From 1ff2de9658341cd3b40c37373d56a2c7e167b7c6 Mon Sep 17 00:00:00 2001 From: georgeyiasemis Date: Fri, 17 May 2024 11:49:21 +0200 Subject: [PATCH 1/8] JSSL/SSL vsharp engine --- direct/nn/ssl/mri_models.py | 2 +- direct/nn/vsharp/vsharp_engine.py | 443 +++++++++++++++++++++++++- tests/tests_ssl/test_vsharp_engine.py | 194 +++++++++++ 3 files changed, 635 insertions(+), 4 deletions(-) create mode 100644 tests/tests_ssl/test_vsharp_engine.py diff --git a/direct/nn/ssl/mri_models.py b/direct/nn/ssl/mri_models.py index 0fe7caec..b56d2990 100644 --- a/direct/nn/ssl/mri_models.py +++ b/direct/nn/ssl/mri_models.py @@ -19,7 +19,7 @@ from direct.utils import detach_dict, dict_to_device, normalize_image from direct.utils.events import get_event_storage -__all__ = ["SSLMRIModelEngine"] +__all__ = ["SSLMRIModelEngine", "JSSLMRIModelEngine"] class SSLMRIModelEngine(MRIModelEngine): diff --git a/direct/nn/vsharp/vsharp_engine.py b/direct/nn/vsharp/vsharp_engine.py index 0ec3f8d4..ad745f8b 100644 --- a/direct/nn/vsharp/vsharp_engine.py +++ b/direct/nn/vsharp/vsharp_engine.py @@ -1,6 +1,18 @@ # Copyright (c) DIRECT Contributors -"""Engine for vSHARP 2D model.""" +"""Engines for vSHARP 2D and 3D models [1]. + +Includes supervised, self-supervised and joint supervised and self-supervised learning [2] engines. + +References +---------- +.. [1] Yiasemis, G., Moriakov, N., Sánchez, C.I., Sonke, J.-J., Teuwen, J.: JSSL: Joint Supervised and + Self-supervised Learning for MRI Reconstruction, http://arxiv.org/abs/2311.15856, (2023). + https://doi.org/10.48550/arXiv.2311.15856. +.. [2] Yiasemis, G., Moriakov, N., Sánchez, C.I., Sonke, J.-J., Teuwen, J.: JSSL: Joint Supervised and + Self-supervised Learning for MRI Reconstruction, http://arxiv.org/abs/2311.15856, (2023). + https://doi.org/10.48550/arXiv.2311.15856. +""" from __future__ import annotations @@ -14,12 +26,13 @@ from direct.data import transforms as T from direct.engine import DoIterationOutput from direct.nn.mri_models import MRIModelEngine +from direct.nn.ssl.mri_models import JSSLMRIModelEngine, SSLMRIModelEngine from direct.types import TensorOrNone from direct.utils import detach_dict, dict_to_device class VSharpNet3DEngine(MRIModelEngine): - """VSharpNet Engine.""" + """VSharpNet 3D Model Engine.""" def __init__( self, @@ -31,7 +44,7 @@ def __init__( mixed_precision: bool = False, **models: nn.Module, ): - """Inits :class:`VSharpNetEngine`. + """Inits :class:`VSharpNet3DEngine`. Parameters ---------- @@ -270,3 +283,427 @@ def forward_function(self, data: dict[str, Any]) -> tuple[torch.Tensor, torch.Te ) return output_images, output_kspace + + +class VSharpNetSSLEngine(SSLMRIModelEngine): + """Self-supervised Learning vSHARP Model 2D Engine. + + Used for the main experiments for SSL in the JSSL paper [1]. + + Parameters + ---------- + cfg: BaseConfig + Configuration file. + model: nn.Module + Model. + device: str + Device. Can be "cuda:{idx}" or "cpu". + forward_operator: Callable[[tuple[Any, ...]], torch.Tensor], optional + The forward operator. Default: None. + backward_operator: Callable[[tuple[Any, ...]], torch.Tensor], optional + The backward operator. Default: None. + mixed_precision: bool + Use mixed precision. Default: False. + **models: nn.Module + Additional models. + + + References + ---------- + .. [1] Yiasemis, G., Moriakov, N., Sánchez, C.I., Sonke, J.-J., Teuwen, J.: JSSL: Joint Supervised and + Self-supervised Learning for MRI Reconstruction, http://arxiv.org/abs/2311.15856, (2023). + https://doi.org/10.48550/arXiv.2311.15856. + """ + + def __init__( + self, + cfg: BaseConfig, + model: nn.Module, + device: str, + forward_operator: Optional[Callable] = None, + backward_operator: Optional[Callable] = None, + mixed_precision: bool = False, + **models: nn.Module, + ): + """Inits :class:`VSharpNetSSLEngine`. + + Parameters + ---------- + cfg: BaseConfig + Configuration file. + model: nn.Module + Model. + device: str + Device. Can be "cuda:{idx}" or "cpu". + forward_operator: Callable[[tuple[Any, ...]], torch.Tensor], optional + The forward operator. Default: None. + backward_operator: Callable[[tuple[Any, ...]], torch.Tensor], optional + The backward operator. Default: None. + mixed_precision: bool + Use mixed precision. Default: False. + **models: nn.Module + Additional models. + """ + super().__init__( + cfg, + model, + device, + forward_operator=forward_operator, + backward_operator=backward_operator, + mixed_precision=mixed_precision, + **models, + ) + + def forward_function(self, data: dict[str, Any]) -> None: + """Forward function for :class:`VSharpNetSSLEngine`.""" + raise NotImplementedError( + "Forward function for SSL vSHARP engine is not implemented. `VSharpNetSSLEngine` " + "implements the `_do_iteration` method itself so the forward function should not be " + "called." + ) + + def _do_iteration( + self, + data: dict[str, Any], + loss_fns: Optional[dict[str, Callable]] = None, + regularizer_fns: Optional[dict[str, Callable]] = None, + ) -> DoIterationOutput: + """This function implements the `_do_iteration` for the SSL vSHARP model. + + Returns + ------- + DoIterationOutput + Output of the iteration. + + + It assumes different behavior for training and inference. During training, it expects the input data + to contain keys "input_kspace" and "input_sampling_mask", otherwise, it expects the input data to contain + keys "masked_kspace" and "sampling_mask". + + Parameters + ---------- + data : dict[str, Any] + Input data dictionary. The dictionary should contain the following keys: + - "input_kspace" if training, otherwise "masked_kspace". + - "input_sampling_mask" if training, otherwise "sampling_mask". + - "target_sampling_mask": Sampling mask for the target k-space if training. + - "sensitivity_map": Sensitivity map. + - "target": Target image. + - "padding": Padding, optionally. + loss_fns : Optional[dict[str, Callable]], optional + Loss functions, optional. + regularizer_fns : Optional[dict[str, Callable]], optional + Regularizer functions, optional. + + """ + + # loss_fns can be None, e.g. during validation + if loss_fns is None: + loss_fns = {} + + if regularizer_fns is None: + regularizer_fns = {} + + # Move data to device + data = dict_to_device(data, self.device) + + # Get the k-space and mask which differ during training and inference for SSL + if self.model.training: + kspace, mask = data["input_kspace"], data["input_sampling_mask"] + else: + kspace, mask = data["masked_kspace"], data["sampling_mask"] + + # Initialize loss and regularizer dictionaries + loss_dict = {k: torch.tensor([0.0], dtype=data["target"].dtype).to(self.device) for k in loss_fns.keys()} + regularizer_dict = { + k: torch.tensor([0.0], dtype=data["target"].dtype).to(self.device) for k in regularizer_fns.keys() + } + + with autocast(enabled=self.mixed_precision): + data["sensitivity_map"] = self.compute_sensitivity_map(data["sensitivity_map"]) + + output_images = self.model( + masked_kspace=kspace, + sampling_mask=mask, + sensitivity_map=data["sensitivity_map"], + ) + + if self.model.training: + if len(output_images) > 1: + # Initialize auxiliary loss weights with a logarithmic scale if multiple auxiliary steps + auxiliary_loss_weights = torch.logspace(-1, 0, steps=len(output_images)).to(output_images[0]) + else: + # Initialize auxiliary loss weights with a single value of 1.0 if single step + auxiliary_loss_weights = torch.ones(1).to(output_images[0]) + + for i in range(len(output_images)): + # Data consistency + output_kspace = T.apply_padding( + kspace + self._forward_operator(output_images[i], data["sensitivity_map"], ~mask), + padding=data.get("padding", None), + ) + # Project predicted k-space onto target k-space if SSL + output_kspace = T.apply_mask(output_kspace, data["target_sampling_mask"], return_mask=False) + + # Compute k-space loss per auxiliary step + loss_dict = self.compute_loss_on_data( + loss_dict, loss_fns, data, None, output_kspace, auxiliary_loss_weights[i] + ) + regularizer_dict = self.compute_loss_on_data( + regularizer_dict, regularizer_fns, data, None, output_kspace, auxiliary_loss_weights[i] + ) + + # SENSE reconstruction + output_images[i] = T.modulus( + T.reduce_operator( + self.backward_operator(output_kspace, dim=self._spatial_dims), + data["sensitivity_map"], + self._coil_dim, + ) + ) + + # Compute image loss per auxiliary step + loss_dict = self.compute_loss_on_data( + loss_dict, loss_fns, data, output_images[i], None, auxiliary_loss_weights[i] + ) + regularizer_dict = self.compute_loss_on_data( + regularizer_dict, regularizer_fns, data, output_images[i], None, auxiliary_loss_weights[i] + ) + + loss = sum(loss_dict.values()) + sum(regularizer_dict.values()) # type: ignore + self._scaler.scale(loss).backward() + + output_image = output_images[-1] + else: + output_kspace = T.apply_padding( + kspace + self._forward_operator(output_images[-1], data["sensitivity_map"], ~mask), + padding=data.get("padding", None), + ) + # SENSE reconstruction using data consistent k-space + output_image = T.modulus( + T.reduce_operator( + self.backward_operator(output_kspace, dim=self._spatial_dims), + data["sensitivity_map"], + self._coil_dim, + ) + ) + + loss_dict = detach_dict(loss_dict) # Detach dict, only used for logging. + regularizer_dict = detach_dict(regularizer_dict) + + return DoIterationOutput( + output_image=output_image, + sensitivity_map=data["sensitivity_map"], + data_dict={**loss_dict, **regularizer_dict}, + ) + + +class VSharpNetJSSLEngine(JSSLMRIModelEngine): + """Joint Supervised and Self-supervised Learning vSHARP Model 2D Engine. + + Used for the main experiments in the JSSL paper [1]. + + Parameters + ---------- + cfg: BaseConfig + Configuration file. + model: nn.Module + Model. + device: str + Device. Can be "cuda:{idx}" or "cpu". + forward_operator: Callable[[tuple[Any, ...]], torch.Tensor], optional + The forward operator. Default: None. + backward_operator: Callable[[tuple[Any, ...]], torch.Tensor], optional + The backward operator. Default: None. + mixed_precision: bool + Use mixed precision. Default: False. + **models: nn.Module + Additional models. + + + References + ---------- + .. [1] Yiasemis, G., Moriakov, N., Sánchez, C.I., Sonke, J.-J., Teuwen, J.: JSSL: Joint Supervised and + Self-supervised Learning for MRI Reconstruction, http://arxiv.org/abs/2311.15856, (2023). + https://doi.org/10.48550/arXiv.2311.15856. + """ + + def __init__( + self, + cfg: BaseConfig, + model: nn.Module, + device: str, + forward_operator: Optional[Callable] = None, + backward_operator: Optional[Callable] = None, + mixed_precision: bool = False, + **models: nn.Module, + ): + """Inits :class:`VSharpNetJSSLEngine`. + + Parameters + ---------- + cfg: BaseConfig + Configuration file. + model: nn.Module + Model. + device: str + Device. Can be "cuda:{idx}" or "cpu". + forward_operator: Callable[[tuple[Any, ...]], torch.Tensor], optional + The forward operator. Default: None. + backward_operator: Callable[[tuple[Any, ...]], torch.Tensor], optional + The backward operator. Default: None. + mixed_precision: bool + Use mixed precision. Default: False. + **models: nn.Module + Additional models. + """ + super().__init__( + cfg, + model, + device, + forward_operator=forward_operator, + backward_operator=backward_operator, + mixed_precision=mixed_precision, + **models, + ) + + def forward_function(self, data: dict[str, Any]) -> None: + """Forward function for :class:`VSharpNetJSSLEngine`.""" + raise NotImplementedError( + "Forward function for JSSL vSHARP is not implemented. `VSharpNetJSSLEngine` " + "implements the `_do_iteration` method itself so the forward function should not be " + "called." + ) + + def _do_iteration( + self, + data: dict[str, Any], + loss_fns: Optional[dict[str, Callable]] = None, + regularizer_fns: Optional[dict[str, Callable]] = None, + ) -> DoIterationOutput: + """This function implements the `_do_iteration` for the JSSL vSHARP model. + + Returns + ------- + DoIterationOutput + Output of the iteration. + + + It assumes different behavior for SSL training and inference. During SSL training, it expects the input data + to contain keys "input_kspace" and "input_sampling_mask", otherwise, it expects the input data to contain + keys "masked_kspace" and "sampling_mask". + + Parameters + ---------- + data : dict[str, Any] + Input data dictionary. The dictionary should contain the following keys: + - "is_ssl": Boolean indicating if the sample is for SSL training. + - "input_kspace" if SSL training, otherwise "masked_kspace". + - "input_sampling_mask" if SSL training, otherwise "sampling_mask". + - "target_sampling_mask": Sampling mask for the target k-space if SSL training. + - "sensitivity_map": Sensitivity map. + - "target": Target image. + - "padding": Padding, optionally. + loss_fns : Optional[dict[str, Callable]], optional + Loss functions, optional. + regularizer_fns : Optional[dict[str, Callable]], optional + Regularizer functions, optional. + + """ + + # loss_fns can be None, e.g. during validation + if loss_fns is None: + loss_fns = {} + + if regularizer_fns is None: + regularizer_fns = {} + + # Move data to device + data = dict_to_device(data, self.device) + + # Get a boolean indicating if the sample is for SSL training + # This will expect the input data to contain the keys "input_kspace" and "input_sampling_mask" if SSL training + is_ssl = data["is_ssl"][0] + + # Get the k-space and mask which differ if SSL training or supervised training + # The also differ during training and inference for SSL + if is_ssl and self.model.training: + kspace, mask = data["input_kspace"], data["input_sampling_mask"] + else: + kspace, mask = data["masked_kspace"], data["sampling_mask"] + + # Initialize loss and regularizer dictionaries + loss_dict = {k: torch.tensor([0.0], dtype=data["target"].dtype).to(self.device) for k in loss_fns.keys()} + regularizer_dict = { + k: torch.tensor([0.0], dtype=data["target"].dtype).to(self.device) for k in regularizer_fns.keys() + } + + with autocast(enabled=self.mixed_precision): + data["sensitivity_map"] = self.compute_sensitivity_map(data["sensitivity_map"]) + + output_images = self.model( + masked_kspace=kspace, + sampling_mask=mask, + sensitivity_map=data["sensitivity_map"], + ) + + if self.model.training: + if len(output_images) > 1: + # Initialize auxiliary loss weights with a logarithmic scale if multiple auxiliary steps + auxiliary_loss_weights = torch.logspace(-1, 0, steps=len(output_images)).to(output_images[0]) + else: + # Initialize auxiliary loss weights with a single value of 1.0 if single step + auxiliary_loss_weights = torch.ones(1).to(output_images[0]) + + for i in range(len(output_images)): + # Data consistency + output_kspace = T.apply_padding( + kspace + self._forward_operator(output_images[i], data["sensitivity_map"], ~mask), + padding=data.get("padding", None), + ) + if is_ssl: + # Project predicted k-space onto target k-space if SSL + output_kspace = T.apply_mask(output_kspace, data["target_sampling_mask"], return_mask=False) + + # Compute k-space loss per auxiliary step + loss_dict = self.compute_loss_on_data( + loss_dict, loss_fns, data, None, output_kspace, auxiliary_loss_weights[i] + ) + regularizer_dict = self.compute_loss_on_data( + regularizer_dict, regularizer_fns, data, None, output_kspace, auxiliary_loss_weights[i] + ) + + # SENSE reconstruction if SSL else modulus if supervised + output_images[i] = T.modulus( + T.reduce_operator( + self.backward_operator(output_kspace, dim=self._spatial_dims), + data["sensitivity_map"], + self._coil_dim, + ) + if is_ssl + else output_images[i] + ) + + # Compute image loss per auxiliary step + loss_dict = self.compute_loss_on_data( + loss_dict, loss_fns, data, output_images[i], None, auxiliary_loss_weights[i] + ) + regularizer_dict = self.compute_loss_on_data( + regularizer_dict, regularizer_fns, data, output_images[i], None, auxiliary_loss_weights[i] + ) + + loss = sum(loss_dict.values()) + sum(regularizer_dict.values()) # type: ignore + self._scaler.scale(loss).backward() + + output_image = output_images[-1] + else: + output_image = T.modulus(output_images[-1]) + + loss_dict = detach_dict(loss_dict) # Detach dict, only used for logging. + regularizer_dict = detach_dict(regularizer_dict) + + return DoIterationOutput( + output_image=output_image, + sensitivity_map=data["sensitivity_map"], + data_dict={**loss_dict, **regularizer_dict}, + ) diff --git a/tests/tests_ssl/test_vsharp_engine.py b/tests/tests_ssl/test_vsharp_engine.py new file mode 100644 index 00000000..3cfb9a92 --- /dev/null +++ b/tests/tests_ssl/test_vsharp_engine.py @@ -0,0 +1,194 @@ +# Copyright (c) DIRECT Contributors + +"""Tests for SSL/JSSL engines in direct.nn.vsharp.vsharp_engine module.""" + +import functools + +import numpy as np +import pytest +import torch + +from direct.config.defaults import DefaultConfig, FunctionConfig, LossConfig, TrainingConfig, ValidationConfig +from direct.data.transforms import fft2, ifft2 +from direct.nn.vsharp.config import VSharpNet3DConfig, VSharpNetConfig +from direct.nn.vsharp.vsharp import VSharpNet, VSharpNet3D +from direct.nn.vsharp.vsharp_engine import VSharpNetJSSLEngine, VSharpNetSSLEngine + + +def create_sample(**kwargs): + sample = dict() + for k, v in locals()["kwargs"].items(): + sample[k] = v + return sample + + +@pytest.mark.parametrize( + "shape", + [(4, 3, 10, 16, 2), (5, 1, 10, 12, 2)], +) +@pytest.mark.parametrize( + "loss_fns", + [["l1_loss", "kspace_nmse_loss", "kspace_nmae_loss"]], +) +@pytest.mark.parametrize( + "num_steps, num_steps_dc_gd, num_filters, num_pool_layers", + [[4, 2, 10, 2]], +) +@pytest.mark.parametrize( + "normalized", + [True, False], +) +def test_vsharpnet_ssl_engine(shape, loss_fns, num_steps, num_steps_dc_gd, num_filters, num_pool_layers, normalized): + # Operators + forward_operator = functools.partial(fft2, centered=True) + backward_operator = functools.partial(ifft2, centered=True) + # Configs + loss_config = LossConfig(losses=[FunctionConfig(loss) for loss in loss_fns]) + training_config = TrainingConfig(loss=loss_config) + validation_config = ValidationConfig(crop=None) + model_config = VSharpNetConfig( + num_steps=num_steps, + num_steps_dc_gd=num_steps_dc_gd, + image_unet_num_filters=num_filters, + image_unet_num_pool_layers=num_pool_layers, + auxiliary_steps=-1, + ) + config = DefaultConfig(training=training_config, validation=validation_config, model=model_config) + # Models + model = VSharpNet( + forward_operator, + backward_operator, + num_steps=model_config.num_steps, + num_steps_dc_gd=model_config.num_steps_dc_gd, + image_unet_num_filters=model_config.image_unet_num_filters, + image_unet_num_pool_layers=model_config.image_unet_num_pool_layers, + auxiliary_steps=model_config.auxiliary_steps, + ) + sensitivity_model = torch.nn.Conv2d(2, 2, kernel_size=1) + # Define engine + engine = VSharpNetSSLEngine(config, model, "cpu", fft2, ifft2, sensitivity_model=sensitivity_model) + engine.ndim = 2 + # Simulate training + # Test _do_iteration function with a single data batch + data = create_sample( + input_sampling_mask=torch.from_numpy(np.random.rand(1, 1, shape[2], shape[3], 1)).round().bool(), + target_sampling_mask=torch.from_numpy(np.random.rand(1, 1, shape[2], shape[3], 1)).round().bool(), + input_kspace=torch.from_numpy(np.random.randn(shape[0], shape[1], shape[2], shape[3], 2)).float(), + kspace=torch.from_numpy(np.random.randn(shape[0], shape[1], shape[2], shape[3], 2)).float(), + sensitivity_map=torch.from_numpy(np.random.randn(shape[0], shape[1], shape[2], shape[3], 2)).float(), + target=torch.from_numpy(np.random.randn(shape[0], shape[2], shape[3])).float(), + scaling_factor=torch.ones(shape[0]), + ) + loss_fns = engine.build_loss() + out = engine._do_iteration(data, loss_fns) + out.output_image.shape == (shape[0],) + tuple(shape[2:-1]) + + # Simulate validation + engine.model.eval() + # Test _do_iteration function with a single data batch + data = create_sample( + sampling_mask=torch.from_numpy(np.random.rand(1, 1, shape[2], shape[3], 1)).round().bool(), + masked_kspace=torch.from_numpy(np.random.randn(shape[0], shape[1], shape[2], shape[3], 2)).float(), + kspace=torch.from_numpy(np.random.randn(shape[0], shape[1], shape[2], shape[3], 2)).float(), + sensitivity_map=torch.from_numpy(np.random.randn(shape[0], shape[1], shape[2], shape[3], 2)).float(), + target=torch.from_numpy(np.random.randn(shape[0], shape[2], shape[3])).float(), + scaling_factor=torch.ones(shape[0]), + ) + loss_fns = engine.build_loss() + out = engine._do_iteration(data, loss_fns) + assert out.output_image.shape == (shape[0],) + tuple(shape[2:-1]) + + +@pytest.mark.parametrize( + "shape", + [(4, 3, 10, 16, 2), (5, 1, 10, 12, 2)], +) +@pytest.mark.parametrize( + "loss_fns", + [["l1_loss", "kspace_nmse_loss", "kspace_nmae_loss"]], +) +@pytest.mark.parametrize( + "num_steps, num_steps_dc_gd, num_filters, num_pool_layers", + [[4, 2, 10, 2]], +) +@pytest.mark.parametrize( + "normalized", + [True, False], +) +def test_vsharpnet_jssl_engine(shape, loss_fns, num_steps, num_steps_dc_gd, num_filters, num_pool_layers, normalized): + # Operators + forward_operator = functools.partial(fft2, centered=True) + backward_operator = functools.partial(ifft2, centered=True) + # Configs + loss_config = LossConfig(losses=[FunctionConfig(loss) for loss in loss_fns]) + training_config = TrainingConfig(loss=loss_config) + validation_config = ValidationConfig(crop=None) + model_config = VSharpNetConfig( + num_steps=num_steps, + num_steps_dc_gd=num_steps_dc_gd, + image_unet_num_filters=num_filters, + image_unet_num_pool_layers=num_pool_layers, + auxiliary_steps=-1, + ) + config = DefaultConfig(training=training_config, validation=validation_config, model=model_config) + # Models + model = VSharpNet( + forward_operator, + backward_operator, + num_steps=model_config.num_steps, + num_steps_dc_gd=model_config.num_steps_dc_gd, + image_unet_num_filters=model_config.image_unet_num_filters, + image_unet_num_pool_layers=model_config.image_unet_num_pool_layers, + auxiliary_steps=model_config.auxiliary_steps, + ) + sensitivity_model = torch.nn.Conv2d(2, 2, kernel_size=1) + # Define engine + engine = VSharpNetJSSLEngine(config, model, "cpu", fft2, ifft2, sensitivity_model=sensitivity_model) + engine.ndim = 2 + + # Simulate training (SSL) + # Test _do_iteration function with a single data batch + data = create_sample( + input_sampling_mask=torch.from_numpy(np.random.rand(1, 1, shape[2], shape[3], 1)).round().bool(), + target_sampling_mask=torch.from_numpy(np.random.rand(1, 1, shape[2], shape[3], 1)).round().bool(), + input_kspace=torch.from_numpy(np.random.randn(shape[0], shape[1], shape[2], shape[3], 2)).float(), + kspace=torch.from_numpy(np.random.randn(shape[0], shape[1], shape[2], shape[3], 2)).float(), + sensitivity_map=torch.from_numpy(np.random.randn(shape[0], shape[1], shape[2], shape[3], 2)).float(), + target=torch.from_numpy(np.random.randn(shape[0], shape[2], shape[3])).float(), + scaling_factor=torch.ones(shape[0]), + is_ssl=torch.ones(shape[0]).bool(), + ) + loss_fns = engine.build_loss() + out = engine._do_iteration(data, loss_fns) + assert out.output_image.shape == (shape[0],) + tuple(shape[2:-1]) + + # Simulate training (SL) + # Test _do_iteration function with a single data batch + data = create_sample( + sampling_mask=torch.from_numpy(np.random.rand(1, 1, shape[2], shape[3], 1)).round().bool(), + masked_kspace=torch.from_numpy(np.random.randn(shape[0], shape[1], shape[2], shape[3], 2)).float(), + kspace=torch.from_numpy(np.random.randn(shape[0], shape[1], shape[2], shape[3], 2)).float(), + sensitivity_map=torch.from_numpy(np.random.randn(shape[0], shape[1], shape[2], shape[3], 2)).float(), + target=torch.from_numpy(np.random.randn(shape[0], shape[2], shape[3])).float(), + scaling_factor=torch.ones(shape[0]), + is_ssl=torch.zeros(shape[0]).bool(), + ) + loss_fns = engine.build_loss() + out = engine._do_iteration(data, loss_fns) + assert out.output_image.shape == (shape[0],) + tuple(shape[2:-1]) + + # Simulate validation + engine.model.eval() + # Test _do_iteration function with a single data batch + data = create_sample( + sampling_mask=torch.from_numpy(np.random.rand(1, 1, shape[2], shape[3], 1)).round().bool(), + masked_kspace=torch.from_numpy(np.random.randn(shape[0], shape[1], shape[2], shape[3], 2)).float(), + kspace=torch.from_numpy(np.random.randn(shape[0], shape[1], shape[2], shape[3], 2)).float(), + sensitivity_map=torch.from_numpy(np.random.randn(shape[0], shape[1], shape[2], shape[3], 2)).float(), + target=torch.from_numpy(np.random.randn(shape[0], shape[2], shape[3])).float(), + scaling_factor=torch.ones(shape[0]), + is_ssl=torch.zeros(shape[0]).bool(), + ) + loss_fns = engine.build_loss() + out = engine._do_iteration(data, loss_fns) + assert out.output_image.shape == (shape[0],) + tuple(shape[2:-1]) From 40e1cf5c5fe46ed00342cbe5ee6922740daec08f Mon Sep 17 00:00:00 2001 From: georgeyiasemis Date: Fri, 17 May 2024 14:50:20 +0200 Subject: [PATCH 2/8] Add readme and lists --- projects/JSSL/README.rst | 76 ++ projects/JSSL/lists/test_prostate.lst | 46 + .../lists/train_brain_16_coils_640x320.lst | 726 +++++++++++++ .../lists/train_brain_16_coils_768x396.lst | 630 ++++++++++++ .../lists/train_brain_20_coils_640x320.lst | 558 ++++++++++ .../lists/train_brain_20_coils_768x396.lst | 557 ++++++++++ .../lists/train_brain_4_coils_512x276.lst | 40 + .../lists/train_brain_4_coils_640x320.lst | 695 +++++++++++++ .../lists/train_brain_4_coils_640x322.lst | 356 +++++++ .../lists/train_brain_4_coils_768x392.lst | 104 ++ .../lists/train_brain_6_coils_640x320.lst | 51 + projects/JSSL/lists/train_knee.lst | 973 ++++++++++++++++++ .../JSSL/lists/train_prostate_10_coils.lst | 1 + .../JSSL/lists/train_prostate_14_coils.lst | 7 + .../JSSL/lists/train_prostate_16_coils.lst | 14 + .../JSSL/lists/train_prostate_20_coils.lst | 153 +++ .../JSSL/lists/train_prostate_24_coils.lst | 4 + .../JSSL/lists/train_prostate_26_coils.lst | 34 + .../JSSL/lists/train_prostate_30_coils.lst | 5 + projects/JSSL/lists/val_prostate.lst | 48 + 20 files changed, 5078 insertions(+) create mode 100644 projects/JSSL/README.rst create mode 100644 projects/JSSL/lists/test_prostate.lst create mode 100644 projects/JSSL/lists/train_brain_16_coils_640x320.lst create mode 100644 projects/JSSL/lists/train_brain_16_coils_768x396.lst create mode 100644 projects/JSSL/lists/train_brain_20_coils_640x320.lst create mode 100644 projects/JSSL/lists/train_brain_20_coils_768x396.lst create mode 100644 projects/JSSL/lists/train_brain_4_coils_512x276.lst create mode 100644 projects/JSSL/lists/train_brain_4_coils_640x320.lst create mode 100644 projects/JSSL/lists/train_brain_4_coils_640x322.lst create mode 100644 projects/JSSL/lists/train_brain_4_coils_768x392.lst create mode 100644 projects/JSSL/lists/train_brain_6_coils_640x320.lst create mode 100644 projects/JSSL/lists/train_knee.lst create mode 100644 projects/JSSL/lists/train_prostate_10_coils.lst create mode 100644 projects/JSSL/lists/train_prostate_14_coils.lst create mode 100644 projects/JSSL/lists/train_prostate_16_coils.lst create mode 100644 projects/JSSL/lists/train_prostate_20_coils.lst create mode 100644 projects/JSSL/lists/train_prostate_24_coils.lst create mode 100644 projects/JSSL/lists/train_prostate_26_coils.lst create mode 100644 projects/JSSL/lists/train_prostate_30_coils.lst create mode 100644 projects/JSSL/lists/val_prostate.lst diff --git a/projects/JSSL/README.rst b/projects/JSSL/README.rst new file mode 100644 index 00000000..2f77cf07 --- /dev/null +++ b/projects/JSSL/README.rst @@ -0,0 +1,76 @@ +JSSL: Joint Supervised and Self-supervised Learning for MRI Reconstruction +========================================================================== + +.. figure:: https://github.com/NKI-AI/direct/assets/71031687/97f1fa27-f4e4-44e2-b54a-7ac149f3c01d + :alt: fig + :name: fig1 + + Figure 1: The training process for the proposed Joint Supervised and Self-supervised Learning (JSSL) method is + divided into two phases: (1) Supervised Learning (SL) using fully sampled k-space data from proxy datasets. + During this phase, the model is trained to predict fully sampled data from retrospectively subsampled proxy data. + (2) Self-supervised Learning. + + +This project contains necessary configuration files to reproduce experiments of the paper +`JSSL: Joint Supervised and Self-supervised Learning for MRI Reconstruction `_. + + +Setting up data directory +------------------------- + +Prerequisites +~~~~~~~~~~~~~ + +Before you begin, make sure you have downloaded the all three fastMRI datasets - brain, knee and prostate. +For more information for downloading you can check out the `fastMRI website `_. + +Prostate Dataset Setup +~~~~~~~~~~~~~~~~~~~~~~ + +In this project, we use the `prostate dataset `_. from the fastMRI +as the target dataset. After downloading the dataset, you need to convert the data to necessary format. +Raw T2 prostate k-space data are provided with dimensions (averages, slices, coils, readout, phase). It is required to +convert the data to h5 format with dimensions (slices, coils, readout, phase) to match proxy datasets (brain and knee). +To do that you can use the GRAPPA T2 reconstruction code provided in the fastMRI Prostate `repository +`_. + + +Assumed Base Path Structure +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +To run the JSSL experiments with the provided configuration files in direct it's recommended that all data are stored +in the same directory or symlinked to the same directory. The configuration files assume that the data is stored in the +following structure: + +.. code-block:: text + + base_path + ├── training + │ ├── file_brain_AXT1_<..>.h5 + │ ├── file_brain_AXFLAIR_<..>.h5 + │ ├── ... + │ ├── file100<...>.h5 (knee) + │ ├── file101<...>.h5 (knee) + │ ├── ... + │ ├── file_prostate_AXT2_<...>.h5 + │ └── ... + ├── validation + │ ├── file_prostate_AXT2_<...>.h5 + │ └── ... + ├── test + │ ├── file_prostate_AXT2_<...>.h5 + | └── ... + + +The `base_path` is the root directory where all the data is stored. The `base_path` should contain +three subdirectories: `training`, `validation` and `test`. The `training` directory should contain all the training data +for the three datasets. The `validation` and `test` directories should contain the validation and test data for the +prostate dataset. The filenames should be the same as the ones in the fastMRI dataset. + + +Filenames lists +~~~~~~~~~~~~~~~ +Provided configuration files assume that `direct/projects/JSSL/lists/` contains `.lst` files for each dataset +which contains the list of filenames for training, validation and test datasets. Each list categorizes the filenames +based on the dataset they belong to, as well as shape and number of coils. This is necessary for the dataloader to +collate the data for batch size greater than 1. The filenames should be the same as the ones in the data directory. \ No newline at end of file diff --git a/projects/JSSL/lists/test_prostate.lst b/projects/JSSL/lists/test_prostate.lst new file mode 100644 index 00000000..7e941497 --- /dev/null +++ b/projects/JSSL/lists/test_prostate.lst @@ -0,0 +1,46 @@ +file_prostate_AXT2_0004.h5 +file_prostate_AXT2_0091.h5 +file_prostate_AXT2_0178.h5 +file_prostate_AXT2_0222.h5 +file_prostate_AXT2_0299.h5 +file_prostate_AXT2_0028.h5 +file_prostate_AXT2_0100.h5 +file_prostate_AXT2_0180.h5 +file_prostate_AXT2_0224.h5 +file_prostate_AXT2_0300.h5 +file_prostate_AXT2_0036.h5 +file_prostate_AXT2_0104.h5 +file_prostate_AXT2_0183.h5 +file_prostate_AXT2_0225.h5 +file_prostate_AXT2_0304.h5 +file_prostate_AXT2_0037.h5 +file_prostate_AXT2_0125.h5 +file_prostate_AXT2_0184.h5 +file_prostate_AXT2_0256.h5 +file_prostate_AXT2_0305.h5 +file_prostate_AXT2_0038.h5 +file_prostate_AXT2_0135.h5 +file_prostate_AXT2_0193.h5 +file_prostate_AXT2_0265.h5 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17 May 2024 15:41:07 +0200 Subject: [PATCH 3/8] Add configs --- projects/JSSL/README.rst | 44 +- projects/JSSL/configs/unet_jssl.yaml | 868 +++++ projects/JSSL/configs/unet_ssl.yaml | 377 ++ projects/JSSL/configs/varnet_jssl.yaml | 868 +++++ projects/JSSL/configs/varnet_ssl.yaml | 377 ++ projects/JSSL/configs/vsharp_jssl.yaml | 872 +++++ .../JSSL/configs/vsharp_jssl_oversampled.yaml | 3000 ++++++++++++++++ .../JSSL/configs/vsharp_jssl_single_q.yaml | 788 +++++ projects/JSSL/configs/vsharp_sl_all.yaml | 689 ++++ .../configs/vsharp_sl_all_oversampled.yaml | 2089 +++++++++++ .../JSSL/configs/vsharp_sl_prostate_only.yaml | 289 ++ projects/JSSL/configs/vsharp_ssl.yaml | 381 ++ projects/JSSL/configs/vsharp_ssl_all.yaml | 989 ++++++ .../configs/vsharp_ssl_all_oversampled.yaml | 3117 +++++++++++++++++ .../JSSL/configs/vsharp_ssl_all_single_q.yaml | 851 +++++ .../JSSL/configs/vsharp_ssl_single_q.yaml | 339 ++ 16 files changed, 15933 insertions(+), 5 deletions(-) create mode 100644 projects/JSSL/configs/unet_jssl.yaml create mode 100644 projects/JSSL/configs/unet_ssl.yaml create mode 100644 projects/JSSL/configs/varnet_jssl.yaml create mode 100644 projects/JSSL/configs/varnet_ssl.yaml create mode 100644 projects/JSSL/configs/vsharp_jssl.yaml create mode 100644 projects/JSSL/configs/vsharp_jssl_oversampled.yaml create mode 100644 projects/JSSL/configs/vsharp_jssl_single_q.yaml create mode 100644 projects/JSSL/configs/vsharp_sl_all.yaml create mode 100644 projects/JSSL/configs/vsharp_sl_all_oversampled.yaml create mode 100644 projects/JSSL/configs/vsharp_sl_prostate_only.yaml create mode 100644 projects/JSSL/configs/vsharp_ssl.yaml create mode 100644 projects/JSSL/configs/vsharp_ssl_all.yaml create mode 100644 projects/JSSL/configs/vsharp_ssl_all_oversampled.yaml create mode 100644 projects/JSSL/configs/vsharp_ssl_all_single_q.yaml create mode 100644 projects/JSSL/configs/vsharp_ssl_single_q.yaml diff --git a/projects/JSSL/README.rst b/projects/JSSL/README.rst index 2f77cf07..0dc18c41 100644 --- a/projects/JSSL/README.rst +++ b/projects/JSSL/README.rst @@ -1,6 +1,10 @@ JSSL: Joint Supervised and Self-supervised Learning for MRI Reconstruction ========================================================================== +This project contains necessary configuration files to reproduce experiments of the paper +`JSSL: Joint Supervised and Self-supervised Learning for MRI Reconstruction `_. + + .. figure:: https://github.com/NKI-AI/direct/assets/71031687/97f1fa27-f4e4-44e2-b54a-7ac149f3c01d :alt: fig :name: fig1 @@ -11,10 +15,6 @@ JSSL: Joint Supervised and Self-supervised Learning for MRI Reconstruction (2) Self-supervised Learning. -This project contains necessary configuration files to reproduce experiments of the paper -`JSSL: Joint Supervised and Self-supervised Learning for MRI Reconstruction `_. - - Setting up data directory ------------------------- @@ -73,4 +73,38 @@ Filenames lists Provided configuration files assume that `direct/projects/JSSL/lists/` contains `.lst` files for each dataset which contains the list of filenames for training, validation and test datasets. Each list categorizes the filenames based on the dataset they belong to, as well as shape and number of coils. This is necessary for the dataloader to -collate the data for batch size greater than 1. The filenames should be the same as the ones in the data directory. \ No newline at end of file +collate the data for batch size greater than 1. The filenames should be the same as the ones in the data directory. + +Experiments +----------- + +Configuration Files +~~~~~~~~~~~~~~~~~~~ + +We provide configuration files for JSSL, SSL and all ablation settings as presented in the main paper, +as well as the supplementary material. The configuration files are stored +in the `JSSL projects folder `_. + + +Training +~~~~~~~~ + +In `direct/` run the following command to commence training: + +.. code-block:: bash + + direct train \ + --training-root /training/ \ + --validation-root /validation/ \ + --cfg projects/JSSL/configs/.yaml \ + --num-gpus \ + --num-workers --resume + + +For instance, to perform JSSL training with the vSHARP model, replace `.yaml` +with `vsharp_jssl.yaml`. + +Note +~~~~ +Note that `jssl`, `sl` and `ssl` in the configuration file names stand for Joint Supervised and Self-supervised +Learning, Supervised Learning, and Self-supervised Learning, respectively. \ No newline at end of file diff --git a/projects/JSSL/configs/unet_jssl.yaml b/projects/JSSL/configs/unet_jssl.yaml new file mode 100644 index 00000000..5e531baf --- /dev/null +++ b/projects/JSSL/configs/unet_jssl.yaml @@ -0,0 +1,868 @@ +physics: + forward_operator: fft2 + backward_operator: ifft2 +training: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/train_knee.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_knee + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_6_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_6_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_768x392.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_768x392 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x322.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_640x322 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_512x276.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_512x276 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_20_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_20_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_16_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_16_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL2 + batch_size: 4 + optimizer: Adam + lr: 0.003 + weight_decay: 0 + lr_step_size: 50000 + lr_gamma: 0.8 + lr_warmup_iter: 3000 + num_iterations: 250000 + gradient_steps: 1 + gradient_clipping: 0 + gradient_debug: false + checkpointer: + checkpoint_steps: 4000 + validation_steps: 20000 + loss: + crop: header + losses: + - + function: l1_loss + multiplier: 2 + - + function: ssim_loss + multiplier: 2 + - + function: hfen_l2_norm_loss + multiplier: 1 + - + function: hfen_l1_norm_loss + multiplier: 1 + - + function: kspace_nmae_loss + multiplier: 2 + - + function: kspace_nmse_loss + multiplier: 2 +validation: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 4 + center_fractions: + - 0.08 + scale_percentile: 0.995 + use_seed: true + text_description: 4x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 8 + center_fractions: + - 0.04 + scale_percentile: 0.995 + use_seed: true + text_description: 8x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 16 + center_fractions: + - 0.02 + scale_percentile: 0.995 + use_seed: true + text_description: 16x + crop: header + metrics: + - fastmri_psnr + - fastmri_ssim + batch_size: 20 +model: + model_name: unet.unet_2d.Unet2d + num_filters: 64 + image_initialization: SENSE + engine_name: UNetJSSLEngine + normalized: true +additional_models: + sensitivity_model: + model_name: unet.unet_2d.UnetModel2d + in_channels: 2 + out_channels: 2 + num_filters: 16 + num_pool_layers: 4 +logging: + tensorboard: + num_images: 4 diff --git a/projects/JSSL/configs/unet_ssl.yaml b/projects/JSSL/configs/unet_ssl.yaml new file mode 100644 index 00000000..87157e87 --- /dev/null +++ b/projects/JSSL/configs/unet_ssl.yaml @@ -0,0 +1,377 @@ +physics: + forward_operator: fft2 + backward_operator: ifft2 +training: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + batch_size: 4 + optimizer: Adam + lr: 0.003 + weight_decay: 0 + lr_step_size: 50000 + lr_gamma: 0.8 + lr_warmup_iter: 3000 + num_iterations: 250000 + gradient_steps: 1 + gradient_clipping: 0 + gradient_debug: false + checkpointer: + checkpoint_steps: 4000 + validation_steps: 20000 + loss: + crop: header + losses: + - + function: l1_loss + multiplier: 2 + - + function: ssim_loss + multiplier: 2 + - + function: hfen_l2_norm_loss + multiplier: 1 + - + function: hfen_l1_norm_loss + multiplier: 1 + - + function: kspace_nmae_loss + multiplier: 2 + - + function: kspace_nmse_loss + multiplier: 2 +validation: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 4 + center_fractions: + - 0.08 + scale_percentile: 0.995 + use_seed: true + text_description: 4x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 8 + center_fractions: + - 0.04 + scale_percentile: 0.995 + use_seed: true + text_description: 8x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 16 + center_fractions: + - 0.02 + scale_percentile: 0.995 + use_seed: true + text_description: 16x + crop: header + metrics: + - fastmri_psnr + - fastmri_ssim + batch_size: 20 +model: + model_name: unet.unet_2d.Unet2d + num_filters: 64 + image_initialization: SENSE + engine_name: UNetSSLEngine + normalized: true +additional_models: + sensitivity_model: + model_name: unet.unet_2d.UnetModel2d + in_channels: 2 + out_channels: 2 + num_filters: 16 + num_pool_layers: 4 +logging: + tensorboard: + num_images: 4 diff --git a/projects/JSSL/configs/varnet_jssl.yaml b/projects/JSSL/configs/varnet_jssl.yaml new file mode 100644 index 00000000..b0712e4d --- /dev/null +++ b/projects/JSSL/configs/varnet_jssl.yaml @@ -0,0 +1,868 @@ +physics: + forward_operator: fft2 + backward_operator: ifft2 +training: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/train_knee.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_knee + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_6_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_6_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_768x392.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_768x392 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x322.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_640x322 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_512x276.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_512x276 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_20_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_20_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_16_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_16_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + ssl_transforms: ssdu + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + ssl_transforms: ssdu + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + ssl_transforms: ssdu + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + ssl_transforms: ssdu + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + ssl_transforms: ssdu + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + ssl_transforms: ssdu + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + ssl_transforms: ssdu + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + ssl_transforms: ssdu + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + ssl_transforms: ssdu + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + ssl_transforms: ssdu + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + ssl_transforms: ssdu + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + ssl_transforms: ssdu + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + ssl_transforms: ssdu + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + ssl_transforms: ssdu + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL2 + batch_size: 4 + optimizer: Adam + lr: 0.003 + weight_decay: 0 + lr_step_size: 50000 + lr_gamma: 0.8 + lr_warmup_iter: 3000 + num_iterations: 250000 + gradient_steps: 1 + gradient_clipping: 0 + gradient_debug: false + checkpointer: + checkpoint_steps: 4000 + validation_steps: 20000 + loss: + crop: header + losses: + - + function: l1_loss + multiplier: 2 + - + function: ssim_loss + multiplier: 2 + - + function: hfen_l2_norm_loss + multiplier: 1 + - + function: hfen_l1_norm_loss + multiplier: 1 + - + function: kspace_nmae_loss + multiplier: 2 + - + function: kspace_nmse_loss + multiplier: 2 +validation: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 4 + center_fractions: + - 0.08 + scale_percentile: 0.995 + use_seed: true + text_description: 4x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 8 + center_fractions: + - 0.04 + scale_percentile: 0.995 + use_seed: true + text_description: 8x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 16 + center_fractions: + - 0.02 + scale_percentile: 0.995 + use_seed: true + text_description: 16x + crop: header + metrics: + - fastmri_psnr + - fastmri_ssim + batch_size: 20 +model: + model_name: varnet.varnet.EndToEndVarNet + num_layers: 6 + regularizer_num_filters: 16 + regularizer_num_pull_layers: 4 + engine_name: EndToEndVarNetJSSLEngine +additional_models: + sensitivity_model: + model_name: unet.unet_2d.UnetModel2d + in_channels: 2 + out_channels: 2 + num_filters: 16 + num_pool_layers: 4 +logging: + tensorboard: + num_images: 4 diff --git a/projects/JSSL/configs/varnet_ssl.yaml b/projects/JSSL/configs/varnet_ssl.yaml new file mode 100644 index 00000000..999949eb --- /dev/null +++ b/projects/JSSL/configs/varnet_ssl.yaml @@ -0,0 +1,377 @@ +physics: + forward_operator: fft2 + backward_operator: ifft2 +training: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + batch_size: 4 + optimizer: Adam + lr: 0.003 + weight_decay: 0 + lr_step_size: 50000 + lr_gamma: 0.8 + lr_warmup_iter: 3000 + num_iterations: 250000 + gradient_steps: 1 + gradient_clipping: 0 + gradient_debug: false + checkpointer: + checkpoint_steps: 4000 + validation_steps: 20000 + loss: + crop: header + losses: + - + function: l1_loss + multiplier: 2 + - + function: ssim_loss + multiplier: 2 + - + function: hfen_l2_norm_loss + multiplier: 1 + - + function: hfen_l1_norm_loss + multiplier: 1 + - + function: kspace_nmae_loss + multiplier: 2 + - + function: kspace_nmse_loss + multiplier: 2 +validation: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 4 + center_fractions: + - 0.08 + scale_percentile: 0.995 + use_seed: true + text_description: 4x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 8 + center_fractions: + - 0.04 + scale_percentile: 0.995 + use_seed: true + text_description: 8x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 16 + center_fractions: + - 0.02 + scale_percentile: 0.995 + use_seed: true + text_description: 16x + crop: header + metrics: + - fastmri_psnr + - fastmri_ssim + batch_size: 20 +model: + model_name: varnet.varnet.EndToEndVarNet + num_layers: 6 + regularizer_num_filters: 16 + regularizer_num_pull_layers: 4 + engine_name: EndToEndVarNetSSLEngine +additional_models: + sensitivity_model: + model_name: unet.unet_2d.UnetModel2d + in_channels: 2 + out_channels: 2 + num_filters: 16 + num_pool_layers: 4 +logging: + tensorboard: + num_images: 4 diff --git a/projects/JSSL/configs/vsharp_jssl.yaml b/projects/JSSL/configs/vsharp_jssl.yaml new file mode 100644 index 00000000..f046abdd --- /dev/null +++ b/projects/JSSL/configs/vsharp_jssl.yaml @@ -0,0 +1,872 @@ +physics: + forward_operator: fft2 + backward_operator: ifft2 +training: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/train_knee.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_knee + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_6_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_6_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_768x392.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_768x392 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x322.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_640x322 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_512x276.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_512x276 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_20_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_20_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_16_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_16_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL2 + batch_size: 2 + optimizer: Adam + lr: 0.003 + weight_decay: 0 + lr_step_size: 150000 + lr_gamma: 0.8 + lr_warmup_iter: 3000 + num_iterations: 1000000 + gradient_steps: 1 + gradient_clipping: 0 + gradient_debug: false + checkpointer: + checkpoint_steps: 2000 + validation_steps: 10000 + loss: + crop: header + losses: + - + function: l1_loss + multiplier: 2 + - + function: ssim_loss + multiplier: 2 + - + function: hfen_l2_norm_loss + multiplier: 1 + - + function: hfen_l1_norm_loss + multiplier: 1 + - + function: kspace_nmae_loss + multiplier: 2 + - + function: kspace_nmse_loss + multiplier: 2 +validation: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 4 + center_fractions: + - 0.08 + scale_percentile: 0.995 + use_seed: true + text_description: 4x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 8 + center_fractions: + - 0.04 + scale_percentile: 0.995 + use_seed: true + text_description: 8x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 16 + center_fractions: + - 0.02 + scale_percentile: 0.995 + use_seed: true + text_description: 16x + crop: header + metrics: + - fastmri_psnr + - fastmri_ssim + batch_size: 20 +model: + model_name: vsharp.vsharp.VSharpNet + engine_name: VSharpNetJSSLEngine + num_steps: 12 + num_steps_dc_gd: 10 + image_init: SENSE + no_parameter_sharing: true + image_model_architecture: UNET + image_unet_num_filters: 32 + auxiliary_steps: -1 +additional_models: + sensitivity_model: + model_name: unet.unet_2d.UnetModel2d + in_channels: 2 + out_channels: 2 + num_filters: 16 + num_pool_layers: 4 +logging: + tensorboard: + num_images: 4 diff --git a/projects/JSSL/configs/vsharp_jssl_oversampled.yaml b/projects/JSSL/configs/vsharp_jssl_oversampled.yaml new file mode 100644 index 00000000..7e6554c4 --- /dev/null +++ b/projects/JSSL/configs/vsharp_jssl_oversampled.yaml @@ -0,0 +1,3000 @@ +physics: + forward_operator: fft2 + backward_operator: ifft2 +training: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/train_knee.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_knee + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_6_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_6_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_768x392.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_768x392 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x322.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_640x322 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_512x276.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_512x276 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_20_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_20_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_16_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_16_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL10 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL10 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL10 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL10 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL10 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL10 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL10 + batch_size: 1 + optimizer: Adam + lr: 0.003 + weight_decay: 0 + lr_step_size: 150000 + lr_gamma: 0.8 + lr_warmup_iter: 3000 + num_iterations: 1000000 + gradient_steps: 1 + gradient_clipping: 0 + gradient_debug: false + checkpointer: + checkpoint_steps: 2000 + validation_steps: 20000 + loss: + crop: header + losses: + - + function: l1_loss + multiplier: 2 + - + function: ssim_loss + multiplier: 2 + - + function: hfen_l2_norm_loss + multiplier: 1 + - + function: hfen_l1_norm_loss + multiplier: 1 + - + function: kspace_nmae_loss + multiplier: 2 + - + function: kspace_nmse_loss + multiplier: 2 +validation: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 4 + center_fractions: + - 0.08 + scale_percentile: 0.995 + use_seed: true + text_description: 4x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 8 + center_fractions: + - 0.04 + scale_percentile: 0.995 + use_seed: true + text_description: 8x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 16 + center_fractions: + - 0.02 + scale_percentile: 0.995 + use_seed: true + text_description: 16x + crop: header + metrics: + - fastmri_psnr + - fastmri_ssim + batch_size: 20 +model: + model_name: vsharp.vsharp.VSharpNet + engine_name: VSharpNetJSSLEngine + num_steps: 12 + num_steps_dc_gd: 10 + image_init: SENSE + no_parameter_sharing: true + image_model_architecture: UNET + image_unet_num_filters: 32 + auxiliary_steps: -1 +additional_models: + sensitivity_model: + model_name: unet.unet_2d.UnetModel2d + in_channels: 2 + out_channels: 2 + num_filters: 16 + num_pool_layers: 4 +logging: + tensorboard: + num_images: 4 diff --git a/projects/JSSL/configs/vsharp_jssl_single_q.yaml b/projects/JSSL/configs/vsharp_jssl_single_q.yaml new file mode 100644 index 00000000..59a5e3ed --- /dev/null +++ b/projects/JSSL/configs/vsharp_jssl_single_q.yaml @@ -0,0 +1,788 @@ +physics: + forward_operator: fft2 + backward_operator: ifft2 +training: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/train_knee.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_knee + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_6_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_6_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_768x392.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_768x392 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x322.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_640x322 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_512x276.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_512x276 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_20_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_20_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_16_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_16_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL2 + batch_size: 2 + optimizer: Adam + lr: 0.003 + weight_decay: 0 + lr_step_size: 150000 + lr_gamma: 0.8 + lr_warmup_iter: 3000 + num_iterations: 1000000 + gradient_steps: 1 + gradient_clipping: 0 + gradient_debug: false + checkpointer: + checkpoint_steps: 2000 + validation_steps: 10000 + loss: + crop: header + losses: + - + function: l1_loss + multiplier: 2 + - + function: ssim_loss + multiplier: 2 + - + function: hfen_l2_norm_loss + multiplier: 1 + - + function: hfen_l1_norm_loss + multiplier: 1 + - + function: kspace_nmae_loss + multiplier: 2 + - + function: kspace_nmse_loss + multiplier: 2 +validation: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 4 + center_fractions: + - 0.08 + scale_percentile: 0.995 + use_seed: true + text_description: 4x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 8 + center_fractions: + - 0.04 + scale_percentile: 0.995 + use_seed: true + text_description: 8x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 16 + center_fractions: + - 0.02 + scale_percentile: 0.995 + use_seed: true + text_description: 16x + crop: header + metrics: + - fastmri_psnr + - fastmri_ssim + batch_size: 20 +model: + model_name: vsharp.vsharp.VSharpNet + engine_name: VSharpNetJSSLEngine + num_steps: 12 + num_steps_dc_gd: 10 + image_init: SENSE + no_parameter_sharing: true + image_model_architecture: UNET + image_unet_num_filters: 32 + auxiliary_steps: -1 +additional_models: + sensitivity_model: + model_name: unet.unet_2d.UnetModel2d + in_channels: 2 + out_channels: 2 + num_filters: 16 + num_pool_layers: 4 +logging: + tensorboard: + num_images: 4 diff --git a/projects/JSSL/configs/vsharp_sl_all.yaml b/projects/JSSL/configs/vsharp_sl_all.yaml new file mode 100644 index 00000000..fe722789 --- /dev/null +++ b/projects/JSSL/configs/vsharp_sl_all.yaml @@ -0,0 +1,689 @@ +physics: + forward_operator: fft2 + backward_operator: ifft2 +training: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/train_knee.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_knee + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_6_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_6_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_768x392.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_768x392 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x322.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_640x322 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_512x276.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_512x276 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_20_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_20_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_16_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_16_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_10_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_14_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_16_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_20_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_24_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_26_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_30_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_10_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_14_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_16_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_20_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_24_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_26_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_30_coils-2 + batch_size: 2 + optimizer: Adam + lr: 0.003 + weight_decay: 0 + lr_step_size: 150000 + lr_gamma: 0.8 + lr_warmup_iter: 3000 + num_iterations: 1000000 + gradient_steps: 1 + gradient_clipping: 0 + gradient_debug: false + checkpointer: + checkpoint_steps: 2000 + validation_steps: 10000 + loss: + crop: header + losses: + - + function: l1_loss + multiplier: 2 + - + function: ssim_loss + multiplier: 2 + - + function: hfen_l2_norm_loss + multiplier: 1 + - + function: hfen_l1_norm_loss + multiplier: 1 + - + function: kspace_nmae_loss + multiplier: 2 + - + function: kspace_nmse_loss + multiplier: 2 +validation: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 4 + center_fractions: + - 0.08 + scale_percentile: 0.995 + use_seed: true + text_description: 4x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 8 + center_fractions: + - 0.04 + scale_percentile: 0.995 + use_seed: true + text_description: 8x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 16 + center_fractions: + - 0.02 + scale_percentile: 0.995 + use_seed: true + text_description: 16x + crop: header + metrics: + - fastmri_psnr + - fastmri_ssim + batch_size: 20 +model: + model_name: vsharp.vsharp.VSharpNet + num_steps: 12 + num_steps_dc_gd: 10 + image_init: SENSE + no_parameter_sharing: true + image_model_architecture: UNET + image_unet_num_filters: 32 + auxiliary_steps: -1 +additional_models: + sensitivity_model: + model_name: unet.unet_2d.UnetModel2d + in_channels: 2 + out_channels: 2 + num_filters: 16 + num_pool_layers: 4 +logging: + tensorboard: + num_images: 4 diff --git a/projects/JSSL/configs/vsharp_sl_all_oversampled.yaml b/projects/JSSL/configs/vsharp_sl_all_oversampled.yaml new file mode 100644 index 00000000..473d7923 --- /dev/null +++ b/projects/JSSL/configs/vsharp_sl_all_oversampled.yaml @@ -0,0 +1,2089 @@ +physics: + forward_operator: fft2 + backward_operator: ifft2 +training: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/train_knee.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_knee + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_6_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_6_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_768x392.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_768x392 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x322.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_640x322 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_512x276.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_4_coils_512x276 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_20_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_20_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_16_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_brain_16_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_10_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_14_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_16_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_20_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_24_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_26_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_30_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_10_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_14_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_16_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_20_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_24_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_26_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_30_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_10_coils-3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_14_coils-3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_16_coils-3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_20_coils-3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_24_coils-3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_26_coils-3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_30_coils-3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_10_coils-4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_14_coils-4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_16_coils-4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_20_coils-4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_24_coils-4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_26_coils-4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_30_coils-4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_10_coils-5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_14_coils-5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_16_coils-5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_20_coils-5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_24_coils-5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_26_coils-5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_30_coils-5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_10_coils-6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_14_coils-6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_16_coils-6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_20_coils-6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_24_coils-6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_26_coils-6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_30_coils-6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_10_coils-7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_14_coils-7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_16_coils-7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_20_coils-7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_24_coils-7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_26_coils-7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_30_coils-7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_10_coils-8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_14_coils-8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_16_coils-8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_20_coils-8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_24_coils-8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_26_coils-8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_30_coils-8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_10_coils-9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_14_coils-9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_16_coils-9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_20_coils-9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_24_coils-9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_26_coils-9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_30_coils-9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_10_coils-10 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_14_coils-10 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_16_coils-10 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_20_coils-10 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_24_coils-10 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_26_coils-10 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_30_coils-10 + batch_size: 1 + optimizer: Adam + lr: 0.003 + weight_decay: 0 + lr_step_size: 150000 + lr_gamma: 0.8 + lr_warmup_iter: 3000 + num_iterations: 1000000 + gradient_steps: 1 + gradient_clipping: 0 + gradient_debug: false + checkpointer: + checkpoint_steps: 2000 + validation_steps: 20000 + loss: + crop: header + losses: + - + function: l1_loss + multiplier: 2 + - + function: ssim_loss + multiplier: 2 + - + function: hfen_l2_norm_loss + multiplier: 1 + - + function: hfen_l1_norm_loss + multiplier: 1 + - + function: kspace_nmae_loss + multiplier: 2 + - + function: kspace_nmse_loss + multiplier: 2 +validation: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 4 + center_fractions: + - 0.08 + scale_percentile: 0.995 + use_seed: true + text_description: 4x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 8 + center_fractions: + - 0.04 + scale_percentile: 0.995 + use_seed: true + text_description: 8x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 16 + center_fractions: + - 0.02 + scale_percentile: 0.995 + use_seed: true + text_description: 16x + crop: header + metrics: + - fastmri_psnr + - fastmri_ssim + batch_size: 20 +model: + model_name: vsharp.vsharp.VSharpNet + num_steps: 12 + num_steps_dc_gd: 10 + image_init: SENSE + no_parameter_sharing: true + image_model_architecture: UNET + image_unet_num_filters: 32 + auxiliary_steps: -1 +additional_models: + sensitivity_model: + model_name: unet.unet_2d.UnetModel2d + in_channels: 2 + out_channels: 2 + num_filters: 16 + num_pool_layers: 4 +logging: + tensorboard: + num_images: 4 diff --git a/projects/JSSL/configs/vsharp_sl_prostate_only.yaml b/projects/JSSL/configs/vsharp_sl_prostate_only.yaml new file mode 100644 index 00000000..53273d55 --- /dev/null +++ b/projects/JSSL/configs/vsharp_sl_prostate_only.yaml @@ -0,0 +1,289 @@ +physics: + forward_operator: fft2 + backward_operator: ifft2 +training: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_10_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_14_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_16_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_20_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_24_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_26_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + text_description: train_prostate_30_coils-1 + batch_size: 2 + optimizer: Adam + lr: 0.003 + weight_decay: 0 + lr_step_size: 150000 + lr_gamma: 0.8 + lr_warmup_iter: 3000 + num_iterations: 1000000 + gradient_steps: 1 + gradient_clipping: 0 + gradient_debug: false + checkpointer: + checkpoint_steps: 2000 + validation_steps: 10000 + loss: + crop: header + losses: + - + function: l1_loss + multiplier: 2 + - + function: ssim_loss + multiplier: 2 + - + function: hfen_l2_norm_loss + multiplier: 1 + - + function: hfen_l1_norm_loss + multiplier: 1 + - + function: kspace_nmae_loss + multiplier: 2 + - + function: kspace_nmse_loss + multiplier: 2 +validation: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 4 + center_fractions: + - 0.08 + scale_percentile: 0.995 + use_seed: true + text_description: 4x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 8 + center_fractions: + - 0.04 + scale_percentile: 0.995 + use_seed: true + text_description: 8x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 16 + center_fractions: + - 0.02 + scale_percentile: 0.995 + use_seed: true + text_description: 16x + crop: header + metrics: + - fastmri_psnr + - fastmri_ssim + batch_size: 20 +model: + model_name: vsharp.vsharp.VSharpNet + num_steps: 12 + num_steps_dc_gd: 10 + image_init: SENSE + no_parameter_sharing: true + image_model_architecture: UNET + image_unet_num_filters: 32 + auxiliary_steps: -1 +additional_models: + sensitivity_model: + model_name: unet.unet_2d.UnetModel2d + in_channels: 2 + out_channels: 2 + num_filters: 16 + num_pool_layers: 4 +logging: + tensorboard: + num_images: 4 diff --git a/projects/JSSL/configs/vsharp_ssl.yaml b/projects/JSSL/configs/vsharp_ssl.yaml new file mode 100644 index 00000000..a7d8b2af --- /dev/null +++ b/projects/JSSL/configs/vsharp_ssl.yaml @@ -0,0 +1,381 @@ +physics: + forward_operator: fft2 + backward_operator: ifft2 +training: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + batch_size: 2 + optimizer: Adam + lr: 0.003 + weight_decay: 0 + lr_step_size: 1500000 + lr_gamma: 0.8 + lr_warmup_iter: 3000 + num_iterations: 500000 + gradient_steps: 1 + gradient_clipping: 0 + gradient_debug: false + checkpointer: + checkpoint_steps: 2000 + validation_steps: 10000 + loss: + crop: header + losses: + - + function: l1_loss + multiplier: 2 + - + function: ssim_loss + multiplier: 2 + - + function: hfen_l2_norm_loss + multiplier: 1 + - + function: hfen_l1_norm_loss + multiplier: 1 + - + function: kspace_nmae_loss + multiplier: 2 + - + function: kspace_nmse_loss + multiplier: 2 +validation: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 4 + center_fractions: + - 0.08 + scale_percentile: 0.995 + use_seed: true + text_description: 4x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 8 + center_fractions: + - 0.04 + scale_percentile: 0.995 + use_seed: true + text_description: 8x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 16 + center_fractions: + - 0.02 + scale_percentile: 0.995 + use_seed: true + text_description: 16x + crop: header + metrics: + - fastmri_psnr + - fastmri_ssim + batch_size: 20 +model: + model_name: vsharp.vsharp.VSharpNet + engine_name: VSharpNetSSLEngine + num_steps: 12 + num_steps_dc_gd: 10 + image_init: SENSE + no_parameter_sharing: true + image_model_architecture: UNET + image_unet_num_filters: 32 + auxiliary_steps: -1 +additional_models: + sensitivity_model: + model_name: unet.unet_2d.UnetModel2d + in_channels: 2 + out_channels: 2 + num_filters: 16 + num_pool_layers: 4 +logging: + tensorboard: + num_images: 4 diff --git a/projects/JSSL/configs/vsharp_ssl_all.yaml b/projects/JSSL/configs/vsharp_ssl_all.yaml new file mode 100644 index 00000000..6672b719 --- /dev/null +++ b/projects/JSSL/configs/vsharp_ssl_all.yaml @@ -0,0 +1,989 @@ +physics: + forward_operator: fft2 + backward_operator: ifft2 +training: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/train_knee.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_knee + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_6_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_brain_6_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_768x392.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_brain_4_coils_768x392 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x322.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_brain_4_coils_640x322 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_brain_4_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_512x276.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_brain_4_coils_512x276 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_brain_20_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_brain_20_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_16_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_brain_16_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-2 + batch_size: 2 + optimizer: Adam + lr: 0.003 + weight_decay: 0 + lr_step_size: 150000 + lr_gamma: 0.8 + lr_warmup_iter: 3000 + num_iterations: 1000000 + gradient_steps: 1 + gradient_clipping: 0 + gradient_debug: false + checkpointer: + checkpoint_steps: 2000 + validation_steps: 10000 + loss: + crop: header + losses: + - + function: l1_loss + multiplier: 2 + - + function: ssim_loss + multiplier: 2 + - + function: hfen_l2_norm_loss + multiplier: 1 + - + function: hfen_l1_norm_loss + multiplier: 1 + - + function: kspace_nmae_loss + multiplier: 2 + - + function: kspace_nmse_loss + multiplier: 2 +validation: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 4 + center_fractions: + - 0.08 + scale_percentile: 0.995 + use_seed: true + text_description: 4x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 8 + center_fractions: + - 0.04 + scale_percentile: 0.995 + use_seed: true + text_description: 8x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 16 + center_fractions: + - 0.02 + scale_percentile: 0.995 + use_seed: true + text_description: 16x + crop: header + metrics: + - fastmri_psnr + - fastmri_ssim + batch_size: 20 +model: + model_name: vsharp.vsharp.VSharpNet + engine_name: VSharpNetSSLEngine + num_steps: 12 + num_steps_dc_gd: 10 + image_init: SENSE + no_parameter_sharing: true + image_model_architecture: UNET + image_unet_num_filters: 32 + auxiliary_steps: -1 +additional_models: + sensitivity_model: + model_name: unet.unet_2d.UnetModel2d + in_channels: 2 + out_channels: 2 + num_filters: 16 + num_pool_layers: 4 +logging: + tensorboard: + num_images: 4 diff --git a/projects/JSSL/configs/vsharp_ssl_all_oversampled.yaml b/projects/JSSL/configs/vsharp_ssl_all_oversampled.yaml new file mode 100644 index 00000000..5d7daa36 --- /dev/null +++ b/projects/JSSL/configs/vsharp_ssl_all_oversampled.yaml @@ -0,0 +1,3117 @@ +physics: + forward_operator: fft2 + backward_operator: ifft2 +training: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/train_knee.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_knee + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_6_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_brain_6_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_768x392.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_brain_4_coils_768x392 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x322.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_brain_4_coils_640x322 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_brain_4_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_512x276.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_brain_4_coils_512x276 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_brain_20_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_brain_20_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_16_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_brain_16_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 10 + - 10 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL3 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL4 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL6 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL7 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL8 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL9 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-SSL10 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-SSL10 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-SSL10 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-SSL10 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-SSL10 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-SSL10 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.2 + - 0.3 + - 0.4 + - 0.5 + - 0.6 + - 0.7 + - 0.8 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-SSL10 + batch_size: 2 + optimizer: Adam + lr: 0.003 + weight_decay: 0 + lr_step_size: 150000 + lr_gamma: 0.8 + lr_warmup_iter: 3000 + num_iterations: 1000000 + gradient_steps: 1 + gradient_clipping: 0 + gradient_debug: false + checkpointer: + checkpoint_steps: 2000 + validation_steps: 20000 + loss: + crop: header + losses: + - + function: l1_loss + multiplier: 2 + - + function: ssim_loss + multiplier: 2 + - + function: hfen_l2_norm_loss + multiplier: 1 + - + function: hfen_l1_norm_loss + multiplier: 1 + - + function: kspace_nmae_loss + multiplier: 2 + - + function: kspace_nmse_loss + multiplier: 2 +validation: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 4 + center_fractions: + - 0.08 + scale_percentile: 0.995 + use_seed: true + text_description: 4x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 8 + center_fractions: + - 0.04 + scale_percentile: 0.995 + use_seed: true + text_description: 8x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 16 + center_fractions: + - 0.02 + scale_percentile: 0.995 + use_seed: true + text_description: 16x + crop: header + metrics: + - fastmri_psnr + - fastmri_ssim + batch_size: 20 +model: + model_name: vsharp.vsharp.VSharpNet + engine_name: VSharpNetSSLEngine + num_steps: 12 + num_steps_dc_gd: 10 + image_init: SENSE + no_parameter_sharing: true + image_model_architecture: UNET + image_unet_num_filters: 32 + auxiliary_steps: -1 +additional_models: + sensitivity_model: + model_name: unet.unet_2d.UnetModel2d + in_channels: 2 + out_channels: 2 + num_filters: 16 + num_pool_layers: 4 +logging: + tensorboard: + num_images: 4 diff --git a/projects/JSSL/configs/vsharp_ssl_all_single_q.yaml b/projects/JSSL/configs/vsharp_ssl_all_single_q.yaml new file mode 100644 index 00000000..557b6889 --- /dev/null +++ b/projects/JSSL/configs/vsharp_ssl_all_single_q.yaml @@ -0,0 +1,851 @@ +physics: + forward_operator: fft2 + backward_operator: ifft2 +training: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/train_knee.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_knee + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_6_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_brain_6_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_768x392.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_brain_4_coils_768x392 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x322.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_brain_4_coils_640x322 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_brain_4_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_4_coils_512x276.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_brain_4_coils_512x276 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_brain_20_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_20_coils_640x320.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_brain_20_coils_640x320 + - + name: FastMRI + filenames_lists: + - ../lists/train_brain_16_coils_768x396.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIRandom + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_brain_16_coils_768x396 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-1 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_10_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_14_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_16_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_20_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_24_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_26_coils-2 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + use_seed: false + delete_kspace: false + transforms_type: SSL_SSDU + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + text_description: train_prostate_30_coils-2 + batch_size: 1 + optimizer: Adam + lr: 0.003 + weight_decay: 0 + lr_step_size: 150000 + lr_gamma: 0.8 + lr_warmup_iter: 3000 + num_iterations: 1000000 + gradient_steps: 1 + gradient_clipping: 0 + gradient_debug: false + checkpointer: + checkpoint_steps: 2000 + validation_steps: 20000 + loss: + crop: header + losses: + - + function: l1_loss + multiplier: 2 + - + function: ssim_loss + multiplier: 2 + - + function: hfen_l2_norm_loss + multiplier: 1 + - + function: hfen_l1_norm_loss + multiplier: 1 + - + function: kspace_nmae_loss + multiplier: 2 + - + function: kspace_nmse_loss + multiplier: 2 +validation: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 4 + center_fractions: + - 0.08 + scale_percentile: 0.995 + use_seed: true + text_description: 4x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 8 + center_fractions: + - 0.04 + scale_percentile: 0.995 + use_seed: true + text_description: 8x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 16 + center_fractions: + - 0.02 + scale_percentile: 0.995 + use_seed: true + text_description: 16x + crop: header + metrics: + - fastmri_psnr + - fastmri_ssim + batch_size: 20 +model: + model_name: vsharp.vsharp.VSharpNet + engine_name: VSharpNetSSLEngine + num_steps: 12 + num_steps_dc_gd: 10 + image_init: SENSE + no_parameter_sharing: true + image_model_architecture: UNET + image_unet_num_filters: 32 + auxiliary_steps: -1 +additional_models: + sensitivity_model: + model_name: unet.unet_2d.UnetModel2d + in_channels: 2 + out_channels: 2 + num_filters: 16 + num_pool_layers: 4 +logging: + tensorboard: + num_images: 4 diff --git a/projects/JSSL/configs/vsharp_ssl_single_q.yaml b/projects/JSSL/configs/vsharp_ssl_single_q.yaml new file mode 100644 index 00000000..e7831a57 --- /dev/null +++ b/projects/JSSL/configs/vsharp_ssl_single_q.yaml @@ -0,0 +1,339 @@ +physics: + forward_operator: fft2 + backward_operator: ifft2 +training: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_10_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_14_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_16_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_20_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_24_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_26_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + - + name: FastMRI + filenames_lists: + - ../lists/train_prostate_30_coils.lst + transforms: + crop: reconstruction_size + estimate_sensitivity_maps: true + sensitivity_maps_type: rss_estimate + scaling_key: masked_kspace + image_center_crop: false + random_flip_probability: 0.5 + random_rotation_probability: 0.5 + masking: + name: FastMRIEquispaced + accelerations: + - 4 + - 8 + - 16 + center_fractions: + - 0.08 + - 0.04 + - 0.02 + scale_percentile: 0.995 + delete_kspace: false + transforms_type: SSL_SSDU + use_seed: false + mask_split_ratio: + - 0.5 + mask_split_acs_region: + - 4 + - 4 + mask_split_gaussian_std: 3.5 + batch_size: 2 + optimizer: Adam + lr: 0.003 + weight_decay: 0 + lr_step_size: 150000 + lr_gamma: 0.8 + lr_warmup_iter: 3000 + num_iterations: 1000000 + gradient_steps: 1 + gradient_clipping: 0 + gradient_debug: false + checkpointer: + checkpoint_steps: 2000 + validation_steps: 10000 + loss: + crop: header + losses: + - + function: l1_loss + multiplier: 2 + - + function: ssim_loss + multiplier: 2 + - + function: hfen_l2_norm_loss + multiplier: 1 + - + function: hfen_l1_norm_loss + multiplier: 1 + - + function: kspace_nmae_loss + multiplier: 2 + - + function: kspace_nmse_loss + multiplier: 2 +validation: + datasets: + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 4 + center_fractions: + - 0.08 + scale_percentile: 0.995 + use_seed: true + text_description: 4x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 8 + center_fractions: + - 0.04 + scale_percentile: 0.995 + use_seed: true + text_description: 8x + - + name: FastMRI + filenames_lists: + - ../lists/val_prostate.lst + transforms: + estimate_sensitivity_maps: true + scaling_key: masked_kspace + masking: + name: FastMRIEquispaced + accelerations: + - 16 + center_fractions: + - 0.02 + scale_percentile: 0.995 + use_seed: true + text_description: 16x + crop: header + metrics: + - fastmri_psnr + - fastmri_ssim + batch_size: 20 +model: + model_name: vsharp.vsharp.VSharpNet + engine_name: VSharpNetSSLEngine + num_steps: 12 + num_steps_dc_gd: 10 + image_init: SENSE + no_parameter_sharing: true + image_model_architecture: UNET + image_unet_num_filters: 32 + auxiliary_steps: -1 +additional_models: + sensitivity_model: + model_name: unet.unet_2d.UnetModel2d + in_channels: 2 + out_channels: 2 + num_filters: 16 + num_pool_layers: 4 +logging: + tensorboard: + num_images: 4 From 31b2eb5ae80ca71a2911a4b587088fe52cadce11 Mon Sep 17 00:00:00 2001 From: georgeyiasemis Date: Fri, 17 May 2024 15:50:39 +0200 Subject: [PATCH 4/8] Update readme --- projects/JSSL/README.rst | 47 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/projects/JSSL/README.rst b/projects/JSSL/README.rst index 0dc18c41..526eb976 100644 --- a/projects/JSSL/README.rst +++ b/projects/JSSL/README.rst @@ -104,6 +104,53 @@ In `direct/` run the following command to commence training: For instance, to perform JSSL training with the vSHARP model, replace `.yaml` with `vsharp_jssl.yaml`. + +Inference +~~~~~~~~~ + +For inference, append the following to the configuration file: + +.. code-block:: yaml + + inference: + batch_size: 4 + dataset: + name: FastMRI + transforms: + cropping: + crop: null + sensitivity_map_estimation: + estimate_sensitivity_maps: true + normalization: + scaling_key: masked_kspace + scale_percentile: 0.995 + masking: + name: FastMRIEquispaced + accelerations: + - + center_fractions: + -
+ text_description: inference + crop: header + + +Replace `` and `
` with the desired acceleration and center fraction values. +To replicate the results in the paper, use the following values: 2 and 0.16, 4 and 0.08, 8 and 0.04, 16 and 0.02, +respectively for the acceleration and center fraction values. + + +In `direct/` run the following command to perform inference, for instance on 4x: + +.. code-block:: bash + + direct predict + --checkpoint \ + --cfg projects/JSSL/configs/.yaml \ + --data-root /test/ \ + --filenames-filter projects/JSSL/lists/test_prostate.lst \ + --num-gpus --num-workers \ + + Note ~~~~ Note that `jssl`, `sl` and `ssl` in the configuration file names stand for Joint Supervised and Self-supervised From 0675e735397649624d828b7093e6080bcae0da5b Mon Sep 17 00:00:00 2001 From: georgeyiasemis Date: Fri, 17 May 2024 15:53:24 +0200 Subject: [PATCH 5/8] Add jssl to docs --- docs/index.rst | 1 + docs/jssl.rst | 1 + 2 files changed, 2 insertions(+) create mode 100644 docs/jssl.rst diff --git a/docs/index.rst b/docs/index.rst index bbc55500..a27bf818 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -64,6 +64,7 @@ images such as MRIs from partially observed or noisy input data. cvpr2022_recurrentvarnet shepp_logan cmrxrecon + jssl .. toctree:: :maxdepth: 2 diff --git a/docs/jssl.rst b/docs/jssl.rst new file mode 100644 index 00000000..b18c1796 --- /dev/null +++ b/docs/jssl.rst @@ -0,0 +1 @@ +.. include:: ../projects/JSSL/README.rst From c7735ba777032349efafd0ac08987238cfa02b35 Mon Sep 17 00:00:00 2001 From: georgeyiasemis Date: Fri, 17 May 2024 17:03:49 +0200 Subject: [PATCH 6/8] Minor fix --- projects/JSSL/configs/varnet_jssl.yaml | 28 +++++++++++++------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/projects/JSSL/configs/varnet_jssl.yaml b/projects/JSSL/configs/varnet_jssl.yaml index b0712e4d..e028b857 100644 --- a/projects/JSSL/configs/varnet_jssl.yaml +++ b/projects/JSSL/configs/varnet_jssl.yaml @@ -252,7 +252,7 @@ training: scale_percentile: 0.995 use_seed: false delete_kspace: false - ssl_transforms: ssdu + transforms_type: SSL_SSDU mask_split_ratio: - 0.2 - 0.3 @@ -290,7 +290,7 @@ training: scale_percentile: 0.995 use_seed: false delete_kspace: false - ssl_transforms: ssdu + transforms_type: SSL_SSDU mask_split_ratio: - 0.2 - 0.3 @@ -328,7 +328,7 @@ training: scale_percentile: 0.995 use_seed: false delete_kspace: false - ssl_transforms: ssdu + transforms_type: SSL_SSDU mask_split_ratio: - 0.2 - 0.3 @@ -366,7 +366,7 @@ training: scale_percentile: 0.995 use_seed: false delete_kspace: false - ssl_transforms: ssdu + transforms_type: SSL_SSDU mask_split_ratio: - 0.2 - 0.3 @@ -404,7 +404,7 @@ training: scale_percentile: 0.995 use_seed: false delete_kspace: false - ssl_transforms: ssdu + transforms_type: SSL_SSDU mask_split_ratio: - 0.2 - 0.3 @@ -442,7 +442,7 @@ training: scale_percentile: 0.995 use_seed: false delete_kspace: false - ssl_transforms: ssdu + transforms_type: SSL_SSDU mask_split_ratio: - 0.2 - 0.3 @@ -480,7 +480,7 @@ training: scale_percentile: 0.995 use_seed: false delete_kspace: false - ssl_transforms: ssdu + transforms_type: SSL_SSDU mask_split_ratio: - 0.2 - 0.3 @@ -518,7 +518,7 @@ training: scale_percentile: 0.995 use_seed: false delete_kspace: false - ssl_transforms: ssdu + transforms_type: SSL_SSDU mask_split_ratio: - 0.2 - 0.3 @@ -556,7 +556,7 @@ training: scale_percentile: 0.995 use_seed: false delete_kspace: false - ssl_transforms: ssdu + transforms_type: SSL_SSDU mask_split_ratio: - 0.2 - 0.3 @@ -594,7 +594,7 @@ training: scale_percentile: 0.995 use_seed: false delete_kspace: false - ssl_transforms: ssdu + transforms_type: SSL_SSDU mask_split_ratio: - 0.2 - 0.3 @@ -632,7 +632,7 @@ training: scale_percentile: 0.995 use_seed: false delete_kspace: false - ssl_transforms: ssdu + transforms_type: SSL_SSDU mask_split_ratio: - 0.2 - 0.3 @@ -670,7 +670,7 @@ training: scale_percentile: 0.995 use_seed: false delete_kspace: false - ssl_transforms: ssdu + transforms_type: SSL_SSDU mask_split_ratio: - 0.2 - 0.3 @@ -708,7 +708,7 @@ training: scale_percentile: 0.995 use_seed: false delete_kspace: false - ssl_transforms: ssdu + transforms_type: SSL_SSDU mask_split_ratio: - 0.2 - 0.3 @@ -746,7 +746,7 @@ training: scale_percentile: 0.995 use_seed: false delete_kspace: false - ssl_transforms: ssdu + transforms_type: SSL_SSDU mask_split_ratio: - 0.2 - 0.3 From bbcdc5a885dd689f42e72d58eb7666103df3e04a Mon Sep 17 00:00:00 2001 From: georgeyiasemis Date: Mon, 20 May 2024 22:58:37 +0200 Subject: [PATCH 7/8] Minor codacy fix --- direct/nn/vsharp/vsharp_engine.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/direct/nn/vsharp/vsharp_engine.py b/direct/nn/vsharp/vsharp_engine.py index ad745f8b..57d9ad50 100644 --- a/direct/nn/vsharp/vsharp_engine.py +++ b/direct/nn/vsharp/vsharp_engine.py @@ -436,7 +436,7 @@ def _do_iteration( # Initialize auxiliary loss weights with a single value of 1.0 if single step auxiliary_loss_weights = torch.ones(1).to(output_images[0]) - for i in range(len(output_images)): + for i, _ in enumerate(output_images): # Data consistency output_kspace = T.apply_padding( kspace + self._forward_operator(output_images[i], data["sensitivity_map"], ~mask), @@ -655,7 +655,7 @@ def _do_iteration( # Initialize auxiliary loss weights with a single value of 1.0 if single step auxiliary_loss_weights = torch.ones(1).to(output_images[0]) - for i in range(len(output_images)): + for i, _ in enumerate(output_images): # Data consistency output_kspace = T.apply_padding( kspace + self._forward_operator(output_images[i], data["sensitivity_map"], ~mask), From c75a838d18d5ad8b0c25c7506dd98131ee230b90 Mon Sep 17 00:00:00 2001 From: georgeyiasemis Date: Mon, 20 May 2024 23:03:00 +0200 Subject: [PATCH 8/8] Minor codacy fix --- direct/nn/vsharp/vsharp_engine.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/direct/nn/vsharp/vsharp_engine.py b/direct/nn/vsharp/vsharp_engine.py index 57d9ad50..93a0f7db 100644 --- a/direct/nn/vsharp/vsharp_engine.py +++ b/direct/nn/vsharp/vsharp_engine.py @@ -436,10 +436,10 @@ def _do_iteration( # Initialize auxiliary loss weights with a single value of 1.0 if single step auxiliary_loss_weights = torch.ones(1).to(output_images[0]) - for i, _ in enumerate(output_images): + for i, output_image in enumerate(output_images): # Data consistency output_kspace = T.apply_padding( - kspace + self._forward_operator(output_images[i], data["sensitivity_map"], ~mask), + kspace + self._forward_operator(output_image, data["sensitivity_map"], ~mask), padding=data.get("padding", None), ) # Project predicted k-space onto target k-space if SSL @@ -655,10 +655,10 @@ def _do_iteration( # Initialize auxiliary loss weights with a single value of 1.0 if single step auxiliary_loss_weights = torch.ones(1).to(output_images[0]) - for i, _ in enumerate(output_images): + for i, output_image in enumerate(output_images): # Data consistency output_kspace = T.apply_padding( - kspace + self._forward_operator(output_images[i], data["sensitivity_map"], ~mask), + kspace + self._forward_operator(output_image, data["sensitivity_map"], ~mask), padding=data.get("padding", None), ) if is_ssl: