rtfMRI

A MATLAB toolbox enabling real-time fMRI image processing and BOLD signal extraction.

Dependencies

• Windows Subsystem for Linux
  • FSL
  • AFNI
• ToolboxToolbox

Usage

In MATLAB, run tbUseProject('neurofeedback'); in the console, then set your working directory to toolboxes/rtfmri. To begin, run runpipeline(...)

This module will pull in image files from scannerPath and extract BOLD signal data, which is combined into a timeseries written to fMRI_timeseries.txt.

Testing

• Example
  • This will use sample neuroimaging data to ensure that the pipeline is set up correctly
  • Run example; from the console
• Simulate
  • This will simulate the functionality of an MRI scanner to test any changes to the pipeline
  • Open up two instances of MATLAB
    • In the first (1), run simulatescanner;
    • In the second (2), run runpipeline()
    • After registration is completed in (2), follow the intructions to start the pipeline
    • After starting the pipeline, start the simulated scanner in (1)

Parameters

There are two ways to control the values of parameters in rtfmri: by file (default) or by command-line arguments. Changing parameter values by file is as simple as finding the desired parameter in rtgetparams() and editing its value. If you find yourself testing different parameter values often, setting the debug flag in runpipeline.m to 1 allows you to enter parameters and values as command line arguments (see example in runpipeline.m).

Important Locations

• fMRI_timeseries.txt: subjectProcessedPath/processed/run#/