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When using this code please cite the paper:
S. Roy, J. A. Butman, D. L. Pham, 
"Robust Skull Stripping Using Multiple MR Image Contrasts Insensitive to Pathology",
NeuroImage.
http://www.sciencedirect.com/science/article/pii/S1053811916306176
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This software is intended to be used in Linux 64bit operating system

1) The main script is MONSTR.sh. It requires AFNI, FSL, ANTs to be installed and added to the PATH 
environment variable.
https://afni.nimh.nih.gov/afni/download/afni/releases/latest
http://fsl.fmrib.ox.ac.uk/fsldownloads/fsldownloadmain.html
http://stnava.github.io/ANTs/

2) The script requires Matlab 2015b runtime compiler. If you do not have the Matlab Compiler Runtime 
v9.0, please download it from Mathworks:

http://www.mathworks.com/products/compiler/mcr/

Unzip and install it in a suitable folder.

3) Open run_image_dilate.sh and run_create_brainmask.sh, change the MCRROOT variable to the installed 
v90 directory

4) Three sets of atlases are provided. See attached AtlasDescription.txt for information on each type
of atlas. The atlases are from ADNI-29, NAMIC-20 and TBI-19 dataset, as described in the paper.

5) Example usage:
MONSTR.sh --t1 Subject_MPRAGE.nii --t2 Subject_T2.nii --ncpu 12 --atlasdir TBI_atlas/ --natlas 5 --o ./ --rad 6

See MONSTR.sh for more details.