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Equation-based brain immunology simulator
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mhoore/braimmu
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Here you see how you can run a simulation: For running this code, your system needs message passing interface (mpi) compiler on c++ (mpicxx) to be already installed on your machine. 1- Go to ./src folder and enter the below command >> make 2- If the code compiled well, a file named "braimmu.exe" would be generated. 3- Run an example simulation using one of input scripts, in.run or in.cuda in ./example/ directory: Note: number of cores should match the partitions specifications inside the input script >> mpirun -np 4 ../src/braimmu.exe connectome conn.run 4- The brain atlases are used as initial conditions, and taken from multiple sources: * Neuroimaging and Surgical Technologies Lab, "http://nist.mni.mcgill.ca/?p=904": ICBM 2009c Nonlinear Symmetric 1×1x1mm template: NIFTI 55MB ./base/wm.nii --> white matter: mni_icbm152_wm_tal_nlin_sym_09c.nii ./base/gm.nii --> gray matter: mni_icbm152_gm_tal_nlin_sym_09c.nii ./base/csf.nii --> cerebrospinal fluid: mni_icbm152_csf_tal_nlin_sym_09c.nii * Courtesy of Dr. Vladimir S. Fonov, McGill University, Montreal Neurological Institute, Brain Imaging Center: ./base/voi.nii --> volume of interest (VOI): mni_icbm152_lob_tal_nlin_sym_09c.nii ./base/voi.txt --> VOIs descriptions * UCLA Brain Mapping Center, "http://www.bmap.ucla.edu/portfolio/atlases/ICBM_DTI-81_Atlas/": ICBM DTI-81 Atlas ./base/rgb.nii --> neural connectome: ICBM_COLOR.nii 5- Enjoy!
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