User Guide

Contents

Installation

We have included mriqc in the PyPi resource

pip install mriqc

Dependencies

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

sudo apt-get 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 profile used run mriqc.

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

Running mriqc

The software automatically finds the data the input folder if it follows the BIDS standard [BIDS]. A fast and easy way to check that your dataset fulfills the BIDS standard is the BIDS validator.

Running mriqc only requires:

mriqc -B ~/Data/bids_dataset -o out/ -w work/

It is possible to run mriqc on specific subjects using

mriqc -B ~/Data/bids_dataset -S S001 S002 -o out/ -w work/

where S001 and S002 are subject identifiers, corresponding to the folders sub-S001 and sub-S002 in the BIDS tree. Here, it is also accepted to use the sub- prefix

mriqc -B ~/Data/bids_dataset -S sub-S001 sub-S002 -o out/ -w work/

Depending on the input images, the resulting outputs will vary as described next.