Low-field MRI denoising without ground truth

We demonstrate self-supervised (blind) denoising of a low-field MRI scan without ground truth data.

In low-field MRI, images have high noise due to the fixed permanent magnet, and acquiring clean reference images is often impossible. One could average the images over multiple repetitions, but if there’s any patient motion, the image would be blurry.

Here, we fine-tune the Reconstruct Anything Model (deepinv.models.RAM) [1] on a single noisy scan using the self-supervised Recorrupted2Recorrupted loss [2]. Play around with different self-supervised denoising losses (see Self-Supervised Learning) and models!

Note that, if more data is available, better results can be obtained by fine-tuning on more samples.

import torch
import deepinv as dinv

device = dinv.utils.get_device()

Selected GPU 0 with 4064.25 MiB free memory

Load data

We load a single low-field T1 MRI scan (Oper 0.3T) from the M4Raw dataset [3], which contains multiple repetitions of the same scan with inter-scan motion. We use the first repetition as our noisy measurement, and average all three repetitions to create a “reference” (which is still blurry due to motion).

def open_m4raw(fname: str) -> torch.Tensor:
    """Load M4Raw slice"""
    x = dinv.io.load_ismrmd(fname, data_slice=8).unsqueeze(
        0
    )  # Load middle slice, shape 12NHW
    x = dinv.utils.MRIMixin().kspace_to_im(x)  # Convert to image space
    x = dinv.utils.MRIMixin().rss(
        x, multicoil=True
    )  # Root-sum-square following original paper, shape 11HW
    x = dinv.utils.normalize_signal(x, mode="min_max")  # Normalise to 0-1
    return x


DATA_DIR = dinv.utils.get_data_home() / "m4raw" / "motion"
DATA_DIR.mkdir(parents=True, exist_ok=True)

dinv.utils.download_example("demo_m4raw_inter-scan_motion_0.h5", DATA_DIR)
dinv.utils.download_example("demo_m4raw_inter-scan_motion_1.h5", DATA_DIR)
dinv.utils.download_example("demo_m4raw_inter-scan_motion_2.h5", DATA_DIR)

y = open_m4raw(DATA_DIR / "demo_m4raw_inter-scan_motion_0.h5")

x = torch.cat(
    [
        open_m4raw(DATA_DIR / "demo_m4raw_inter-scan_motion_0.h5"),
        open_m4raw(DATA_DIR / "demo_m4raw_inter-scan_motion_1.h5"),
        open_m4raw(DATA_DIR / "demo_m4raw_inter-scan_motion_2.h5"),
    ]
).mean(
    dim=0, keepdim=True
)  # Average 3 repetitions

Since the data is raw, we estimate the noise level in both the single scan and the averaged scan using patch covariance. Note that the averaged scan has lower noise as expected, but observe the motion blurring!

noise_estimator = dinv.models.PatchCovarianceNoiseEstimator()

dinv.utils.plot(
    {"Noisy scan": y, "3x rep, averaged": x},
    subtitles=[
        f"sigma: {noise_estimator(y).item():.4f}",
        f"sigma: {noise_estimator(x).item():.4f}",
    ],
)

Physics

We define a simple denoising physics with Gaussian noise matching the estimated noise level.

with torch.no_grad():
    sigma = noise_estimator(y.to(device))
physics = dinv.physics.Denoising(dinv.physics.GaussianNoise(sigma=sigma), device=device)

Zero-shot reconstruction

First, we apply the pre-trained RAM model as a zero-shot denoiser without any training.

model = dinv.models.RAM(device=device)
with torch.no_grad():
    x_net = model(y.to(device), physics)

Self-supervised fine-tuning

We create a dataset from the single noisy scan and fine-tune RAM using the R2R loss. See the dedicated R2R example for more.

Note

We train for 50 epochs on GPU. For faster execution on CPU, set epochs to a smaller value.

dataset = dinv.datasets.TensorDataset(y=y)

trainer = dinv.Trainer(
    model=model,
    physics=physics,
    train_dataloader=torch.utils.data.DataLoader(dataset, batch_size=1),
    optimizer=torch.optim.AdamW(model.parameters(), lr=1e-5),
    epochs=1 if str(device) == "cpu" else 50,
    losses=dinv.loss.R2RLoss(noise_model=None),
    metrics=None,
    device=device,
    save_path=None,
)
model = trainer.train()
model = model.eval()

/local/jtachell/deepinv/deepinv/deepinv/training/trainer.py:1354: UserWarning: non_blocking_transfers=True but DataLoader.pin_memory=False; set pin_memory=True to overlap host-device copies with compute.
  self.setup_train()
The model has 35618813 trainable parameters
/local/jtachell/deepinv/deepinv/deepinv/training/trainer.py:549: UserWarning: Update progress bar frequency of 1 may slow down training on GPU. Consider setting freq_update_progress_bar > 1.
  warnings.warn(

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Train epoch 38/50: 100%|██████████| 1/1 [00:00<00:00,  5.84it/s, TotalLoss=0.00364]

  0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 39/50:   0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 39/50:   0%|          | 0/1 [00:00<?, ?it/s, TotalLoss=0.00363]
Train epoch 39/50: 100%|██████████| 1/1 [00:00<00:00,  5.87it/s, TotalLoss=0.00363]
Train epoch 39/50: 100%|██████████| 1/1 [00:00<00:00,  5.86it/s, TotalLoss=0.00363]

  0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 40/50:   0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 40/50:   0%|          | 0/1 [00:00<?, ?it/s, TotalLoss=0.00358]
Train epoch 40/50: 100%|██████████| 1/1 [00:00<00:00,  5.73it/s, TotalLoss=0.00358]
Train epoch 40/50: 100%|██████████| 1/1 [00:00<00:00,  5.72it/s, TotalLoss=0.00358]

  0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 41/50:   0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 41/50:   0%|          | 0/1 [00:00<?, ?it/s, TotalLoss=0.00358]
Train epoch 41/50: 100%|██████████| 1/1 [00:00<00:00,  5.93it/s, TotalLoss=0.00358]
Train epoch 41/50: 100%|██████████| 1/1 [00:00<00:00,  5.91it/s, TotalLoss=0.00358]

  0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 42/50:   0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 42/50:   0%|          | 0/1 [00:00<?, ?it/s, TotalLoss=0.00361]
Train epoch 42/50: 100%|██████████| 1/1 [00:00<00:00,  6.05it/s, TotalLoss=0.00361]
Train epoch 42/50: 100%|██████████| 1/1 [00:00<00:00,  6.03it/s, TotalLoss=0.00361]

  0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 43/50:   0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 43/50:   0%|          | 0/1 [00:00<?, ?it/s, TotalLoss=0.00362]
Train epoch 43/50: 100%|██████████| 1/1 [00:00<00:00,  6.08it/s, TotalLoss=0.00362]
Train epoch 43/50: 100%|██████████| 1/1 [00:00<00:00,  6.07it/s, TotalLoss=0.00362]

  0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 44/50:   0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 44/50:   0%|          | 0/1 [00:00<?, ?it/s, TotalLoss=0.00358]
Train epoch 44/50: 100%|██████████| 1/1 [00:00<00:00,  6.26it/s, TotalLoss=0.00358]
Train epoch 44/50: 100%|██████████| 1/1 [00:00<00:00,  6.25it/s, TotalLoss=0.00358]

  0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 45/50:   0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 45/50:   0%|          | 0/1 [00:00<?, ?it/s, TotalLoss=0.00363]
Train epoch 45/50: 100%|██████████| 1/1 [00:00<00:00,  5.77it/s, TotalLoss=0.00363]
Train epoch 45/50: 100%|██████████| 1/1 [00:00<00:00,  5.76it/s, TotalLoss=0.00363]

  0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 46/50:   0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 46/50:   0%|          | 0/1 [00:00<?, ?it/s, TotalLoss=0.00362]
Train epoch 46/50: 100%|██████████| 1/1 [00:00<00:00,  6.14it/s, TotalLoss=0.00362]
Train epoch 46/50: 100%|██████████| 1/1 [00:00<00:00,  6.13it/s, TotalLoss=0.00362]

  0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 47/50:   0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 47/50:   0%|          | 0/1 [00:00<?, ?it/s, TotalLoss=0.00362]
Train epoch 47/50: 100%|██████████| 1/1 [00:00<00:00,  5.76it/s, TotalLoss=0.00362]
Train epoch 47/50: 100%|██████████| 1/1 [00:00<00:00,  5.75it/s, TotalLoss=0.00362]

  0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 48/50:   0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 48/50:   0%|          | 0/1 [00:00<?, ?it/s, TotalLoss=0.0036]
Train epoch 48/50: 100%|██████████| 1/1 [00:00<00:00,  5.64it/s, TotalLoss=0.0036]
Train epoch 48/50: 100%|██████████| 1/1 [00:00<00:00,  5.63it/s, TotalLoss=0.0036]

  0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 49/50:   0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 49/50:   0%|          | 0/1 [00:00<?, ?it/s, TotalLoss=0.00358]
Train epoch 49/50: 100%|██████████| 1/1 [00:00<00:00,  6.12it/s, TotalLoss=0.00358]
Train epoch 49/50: 100%|██████████| 1/1 [00:00<00:00,  6.10it/s, TotalLoss=0.00358]

  0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 50/50:   0%|          | 0/1 [00:00<?, ?it/s]
Train epoch 50/50:   0%|          | 0/1 [00:00<?, ?it/s, TotalLoss=0.00358]
Train epoch 50/50: 100%|██████████| 1/1 [00:00<00:00,  6.18it/s, TotalLoss=0.00358]
Train epoch 50/50: 100%|██████████| 1/1 [00:00<00:00,  6.17it/s, TotalLoss=0.00358]

Evaluation

We see that the zero-shot recon is denoised, but details are blurry. The fine-tuned recon has clearer details, which is both less noisy than than the input data, but less blurry than the averaged image.

with torch.no_grad():
    x_ft = model(y.to(device), physics)

dinv.utils.plot(
    {
        "Noisy scan": y,
        "3x rep, averaged": x,
        "Zero-shot RAM": x_net,
        "Fine-tuned RAM": x_ft,
    },
)

References:

[1]

Matthieu Terris, Samuel Hurault, Maxime Song, and Julián Tachella. Reconstruct anything model: a lightweight foundation model for computational imaging. arXiv preprint arXiv:2503.08915, 2025.

[2]

Tongyao Pang, Huan Zheng, Yuhui Quan, and Hui Ji. Recorrupted-to-recorrupted: unsupervised deep learning for image denoising. In Proceedings of the IEEE/CVF conference on computer vision and pattern recognition, 2043–2052. 2021.

[3]

Mengye Lyu, Lifeng Mei, Shoujin Huang, Sixing Liu, Yi Li, Kexin Yang, Yilong Liu, Yu Dong, Linzheng Dong, and Ed X Wu. M4raw: a multi-contrast, multi-repetition, multi-channel mri k-space dataset for low-field mri research. Scientific Data, 10(1):264, 2023.