Installation¶
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 https://raw.githubusercontent.com/poldracklab/mriqc/master/requirements.txt
pip install git+https://github.com/poldracklab/mriqc.git
Warning
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.