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---
language:
- en
license: apache-2.0
library_name: atommic
datasets:
- SKMTEA
thumbnail: null
tags:
- image-segmentation
- UNet
- ATOMMIC
- pytorch
model-index:
- name: SEG_UNet_SKMTEA
results: []
---
## Model Overview
AttentionUNet for MRI Segmentation on the SKMTEA dataset.
## ATOMMIC: Training
To train, fine-tune, or test the model you will need to install [ATOMMIC](https://github.com/wdika/atommic). We recommend you install it after you've installed latest Pytorch version.
```
pip install atommic['all']
```
## How to Use this Model
The model is available for use in ATOMMIC, and can be used as a pre-trained checkpoint for inference or for fine-tuning on another dataset.
Corresponding configuration YAML files can be found [here](https://github.com/wdika/atommic/tree/main/projects/SEG/SKMTEA/conf).
### Automatically instantiate the model
```base
pretrained: true
checkpoint: https://huggingface.co/wdika/SEG_UNet_SKMTEA/blob/main/SEG_UNet_SKMTEA.atommic
mode: test
```
### Usage
You need to download the SKM-TEA dataset to effectively use this model. Check the [SKMTEA](https://github.com/wdika/atommic/blob/main/projects/SEG/SKMTEA/README.md) page for more information.
## Model Architecture
```base
model:
model_name: SEGMENTATIONUNET
segmentation_module: UNet
segmentation_module_input_channels: 1
segmentation_module_output_channels: 4
segmentation_module_channels: 32
segmentation_module_pooling_layers: 5
segmentation_module_dropout: 0.0
segmentation_module_normalize: false
segmentation_loss:
dice: 1.0
dice_loss_include_background: true # always set to true if the background is removed
dice_loss_to_onehot_y: false
dice_loss_sigmoid: false
dice_loss_softmax: false
dice_loss_other_act: none
dice_loss_squared_pred: false
dice_loss_jaccard: false
dice_loss_flatten: false
dice_loss_reduction: mean_batch
dice_loss_smooth_nr: 1e-5
dice_loss_smooth_dr: 1e-5
dice_loss_batch: true
dice_metric_include_background: true # always set to true if the background is removed
dice_metric_to_onehot_y: false
dice_metric_sigmoid: false
dice_metric_softmax: false
dice_metric_other_act: none
dice_metric_squared_pred: false
dice_metric_jaccard: false
dice_metric_flatten: false
dice_metric_reduction: mean_batch
dice_metric_smooth_nr: 1e-5
dice_metric_smooth_dr: 1e-5
dice_metric_batch: true
segmentation_classes_thresholds: [0.5, 0.5, 0.5, 0.5]
segmentation_activation: sigmoid
magnitude_input: true
log_multiple_modalities: false # log all modalities in the same image, e.g. T1, T2, T1ce, FLAIR will be concatenated
normalization_type: minmax
normalize_segmentation_output: true
complex_data: false
```
## Training
```base
optim:
name: adam
lr: 1e-4
betas:
- 0.9
- 0.98
weight_decay: 0.0
sched:
name: InverseSquareRootAnnealing
min_lr: 0.0
last_epoch: -1
warmup_ratio: 0.1
trainer:
strategy: ddp_find_unused_parameters_false
accelerator: gpu
devices: 1
num_nodes: 1
max_epochs: 20
precision: 16-mixed # '16-mixed', 'bf16-mixed', '32-true', '64-true', '64', '32', '16', 'bf16'
enable_checkpointing: false
logger: false
log_every_n_steps: 50
check_val_every_n_epoch: -1
max_steps: -1
```
## Performance
Evaluation can be performed using the segmentation [evaluation](https://github.com/wdika/atommic/blob/main/tools/evaluation/segmentation.py) script for the segmentation task, with --evaluation_type per_slice.
Results
-------
Evaluation
----------
DICE = 0.9123 +/- 0.05847 F1 = 0.6509 +/- 0.4487 HD95 = 6.618 +/- 1.793 IOU = 0.5158 +/- 0.3499
## References
[1] [ATOMMIC](https://github.com/wdika/atommic)
[2] Desai AD, Schmidt AM, Rubin EB, et al. SKM-TEA: A Dataset for Accelerated MRI Reconstruction with Dense Image Labels for Quantitative Clinical Evaluation. 2022 |