Modifier Axis¶

The Modifier axis identifies acquisition enhancements applied to the base technique. It answers the question: "How was the acquisition modified from the standard technique?"

Overview¶

Modifiers are additive - multiple modifiers can apply to a single series. Output is a comma-separated list (alphabetically sorted).

Category	Modifiers	Purpose
IR Contrast	FLAIR, STIR, DIR, PSIR, IR	Tissue nulling via inversion recovery
Fat Suppression	FatSat, WaterExc, Dixon	Remove/separate fat signal
Signal Modifiers	MT, FlowComp, MoCo	Modify tissue/flow signals
Trajectory	Radial, Spiral	Non-Cartesian k-space
Blood Signal	BlackBlood, BrightBlood	Vessel visualization

Key Concepts¶

Additive Logic¶

Unlike Technique (single value), multiple modifiers can coexist:

T2-FLAIR + FatSat → modifier_csv = "FatSat,FLAIR"
Dixon + Radial    → modifier_csv = "Dixon,Radial"

Mutual Exclusion Groups¶

Some modifiers are mutually exclusive within their group:

Group	Members	Rule
IR_CONTRAST	FLAIR, STIR, DIR, PSIR, IR	Highest priority wins
TRAJECTORY	Radial, Spiral	Highest priority wins

Within IR_CONTRAST, you can't have both FLAIR and STIR - they use different TI values for different tissue nulling.

Output Format¶

Modifiers are output as modifier_csv: - Comma-separated - Alphabetically sorted - Empty string if no modifiers

Examples: - "FLAIR" - Single modifier - "Dixon,FatSat" - Multiple modifiers - "" - No modifiers detected

Detection Strategy¶

Same three-tier approach as other axes (first match wins per modifier):

Tier 1: Exclusive Flag (95% confidence)¶

FLAIR:
  detection:
    exclusive: is_flair

Tier 2: Keywords Match (85% confidence)¶

FLAIR:
  keywords:
    - "flair"
    - "dark fluid"

Tier 3: Combination (75% confidence)¶

Dixon:
  detection:
    combination:
      - has_in_phase
      - has_out_phase

IR Contrast Modifiers¶

Inversion Recovery modifiers use a 180° inversion pulse with specific TI to null different tissues.

FLAIR (Fluid-Attenuated IR)¶

TI: ~2000-2500ms at 3T (nulls CSF)

Detection: - Exclusive flag: is_flair - Keywords: flair, dark fluid, da fl

Physics: Long TI nulls CSF signal, making periventricular lesions more visible.

Clinical use: - MS lesion detection - Stroke imaging - Tumor visualization near ventricles

T1-FLAIR vs T2-FLAIR

FLAIR is a modifier, not a base contrast. The base (T1w vs T2w) is determined by TE. Most clinical FLAIR is T2-FLAIR.

STIR (Short-TI IR)¶

TI: ~150-200ms at 3T (nulls fat)

Detection: - Exclusive flag: has_stir - Keywords: stir, short tau, tirm

Physics: Short TI nulls fat signal regardless of B0 homogeneity.

Clinical use: - Robust fat suppression - Bone marrow edema - Orbital imaging

Caveat: Also suppresses gadolinium-enhanced tissue (short T1).

DIR (Double IR)¶

Physics: Two inversion pulses to null two tissue types.

Detection: - Exclusive flag: is_dir - Keywords: dir, double ir, dual ir

Common configuration: CSF + white matter nulling → gray matter only visible.

Clinical use: - Cortical lesion detection in MS - Gray matter imaging

PSIR (Phase-Sensitive IR)¶

Physics: Preserves magnetization sign (not just magnitude).

Detection: - Exclusive flag: has_psir - Keywords: psir, phase sensitive

Benefit: Improved gray/white contrast and dynamic range.

Clinical use: Often combined with MPRAGE for better tissue delineation.

IR (Generic)¶

Detection: - Exclusive flag: has_ir_se (SE-based IR only) - Keywords: inversion recovery

Note: Fallback when no specific IR variant matches. Uses has_ir_se to exclude GRE-based IR (MPRAGE, MP2RAGE) where IR is part of the technique, not a modifier.

Fat Suppression Modifiers¶

FatSat (Frequency-Selective)¶

Physics: Spectral saturation pulse at fat frequency before excitation.

Detection: - Exclusive flag: has_fat_sat - Keywords: fatsat, fat sat, chemsat, spair

Vendor names: - Generic: FatSat - Philips: SPIR, SPAIR

Requirement: Good B0 homogeneity for effective suppression.

WaterExc (Water-Only Excitation)¶

Physics: Binomial or spectral-spatial pulse that excites only water protons.

Detection: - Exclusive flag: has_water_excitation - Keywords: water excitation, proset, wex

Characteristics: - Faster than fat saturation - Less robust at air-tissue interfaces - Alternative to FatSat

Dixon (Fat-Water Separation)¶

Physics: Acquires in-phase and out-of-phase echoes to separate fat and water.

Detection: - Exclusive flag: has_dixon - Keywords: dixon, ideal, mdixon, lava-flex - Combination: has_in_phase + has_out_phase

Outputs: - Water-only image - Fat-only image - In-phase image - Out-of-phase image

Vendor names: - GE: IDEAL - Philips: mDixon - Siemens: Dixon

Signal Modifiers¶

MT (Magnetization Transfer)¶

Physics: Off-resonance RF saturates bound (macromolecular) protons. Saturation transfers to free water.

Detection: - Exclusive flag: has_mtc - Keywords: magnetization transfer, mtc

Effect: Tissues with bound protons (myelin, collagen) show signal loss.

Clinical use: - Myelin integrity assessment - MS lesion characterization

FlowComp (Flow Compensation)¶

Physics: Gradient waveforms designed to null velocity-induced phase.

Detection: - Exclusive flag: has_flow_comp - Keywords: flow comp, flowcomp, gmn, fc

Purpose: Reduces flow artifacts in vessels.

Variants: - First-order (velocity) - Higher-order (acceleration)

MoCo (Motion Correction)¶

Physics: Retrospective or prospective motion correction.

Detection: - Exclusive flag: has_moco - Keywords: moco, mocoseries, motion correct

Applications: - fMRI - Diffusion imaging - Pediatric/uncooperative patients

Note: Often indicated in DICOM ImageType as "MOCO" or "MOTIONCORRECTION".

Trajectory Modifiers¶

Radial (PROPELLER/BLADE)¶

Physics: Radial k-space spokes through center.

Detection: - Exclusive flag: is_radial - Keywords: propeller, blade, multivane, radial

Vendor names: - GE: PROPELLER - Siemens: BLADE - Philips: MultiVane

Benefit: Motion-robust due to oversampled k-space center.

Spiral¶

Physics: Spiral readout from k-space center.

Detection: - Exclusive flag: is_spiral - Keywords: spiral

Characteristics: - Very efficient k-space coverage - Sensitive to off-resonance artifacts - Used in ASL, fMRI research

Blood Signal Modifiers¶

BlackBlood¶

Physics: Double IR or motion-sensitizing prep to null flowing blood.

Detection: Keywords only: black blood, blackblood, dark blood

Clinical use: - Vessel wall imaging - Cardiac imaging - Plaque characterization

BrightBlood¶

Physics: Inflow enhancement (TOF-like) for bright arterial blood.

Detection: Keywords only: bright blood, brightblood

Clinical use: - Cardiac imaging - Angiography variants

Exclusion Group Logic¶

When multiple modifiers from the same exclusion group match, highest priority wins:

IR_CONTRAST Group¶

Modifier	Priority	TI Range
FLAIR	1	~2000-2500ms (CSF null)
STIR	2	~150-200ms (fat null)
DIR	3	Two TIs
PSIR	4	Phase-sensitive
IR	99	Generic fallback

If both FLAIR and STIR keywords appear, FLAIR wins (lower priority number = higher priority).

TRAJECTORY Group¶

Modifier	Priority
Radial	1
Spiral	2

Confidence Levels¶

Detection Method	Confidence
Exclusive flag	95%
Keywords match	85%
Combination (AND)	75%
No modifiers (valid)	80%

Note: "No modifiers detected" is a valid, confident result - many series have no modifiers.

Common Combinations¶

Series Type	Typical Modifiers
T2-FLAIR	`FLAIR`
STIR	`STIR`
T1 post-contrast FatSat	`FatSat`
Dixon VIBE	`Dixon`
PROPELLER T2	`Radial`
FLAIR with fat suppression	`FatSat,FLAIR`
Black blood TSE	`BlackBlood`

Modifier vs Technique¶

Some acquisitions could be viewed as either:

Acquisition	Classification
STIR	Technique: TSE/IR-TSE, Modifier: STIR
FLAIR	Technique: TSE, Modifier: FLAIR
MPRAGE	Technique: MPRAGE (IR is part of technique)
PROPELLER T2	Technique: TSE, Modifier: Radial

Rule: IR is a modifier for SE sequences, but part of the technique for GRE (MPRAGE, MP2RAGE).

YAML Configuration¶

Modifiers are configured in backend/src/classification/detection_yaml/modifier-detection.yaml:

exclusion_groups:
  IR_CONTRAST:
    description: "IR-based contrast modifiers"
    members: ["FLAIR", "STIR", "DIR", "PSIR"]
    fallback: "IR"

  TRAJECTORY:
    members: ["Radial", "Spiral"]

modifiers:
  FLAIR:
    name: "FLAIR"
    group: "IR_CONTRAST"
    priority: 1
    keywords:
      - "flair"
      - "dark fluid"
    detection:
      exclusive: is_flair

  FatSat:
    name: "FatSat"
    group: null  # Independent - can combine with any
    keywords:
      - "fatsat"
      - "spair"
    detection:
      exclusive: has_fat_sat

rules:
  priority_order:
    - "FLAIR"
    - "STIR"
    # ... IR group first
    - "FatSat"
    - "Dixon"
    # ... independent modifiers

Convenience Checks¶

The detector provides helper methods:

# Check if any IR modifier present
detector.has_ir_modifier(result)  # True if FLAIR, STIR, DIR, PSIR, or IR

# Check if any fat suppression
detector.has_fat_suppression(result)  # True if FatSat, WaterExc, STIR, or Dixon

# Check if trajectory modifier
detector.has_trajectory_modifier(result)  # True if Radial or Spiral