This script runs FDR on a COPE image (after an FSL analysis).
It does make a few assumptions, for instance that you are inside the “stats” directory of an FSL FEAT analysis. It is amply commented and you can easily edit it to fit your circumstances. A few variables (like the mask) are set at the beginning at the script.
Here is the header information:
#(Launch from the stats folder)
# Usage ./fdr cope# q ( or: source fdr 1 0.05 )
# cope# is the number of the cope you want to threshold
# q is the familywise (corrected) alpha level you want to use (e.g., 0.05)
# Example usage: source fdr.tcsh 1 0.05
# (you might have to set the permissions the first time, e.g., chmod 755 fdr.tcsh )
#
# script edited by Martin Monti (monti@psych.ucla.edu)
#
Download the script from here