Warning: This document is for an old version of smriprep. The main version is master.


There are two ways of getting sMRIPrep installed:

Once you have your bare-metal environment set-up (first option above), the next step is executing the smriprep command-line. The smriprep command-line options are documented in the Usage section. The smriprep command-line adheres to the BIDS-Apps recommendations for the user interface. Therefore, the command-line has the following structure:

$ smriprep <input_bids_path> <derivatives_path> <analysis_level> <named_options>

On the other hand, if you chose a container infrastructure, then the command-line will be composed of a preamble to configure the container execution followed by the smriprep command-line options as if you were running it on a bare-metal installation. The command-line structure above is then modified as follows:

$ <container_command_and_options> <container_image> \
     <input_bids_path> <derivatives_path> <analysis_level> <smriprep_named_options>

Therefore, once specified, the container options and the image to be run the command line is the same as for the bare-metal installation but dropping the smriprep executable name.

Container technologies: Docker and Singularity

Container technologies are operating-system-level virtualization methods to run Linux systems using the host’s Linux kernel. This is a lightweight approach to virtualization, as compares to virtual machines.

Manually Prepared Environment (Python 3.5+)


This method is not recommended! Please checkout container alternatives such as Docker, or Singularity.

Make sure all of sMRIPrep’s External Dependencies are installed. These tools must be installed and their binaries available in the system’s $PATH. A relatively interpretable description of how your environment can be set-up is found in the Dockerfile. As an additional installation setting, FreeSurfer requires a license file (see The FreeSurfer license).

On a functional Python 3.5 (or above) environment with pip installed, sMRIPrep can be installed using the habitual command

$ python -m pip install smriprep

Check your installation with the --version argument

$ smriprep --version

External Dependencies

sMRIPrep is written using Python 3.5 (or above), and is based on nipype.

sMRIPrep requires some other neuroimaging software tools that are not handled by the Python’s packaging system (Pypi) used to deploy the smriprep package: