The neuroscout command line interface allows you to easily execute analyses created on neuroscout.org. neuroscout-cli automatically fetches analysis dependencies (including data, and analysis specifications), fits a GLM model to the BIDS dataset, and produces shareable reports of the results.
neuroscout-cli uses FitLins to estimate linear models using the BIDS model specification.
The easiest way to get Neuroscout running is using Docker. Just pull it from Docker hub!
docker pull neuroscout/neuroscout-cli
Neuroscout is easy to use. Assuming you've already created an analysis on neuroscout.org, and have its analysis id (e.g.: 5xH937f) you can run it in one line:
docker run -it neuroscout/neuroscout-cli run 5xH937f
Neuroscout will download the necessary images, analysis bundle, and fit your model.
To cache the downloaded data, and output the results to a separate folder, mount the appropriate volumes:
docker run -it -v /local/datadir:/data -v /local/outdir:/out neuroscout/neuroscout-cli run 5xH937f -o /out
See the output of neuroscout --help for more information:
Usage:
neuroscout run <bundle_id> [-dn -w <work_dir> -o <out_dir> -i <install_dir> --n-cpus=<n>]
neuroscout install <bundle_id> [-dn -i <install_dir>]
neuroscout ls <bundle_id>
neuroscout -h | --help
neuroscout --version
Options:
-i <install_dir> Directory to download dataset and bundle [default: .]
-o <out_dir> Output directory [default: bundle_dir]
-w <work_dir> Working directory
--n-cpus=<n> Maximum number of threads across all processes [default: 1]
-n, --no-download Dont download dataset (if available locally)
-h --help Show this screen
-v, --version Show version
-d, --debug Debug mode
Commands:
run Runs a first level, group level, or full analysis.
install Installs a bundle and/or dataset.
ls Lists the available files in a bundle's dataset.
