brainweb tissue segmentation

Dataset

Creation dataset by Brainweb Simulator.

The Following figure shows the configs in Simulator

dataset generated in three mode: ""MS mild"", ""MS moderate"", """MS severe""

Preprocessing

1. convert 3D T1 (.mnc) to 2D
2. normalization
3. remove extra tissues from T1
4. remove extra tissues from mask

T1 after Preprocessing

mask after Preprocessing

Train

1. Install dependencies:

 pip install -r requirements.txt

2. Training

python train.py --dataset /path/to/hdf5 --BS_train batch_size --BS_test batch_size --img_h image_height --img_w image_width --epochs epochs_number --model_name /model/path

Example:**

python train.py --dataset sample/dataset_without_noise_csf_1.hdf5 --BS_train 32 --BS_test 32 --img_h 256 --img_w 176 --epochs 40 --model_name csf_tissue

Evaluation

python test.py --images /path/to/images/T1  --labels /path/to/groundtruth --model_path /path/to/model --save_output True/False

Results

	CSF	GM	WM
mIOU	0.69	0.83	0.72