Containerized versions

If you have Docker installed, the quickest way to get mriqc to work is following the running with docker guide.

We recommend trying containerized versions first to avoid installation issues. MRIQC uses bleeding-edge (oftentimes unreleased) versions of nipype and niworkflows and “bare-metal” installations can be hard. Nonetheless, we offer support on our github repository.

“Bare-metal” installation (only Python 3)

If, for some reason, you really need a bare-metal installation, MRIQC can be installed as follows. First, please make sure you have the execution system dependencies installed (see below). Second, the latest development version of MRIQC can be installed from github using pip on a Python 3 environment:

pip install -r
pip install git+


As of MRIQC 0.9.4, Python 2 is no longer supported.

Execution system dependencies

If you are using a linux distribution with neurodebian, installation should be as easy as:

sudo apt-get install fsl afni ants
sudo ln -sf /usr/lib/ants/N4BiasFieldCorrection /usr/local/bin/

After installation, make sure that all the necessary binaries are added to the $PATH environment variable, for the user that will run mriqc.

Otherwise, you can follow each software installation guide: FSL, AFNI, and ANTs.