biomedia/cardiac_segmentation repository overview

⁠Cardiac segmentation pipeline

Original author: Wenjia Bai⁠ Docker version: Jonathan Passerat-Palmbach⁠

⁠Pre-requisites

• Install docker⁠
• Download the input data files: (or find a subset here -> /homes/jpassera/playground/dummy_data_biobank) scp -r [email protected]:/homes/jpassera/playground/dummy_data_biobank .

⁠How to run

# change to downloaded directory
pushd dummy_data_biobank
# retrieve latest image
docker pull biomedia/cardiac_segmentation
# run the pipeline on a single subject (results written back to `pwd`/data)
docker run --rm -v `pwd`/template:/tmp/template:ro -v `pwd`/atlas:/tmp/atlas:ro -v `pwd`/data:/tmp/bids_dataset biomedia/cardiac_segmentation <subject_id>

⁠Information

Subjects data originating from the UK Biobank project⁠

Atlas files described in the following papers, please contact the original authors to obtain the data.

Insert links to download the atlases

Clinical paper [1] de Marvao A, Dawes TJ, Shi W, Minas C, Keenan NG, Diamond T, Durighel G, Montana G, Rueckert D, Cook SA, O’Regan DP.(2014) Population-based studies of myocardial hypertrophy: high resolution cardiovascular magnetic resonance atlases improve statistical power. J Cardiovasc Magn Reson. 16:16

Methodology paper [2] W.Bai, W. Shi, A. de Marvao, T.J.W. Dawes, D.P. O’Regan, S.A. Cook, D. Rueckert. A bi-ventricular cardiac atlas built from 1000+ high resolution MR images of healthy subjects and an analysis of shape and motion. Medical Image Analysis, 26(1):133-145, 2015.