demos

Dependencies

• six
• Python
• Tensorflow
• Nibabel
• Numpy
• Scipy
• configparser

Usage

To install dependencies

Run pip install -r requirements-gpu.txt to install all dependencies with GPU support,

Run pip install -r requirements-cpu.txt for a CPU support only version.

For more information on installing Tensorflow, please follow https://www.tensorflow.org/install/

(a) Running the demos:

Please see the README.md in each folder of this directory for more details.

(b) Running a NiftyNet "toynet" example:

To train a "toynet" specified in network/toynet.py:

cd NiftyNet/
wget -N https://www.dropbox.com/s/y7mdh4m9ptkibax/example_volumes.tar.gz
tar -xzvf example_volumes.tar.gz
net_segment train --net_name toynet \
    --image_size 42 --label_size 42 --batch_size 1

(GPU computing is enabled by default; to train with CPU only please use --num_gpus 0)

After the training process, to do segmentation with a trained "toynet":

cd NiftyNet/
net_segment inference --net_name toynet \
    --save_seg_dir ./seg_output \
    --image_size 80 --label_size 80 --batch_size 8

Image data in nifty format (extension .nii or .nii.gz) are supported.

(c) To customise configurations

Commandline parameters override the default settings defined in config/default_config.ini.

Alternatively, to run with a customised config file:

cd NiftyNet/
# training
net_segment train -c /path/to/customised_config
# inference
net_segment inference -c /path/to/customised_config

where /path/to/customised_config implements all parameters listed by running:

net_segment -h