fMRwhy: BIDS-compatible fMRI analysis with SPM12

fMRwhy is a MATLAB- and SPM12-based toolbox with a variety of helper functions and BIDS-compatible workflows to assist in your fMRI quality checking, preprocessing and analysis journey.

License Documentation Status

About

_images/fmrwhy_logo_2020.png

With fMRwhy you are provided with the tools and shown how to calculate interesting quality metrics, how to visualize outcomes, how to analyse your data with batch scripts, and how to build a BIDS compatible analysis pipeline, all to flexible levels of automation. fMRwhy does not help with the why questions, which are arguably the most important ones that need to be considered right at the start of your fMRI research journey.

fMRwhy currently has the following features:

  • Focus on functional MRI

  • BIDS-compatibility

  • Visual fMRI quality control

  • Multi-echo fMRI preprocessing

  • Accessible and extensible SPM12 batch processing

  • Processing utilities

Background

fMRwhy started as a loose collection of MATLAB- and SPM12-based scripts created to reproduce useful quality control measures and interesting visualizations as reported in journal articles, such as calculating the temporal signal-to-noise ratio of an fMRI time series or creating a carpet plot from fMRI data. The core idea behind this was: if the results of our research are supported by useful quality control methods, why not implement these in a reproducible and extensible way so that the greater community can benefit from and contribute to it? This evolved over time into a modular set of SPM12 batch process wrapper functions that simplified the process of creating reproducible fMRI preprocessing and quality reporting scripts. With the goal of allowing automated quality reporting workflows, BIDS-compatibility was added using bids-matlab as a dependency.

Indices and tables