highres3dnet_brain_parcellation_model_zoo.md

Automatic brain parcellation on T1 MR with a high-resolution 3D net

This page describes how to acquire and use the network described in:

Li W., Wang G., Fidon L., Ourselin S., Cardoso M.J., Vercauteren T. (2017) On the Compactness, Efficiency, and Representation of 3D Convolutional Networks: Brain Parcellation as a Pretext Task. In: Information Processing in Medical Imaging. IPMI 2017

This network parcellates 160 types of structures (including 155 neuroanatomical structures) from brain MR images.

Downloading model zoo files

The network weights and examples data can be downloaded with the command

net_download highres3dnet_brain_parcellation_model_zoo

(Replace net_download with python net_download.py if you cloned the NiftyNet repository.)

Generating segmentations for example data

Generate segmentations for the included example image with the command

net_segment inference -c ~/niftynet/extensions/highres3dnet_brain_parcellation/highres3dnet_config_eval.ini

Replace net_segment with python net_segment.py if you cloned the NiftyNet repository.