feta-inference

Inference pipeline for our participation in the FeTA challenge 2021.

Team name: TRABIT

Installation

Download the two folders in https://drive.google.com/drive/folders/1V5PBETb89GEA3oSNidTpQRtNADjcdp_0?usp=sharing

Move them to feta-inference/data

Build the docker image by running

cd feta-inference
sh build_docker.sh

The tag for the docker image should be feta_challenge/trabit:latest

Run inference using docker

After you have built the docker image, you can create a docker container and obtain the predicted fetal brain segmentation by running

sh example_docker_inference.sh

The script example_docker_inference.sh is based on the instructions found at https://feta-2021.grand-challenge.org/Submission/

Note that you have to rebuild the docker image for changes in the code to be taken into account.