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Installation

There are four ways to use fmriprep: on the free cloud service OpenNeuro.org, in a Docker Container, in a Singularity Container, or in a Manually Prepared Environment (Python 3.5+). Using OpenNeuro or a local container method is highly recommended. Once you are ready to run fmriprep, see Usage_ for details.

OpenNeuro

fmriprep is available on the free cloud platform OpenNeuro.org. After uploading your BIDS-compatible dataset to OpenNeuro you will be able to run fmriprep for free using OpenNeuro servers. This is the easiest way to run fmriprep, as there is no installation required.

Docker Container

In order to run fmriprep in a Docker container, Docker must be installed. Once Docker is installed, the recommended way to run fmriprep is to use the fmriprep-docker_ wrapper, which requires Python and an Internet connection.

To install:

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

When run, fmriprep-docker will generate a Docker command line for you, print it out for reporting purposes, and then run the command, e.g.:

$ fmriprep-docker /path/to/data/dir /path/to/output/dir participant
RUNNING: docker run --rm -it -v /path/to/data/dir:/data:ro \
    -v /path/to_output/dir:/out poldracklab/fmriprep:1.0.0 \
    /data /out participant
...

You may also 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 \
    participant

For example:

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

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

Singularity Container

For security reasons, many HPCs (e.g., TACC) do not allow Docker containers, but do allow Singularity containers.

Preparing a Singularity image (Singularity version >= 2.5)

If the version of Singularity on your HPC is modern enough you can create Singularity image directly on the HCP. This is as simple as:

$ singularity build /my_images/fmriprep-<version>.simg docker://poldracklab/fmriprep:<version>

Where <version> should be replaced with the desired version of fMRIPrep that you want to download.

Preparing a Singularity image (Singularity version < 2.5)

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 \
    poldracklab/fmriprep:<version>

Where <version> should be replaced with the desired version of fMRIPrep that you want to download.

Beware of the back slashes, expected for Windows systems. For *nix users the command translates as follows:

$ docker run --privileged -t --rm \
    -v /var/run/docker.sock:/var/run/docker.sock \
    -v /absolute/path/to/output/folder:/output \
    singularityware/docker2singularity \
    poldracklab/fmriprep:<version>

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

$ scp poldracklab_fmriprep*.img user@hcpserver.edu:/my_images

Running a Singularity Image

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

$ singularity run --cleanenv /my_images/fmriprep-1.1.2.simg \
    path/to/data/dir path/to/output/dir \
    participant \
    --participant-label label

Note

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 using the --cleanenv singularity flag in production use. For example:

$ singularity run --cleanenv ~/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 \
  --omp-nthreads 16

or, unset the PYTHONPATH variable before running:

$ unset 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 \
  --omp-nthreads 16

Note

Depending on how Singularity is configured on your cluster it might or might not automatically bind (mount or expose) host folders to the container. If this is not done automatically you will need to bind the necessary folders using the -B <host_folder>:<container_folder> Singularity argument. For example:

$ singularity run --cleanenv -B /work:/work ~/poldracklab_fmriprep_latest-2016-12-04-5b74ad9a4c4d.simg \
  /work/my_dataset/ /work/my_dataset/derivatives/fmriprep \
  participant \
  --participant-label 387 --nthreads 16 \
  --omp-nthreads 16

Manually Prepared Environment (Python 3.5+)

Warning

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. 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 :ref:`fs_license`).

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

$ pip install fmriprep

Check your installation with the --version argument

$ fmriprep --version

External Dependencies

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 the fmriprep package:

The FreeSurfer license

FMRIPREP uses FreeSurfer tools, which require a license to run.

To obtain a FreeSurfer license, simply register for free at https://surfer.nmr.mgh.harvard.edu/registration.html.

When using manually-prepared environments or singularity, FreeSurfer will search for a license key file first using the $FS_LICENSE environment variable and then in the default path to the license key file ($FREESURFER_HOME/license.txt). If using the --cleanenv flag and $FS_LICENSE is set, use --fs-license-file $FS_LICENSE to pass the license file location to fMRIPrep.

It is possible to run the docker container pointing the image to a local path where a valid license file is stored. For example, if the license is stored in the $HOME/.licenses/freesurfer/license.txt file on the host system:

$ docker run -ti --rm \
    -v $HOME/fullds005:/data:ro \
    -v $HOME/dockerout:/out \
    -v $HOME/.licenses/freesurfer/license.txt:/opt/freesurfer/license.txt \
    poldracklab/fmriprep:latest \
    /data /out/out \
    participant \
    --ignore fieldmaps

Using FreeSurfer can also be enabled when using fmriprep-docker:

$ fmriprep-docker --fs-license-file $HOME/.licenses/freesurfer/license.txt \
    /path/to/data/dir /path/to/output/dir participant
RUNNING: docker run --rm -it -v /path/to/data/dir:/data:ro \
    -v /home/user/.licenses/freesurfer/license.txt:/opt/freesurfer/license.txt \
    -v /path/to_output/dir:/out poldracklab/fmriprep:1.0.0 \
    /data /out participant
...

If the environment variable $FS_LICENSE is set in the host system, then it will automatically used by fmriprep-docker. For instance, the following would be equivalent to the latest example:

$ export FS_LICENSE=$HOME/.licenses/freesurfer/license.txt
$ fmriprep-docker /path/to/data/dir /path/to/output/dir participant
RUNNING: docker run --rm -it -v /path/to/data/dir:/data:ro \
    -v /home/user/.licenses/freesurfer/license.txt:/opt/freesurfer/license.txt \
    -v /path/to_output/dir:/out poldracklab/fmriprep:1.0.0 \
    /data /out participant
...