Population Receptive Field (pRF)

Code for fitting population receptive fields (Dumoulin & Wandell, 2008) for multidimensional models. Includes optional compressive spatial summation exponential parameter (Kay et al., 2013).

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Demonstration

1. Add pathing to pRF package

   addpath(genpath('PathToPackage'));

2. Open demopRF.m

   open demopRF

3. Edit Pathing to Directories

   • Edit directories section as based on your computer's pathing
   
   

   % paths = createPaths(); % initialize paths structure
   % paths.data = fullfile(paths.main, 'DemoData'); % path to demostration data directory
   % paths.results = fullfile(paths.main, 'DemoExampleResults'); % path to output results directory
   % paths = createPaths(paths); % create paths if they do not already exist

4. Run demopRF.m

   • Estimates pRF parameters, mu & sigma & exp, along with Boynton HRF parameters, tau & delta, for the demonstration data
   • Plots histogram of estimated pRF parameters mu, sigma, exp, and corr
   • Plots pRF model predicted voxel time courses vs. actual voxel time courses
   • Plots estimated Boynton HRF as a function of time

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Tutorial

I've written a tutorial that walks through the concepts of pRF modeling in case you're new to the topic.

pRF Tutorial

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Latest Version

Version 3.0

• createScan.m can now also take in FreeSurfer .nii, .nii.gz, .mgz files along with .label files (to select ROIs)
• Edited HRF options, can now provide other parameterized HRF function other than the BoyntonHRF such as the TwoGammaHRF from SPM
• Edited HRF estimating methods, can now iteratively fit HRF parameters either voxels that past a correlation threshold and/or are in the top percentage of initial correlation fits
• Incorporated timing interpolation if stimulus image and voxel time courses were collected at different sampling rates
• Add plotHRF.m to visualize the HRF used to fit the pRF model
• Optimizing for redundant code calls and efficiency. Also reduced nested structure layers
• General documentation editing for spelling errors and clarity

Version Log

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Contributor(s)

Kelly Chang - @kellychang4 - kchang4@uw.edu

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Dependencies

• BVQXtools/NeuroElf
• mrVista/FreeSurfer

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References

Dumoulin, S. O., & Wandell, B. A. (2008). Population receptive field estimates in human visual cortex. Neuroimage, 39(2), 647-660.

Kay, K. N., Winawer, J., Mezer, A., & Wandell, B. A. (2013). Compressive spatial summation in human visual cortex. Journal of neurophysiology, 110(2), 481-494.