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
MRIQC uses bleeding-edge (oftentimes unreleased) versions of
niworkflows and “bare-metal” installations can
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
pip on a Python 3 environment:
pip install -r https://raw.githubusercontent.com/poldracklab/mriqc/master/requirements.txt pip install git+https://github.com/poldracklab/mriqc.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
variable, for the user that will run