My new TEDx talk @ Claremont College is online:
We congratulate Micah Johnson (GS 2nd) for being awarded a prestigious NSF graduate fellowship!
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 (firstname.lastname@example.org)
Download the script from here
Latest interview to Prof Monti on the topic of brain death and its criteria:
- Los Angeles Times (online): What constitutes brain death?
- Los Angeles Times (print): Criteria vary for brain death diagnosis.
- Definition of brain death depends on hospital, study finds.
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 injury. Annals 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).
Atrophy in Patients as compared to Healthy Volunteers
Atrophy correlating with clinical scores of motor behavior/communication and arousal
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.
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