using heavily T2-weighted imaging. This makes static fluids like bile and pancreatic juice appear bright, without invasive procedures or ionizing radiation. Stones contain no free fluid, so they appear as dark filling defects against that bright background.

The protocol combines routine upper-abdominal sequences with dedicated MRCP acquisitions, so we assess both the abdominal organs and the fine duct anatomy in one study.

After liver tests and abdominal ultrasound, MRCP is a first-line non-invasive test for suspected common bile duct stones and biliary obstruction, alongside endoscopic ultrasound.

How to Balance the 3 Trade-offs in MRCP

In MRI, we always face a trade-off between 3 key metrics:

1. Scan Time: How fast a pulse sequence can be completed.
2. Resolution: How much detail the image can display.
3. SNR: How clear the image is, meaning how much signal we have compared with noise.

Improving one of these metrics often reduces the performance of the others. To decide what trade-offs to make, we must consider the needs of each clinical situation.

For MRCP, we face three specific challenges:

• Tiny structures. The main pancreatic duct is usually only a few millimeters wide, with published reference values of roughly 3 mm below age 65 and 4 mm from age 65, and stones or strictures can be smaller still. Without high spatial resolution, partial volume averaging blurs them together and small findings vanish.
• Fluid-based contrast. The duct signal comes mainly from fluid. Heavily T2-weighted imaging keeps static bile and pancreatic juice bright against a darker background, so we need enough SNR to hold the bright-fluid to dark-stone distinction clear. That gets SNR-sensitive when voxels are small and echo times are long.
• Constant motion. The upper abdomen moves with breathing and bowel motion, and the high-detail scan takes minutes.

Therefore, we typically:

1. Prioritize resolution because the fine duct detail is the diagnosis, and
2. Keep SNR high enough for clarity.

But neither matters until motion is controlled, and one scan usually cannot maximize resolution, SNR, and speed at once.

So the protocol takes a two-pronged approach, splitting its sequences into two groups: one optimized for detail, one for speed.

1. The respiratory-triggered sequence group: scan time comes last

These sequences acquire data during a consistent part of the breathing cycle, usually near end-expiration, which reduces motion rather than freezing it, at the cost of minutes.

Scan time is what all three sequences in this group spend last, but what they spend it on differs: the 3D MRCP spends it on resolution, while the coronal T2 and axial T2 fat-sat spend it on coverage and inflammation contrast instead.

The 3D MRCP is the most important sequence. Its thin near-isotropic voxels, roughly 1.4 mm in-plane by 1.6 mm slice, resolve small stones and fine ducts and reconstruct in any plane, and its volumetric readout supplies the SNR those thin slices spend. The coronal and fat-suppressed T2 images ride along in the same group, trading time for clean, detailed anatomy.

2. The breath-hold sequence group: 1) scan time, 2) SNR, 3) resolution

These sequences finish inside a single breath-hold or a single shot, so respiratory motion has little chance to blur them, though bowel motion or a failed breath-hold still can.

Speed comes first, and detail is what gets sacrificed. The thick slab collapses through-plane detail into one projection, and single-shot readouts come out softer than the triggered images. This group keeps the study diagnostic when the patient cannot hold still or breathe regularly.

Strategy and Priority for Each MRCP Sequence

This table shows a breakdown of every sequence in standard MRCP protocol, the motion-control strategy we use, and what to prioritize in acquisition.

Note on Other MRCP Variants

Grouping and triggering differ by vendor and site, so a sequence that is respiratory-triggered here may be run breath-hold elsewhere.

Some centers use breath-hold 3D MRCP with compressed sensing to bring near-3D duct detail into one breath-hold, though heavy acceleration can reduce small-duct visibility.

Secretin MRCP changes the trade-off further, adding repeated timed thick-slab images after IV secretin to assess pancreatic duct filling and function, where temporal timing outranks spatial resolution. These are not the sequences demonstrated in this video.

MRCP Health Conditions and the MRI Sequences That Reveal Them

The MRCP study can help us diagnose a wide range of health conditions. The table below lists some of the most common conditions and what pulse sequences reveal them:

The step-by-step guide below will show you how to set up and perform an MRCP protocol in practice.

We will perform the protocol in 3 parts:

1. Set up the Patient and MRI Scanner
2. Plan and Acquire the Protocol Sequences
3. Review the Images

Part 1: Set up the Patient and MRI Scanner

1. Prepare the Patient

MRCP is one of the few protocols where preparation before the patient reaches the table directly affects image quality.

• Fasting: Ask the patient to fast for 4–6 hours when the clinical situation allows. This reduces bright fluid in the stomach and duodenum, and lets the gallbladder distend.
• Negative oral contrast (optional, site-dependent): Bright gastric and duodenal fluid can sit on top of the common bile duct and hide it. Purpose-built agents such as ferumoxsil were once used for this but have since been withdrawn from the market, which is a large part of why many departments now use pineapple juice instead. It works because its manganese content shortens the T2 of the fluid it mixes with, so at MRCP’s very long echo times that fluid loses nearly all signal. No official body recommends a specific volume. Published studies have used 150–400 mL, given 15–30 minutes before scanning, and the amount needed depends on the manganese concentration of the specific juice, so follow a locally validated protocol.
• Breathing coaching: Practice breath-hold instructions before the patient enters the bore, and test both exhale and inhale. Many patients hold their breath far more reliably one way, and picking the better one keeps slice positions consistent between sequences.

2. Position the Patient in the Scanner

Lay the patient supine with the upper abdomen centered at the scanner’s isocenter.

Use an anterior body array coil on top of the upper abdomen, combined with the posterior spine coil integrated into the scanner table. This gives full signal coverage of the liver, gallbladder, biliary tree, and pancreas.

Arms can be positioned above the head or alongside the body. If they rest alongside the body they sit near the field of view in the right-to-left direction, which is why foldover suppression matters on the coronal sequences.

✅ Correct Patient Positioning:

3. Check the Scanner’s Hardware Settings

Once the patient is in place, review your scanner’s hardware settings.

In this guide, we will use the following settings:

This hardware setup is widely used in clinical practice. It balances acquisition time, image quality, and patient comfort.

4. Capture the Initial Localizer Images

Every MRI protocol starts with localizer images of the patient. These images act as a guide for planning the detailed scans we will perform next.

Select the abdominal region, save it, and run the localizers.

We should always capture localizers in three planes:

1. Axial
2. Sagittal
3. Coronal

Once acquired, load the localizer images into the three viewports. Then scroll through each stack to locate a central slice that clearly shows the anatomy of the upper abdomen.

✅ Correct Setup of Localizer Images for MRCP:

Part 2: Plan and Acquire the Protocol Sequences

When all preparations are ready, we can start planning and acquiring the protocol sequences.

Let’s go through the pulse sequences a standard MRCP protocol includes, why we perform them, and how to set them up.

The 6 Sequences of a Standard MRCP Protocol

1. Coronal T2 TSE
2. Axial T2 FS TSE
3. Axial T2 SS-TSE
4. Axial GRE Dixon
5. 3D MRCP
6. Radial SS-TSE FS

Sequences 1, 2, and 5 belong to the respiratory-triggered group. Sequences 3, 4, and 6 belong to the breath-hold group.

In the sections below, we go through how to plan and set up each sequence.

1. Planning Coronal T2 TSE

✅ Correct Planning:

Planning Instructions:

• Plan in the true coronal plane, covering the entire hepatobiliary system.
• Use appropriate geometry parameters:
  • Coverage: From the anterior abdominal wall back to the kidneys, including liver, gallbladder, pancreas, spleen, and upper kidneys.
  • Slice number: 32–38, enough for that anterior-to-posterior block.
  • Slice thickness: 6 mm, thick enough to keep SNR up across the coverage while still resolving duct anatomy.
  • Slice gap: 1 mm, which is 17% of the slice thickness and limits cross-talk without hiding anatomy.
• Set the foldover direction (phase encoding) to right-to-left (RL) and activate foldover suppression, so the arms and body wall do not alias into the image.
• Acquire with respiratory triggering. This is a multi-shot TSE that takes a few minutes, so it follows the breathing cycle rather than a breath-hold.

Tip: You can display your slices in either box view or slice view. Pick whichever helps you check coverage, angle, and position most clearly.

Parameters for Coronal T2 TSE:

2. Planning Axial T2 FS TSE

✅ Correct Planning:

Planning Instructions:

• Plan in the axial plane. Right-click on the axial localizer and set the in-plane position, which also sets the correct orientation under the Geometry tab.
• Use appropriate geometry parameters:
  • Coverage: From the hepatic dome down to the kidneys.
  • Slice number: 32–38.
  • Slice thickness: 6 mm, with a 1 mm gap.
• Review your slice package on top of a high-resolution image, such as the coronal T2, and scroll through to confirm the abdominal dome and kidneys are both covered.
• Set the foldover direction (phase encoding) to anterior-to-posterior (AP) to limit aliasing.
• Foldover suppression can stay off here, since no anatomy extends beyond the field of view in the AP direction. Leaving it off also reduces scan time.
• Acquire with respiratory triggering, the same as the coronal T2.

Parameters for Axial T2 FS TSE:

3. Planning Axial T2 SS-TSE

The SS tag stands for single-shot. This sequence captures the complete k-space for each slice in one shot, which makes it far faster than the multi-shot sequences before it.

✅ Correct Planning:

Planning Instructions:

• Copy the slice geometry and planning from the previous axial T2 FS TSE sequence.
• Keep the same slice angulation, coverage, and positioning so images of different contrasts can be clearly compared.
• Acquire as a breath-hold, at exhale or inhale depending on which your patient performs more reliably.

Parameters for Axial T2 SS-TSE:

4. Planning Axial GRE Dixon

✅ Correct Planning:

Planning Instructions:

• Copy the slice geometry from one of your previous axial sequences using the Custom copy option.
• This time, exclude the phase matrix from the copy and keep everything else. The Dixon runs at a lower phase matrix to hold each breath-hold short.
• Through-plane resolution and central position stay the same, so the radiologist can compare all sequences at matching levels.
• Acquire as a breath-hold.

Parameters for Axial GRE Dixon:

5. Planning 3D MRCP

This is the cornerstone of the study. Everything before it establishes anatomy and context. This sequence maps the duct tree itself.

✅ Correct Planning:

Planning Instructions:

• Bring the sagittal localizer back into a viewport and scroll to a slice showing the upper-abdomen organs clearly. Keep your high-resolution coronal and axial images ready for planning.
• Plan the slab as a coronal. Position on the coronal T2 image, and set the in-plane position. The slab should then sit perpendicular on the axial view.
• Use the axial T2 FS to check the extent of the gallbladder, then scroll down to find the common bile duct and pancreatic duct. These are the structures to cover in every case.
• Use appropriate geometry parameters:
  • Slice number: 75–85, enough to cover the hepatobiliary system and no more. Every extra slice costs time on an already long sequence.
  • Slice thickness: 1.6 mm, thin near-isotropic voxels.
  • Slice gap: 0 mm, contiguous slices are required for a true 3D volume.
• Angle the slab strategically so it captures those structures without including surrounding anatomy that adds nothing here.
• Acquire with respiratory triggering. Verify the patient’s breathing is consistent, otherwise the listed scan time will stretch out significantly.

Parameters for 3D MRCP:

6. Planning Radial SS-TSE FS

This is a thick-slab, projection-style acquisition. Instead of a stack of parallel slices, it rotates a small number of thick slices around a single central axis.

✅ Correct Planning:

Planning Instructions:

• Bring back a high-resolution coronal T2 image for planning.
• Set the first slice perpendicular on the axial image and center it. That slice sits in a true coronal plane through the biliary tree.
• Enable radial slices, and set the number of slices.
• The slices rotate at a fixed angle around that initial position. Completing 360° gives multiple projection views of the duct tree from different angles.
• Typically 9–12 slices are enough, since each views the ducts from a different angle.
• Acquire as breath-holds in the same direction used on the single-shot sequence, so slice positions stay consistent.

Parameters for Radial SS-TSE FS:

How to Avoid Artifacts When Planning the Sequences

The table below lists the 5 common MRCP artifacts, and what techniques you can use to avoid them:

Part 3: Review the Images

Finally, we will review the images to ensure all the anatomical information we need is clear.

These key structures must be clearly visible in an MRCP:

1. Intrahepatic bile ducts, right and left hepatic ducts
2. Common hepatic duct and cystic duct
3. Gallbladder, including wall and contents
4. Common bile duct along its full length to the ampulla
5. Main pancreatic duct
6. Pancreatic parenchyma
7. Liver, spleen, and upper kidneys

Below, we will go through all the different image contrasts and explain their specific role in an MRCP study.

Coronal T2 TSE – Anatomical Overview of the Upper Abdomen

The coronal T2 gives a high-resolution anatomical overview of the upper abdomen, showing the liver, pancreas, gallbladder, biliary tree, and surrounding structures in a plane that runs along the axis of the biliary system.

It is valuable for detecting edema, inflammation, masses, and fluid collections, and for establishing anatomical orientation before the dedicated MRCP acquisitions.

✅ Coronal T2 TSE – Correct Image Example:

Things to Look for in Coronal T2:

• Coverage runs correctly from anterior to posterior, capturing liver, gallbladder, pancreas, spleen, and upper kidneys.
• The biliary tree can be traced across its general course.
• No aliasing from the arms or body wall in the right-to-left direction.
• Large extra-biliary masses and fluid collections are visible.

Axial T2 FS TSE – Inflammation and Edema

Suppressing the fat increases the visibility of fluid, edema, and inflammatory changes, while improving lesion detection within the liver. This sequence is particularly useful for evaluating pancreatitis, cholangitis, fluid collections, and cystic lesions, as well as gallbladder wall thickening in cholecystitis.

✅ Axial T2 FS TSE – Correct Image Example:

Things to Look for in Axial T2 FS:

• Fat is uniformly suppressed across the whole field of view.
• Coverage runs from the hepatic dome down to the kidneys.
• Gallbladder wall thickness and any pericholecystic fluid are clearly assessable.
• Peripancreatic fluid and edema stand out against the darker background.

Axial T2 SS-TSE – Fast Motion-Resistant Duct Screen

The axial T2 single-shot is a reliable overview sequence, helping identify free fluid, biliary dilatation, pancreatic abnormalities, and other upper-abdominal pathology. Because it is planned identically to the axial T2 FS, the two can be compared slice for slice.

✅ Axial T2 SS-TSE – Correct Image Example:

Things to Look for in Axial T2 SS-TSE:

• Slice positions match the axial T2 FS exactly.
• Images look slightly softer even though the matrix matches the axial T2 FS. That blurring comes from the long single-shot echo train and half-Fourier filling, and is the expected cost of speed.
• Contrast on the vital structures remains well-defined.
• Dark filling defects in the CBD are noted but confirmed on 3D MRCP source images, since flow artifact can mimic a stone.

Axial GRE Dixon – Tissue Characterization

The Dixon sequence gives tissue characterization by separating fat and water signal. It is useful for detecting hepatic steatosis, microscopic fat, adrenal adenomas, pancreatic fat infiltration, and hemorrhage, while producing high-quality fat-suppressed images. The top-left corner of the viewport shows which of the four reconstructions you are viewing.

✅ Axial GRE Dixon – Correct Image Examples (4 contrasts):

Things to Look for in Axial GRE Dixon:

• In-phase: overall anatomy, acquired at the echo where fat and water signals add together.
• Out-of-phase: signal drop indicating fat and water in the same voxel, pointing to steatosis or a fat-containing lesion.
• Water map: completely fat-suppressed, showing only water content as bright.
• Fat map: shows only the signal coming from fat.
• Levels match the other axial sequences, from the top of the liver dome down to the kidneys.

3D MRCP – The Cornerstone of the Study

The detailed visualization of the biliary and pancreatic duct systems helps assess ductal anatomy, stones, obstructions, congenital abnormalities, ductal dilatation, and communication with cystic lesions, all without intravenous contrast.

This sequence is normally post-processed to generate MIP (maximum intensity projection) reconstructions. The native source acquisition is what you should always review first.

✅ 3D MRCP – Correct Image Example:

Things to Look for in 3D MRCP:

• The full duct tree is traceable from the intrahepatic ducts to the ampulla.
• The common bile duct and pancreatic duct are covered along their length.
• Background signal is well suppressed, so the ducts dominate the image.
• Always check the thin source images alongside the MIP. MIP reconstruction can hide small stones and exaggerate strictures.
• Any apparent narrowing is cross-checked against the source images and other planes to rule out vascular pulsation from the right hepatic artery or the gastroduodenal artery.

Radial SS-TSE FS – Fast Projection Backup

The heavily T2-weighted thick slab produces projection-like images of the biliary and pancreatic ducts. It is effective for detecting biliary obstruction, choledocholithiasis, ductal dilatation, pancreatic duct abnormalities, and gallbladder pathology, with an appearance similar to conventional cholangiography, with each slice acquired in only one to two seconds.

✅ Radial SS-TSE FS – Correct Image Examples:

Things to Look for in Radial SS-TSE FS:

• The first slice is the central one, giving a true coronal view through the biliary tree.
• Each following slice is rotated by a fixed angle, building a full 360° set of projection views.
• The cross-reference on the axial plane shows which slice you are viewing.
• Contrast is similar to the 3D MRCP, highlighting the same duct structures.
• Detail is coarser than the 3D MRCP. That is the expected trade for motion resistance.

Final Checks:

Before finishing an MRCP, always check these 5 points to ensure diagnostic quality:

1. Complete Duct Coverage: The intrahepatic ducts, common hepatic duct, cystic duct, common bile duct to the ampulla, and main pancreatic duct must all be included on the 3D MRCP.
2. Motion Control: Respiratory-triggered sequences must show consistent triggering with no ghosting, and breath-hold sequences must show no blurring from a broken breath-hold.
3. Source Images Reviewed: Every finding on the MIP must be confirmed on the thin 3D source images, and every suspected stone on the SS-TSE must be confirmed on the 3D MRCP.
4. Consistent Planning: All axial sequences must sit at matching slice positions so contrasts can be compared level for level.
5. Image Quality and Artifacts: Fat suppression must be uniform, background GI fluid adequately dark, and there must be no significant chemical shift, wraparound, or susceptibility artifacts.

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