An app to demo nirs mcx simulations.
- a compatible nvidia gpu
- compatible meaning, at least compute-capability 3.0, see list of here
- nvidia driver installed
- docker
- nvidia-docker
- to configure the simulations, experience with mcx, Monte Carlo eXtreme, is needed.
- understanding of chrisapp would be useful, but not necessary
- incoming: input directory for files.
- outgoing: output directory for files.
- head: NIfTI file containing head to simulate.
- mcx_config: json file containing options for how to run mcx, and vectors for srcpos, srcdir, detpos, and detdir.
{
"mcx" : {
"gpuid": "1",
"prop": [
[0, 0, 1, 1],
[0.014600, 8.28, 0.9, 1.37],
[0.019500, 11.11, 0.9, 1.37]
]
},
"srcpos": [53, 100, 50],
"srcdir": [0.9063077870366499, 0, 0.42261826174069944],
"detpos": [47, 100, 62.5],
"detdir": [0.9063077870366499, 0, 0.42261826174069944]
}
Using the example config and head, here is an example of how to run this plugin using nvidia-docker.
mkdir -p out && nvidia-docker run -v example:/incoming -v out:/outgoing \
jdtatz/pl-nirs-demo-app nirs_demo_app.py /incoming /outgoing \
--head=example_head.nii.gz --mcx_config=example_config.json