Catanese et al. (2016)
Code used for processing, analysis and visualization in Catanese, Carmichael & van der Meer, "Low and high gamma oscillations deviate in opposite directions from zero-phase synchrony in the limbic corticostriatal loop" (2016) Journal of Neurophysiology (preprint)
Once you have checked out the above code, set up your MATLAB path as follows:
restoredefaultpath; % start with clean slate cd('\GitHub\fieldtrip'); % remember to replace paths with yours addpath(genpath('\GitHub\vandermeerlab\code-matlab\shared')); addpath('\GitHub\papers\Catanese_vanderMeer2016\utility'); ft_defaults; % warning can be ignored
To obtain the data, e-mail mvdm at dartmouth dot edu to get access to the lab server. Then, to reproduce the results in the paper, run the following:
- For all event-based analyses (Figures 4, 5, 6 and 9) first run the
subsequent analyses require the resulting
ALL_evtvariable to exist in the workspace.
- Amplitude correlations: MASTER_AmplCorr.m followed by PLOT_AmplCorr.m.
- Phase slopes: MASTER_SpectralConnectivity.m followed by PLOT_SpectralConnectivity.m.
- Ensemble classification: MASTER_ClassifyGammaEvents.m followed by PLOT_Classify.m.
- Analysis of phase lags and slopes for signal generator inputs: MASTER_probe.m.
- For the epoch-based analyses (Figure 3), run this script.
- Phase slope index schematic (Figure 5a): PLOT_PSIexample.m.
- Code for checking the units in FieldTrip's output for the phase angle and phase slopes on simulated data.
We used MATLAB R2014b running on 64-bit Windows 7.
Wiki-based tutorials introducing the codebase architecture, and step-by-step explanations of specific analyses, are here.