MRIQC

MRIQC extracts no-reference IQMs (image quality metrics) from structural (T1w and T2w), functional and diffusion MRI (magnetic resonance imaging) data.

What is it?

MRIQC extracts no-reference IQMs (image quality metrics) from structural (T1w and T2w), functional and diffusion MRI (magnetic resonance imaging) data.

Basically it can help you determine the quality of some MRI images (which can be helpful for very large datasets).

The best way to learn about MRIQC is to read their documentation

Installation

Can be run as a docker (see below), or on its own (local install).

Local install

pip install mriqc

Upgrade

pip install --user --upgrade mriqc

Docker install or upgrade

docker pull nipreps/mriqc:latest

User Guide

mriqc.readthedocs.io/en/latest/docker.html

Example with docker for participant level (for help with docker, see our docker page)

docker run -it --rm -v $PWD:/data:ro \
-v $PWD/derivatives/mriqc:/out \
nipreps/mriqc:latest /data /out \
participant --participant_label <subject-id>

Group level (after you have run MRIQC on all participants):

docker run -it --rm -v $PWD:/data:ro \
-v $PWD/derivatives/mriqc:/out \
nipreps/mriqc:latest /data /out group

Reports

Walkthrough of reports:
mriqc.readthedocs.io/en/stable/reports.html