False discovery rates in TED

The program vtedfdr performs a statistical inference based on the output produced by the program vted. The details of the algorithm are described in Lohmann et al (2016) (see reference below).

The program expects two histogram files as input representing the permuted and non-permuted outputs of “vted”. It produces as output a txt-file containing the false discovery rates (Fdr) for very edge density value. The cutoff above which Fdr falls below the predetermined significance level alpha is also reported. An example calling sequence is shown below:

Example:

vted -in1 A*.v -in2 B*.v -mask mask.v -perm   0 -q 0.99 -hist realhist.txt -out edgelist.v
      vted -in1 A*.v -in2 B*.v -mask mask.v -perm 100 -q 0.99 -hist nullhist.txt
      vtedfdr -real realhist.txt -null nullhist.txt -out fdr.txt -alpha 0.05

The first two calls produce the two histograms needed as input into vtedfdr. The third call to ‘vtedfdr’ uses the two histogram files as input and produces the txt-file “fdr.txt” as output. The file “fdr.txt” can be used to determine a cutoff so that edges with edge densities that exceed this cutoff have a sufficiently low false discovery rate. This cutoff is both reported as terminal output and additionally in the output file fdr.txt.

Reference: Lohmann G, Stelzer J, Zuber V, Buschmann T, Margulies D, et al. (2016): Task-Related Edge Density (TED) - A New Method for Revealing Dynamic Network Formation in fMRI Data of the Human Brain. PLoS ONE 11(6): e0158185. doi: 10.1371/journal.pone.0158185

Parameters of ‘vtedfdr’

-help

Prints usage information.

-null

Null histogram.

-real

Non-permutated real histogram.

-out

Output txt file containing false discovery rates.

-alpha

Significance level. Default: 0.05