qmrpy 0.6.0

Python toolkit for quantitative MRI modeling, fitting, and simulation.

qmrpy

Python toolkit for quantitative MRI (qMRI) modeling, fitting, and simulation.

Statement of need

qMRLab (MATLAB) and DECAES (Julia) provide widely used qMRI reference implementations, but integration into Python workflows can be frictional. qmrpy reimplements key models in Python with a unified API, explicit parameter naming, and reproducible tests so researchers can run model fitting and comparisons inside a single Python environment.

Scope

• Models: T1, T2, B1, QSM, noise, and simulation utilities.
• Interfaces: object-oriented models plus functional wrappers.
• Verification: parity checks for DECAES components and a broad test suite.

Installation

pip install qmrpy

If you use uv:

uv add qmrpy

Quickstart

import numpy as np
from qmrpy.models.t1.vfa_t1 import VfaT1

model = VfaT1(tr_ms=15.0, flip_angle_deg=np.array([2, 5, 10, 15]))

signal = model.forward(m0=1.0, t1_ms=1200.0)
fit = model.fit(signal)
print(fit["t1_ms"], fit["m0"])

Functional API (no object):

import numpy as np
from qmrpy import vfa_t1_fit

signal = np.array([0.02, 0.06, 0.12, 0.18], dtype=float)
fit = vfa_t1_fit(signal, flip_angle_deg=np.array([2, 5, 10, 15]), tr_ms=15.0)
print(fit["t1_ms"], fit["m0"])

EPG-corrected T2 (multi-echo spin-echo):

import numpy as np
from qmrpy.models.t2 import EpgT2

model = EpgT2(n_te=32, te_ms=10.0, t1_ms=1000.0, alpha_deg=180.0)
signal = model.forward(m0=1.0, t2_ms=80.0)
fit = model.fit(signal)
print(fit["t2_ms"], fit["m0"])

Optional B1 correction: forward(..., b1=0.9), fit(..., b1=0.9), or fit_image(..., b1_map=...).

Functional API (EPG-corrected T2):

import numpy as np
from qmrpy import epg_t2_fit, epg_t2_forward

signal = epg_t2_forward(
    m0=1.0, t2_ms=80.0, n_te=32, te_ms=10.0, t1_ms=1000.0, alpha_deg=180.0
)
fit = epg_t2_fit(signal, n_te=32, te_ms=10.0, t1_ms=1000.0, alpha_deg=180.0)
print(fit["t2_ms"], fit["m0"])

B1 mapping integration (example):

import numpy as np
from qmrpy.models.b1 import B1Dam
from qmrpy.models.t2 import EpgT2

b1_model = B1Dam(alpha_deg=60.0)
sig_b1 = b1_model.forward(m0=1.0, b1=0.9)
b1_fit = b1_model.fit(sig_b1)

t2_model = EpgT2(n_te=16, te_ms=10.0, t1_ms=1000.0, alpha_deg=180.0)
sig_t2 = t2_model.forward(m0=1.0, t2_ms=80.0, b1=b1_fit["b1_raw"])
t2_fit = t2_model.fit(sig_t2, b1=b1_fit["b1_raw"])
print(t2_fit["t2_ms"])

Use b1_map for voxel-wise correction: t2_model.fit_image(data, b1_map=..., mask=...).

API overview

• Names use physical quantity + unit (e.g., t1_ms, t2_ms, flip_angle_deg).
• forward(**params) returns simulated signal(s).
• fit(signal, **kwargs) returns a dict for a single voxel.
• fit_image(data, mask=None, **kwargs) returns a dict for images/volumes.
  • data shape is (..., n_obs) and mask matches spatial shape.
• Primary estimates use fixed keys (e.g., t1_ms, t2_ms, m0); auxiliaries use snake_case.

Model modules:

• qmrpy.models.t1
• qmrpy.models.t2
• qmrpy.models.b1
• qmrpy.models.qsm
• qmrpy.models.noise
• qmrpy.sim

Verification highlights

DECAES parity (reference CSV)

Errors against reference CSV in tests/data (regenerate with uv run scripts/summarize_parity.py --no-qmrlab).

reg	abs(alpha-alpha_ref) [deg]	abs(mu-mu_ref)	abs(chi2factor-chi2_ref)	max abs(dist-dist_ref)
none	0	N/A	N/A	2.22045e-15
gcv	1.99e-10	4.79026e-08	N/A	1.12119e-06
lcurve	1.99e-10	0	1.04894e-11	3.29564e-12
chi2	1.99e-10	5.67276e-14	1.28786e-14	4.82459e-12
mdp	1.99e-10	5.66938e-14	1.69642e-13	4.91318e-12

qMRLab parity (optional)

Requires Octave and a qMRLab checkout. The script compares qMRLab-generated signals against qmrpy fits.

QMRLAB_PATH=/path/to/qMRLab uv run scripts/verify_parity.py --model inversion_recovery
QMRLAB_PATH=/path/to/qMRLab uv run scripts/verify_qmrlab_mwf.py
QMRLAB_PATH=/path/to/qMRLab uv run scripts/sweep_qmrlab_mwf.py

Inversion Recovery (Barral, rdNLS):

metric	abs diff
T1 (ms)	0

MWF example:

metric	abs diff
MWF (%)	0.105
T2MW (ms)	0.127
T2IEW (ms)	0.045

Tests

Run the test suite:

uv run --locked -m pytest

Generate a test matrix table (output under output/, not tracked):

uv run scripts/summarize_tests.py

Development

uv sync --extra viz
uv sync --extra viz --extra dev

Citation

For JOSS submission, see paper.md and paper.bib. A Zenodo archive DOI will be added before release.

License

• qmrpy core: MIT (LICENSE)
• Third-party notices: THIRD_PARTY_NOTICES.md