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Code for the analysis of the AVT fMRI high-res experiment.

Dependencies

fMRI and psychophysics experiment

  • Presentation (?????)
  • HRTF (MIT and HPC...)
  • piezzo stimulator (??????)
  • palamedes to analyze (?????)

fMRI analysis

You will need matlab and SPM12 to make use of this code.

Matlab, toolbox and other dependencies Used version Purpose
Matlab 2016a
SPM12 v6685 preprocessing, GLM, ...

Other functions from github and the mathwork file exchange are needed. All of them are shipped with this repo in the lib folder or can be pulled from github as submodules.

So to install all the code and its dependencies you simply to run:

git clone --recurse-submodules https://github.com/Remi-Gau/AVT_analysis.git

Set up

When in the root folder simply run initEnv from the matlab prompt to add all relevant folders to the matlab path.

Settings

Files used to stored settings are in the following folders:

src/settings/
lib/laminar_tools/src/settings/

Compiling mex file for PCM analysis

You might need to compile a a mex file to run the PCM if you are on Linux.

cd(fullfile('lib', 'pcm_toolbox'))
mex traceABtrans.c

Recreating figures

For BOLD and MVPA analysis

The script src/figures/PlotBoldProfile.m will plot the main figures for BOLD profile results.

Development

virtualenv -p /usr/bin/python3.8 env
source env/bin/activate

pip install -r requirements.txt
pre-commit install
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