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 in Annals of Neurology (IF: 11.9): Thalamic and extra-thalamic mechanisms of consciousness after severe brain injury

Lutkenhoff E.S., Chiang J., Tshibanda L., Kamau E., Kirsch M., Pickard J.D., Owen A.M., Monti M.M. (2015) Thalamic and extra-thalamic mechanisms of consciousness after severe brain injuryAnnals of Neurology. [ePub ahead of print].

Traditionally the thalamo-cortical axis is believed to be crucial for the maintenance/recovery of consciousness after brain injury as well as cortical/behavioral arousal. Evan Lutkenhoff (MontiLab post-doc) shows, in a paper now in press in Annals of Neurology, that while the degree of thalamic atrophy is proportional to a patient’s inability to produce voluntary behavior and communicate, the impairment in arousal is unrelated to thalamic atrophy. Rather, level of arousal was connected to the degree of atorphy within the basal ganglia (putamen/globus pallidus).

Lutkenhoff_SubcorticalAtrophyAtrophy in Patients as compared to Healthy Volunteers

Lutkenhoff_SubcorticalAtrophy_pat

Atrophy correlating with clinical scores of motor behavior/communication and arousal

Lutkenhoff_SubcorticalAtrophy_patOnly

New Publication in Neurology (IF: 8.3; with editorial): Thalamo-frontal connectivity mediates top-down cognitive functions in disorders of consciousness

A new MontiLab paper published in Neurology (IF: 8.3) demonstrating the importance of thalamo-frontal connectivity in cognitive function for patients with Disorders of Consciousness.

Monti M.M., Rosenberg M., Finoia P., Kamau E., Pickard J.D., Owen A.M. (2015) Thalamo-frontal connectivity mediates top-down cognitive functions in disorders of consciousness. Neurology, 85:1-7. [Pub ahead of print].

See also the accompanying Editorial by S. Goldman and N. Schiff.

New Publication: better brain extractions with optiBET!

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

GraphicalAbstrac_white3