There are two ways to get fMRIPrep installed:

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

$ fmriprep <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 fmriprep 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> <fmriprep_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 fmriprep 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 3.7+)


This method is not recommended! Please checkout container alternatives in Running fMRIPrep via Docker containers, and Running fMRIPrep via Singularity containers.

Make sure all of fMRIPRep’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 3.7 (or above) environment with pip installed, fMRIPRep can be installed using the habitual command

$ python -m pip install fmriprep

Check your installation with the --version argument

$ fmriprep --version

External Dependencies

fMRIPRep is written using Python 3.7 (or above), and is based on nipype.

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

Not running on a local machine? - Data transfer

If you intend to run fMRIPRep on a remote system, you will need to make your data available within that system first.

For instance, here at the Poldrack Lab we use Stanford’s HPC system, called Sherlock. Sherlock enables the following data transfer options.

Alternatively, more comprehensive solutions such as Datalad will handle data transfers with the appropriate settings and commands. Datalad also performs version control over your data.