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Tools for cmr challenge and configs
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@georgeyiasemis
georgeyiasemis committed Nov 9, 2023
1 parent 7443440 commit 40e10a8
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Showing 7 changed files with 382 additions and 445 deletions.
98 changes: 30 additions & 68 deletions projects/CMRxRecon/configs/base_rvn.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -667,24 +667,6 @@ training:
scale_percentile: 0.99
use_seed: false
delete_kspace: false
-
name: CMRxRecon
text_description: mc_4x_204x448
filenames_lists:
- ../lists/204x448_cine_with_masks_train.lst
extra_keys:
- mask04
transforms:
crop: null
estimate_sensitivity_maps: true
scaling_key: masked_kspace
image_center_crop: false
random_flip: true
random_rotation: false
masking: null
scale_percentile: 0.99
use_seed: false
delete_kspace: false
-
name: CMRxRecon
text_description: mc_4x_246x512
Expand Down Expand Up @@ -775,24 +757,6 @@ training:
scale_percentile: 0.99
use_seed: false
delete_kspace: false
-
name: CMRxRecon
text_description: mc_8x_204x448
filenames_lists:
- ../lists/204x448_cine_with_masks_train.lst
extra_keys:
- mask08
transforms:
crop: null
estimate_sensitivity_maps: true
scaling_key: masked_kspace
image_center_crop: false
random_flip: true
random_rotation: false
masking: null
scale_percentile: 0.99
use_seed: false
delete_kspace: false
-
name: CMRxRecon
text_description: mc_8x_246x512
Expand Down Expand Up @@ -883,24 +847,6 @@ training:
scale_percentile: 0.99
use_seed: false
delete_kspace: false
-
name: CMRxRecon
text_description: mc_10x_204x448
filenames_lists:
- ../lists/204x448_cine_with_masks_train.lst
extra_keys:
- mask10
transforms:
crop: null
estimate_sensitivity_maps: true
scaling_key: masked_kspace
image_center_crop: false
random_flip: true
random_rotation: false
masking: null
scale_percentile: 0.99
use_seed: false
delete_kspace: false
-
name: CMRxRecon
text_description: mc_10x_246x512
Expand Down Expand Up @@ -2543,13 +2489,13 @@ training:
optimizer: Adam
lr: 0.005
weight_decay: 0
batch_size: 1
batch_size: 2
lr_step_size: 75000
lr_gamma: 0.8
lr_warmup_iter: 2000
swa_start_iter: null
num_iterations: 1000000
validation_steps: 500000
validation_steps: 200000
gradient_steps: 1
gradient_clipping: 0
gradient_debug: false
Expand All @@ -2569,12 +2515,12 @@ training:
function: kspace_nmae_loss
multiplier: 3
checkpointer:
checkpoint_steps: 2000
checkpoint_steps: 1000
validation:
datasets:
-
name: CMRxRecon
text_description: val-4x
text_description: val-cine-4x
filenames_lists:
- ../lists/204x448_cine_with_masks_train.lst
extra_keys:
Expand All @@ -2583,19 +2529,35 @@ validation:
crop: null
estimate_sensitivity_maps: true
scaling_key: masked_kspace
image_center_crop: false
random_flip: true
random_rotation: false
masking: null
scale_percentile: 0.99
use_seed: false
delete_kspace: false
batch_size: 20
-
name: CMRxRecon
text_description: val-cine-8x
filenames_lists:
- ../lists/204x448_cine_with_masks_train.lst
extra_keys:
- mask08
transforms:
crop: null
estimate_sensitivity_maps: true
scaling_key: masked_kspace
masking: null
-
name: CMRxRecon
text_description: val-cine-10x
filenames_lists:
- ../lists/204x448_cine_with_masks_train.lst
extra_keys:
- mask10
transforms:
crop: null
estimate_sensitivity_maps: true
scaling_key: masked_kspace
masking: null
batch_size: 1
metrics:
- fastmri_psnr
- fastmri_ssim
- fastmri_nmse
crop: null
- fastmri_psnr
model:
model_name: recurrentvarnet.recurrentvarnet.RecurrentVarNet
num_steps: 10
Expand Down
96 changes: 29 additions & 67 deletions projects/CMRxRecon/configs/base_varnet.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -667,24 +667,6 @@ training:
scale_percentile: 0.99
use_seed: false
delete_kspace: false
-
name: CMRxRecon
text_description: mc_4x_204x448
filenames_lists:
- ../lists/204x448_cine_with_masks_train.lst
extra_keys:
- mask04
transforms:
crop: null
estimate_sensitivity_maps: true
scaling_key: masked_kspace
image_center_crop: false
random_flip: true
random_rotation: false
masking: null
scale_percentile: 0.99
use_seed: false
delete_kspace: false
-
name: CMRxRecon
text_description: mc_4x_246x512
Expand Down Expand Up @@ -775,24 +757,6 @@ training:
scale_percentile: 0.99
use_seed: false
delete_kspace: false
-
name: CMRxRecon
text_description: mc_8x_204x448
filenames_lists:
- ../lists/204x448_cine_with_masks_train.lst
extra_keys:
- mask08
transforms:
crop: null
estimate_sensitivity_maps: true
scaling_key: masked_kspace
image_center_crop: false
random_flip: true
random_rotation: false
masking: null
scale_percentile: 0.99
use_seed: false
delete_kspace: false
-
name: CMRxRecon
text_description: mc_8x_246x512
Expand Down Expand Up @@ -883,24 +847,6 @@ training:
scale_percentile: 0.99
use_seed: false
delete_kspace: false
-
name: CMRxRecon
text_description: mc_10x_204x448
filenames_lists:
- ../lists/204x448_cine_with_masks_train.lst
extra_keys:
- mask10
transforms:
crop: null
estimate_sensitivity_maps: true
scaling_key: masked_kspace
image_center_crop: false
random_flip: true
random_rotation: false
masking: null
scale_percentile: 0.99
use_seed: false
delete_kspace: false
-
name: CMRxRecon
text_description: mc_10x_246x512
Expand Down Expand Up @@ -2549,7 +2495,7 @@ training:
lr_warmup_iter: 2000
swa_start_iter: null
num_iterations: 1000000
validation_steps: 600000
validation_steps: 200000
gradient_steps: 1
gradient_clipping: 0
gradient_debug: false
Expand All @@ -2569,12 +2515,12 @@ training:
function: kspace_nmae_loss
multiplier: 3
checkpointer:
checkpoint_steps: 2000
checkpoint_steps: 1000
validation:
datasets:
-
name: CMRxRecon
text_description: val-4x
text_description: val-cine-4x
filenames_lists:
- ../lists/204x448_cine_with_masks_train.lst
extra_keys:
Expand All @@ -2583,19 +2529,35 @@ validation:
crop: null
estimate_sensitivity_maps: true
scaling_key: masked_kspace
image_center_crop: false
random_flip: true
random_rotation: false
masking: null
scale_percentile: 0.99
use_seed: false
delete_kspace: false
batch_size: 20
-
name: CMRxRecon
text_description: val-cine-8x
filenames_lists:
- ../lists/204x448_cine_with_masks_train.lst
extra_keys:
- mask08
transforms:
crop: null
estimate_sensitivity_maps: true
scaling_key: masked_kspace
masking: null
-
name: CMRxRecon
text_description: val-cine-10x
filenames_lists:
- ../lists/204x448_cine_with_masks_train.lst
extra_keys:
- mask10
transforms:
crop: null
estimate_sensitivity_maps: true
scaling_key: masked_kspace
masking: null
batch_size: 1
metrics:
- fastmri_psnr
- fastmri_ssim
- fastmri_nmse
crop: null
- fastmri_psnr
model:
model_name: varnet.varnet.EndToEndVarNet
num_layers: 12
Expand Down
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