There are three ways to use fmriprep: in a Docker Container, in a Singularity Container, or in a Manually Prepared Environment. Using a container method is highly recommended. Once you are ready to run fmriprep, see Usage for details.

Docker Container

Make sure command-line Docker is installed.

See External Dependencies for more information (e.g., specific versions) on what is included in the fmriprep Docker image.

There are two ways to run fmriprep through Docker; the first, recommended way is to use the fmriprep-docker wrapper. This requires Python and an internet connection.

To install:

$ pip install --user --upgrade fmriprep-docker

To run:

$ fmriprep-docker /path/to/data/dir /path/to/output/dir participant

The second way to run fmriprep is to invoke docker directly.

$ docker run -ti --rm \
    -v filepath/to/data/dir:/data:ro \
    -v filepath/to/output/dir:/out \
    poldracklab/fmriprep:latest \
    /data /out/out \

For example:

$ docker run -ti --rm \
    -v $HOME/fullds005:/data:ro \
    -v $HOME/dockerout:/out \
    poldracklab/fmriprep:latest \
    /data /out/out \
    participant \
    --ignore fieldmaps

Singularity Container

For security reasons, many HPCs (e.g., TACC) do not allow Docker containers, but do allow Singularity containers. In this case, start with a machine (e.g., your personal computer) with Docker installed. Use docker2singularity to create a singularity image. You will need an active internet connection and some time.

$ docker run --privileged -t --rm \
    -v /var/run/docker.sock:/var/run/docker.sock \
    -v D:\host\path\where\to\output\singularity\image:/output \
    singularityware/docker2singularity \

Transfer the resulting Singularity image to the HPC, for example, using scp.

$ scp poldracklab_fmriprep_latest-*.img

If the data to be preprocessed is also on the HPC, you are ready to run fmriprep.

$ singularity run path/to/singularity/image.img \
    path/to/data/dir path/to/output/dir \
    participant \
    --participant_label label

For example:

$ singularity run ~/poldracklab_fmriprep_latest-2016-12-04-5b74ad9a4c4d.img \
    /work/04168/asdf/lonestar/ $WORK/lonestar/output \
    participant \
    --participant_label 387 --nthreads 16 -w $WORK/lonestar/work \
    --ants-nthreads 16


Singularity by default exposes all environment variables from the host inside the container. Because of this your host libraries (such as nipype) could be accidentally used instead of the ones inside the container - if they are included in PYTHONPATH. To avoid such situation we recommend unsetting PYTHONPATH in production use. For example:

$ PYTHONPATH="" singularity run ~/poldracklab_fmriprep_latest-2016-12-04-5b74ad9a4c4d.img \
  /work/04168/asdf/lonestar/ $WORK/lonestar/output \
  participant \
  --participant_label 387 --nthreads 16 -w $WORK/lonestar/work \
  --ants-nthreads 16

Manually Prepared Environment


This method is not recommended! Make sure you would rather do this than use a Docker Container or a Singularity Container.

Make sure all of fmriprep’s External Dependencies are installed. These tools must be installed and their binaries available in the system’s $PATH.

If you have pip installed, install fmriprep

$ pip install fmriprep

If you have your data on hand, you are ready to run fmriprep:

$ fmriprep data/dir output/dir participant --participant_label label

External Dependencies

fmriprep is implemented using nipype, but it requires some other neuroimaging software tools:

  • FSL (version 5.0.9)
  • ANTs (version 2.1.0.Debian-Ubuntu_X64)
  • AFNI (version Debian-16.2.07)
  • C3D (version 1.0.0)
  • FreeSurfer (version 6.0.0)