There are two ways to get fMRIPrep installed:
within a Manually Prepared Environment (Python 3.5+), also known as bare-metal installation; or
Once you have your bare-metal environment set-up (first option above),
the next step is executing the
fmriprep command-line options are documented in the Usage Notes
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
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.
Docker (recommended for PC/laptop and commercial Cloud)¶
Probably, the most popular framework to execute containers is Docker.
If you are to run fMRIPrep on your PC/laptop, this is the RECOMMENDED way of execution.
Please make sure you follow the Docker installation instructions.
You can check your Docker Engine installation running their
$ docker run --rm hello-world
If you have a functional installation, then you should obtain the following output.
Hello from Docker! This message shows that your installation appears to be working correctly. To generate this message, Docker took the following steps: 1. The Docker client contacted the Docker daemon. 1. The Docker daemon pulled the "hello-world" image from the Docker Hub. (amd64) 1. The Docker daemon created a new container from that image which runs the executable that produces the output you are currently reading. 1. The Docker daemon streamed that output to the Docker client, which sent it to your terminal. To try something more ambitious, you can run an Ubuntu container with: $ docker run -it ubuntu bash Share images, automate workflows, and more with a free Docker ID: https://hub.docker.com/ For more examples and ideas, visit: https://docs.docker.com/get-started/
After checking your Docker Engine is capable of running Docker images, then go ahead
and check out our documentation to run the fMRIPrep image.
The list of Docker images ready to use is found at the Docker Hub,
This is the easiest way to run fMRIPrep using Docker.
The Docker wrapper is a Python script that operates the Docker Engine seamlessly
as if you were running
To that end,
fmriprep-docker reinterprets the command-line you are passing and
converts it into a
docker run command.
The wrapper just requires Python and an Internet connection.
Install the wrapper using a Python distribution system, e.g.:
$ python -m pip install --user --upgrade fmriprep-docker
Singularity (recommended for HPC)¶
For security reasons, many HPCs (e.g., TACC) do not allow Docker containers, but do allow Singularity containers. The improved security for multi-tenant systems comes at the price of some limitations and extra steps necessary for execution. Please make sure you follow our tips and tricks to run fMRIPrep’s Singularity images.
Manually Prepared Environment (Python 3.5+)¶
Make sure all of fMRIPRep’s External Dependencies are installed.
These tools must be installed and their binaries available in the
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
fMRIPRep can be installed using the habitual command
$ python -m pip install fmriprep
Check your installation with the
$ fmriprep --version
fMRIPRep is written using Python 3.5 (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
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.