qmri-dro 0.1.0

Digital Reference Objects for quantitative MRI validation

qmri-dro

Digital Reference Objects (DROs) for quantitative MRI validation.

Overview

qmri-dro provides tools for generating synthetic MRI data with known ground truth parameters. This is essential for:

• Validation: Test fitting algorithms against known ground truth
• Education: Demonstrate how MRI parameters affect signal
• Benchmarking: Compare fitting methods (e.g., LLS vs WLLS vs IWLLS)
• Testing: Reproducible synthetic data for unit tests
• Sensitivity analysis: Study noise/parameter effects on results

Installation

pip install qmri-dro

Or with uv:

uv add qmri-dro

Quick Start

DWI Phantom

from qmri.dro import dwi
from qmri.diffusion import adc

# Generate a phantom with known ADC
phantom = dwi.generate(adc=1e-3, s0=1000, snr=50, seed=42)

# Fit and compare to ground truth
result = adc.fit(phantom.signal, phantom.b_values)
print(f"True ADC: {phantom.ground_truth['adc'].value:.2e}")
print(f"Fitted ADC: {result.adc:.2e}")

T1 Phantom

from qmri.dro import relaxometry
from qmri.relaxometry import t1

# Generate IR data with known T1
phantom = relaxometry.generate_t1_ir(
    t1=1.2,
    inversion_times=[0.1, 0.5, 1.0, 2.0, 3.0],
    repetition_time=5.0,
    snr=100,
    seed=42,
)

# Fit and validate
result = t1.fit_ir(phantom.signal, phantom.time_points, repetition_times=5.0)
print(f"True T1: {phantom.ground_truth['t1'].value:.2f} s")
print(f"Fitted T1: {float(result.t1):.2f} s")

ASL Phantom

from qmri.dro import perfusion

# Generate pCASL data with known perfusion
phantom = perfusion.generate_pcasl(
    perfusion_rate=60.0,  # ml/100g/min
    m0=1000.0,
    transit_time=1.0,
    snr=50,
    seed=42,
)

# Access the difference signal
delta_m = phantom.control - phantom.label
print(f"True CBF: {phantom.ground_truth['perfusion_rate'].value} ml/100g/min")

Features

• Noise models: Gaussian and Rician noise with reproducible seeding
• Ground truth tracking: All phantoms include documented ground truth values
• Multi-voxel support: Generate single voxels or calibration phantoms
• Calibration phantoms: Pre-configured phantoms for standardised testing

Documentation

Full documentation: https://gold-standard-phantoms.github.io/qmri

Licence

MIT