Clone this repository somewhere with sufficiently large space. When executed, sample workflow produces 17GB of output. You need to have ANTs and ANTsR installed in your system:
- Instructions for installing ANTS: https://brianavants.wordpress.com/2012/04/13/updated-ants-compile-instructions-april-12-2012/
- Instruction for installing ANTsR: https://github.com/stnava/ANTsR#installation-from-source (method #2 works well).
After both of them are installed, edit the first two lines of src/main.R to specify the root directory where you cloned the repository and where ants/bin is installed on the system. You can then execute the image processing pipeline as
nohup Rscript src/main.R > processing.log&
Image segmentation pipeline (Part I-III) takes approximately 20-30 minutes depending on the availability of computing power. Registrations (Part IV) will take 5-10h, again depending on the available computational power.
Reported results and graphs in Maga et al. 2017 (https://www.ncbi.nlm.nih.gov/pubmed/28656622) can be reproduced by running the src/analysis.R script interactively.
UPDATE: It is now possible to run ANTs/ANTsR in Windows, provided you are using Windows 10 and enabled the linux subsystem. Instructions are available at https://github.com/ANTsX/ANTsR/wiki/Installing-ANTsR-in-Windows-10-(along-with-FSL,-Rstudio,-Freesurfer,-etc).