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Optimize hemodynamic response function parameters.

Project description

Optimize hemodynamic response function parameters.

A free & open source package for finding best-fitting hemodynamic response function (HRF) parameters for fMRI data. Optimization takes place within the framework of population receptive field (pRF) parameters.

The fitting process requires, for every voxel of fMRI data, optimized pRF parameters. These can be obtained using pyprf_feature.

Installation

For installation, follow these steps:

  1. (Optional) Create conda environment
conda create -n env_hrf_opt python=2.7
source activate env_hrf_opt
conda install pip
  1. Clone repository
git clone https://github.com/MSchnei/hrf_opt.git
  1. Install hrf_opt with pip
pip install /path/to/cloned/hrf_opt

How to use

1. Run pyprf_feature to obtain an initial guess of the pRF parameters

See here for more information on how to use pyprf_feature. In brief, open a terminal and run:

pyprf_feature -config path/to/custom_pRF_config.csv

2. Obtain model responses for every voxel for best-fitting pRF model

When pyprf_feature is done, run it again with -save_tc and -mdl_rsp flag. This will save the fitted pRF model time courses and corresponding neural responses to disk:

pyprf_feature -config path/to/custom_pRF_config.csv -save_tc -mdl_rsp

3. Adjust the csv file for hrf_opt

Adjust the information in the config_default.csv file in the hrf_opt folder, such that the provided information is correct. It is recommended to make a specific copy of the csv file for every subject.

4. Run hrf_opt

Open a terminal and run:

hrf_opt -config path/to/custom_hrf_opt_config.csv

References

This application is based on the following work:

  • Dumoulin, S. O., & Wandell, B. A. (2008). Population receptive field estimates in human visual cortex. NeuroImage, 39(2), 647–660. https://doi.org/10.1016/j.neuroimage.2007.09.034
  • Harvey, B. M., & Dumoulin, S. O. (2011). The Relationship between Cortical Magnification Factor and Population Receptive Field Size in Human Visual Cortex: Constancies in Cortical Architecture. Journal of Neuroscience, 31(38), 13604–13612. https://doi.org/10.1523/JNEUROSCI.2572-11.2011

License

The project is licensed under GNU General Public License Version 3.

Project details


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