FDR thresholding script

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

New Publication: better brain extractions with optiBET!


Our in-house script for better brain extractions is now “official”!

If you do brain extractions in any population other than healthy volunteers this tool might be of great use. It’s free and takes only a 1-liner to work: sh optiBET.sh -i <input_image> -options

You download the script, find a link to the paper, and a full description of the tool here: http://montilab.psych.ucla.edu/fmri-wiki/optibet

Here is the visual summary of the 4-step process that makes optiBET capable of brain extractions even in the presence of large pathology