This repository contains the code for "Challenging Current Semi-Supervised Anomaly Segmentation Methods for Brain MRI", accepted to the MICCAI 2021 BrainLes Workshop.
Clone the git project:
$ git clone https://github.com/FeliMe/brain_sas_baseline.git
Create a virtual environment and install the requirements:
$ conda create -f environment.yml
Activate the newly created environment:
$ conda activate anomaly_detection
Download and install ROBEX from https://www.nitrc.org/projects/robex Download the SRI ATLAS from https://www.nitrc.org/projects/sri24/ and place it into DATAROOT/BrainAtlases/
$ python download_data.py --dataset BraTS
$ python download_data.py --dataset BraTS --register
$ python download_data.py --dataset MSLUB
$ python download_data.py --dataset MSLUB --skull_strip
$ python download_data.py --dataset MSLUB --register
$ python download_data.py --dataset WMH
$ python download_data.py --dataset WMH --skull_strip
$ python download_data.py --dataset WMH --register
$ python download_data.py --dataset MSSEG2015
$ python download_data.py --dataset MSSEG2015 --register
$ python baseline.py --test_ds BraTS --img_size 128 --slices_lower_upper 15 125