Software


Dynamic Functional Connectivity
  • Matlab code for determining eigenconnectivities from dynamic functional connectivity measures.

    [1] N. Leonardi, J. Richiardi, M. Gschwind, S. Simoni, J.-M. Annoni, M. Schluep, P. Vuilleumier, D. Van De Ville, "Principal Components of Functional Connectivity: A New Approach to Study Dynamic Brain Connectivity During Rest", NeuroImage, 2013, 83, 937-950

  • Matlab code for simulation of dynamic functional connectivity.

    [2] N. Leonardi, D. Van De Ville, "On Spurious and Real Fluctuations of Dynamic Functional Connectivity During Rest", NeuroImage, in press
Statistical Parametric Connectome (SPC)

R code and manual for two-step procedure applied to connectomes.

[1] D.-E. Meskaldji et al, "Improved statistical evaluation of group differences in connectomes by screening-filtering strategy with application to study maturation of brain connections between childhood and adolescence", NeuroImage, in press

Total Activation

Matlab code for deconvolution of fMRI timecourses.

[1] I. Karahanoglu, C. Caballero Gaudes, F. Lazeyras, D. Van De Ville, "Total Activation: FMRI Deconvolution through Spatio-Temporal Regularization", NeuroImage, 2013, 73, 121-134

Wavelet-based Statistical Parametric Mapping (WSPM)

WSPM toolbox for SPM allowing high-spatial resolution mapping (non-smoothed data) with strong and weak (FDR) type I error control. New version 1.40 now available (SPM8 compatible).

[1] D. Van De Ville, T. Blu, M. Unser, "Integrated Wavelet Processing and Spatial Statistical Testing of fMRI Data", NeuroImage, 2004, 23, 1472-1485
[2] D. Van De Ville, M. Seghier, F. Lazeyras, T. Blu, M. Unser, "WSPM: Wavelet-Based Statistical Parametric Mapping", NeuroImage, 2007, 37, 1205-1217

Spectral graph wavelet transform for multiplex graphs

Matlab code for the extension of the spectral graph wavelet transform (SGWT) for multislice graphs.

[1] N. Leonardi, D. Van De Ville, "Tight Wavelet Frames on Multislice Graphs", IEEE Transactions on Signal Processing, 2013, 61, 3357-3367

Stein's unbiased risk estimate (SURE) for non-local means (NLM)

The original code from Gabriel Peyré has been modified; here's the patch.

[1] D. Van De Ville, M. Kocher, "SURE-Based Non-Local Means", IEEE Signal Processing Letters, 2009, 16, 973-976

Optimal linear expansion of multiple NLM algorithms based on SURE

The software is available for download.

[1] D. Van De Ville, M. Kocher, "Non-Local Means with Dimensionality Reduction and SURE-Based Parameter Selection", IEEE Transactions on Image Processing, 2011, 20, 2683-2690

Wavelet-based functional connectivity pipeline

Wavelet-based functional-connectivity pipeline, maintained by Jonas Richiardi, can be downloaded from here.

[1] J. Richiardi, H. Eryilmaz, S. Schwartz, P. Vuilleumier, D. Van De Ville, "Decoding Brain States from fMRI Connectivity Graphs", NeuroImage, 2011, 56, 616-626 (Special Issue on Brain Decoding)
[2] J. Richiardi, S. Achard, H. Bunke, D. Van De Ville, "Machine Learning with Brain Graphs", IEEE Signal Processing Magazine, 2013, 30, 58-70

Riesz steerable wavelets for rotation-covariant texture learning

Matlab implementation of Riesz steerable wavelets for rotation-covariant texture learning, maintained by Adrien Depeursinge, can be downloaded from here.

[1] A. Depeursinge, A. Foncubierta-Rodriguez, D. Van De Ville, H. Muller, "Rotation-Covariant Feature Learning Using Steerable Riesz Wavelets", IEEE Transactions on Image Processing, 2014, 23, 898-908

Riesz wavelet pyramid

Matlab code for the accompanying paper has been published in IEEE Transactions on Image Processing.