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Fetal-MRI-Segmentation

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### Quick Links

- [Development Branch](https://github.com/GalDude33/Fetal-MRI-Segmentation/tree/dev)

- [Experiments Branch](https://github.com/GalDude33/Fetal-MRI-Segmentation/tree/adapt)

- [Augmentations Notebook](https://github.com/GalDude33/Fetal-MRI-Segmentation/blob/adapt/notebooks/Check_Augmentations.ipynb)

### Fetal Total-Body and Brain 3D Segmentation in MRI scans with limited datasets.

- 3D and 2D segmentation.
- Implemented Advanced Augmentation techniques.
- Achieving results below Radiologist Inter & Intra Observer variability.
- Option to Utilize previous-slice segmentation to improve performance on hard samples.

### Training 

* Install Tensorflow & Keras

* Install dependencies: 
pip install -r requirements.txt

* To run training:
Config currently in dict inside brats/train_fetal.py
```
$ python -m brats.train_fetal --config_dir <config_dir>
```
Where <config_dir> is the folder containing the training configurations (or will be creatad to)

### Write prediction images from the validation data
In the training above, part of the data was held out for validation purposes. 
To write the predicted label maps to file:
```
$ python -m brats.predict --config_dir <config_dir>
```
The predictions will be written in the ```<config_dir>/prediction``` folder along with the input data and ground truth labels for comparison.

### More Instructions and Explanations in the [Wiki](../../wiki)!

### Cool Results

##### 3D Model of the segmented fetal brain
![3D Model of the segmented fetal brain](https://github.com/GalDude33/Fetal-MRI-Segmentation/blob/master/results/brain3.gif?raw=true)
##### 3D Model of the segmented fetal body
![](https://github.com/GalDude33/Fetal-MRI-Segmentation/blob/master/results/fetal.gif?raw=true)
##### Segmentation of fetal brain
![](https://github.com/GalDude33/Fetal-MRI-Segmentation/blob/master/results/brain_seg4.png?raw=true)
##### Segmentation of fetal brain (only border)
![](https://github.com/GalDude33/Fetal-MRI-Segmentation/blob/master/results/brain_seg_border.png?raw=true)
##### Segmentation of fetal body
![](https://github.com/GalDude33/Fetal-MRI-Segmentation/blob/master/results/fetal_seg1.png?raw=true)

	a/README.md		b/README.md
1	### Quick Links	1	### Quick Links
2		2
3	- [Development Branch](https://github.com/GalDude33/Fetal-MRI-Segmentation/tree/dev)	3	- [Development Branch](https://github.com/GalDude33/Fetal-MRI-Segmentation/tree/dev)
4		4
5	- [Experiments Branch](https://github.com/GalDude33/Fetal-MRI-Segmentation/tree/adapt)	5	- [Experiments Branch](https://github.com/GalDude33/Fetal-MRI-Segmentation/tree/adapt)
6		6
7	- [Augmentations Notebook](https://github.com/GalDude33/Fetal-MRI-Segmentation/blob/adapt/notebooks/Check_Augmentations.ipynb)	7	- [Augmentations Notebook](https://github.com/GalDude33/Fetal-MRI-Segmentation/blob/adapt/notebooks/Check_Augmentations.ipynb)
8		8
9	### Fetal Total-Body and Brain 3D Segmentation in MRI scans with limited datasets.	9	### Fetal Total-Body and Brain 3D Segmentation in MRI scans with limited datasets.
10		10
11	- 3D and 2D segmentation.	11	- 3D and 2D segmentation.
12	- Implemented Advanced Augmentation techniques.	12	- Implemented Advanced Augmentation techniques.
13	- Achieving results below Radiologist Inter & Intra Observer variability.	13	- Achieving results below Radiologist Inter & Intra Observer variability.
14	- Option to Utilize previous-slice segmentation to improve performance on hard samples.	14	- Option to Utilize previous-slice segmentation to improve performance on hard samples.
15		15
16	### Training	16	### Training
17		17
18	* Install Tensorflow & Keras	18	* Install Tensorflow & Keras
19		19
20	* Install dependencies:	20	* Install dependencies:
21	pip install -r requirements.txt	21	pip install -r requirements.txt
22		22
23	* To run training:	23	* To run training:
24	Config currently in dict inside brats/train_fetal.py	24	Config currently in dict inside brats/train_fetal.py
25	```	25	```
26	$ python -m brats.train_fetal --config_dir <config_dir>	26	$ python -m brats.train_fetal --config_dir <config_dir>
27	```	27	```
28	Where <config_dir> is the folder containing the training configurations (or will be creatad to)	28	Where <config_dir> is the folder containing the training configurations (or will be creatad to)
29		29
30	### Write prediction images from the validation data	30	### Write prediction images from the validation data
31	In the training above, part of the data was held out for validation purposes.	31	In the training above, part of the data was held out for validation purposes.
32	To write the predicted label maps to file:	32	To write the predicted label maps to file:
33	```	33	```
34	$ python -m brats.predict --config_dir <config_dir>	34	$ python -m brats.predict --config_dir <config_dir>
35	```	35	```
36	The predictions will be written in the ```<config_dir>/prediction``` folder along with the input data and ground truth labels for comparison.	36	The predictions will be written in the ```<config_dir>/prediction``` folder along with the input data and ground truth labels for comparison.
37		37
38	### More Instructions and Explanations in the [Wiki](../../wiki)!	38	### More Instructions and Explanations in the [Wiki](../../wiki)!
39		39
40	### Cool Results	40	### Cool Results
41		41
42	##### 3D Model of the segmented fetal brain	42	##### 3D Model of the segmented fetal brain
43	![3D Model of the segmented fetal brain](results/brain3.gif)	43	![3D Model of the segmented fetal brain](https://github.com/GalDude33/Fetal-MRI-Segmentation/blob/master/results/brain3.gif?raw=true)
44	##### 3D Model of the segmented fetal body	44	##### 3D Model of the segmented fetal body
45	![](results/fetal.gif)	45	![](https://github.com/GalDude33/Fetal-MRI-Segmentation/blob/master/results/fetal.gif?raw=true)
46	##### Segmentation of fetal brain	46	##### Segmentation of fetal brain
47	![](results/brain_seg4.png)	47	![](https://github.com/GalDude33/Fetal-MRI-Segmentation/blob/master/results/brain_seg4.png?raw=true)
48	##### Segmentation of fetal brain (only border)	48	##### Segmentation of fetal brain (only border)
49	![](results/brain_seg_border.png)	49	![](https://github.com/GalDude33/Fetal-MRI-Segmentation/blob/master/results/brain_seg_border.png?raw=true)
50	##### Segmentation of fetal body	50	##### Segmentation of fetal body
51	![](results/fetal_seg1.png)	51	![](https://github.com/GalDude33/Fetal-MRI-Segmentation/blob/master/results/fetal_seg1.png?raw=true)