QA - quality assurance of fMRI data

Github Pages: https://nottingham-neuroimaging.github.io/qa/

What is this?

• A MATLAB-based toolbox to allow quick and easy temporal signal-to-noise-ratio analysis of routine brain/fMRI NIFTI data.
• This is important to ascertain the stability of the scanner, and benchmark the quality of your raw data before any further processing.

MATLAB installation

1. Clone this repository with git clone https://github.com/nottingham-neuroimaging/qa.git
2. Add the path to your MATLAB path.
3. There are 2 options for how to run fMRI_report:
4. If your MATLAB version is 2016a or later, then in the command window type fMRI_report_app
5. If your MATLAB version is older than 2016a, then type fMRI_report
6. In both versions, you will select fMRI data using a GUI and generate mean images and tSNR maps. The difference is that fMRI_report was written using old-school GUIDElines, whereas the newer fMRI_report_app version has the same functionality but is now in the form of a more user-friendly app, especially for debugging/portability etc.

WIP: Is there a python version? Yes!

• This is tested on macOS Sonoma 14.4.1 Apple M1 Chip, with Python ver 3.11.4
• Then run:

cd fMRI_report_python/
pip install -r requirements.txt

• The python version is a work-in-progress jupyter notebook that loads in your nifti data (you will need to set paths to your data). Run:

cd fMRI_report_python/tutorials/
jupyter notebook qa_tutorial.ipynb

• This code uses a lot of function within the functions/snr.py code.
• Example phantom data is in data/
• Thanks to Alex Daniel and his ukat repo for help porting this from MATLAB to python.
• The file qa_run.ipynb is a version that is being altered for use as a container on XNAT.

Help

If you run into any problems or find any issues with the installation process please raise an issue.

Dependencies

• For fMRI_report, there is a zipped folder that contains the toolbox’s dependencies, such as some mrTools and mgl functions. Feel free to ignore if you have already installed these.
• If you are running MATLAB 2016a or later, you can install the app version by navigating to the app tab in the main MATLAB window (third one along, top left), then clicking install app. You can then select the fMRI_report_app.mlappinstall file and it should appear in your app toolbar.