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.
About¶
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.
License Information¶
fMRwhy
is licensed under GNU Lesser General Public License version 2.1.
- Core Features
- Installation
- Quality Reporting
- Multi-echo processing
- Resources
- Contributing to
fMRwhy
- API
fmrwhy.batch
: Wrapper functions for SPM12 batch processesfmrwhy.bidsutils
: Utilities for BIDS-compatibilityfmrwhy.multiecho
: Multi-echo fMRI analysis functionsfmrwhy.qc
: Quality control functionsfmrwhy.realtime
: Real-time fMRI analysis functionsfmrwhy.settings
: Defaults and workflow-specific settingsfmrwhy.utils
: Common utility functionsfmrwhy.workflows
: BIDS-compatible analysis pipelines