
...
Blue outline corresponds to ground truth and red to the final automatic segmentation output.
Images show FLAIR modality after preprocessing and skull stripping.

| Average Case | Median Case |
|:----------:|:---------:|
|![Average case](https://github.com/MaciejMazurowski/brain-segmentation/blob/master/CS_6669.gif?raw=true)|![Median case](https://github.com/MaciejMazurowski/brain-segmentation/blob/master/HT_7473.gif?raw=true)|

The distribution of Dice similarity coefficient (DSC) for the whole dataset of 110 cases used in our study.

![DSC distribution](https://github.com/MaciejMazurowski/brain-segmentation/blob/master/DSC_distribution.png?raw=true)

...

## U-Net architecture

The figure below shows a U-Net architecture implemented in this repository.

![unet](https://github.com/MaciejMazurowski/brain-segmentation/blob/master/unet.png?raw=true)

## Data

![brain-mri-lgg](https://github.com/MaciejMazurowski/brain-segmentation/blob/master/brain-mri-lgg.png?raw=true)


	a/README.md		b/README.md
	...		...
38	Blue outline corresponds to ground truth and red to the final automatic segmentation output.	38	Blue outline corresponds to ground truth and red to the final automatic segmentation output.
39	Images show FLAIR modality after preprocessing and skull stripping.	39	Images show FLAIR modality after preprocessing and skull stripping.
40		40
41	\| Average Case \| Median Case \|	41	\| Average Case \| Median Case \|
42	\|:----------:\|:---------:\|	42	\|:----------:\|:---------:\|
43	\|![Average case](CS_6669.gif)\|![Median case](HT_7473.gif)\|	43	\|![Average case](https://github.com/MaciejMazurowski/brain-segmentation/blob/master/CS_6669.gif?raw=true)\|![Median case](https://github.com/MaciejMazurowski/brain-segmentation/blob/master/HT_7473.gif?raw=true)\|
44		44
45	The distribution of Dice similarity coefficient (DSC) for the whole dataset of 110 cases used in our study.	45	The distribution of Dice similarity coefficient (DSC) for the whole dataset of 110 cases used in our study.
46		46
47	![DSC distribution](https://github.com/MaciejMazurowski/brain-segmentation/blob/master/DSC_distribution.png?raw=true)	47	![DSC distribution](https://github.com/MaciejMazurowski/brain-segmentation/blob/master/DSC_distribution.png?raw=true)
48		48
	...		...
55		55
56	## U-Net architecture	56	## U-Net architecture
57		57
58	The figure below shows a U-Net architecture implemented in this repository.	58	The figure below shows a U-Net architecture implemented in this repository.
59		59
60	![unet](unet.png)	60	![unet](https://github.com/MaciejMazurowski/brain-segmentation/blob/master/unet.png?raw=true)
61		61
62	## Data	62	## Data
63		63
64	![brain-mri-lgg](https://github.com/MaciejMazurowski/brain-segmentation/blob/master/brain-mri-lgg.png?raw=true)	64	![brain-mri-lgg](https://github.com/MaciejMazurowski/brain-segmentation/blob/master/brain-mri-lgg.png?raw=true)
65		65