How to Plan an Anal Fistula MRI Protocol

Intro to Anal Fistula MRIs

How to Perform a Shoulder MRI with Clock Face Method

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

4. Capture the Initial Localizer Images

Before we can perform any MRI protocol, we must always capture initial localizer images of the patient. These images act as a guide for planning the detailed scans we will perform next.

We should always capture localizers in three planes:

1. Axial
2. Sagittal
3. Coronal

Once acquired, upload the initial localizer images into the three viewports.

Then, scroll through each of the image stacks to locate a central slice that clearly shows the anatomy of the anal canal.

✅ Correct Setup of Localizer Images for Anal Fistula MRI:

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 anal fistula MRI protocol includes, why we perform them, and how to set them up.

The 6 Sequences of a Standard Anal Fistula MRI Protocol

1. Sagittal T2 TSE High Resolution
2. Sagittal T2 TSE Fat-Saturated (SPAIR or STIR)
3. Axial T2 TSE Fat-Saturated (SPAIR or STIR)
4. Coronal T2 TSE Fat-Saturated (SPAIR or STIR)
5. Sagittal T1 TSE (Pre-contrast)
6. Sagittal T1 TSE (Post-contrast)

We mainly use T2 Turbo Spin Echo sequences with fat saturation for this study. These sequences make fluid appear bright, which helps us detect fistula tracts, abscesses, and inflammation clearly against darker tissue.

Fat saturation techniques enhance this contrast further by suppressing the bright fat signal. This increases the contrast-to-noise ratio between pathology and normal tissue.

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

1. Sagittal T2 TSE High Resolution

✅ Correct Planning:

Planning Instructions:

• Use the anal canal and rectum as your anatomical references.
• Align the slices as follows:
  • Axial localizer: Position slices through the midline of the anal canal.
  • Coronal localizer: Angle slices to be exactly in the middle of the rectum, following its axis.
• Use appropriate geometry parameters:
  • Slice number: 15–20 to fully cover the perianal region.
  • Slice thickness: 3 mm for high resolution without sacrificing SNR.
  • Slice gap: 0.3 mm (10% of thickness) to prevent crosstalk while maintaining continuity.
• Set the fold-over direction (phase encoding) to foot–head (FH) to reduce wrap and respiratory motion artifacts.
• Ensure coverage from the buttock cheek posteriorly to the upper rectum anteriorly.

Parameters for Sagittal T2 TSE High Resolution:

Choosing Fat Suppression for Anal Fistula MRI: SPAIR vs STIR

The following T2 sequences will use fat suppression.

When imaging anal fistulas, however, it’s very important to select the right fat suppression technique for image quality.

There are two main fat suppression options:

1. SPAIR (Spectral Fat Saturation):SPAIR uses a specific pulse to suppress fat based on its frequency. It's faster than STIR and provides more robust suppression when the magnetic field is uniform.
2. However, SPAIR is very sensitive to field inhomogeneity. In the pelvis, interfaces between water (bladder), gas (bowel), and tissue create field variations that can cause SPAIR to fail.
3. STIR (Inversion Recovery):STIR works by setting an inversion time that nulls fat signal completely. It's less sensitive to field inhomogeneity, making it more reliable when bowel gas or poor patient preparation creates field distortions.

Which to Choose for Anal Fistula MRI:

• First choice: SPAIR when the patient is well-prepared (empty bladder, minimal bowel gas)
• Better choice: STIR when:
  • Scanning at 3T (more field inhomogeneity)
  • Poor patient preparation (full bladder, excessive gas)
  • Emergency scans without prep time
  • SPAIR shows poor suppression on initial images

The typical inversion time for STIR at 1.5T is 150-180 milliseconds. While STIR takes longer than SPAIR, its robust suppression often makes it worth the extra time in pelvic imaging.

2. Sagittal T2 TSE Fat-Saturated (SPAIR or STIR)

✅ Correct Planning:

Planning Instructions:

• Copy the slice geometry and planning from the previous Sagittal T2 TSE sequence.
• Keep the same slice angulation, coverage, and positioning to ensure images of different contrasts can be clearly compared.

Parameters for Sagittal T2 TSE Fat-Saturated:

3. Axial PD Fat-Saturated TSE (SPAIR or STIR)

✅ Correct Planning:

Planning Instructions:

• Use the anal canal and internal anal sphincter as your anatomical references.
• Align the slices as follows:
  • Sagittal localizer: Position slices perpendicular to the anal canal axis.
  • Coronal localizer: Ensure slices are perpendicular to the anal canal.
• Use appropriate geometry parameters:
  • Slice number: 20–25 to cover from above the levator ani to the perineal skin.
  • Slice thickness: 3–4 mm for good resolution while maintaining SNR.
  • Slice gap: 0.3–0.4 mm (10% of thickness) to avoid missing pathology.
• Set the fold-over direction (phase encoding) to right–left (RL) to reduce motion artifacts from bowel.

Parameters for Axial T2 TSE Fat-Saturated:

4. Coronal T2 TSE Fat-Saturated (SPAIR or STIR)

✅ Correct Planning:

Planning Instructions:

• Use the anal canal as your anatomical reference.
• Align the slices as follows:
  • Sagittal localizer: Position slices parallel to the anal canal axis.
  • Axial localizer: Ensure coverage of the ischiorectal fossae bilaterally.
• Use appropriate geometry parameters:
  • Slice number: 15–20 to cover from rectum posteriorly to pubic symphysis anteriorly.
  • Slice thickness: 3–4 mm for adequate resolution.
  • Slice gap: 0.3–0.4 mm (10% of thickness) to maintain continuity.
• Set the fold-over direction (phase encoding) to right–left (RL) to minimize motion artifacts.
• Ensure coverage includes horseshoe tracts and bilateral ischiorectal fossae.

Parameters for Coronal T2 TSE Fat-Saturated:

5. Sagittal T1 TSE (Pre-contrast)

✅ Correct Planning:

Planning Instructions:

• Copy the slice geometry and planning from the previous Sagittal T2 TSE sequence.
• Keep the same slice angulation, coverage, and positioning to ensure images of different contrasts can be clearly compared.

Parameters for Sagittal T1 TSE (Pre-contrast):

6. Sagittal T1 TSE (Post-contrast)

After administering gadolinium contrast (typically 0.1 mmol/kg body weight), wait approximately 30-60 seconds before acquiring post-contrast images.

✅ Correct Planning:

Planning Instructions:

• Copy the slice geometry and planning from the previous pre-contrast T1 TSE sequence.
• Keep the same slice angulation, coverage, and positioning to ensure precise comparison between pre- and post-contrast images.
• Consider adding fat saturation to post-contrast T1 for better visualization of enhancing tissue.

Parameters for Sagittal T1 TSE Post-contrast:

How to Avoid Artifacts When Planning the Sequences

The table below lists the 5 common anal fistula 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 anal fistula MRI:

1. Internal and external anal sphincters
2. Levator ani muscle
3. Ischiorectal fossae
4. Perianal skin and subcutaneous tissue
5. Rectum and anal canal
6. Any fistula tracts, abscesses, or inflammatory changes

Below, we will go through all the different image contrasts and explain their specific role in imaging anal fistulas.

T2 TSE – Highlights Fluid-Filled Tracts and Anatomy

T2-weighted imaging makes fluids appear bright. This contrast is ideal for tissues and abnormalities with high water content.

In anal fistula MRI, T2 sequences are the workhorse for detecting fistula tracts, which appear as bright tubular structures against darker muscle and fat. They help us map the exact course of fistulas through the sphincter complex and identify branching patterns.

We acquire sagittal views to assess the relationship between fistulas and the rectum, and to understand anterior-posterior spread.

✅ Sagittal T2 TSE of Anal Canal – Correct Image Example:

Things to Look for in Sagittal T2 TSE:

• Bright tubular tracts indicating fistulas
• Relationship to internal and external sphincters
• Extension into the rectum or perianal skin
• Any fluid collections or abscesses

T2 Fat-Saturated – Mapping Inflammatory Extent Through Edema

T2 Fat-Saturated imaging suppresses fat while keeping fluid bright. This shows all areas with increased water content, making it the most sensitive sequence for detecting inflammatory spread.

In anal fistula MRI, STIR reveals the full extent of inflammation by highlighting edema in tissues. Any area with increased water appears bright, whether from acute infection or chronic inflammation. This complete map of inflammatory spread helps surgeons plan their approach.

We acquire fat-saturated T2 in all three planes to fully understand the fistula's path and extent:

• Sagittal views show the vertical relationship to the rectum and sphincters.
• Axial views best demonstrate tracts crossing from internal to external sphincter.
• Coronal views reveal horseshoe extensions and bilateral spread that might be missed in other planes.

❌ Failed Spectral Fat Saturation (SPAIR) – Example of Poor Suppression:

Signs of Failed Fat Suppression:

• Heterogeneous fat signal (some areas bright, others dark)
• Poor suppression around gas-tissue interfaces
• Bright fat signal obscuring pathology
• Need to switch to STIR for robust suppression

✅ Sagittal T2 STIR of Anal Canal – Correct Image Example:

Things to Look for in Sagittal T2 Fat-Saturated:

• Bright signal from fluid in fistula tracts
• Edema in surrounding soft tissues (bright signal)
• Relationship between fistula and sphincter complex
• Vertical extent of inflammatory changes

We then acquire axial views perpendicular to the anal canal for the most diagnostic images, as they show tracts crossing from internal to external sphincter clearly.

✅ Axial T2 STIR of Anal Canal – Correct Image Example:

Things to Look for in Axial T2 Fat-Saturated:

• Bright fistula tracts crossing sphincters
• Fluid collections in ischiorectal fossae
• Inflammatory changes in perianal fat
• Relationship to levator ani muscle

✅ Coronal T2 STIR of Anal Canal – Correct Image Example:

Things to Look for in Coronal T2 Fat-Saturated:

• Horseshoe tracts extending laterally
• Bilateral disease spread
• Trans-levator extensions
• Collections in supralevator space

T1 TSE Pre-contrast – Structural Detail and Chronic Changes

T1-weighted imaging makes fat appear bright and fluid dark. This contrast is ideal for fat-rich tissues and structural abnormalities. T1 shows anatomical structures clearly, since it helps us see where different solid tissues like muscle and fat meet.

In anal fistula MRI, pre-contrast T1 sequences provide baseline anatomy and help identify chronic fibrotic changes. They show the normal fat planes between muscles and help detect fat infiltration or obliteration that indicates chronic inflammation.

We acquire pre-contrast T1 in the sagittal plane to match our T2 sequences for direct comparison.

✅ Sagittal T1 TSE Pre-contrast of Anal Canal – Correct Image Example:

Things to Look for in Sagittal T1 Pre-contrast:

• Anatomical landmarks clearly defined
• Fat planes between muscles preserved or obliterated
• Chronic fibrotic changes (intermediate signal)
• Baseline anatomy before contrast enhancement

T1 TSE Post-contrast – Identifying Viable Tissue Through Enhancement

Post-contrast T1 shows where gadolinium accumulates in tissues with active blood supply and leaky vessels. Enhancement indicates viable, vascularized tissue.

In anal fistula MRI, post-contrast T1 differentiates healing tissue from mature scar. Active granulation tissue in fistula walls enhances brightly, while chronic fibrotic tracts show little to no enhancement. Abscesses show characteristic rim enhancement around a dark center of pus.

These contrasts help surgeons identify which tissue can heal versus what needs removal.

We typically acquire post-contrast T1 in the same sagittal plane as pre-contrast for direct comparison. Some protocols may add axial or coronal post-contrast sequences for complex cases.

✅ Sagittal T1 TSE Post-contrast of Anal Canal – Correct Image Example:

Things to Look for in Sagittal T1 Post-contrast:

• Enhancement of fistula tract walls (active disease)
• Rim enhancement around abscesses
• Non-enhancing areas suggesting fibrosis or pus
• Potential tumor enhancement if malignancy suspected

Final Checks:

Before finishing an anal fistula MRI, always check these 5 points to ensure diagnostic quality:

1. Fistula Visualization: All fistula tracts must be clearly visible from internal opening to external opening, including any branches.
2. Sphincter Assessment: Internal and external sphincters must be clearly defined to determine the Parks classification of fistulas.
3. Fat Suppression Quality: STIR or fat-saturated sequences must show uniform suppression to highlight all inflammatory changes.
4. Coverage Completeness: Images must cover from mid-rectum to perineal skin, including bilateral ischiorectal fossae.
5. Image Quality and Artifacts: Images must have strong SNR, sharp detail, and minimal motion, susceptibility, or wrap artifacts.

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