biomedia/malpem repository overview

⁠Brain segmentation pipeline

Original author: Christian Ledig⁠ 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 .

• Retrieve / Link to the atlases from /vol/medic02/users/cl6311/MALPEM_v1.0/

⁠How to run

# change to downloaded directory
pushd dummy_data_biobank
# retrieve latest image
docker pull biomedia/malpem:latest
# concrete example from the install manual
docker run --rm -v `pwd`/atlas:/malpem/atlas:ro -v `pwd`/outputDir:/tmp/outputDir biomedia/malpem -i /malpem/atlas/pincram/limages/full/m100.nii.gz -o /tmp/outputDir -t 8

⁠Information

Subjects data originating from the UK Biobank project⁠

Original package:

⁠Related papers

• Framework and segmentation *

[1] C. Ledig, R. A. Heckemann, A. Hammers, J. C. Lopez, V. F. J. Newcombe, A. Makropoulos, J. Loetjoenen, D. Menon and D. Rueckert, "Robust whole-brain segmentation: Application to traumatic brain injury", Medical Image Analysis, 21(1), pp. 40-58, 2015.

• Brain extraction *

[2] R. Heckemann, C. Ledig, K. R. Gray, P. Aljabar, D. Rueckert, J. V. Hajnal, and A. Hammers, "Brain extraction using label propagation and group agreement: pincram", PLoS ONE, 10(7), pp. e0129211, 2015.