Overview

The Neuroscout Command Line Interface (neuroscout-cli) allows you to execute analyses created on neuroscout.org.

neuroscout-cli makes it easy to run your analysis with no configuration by fetching a self-contained analysis bundle, and downloading the required preprocessed fMRI data using DataLad. neuroscout-cli internally uses FitLins, a python pipeline for fMRI analysis in BIDS, to fit a statistical model to the fMRI data, and produce comprehensive reports. neuroscout-cli automatically uploads the resulting images to Neurovault, and links them to the analysis listing, making it easy to view and share your results.

Getting Started 🚀

If this is your first time running an analysis, follow our interactive guide to Cloud execution on Google Colab to run a demo of Neuroscout-CLI in the cloud without using any local resources!

Note

Google Colab allows you to execute Jupyer Notebooks for free, using two CPUs for ~6 hours. This should be sufficient for individual Neuroscout analyses. A small demonstration can be run live in ~15 mins, and a normal analysis should execute in a few hours.

Documentation and Reference

For comprehensive reference of Neuroscout-CLI , please visit the official Neuroscout-CLI Documentation on ReadTheDocs. These docs are updated as new Neuroscout-CLI versions are released.

Installation

The recommended way to install Neuroscout-CLI is using containers (i.e. Docker or Singularity) to facilitate dependency managment.

Containerized Execution

Docker

For most systems (i.e. laptops and workstations), we recommend using Docker. First, follow the instructions for installing Docker on your system.

Next, follow the Portable Docker Execution guide in the Neuroscout Docs.

Singularity

Singularity containers are a great solution for High Performance Computing (HPC) environments, where Docker cannot typically be used due to more tightly controlled user privileges.

First, check with your HPC administrator that Singularity is available for use. If so, follow our guide on Singularity for HPCs in the offical Neuroscout Docs.

Manually prepared environment using pip

Danger

Manually installing neuroscout-cli can be difficult due to complex dependencies in the SciPy stack, or fMRI-specific tooling. Proceed only if you know what you’re doing.

Use pip to install neuroscout-cli from PyPI:

pip install neuroscout-cli