--- a/README.md +++ b/README.md @@ -1,51 +1,51 @@ -### 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 body - -##### Segmentation of fetal brain - -##### Segmentation of fetal brain (only border) - -##### Segmentation of fetal body - +### 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 body + +##### Segmentation of fetal brain + +##### Segmentation of fetal brain (only border) + +##### Segmentation of fetal body +